Volume 35 Issue 5
May  2022
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LIANG Dan, WANG Tao, LI Jiao Jiao, GUAN Da Wei, ZHANG Guan Ting, LIANG Yu Feng, LI An An, HONG Wen Shan, WANG Li, CHEN Meng Lin, DENG Xiao Ling, CHEN Feng Juan, PAN Xing Fei, JIA Hong Ling, LEI Chun Liang, KE Chang Wen. Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021[J]. Biomedical and Environmental Sciences, 2022, 35(5): 393-401. doi: 10.3967/bes2022.055
Citation: LIANG Dan, WANG Tao, LI Jiao Jiao, GUAN Da Wei, ZHANG Guan Ting, LIANG Yu Feng, LI An An, HONG Wen Shan, WANG Li, CHEN Meng Lin, DENG Xiao Ling, CHEN Feng Juan, PAN Xing Fei, JIA Hong Ling, LEI Chun Liang, KE Chang Wen. Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021[J]. Biomedical and Environmental Sciences, 2022, 35(5): 393-401. doi: 10.3967/bes2022.055

Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021

doi: 10.3967/bes2022.055
Funds:  This work was supported by the grant National Key Research and Development Program of China [2018YFC1603804 and 2021YFC0863300]; Emergency Key Program of Guangzhou Laboratory [EKPG21-27]; and Sino-German Center for Research Promotion (SGC)’s Rapid Response Funding Call for Bilateral Collaborative Proposals Between China and Germany in COVID-19 Related Research [C-0032]
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  • Author Bio:

    LIANG Dan, female, born in 1992, PhD Candidate, majoring in microbiology

    WANG Tao, male, born in 1998, Master Candidate, majoring in laboratory diagnosis of infectious diseases

    LI Jiao Jiao, female, born in 1991, MD, majoring in infectious disease

  • Corresponding author: JIA Hong Ling, E-mail: jiahongling@aliyun.com; Tel: 86-20-85228359; LEI Chun Liang, E-mail: gz8hlcl@126.com; Tel: 86-13802917518; KE Chang Wen, E-mail: kecw1965@aliyun.com; Tel: 86-20-31051236.
  • &These authors contributed equally to this work.
  • Received Date: 2021-11-29
  • Accepted Date: 2022-03-29
  •   Objective   The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARS-CoV-2 from imported cases admitted to the Guangzhou Eighth People’s Hospital, which was appointed by the Guangdong provincial government to treat coronavirus disease 2019 (COVID-19). The SARS-CoV-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated.  Methods   In total, 177 throat swab samples were obtained from COVID-19 patients (from October 2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-CoV-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants.  Results   We observed that the imported cases mainly occurred after January 2021, peaking in May 2021, with the highest proportion observed from cases originating from the United States. The main lineages were found in Europe, Africa, and North America, and B.1.1.7 and B.1.351 were the two major sublineages. Sublineage B.1.618 was the Asian lineage (Indian) found in this study, and B.1.1.228 was not included in the lineage list of the Pangolin web. A reasonably high homology was observed among all samples. The total frequency of mutations showed that the open reading frame 1a (ORF1a) protein had the highest mutation density at the nucleotide level, and the D614G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7b, and ORF9b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in PubMed among all missense mutations.  Conclusion   These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-CoV-2 in Guangdong Province, China.
  • &These authors contributed equally to this work.
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  • [1] World Health Organization. Coronavirus disease (COVID-19) pandemic.https://www.who.int/emergencies/diseases/novel-coronavirus-2019. [2021-06-17].
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    [5] Xiong YB, Tian YX, Ma Y, et al. Factors defining the development of severe illness in patients with COVID-19: a retrospective study. Biomed Environ Sci, 2021; 34, 984−91.
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    [12] Gupta RK. Will SARS-CoV-2 variants of concern affect the promise of vaccines? Nat Rev Immunol, 2021; 21, 340-1.
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    [14] Volz E, Mishra S, Chand M, et al. Transmission of SARS-CoV-2 Lineage B. 1.1. 7 in England: Insights from linking epidemiological and genetic data. medRxiv. 2021.
    [15] Iacobucci G. Covid-19: local councils initiate surge vaccination to tackle B. 1. 617. 2 variant. BMJ, 2021; 373, n1361.
    [16] Guangzhou Municipal Health Commission. Coronavirus disease (COVID-19) pandemic. http://wjw.gz.gov.cn/ztzl/xxfyyqfk/yqtb/content/post_7284283.html. [2021-5]
    [17] Galloway SE, Paul P, MacCannell DR, et al. Emergence of SARS-CoV-2 B. 1.1. 7 lineage - United States, December 29, 2020-January 12, 2021. MMWR Morb Mortal Wkly Rep, 2021; 70, 95-9.
    [18] Horspool AM, Ye CJ, Wong TY, et al. SARS-CoV-2 B. 1.1. 7 and B. 1.351 variants of concern induce lethal disease in K18-hACE2 transgenic mice despite convalescent plasma therapy. bioRxiv, 2021.
    [19] Aleem A, Akbar SAB, Slenker AK. Emerging variants of SARS-CoV-2 and novel therapeutics against coronavirus (COVID-19). StatPearls Publishing. 2021.
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    [22] Ozer EA, Simons LM, Adewumi OM, et al. High prevalence of SARS-CoV-2 B. 1.1. 7 (UK variant) and the novel B. 1.525 lineage in Oyo State, Nigeria. medRxiv, 2021.
    [23] Yurkovetskiy L, Wang X, Pascal KE, et al. Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant. Cell, 2020; 183, 739−51.e8. doi:  10.1016/j.cell.2020.09.032
    [24] Korber B, Fischer WM, Gnanakaran S, et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell, 2020; 182, 812−27.e19. doi:  10.1016/j.cell.2020.06.043
    [25] Volz E, Hill V, McCrone JT, et al. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell, 2021; 184, 64−75.e11. doi:  10.1016/j.cell.2020.11.020
    [26] Nyayanit DA, Sarkale P, Baradkar S, et al. Transcriptome & viral growth analysis of SARS-CoV-2-infected Vero CCL-81 cells. Indian J Med Res, 2020; 152, 70−6.
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    [29] Shi CS, Qi HY, Boularan C, et al. SARS-coronavirus open reading frame-9b suppresses innate immunity by targeting mitochondria and the MAVS/TRAF3/TRAF6 signalosome. J Immunol, 2014; 193, 3080−9. doi:  10.4049/jimmunol.1303196
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Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021

doi: 10.3967/bes2022.055
Funds:  This work was supported by the grant National Key Research and Development Program of China [2018YFC1603804 and 2021YFC0863300]; Emergency Key Program of Guangzhou Laboratory [EKPG21-27]; and Sino-German Center for Research Promotion (SGC)’s Rapid Response Funding Call for Bilateral Collaborative Proposals Between China and Germany in COVID-19 Related Research [C-0032]
  • Author Bio:

  • Corresponding author: JIA Hong Ling, E-mail: jiahongling@aliyun.com; Tel: 86-20-85228359;  LEI Chun Liang, E-mail: gz8hlcl@126.com; Tel: 86-13802917518;  KE Chang Wen, E-mail: kecw1965@aliyun.com; Tel: 86-20-31051236.
  • &These authors contributed equally to this work.

Abstract:   Objective   The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARS-CoV-2 from imported cases admitted to the Guangzhou Eighth People’s Hospital, which was appointed by the Guangdong provincial government to treat coronavirus disease 2019 (COVID-19). The SARS-CoV-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated.  Methods   In total, 177 throat swab samples were obtained from COVID-19 patients (from October 2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-CoV-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants.  Results   We observed that the imported cases mainly occurred after January 2021, peaking in May 2021, with the highest proportion observed from cases originating from the United States. The main lineages were found in Europe, Africa, and North America, and B.1.1.7 and B.1.351 were the two major sublineages. Sublineage B.1.618 was the Asian lineage (Indian) found in this study, and B.1.1.228 was not included in the lineage list of the Pangolin web. A reasonably high homology was observed among all samples. The total frequency of mutations showed that the open reading frame 1a (ORF1a) protein had the highest mutation density at the nucleotide level, and the D614G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7b, and ORF9b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in PubMed among all missense mutations.  Conclusion   These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-CoV-2 in Guangdong Province, China.

&These authors contributed equally to this work.
LIANG Dan, WANG Tao, LI Jiao Jiao, GUAN Da Wei, ZHANG Guan Ting, LIANG Yu Feng, LI An An, HONG Wen Shan, WANG Li, CHEN Meng Lin, DENG Xiao Ling, CHEN Feng Juan, PAN Xing Fei, JIA Hong Ling, LEI Chun Liang, KE Chang Wen. Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021[J]. Biomedical and Environmental Sciences, 2022, 35(5): 393-401. doi: 10.3967/bes2022.055
Citation: LIANG Dan, WANG Tao, LI Jiao Jiao, GUAN Da Wei, ZHANG Guan Ting, LIANG Yu Feng, LI An An, HONG Wen Shan, WANG Li, CHEN Meng Lin, DENG Xiao Ling, CHEN Feng Juan, PAN Xing Fei, JIA Hong Ling, LEI Chun Liang, KE Chang Wen. Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021[J]. Biomedical and Environmental Sciences, 2022, 35(5): 393-401. doi: 10.3967/bes2022.055
    • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogenic agent of coronavirus disease 2019 (COVID-19), has caused a global pandemic and conferred a profound effect on all aspects of society. As of June 15, 2021, 175 million infections have been confirmed, and 3.8 million deaths have been reported all over the world[1]. The Chinese government managed to contain the virus through a series of draconian control measures. However, the number of newly confirmed cases outside of China has been rising rapidly. Thus, China prioritized protecting itself from imported cases from other countries or territories.

      Guangdong Province is known as the “South Gate of China,” with a large number of foreign passengers; hence, the most number of imported cases was detected here compared with other regions of Mainland China [2]. The World Health Organization announced several variants of concern (VOCs) and variants of interest (VOIs) of SARS-CoV-2 on May 31, 2021 [3]. With the increase in the number of genome sequences available in the public database, analysis using more sequences by sampling from a wider area over a longer period was imperative. In the present study, we employed second-generation sequencing to obtain virus sequence information and performed advanced comprehensive methods to analyze the genetic characteristics of SARS-CoV-2 in the imported cases based on the demographic and baseline characteristics of these patients. Our studies enriched the knowledge of the existing epidemic strains of SARS-CoV-2 in the world and provided valuable clues for defense against this infectious disease imported to China.

    • The protocol of the study was reviewed and approved by Guangdong Provincial Center for Disease Control and Prevention (approval number: W96-027E-202121).

    • This study included human throat swab samples that were collected and processed in the Guangdong Provincial Center for Disease Control and Prevention, China, and throat swab samples, which were de-identified prior to analysis, collected from the Guangzhou Eighth People’s Hospital from October 2020 to May 2021. All the samples were inactivated at 56 °C for 30 min. Demographic characteristics and clinical information were collected from electronic medical records.

    • All the throat swab samples were screened by quantitative real-time polymerase chain reaction method using the SARS-CoV-2 NAT kits (BioGerm, Shanghai, China). The positive specimens were processed for NGS using the MGISEQ-2000 platform of the Beijing Genomics Institute (BGI, Shenzhen, China). DNA fragment assembly was performed using the iGenome® VirusDetector system (BGI, Shenzhen, China), with the Wuhan-hu-01 (GenBank access no. MN908947.3) genome as the reference sequence. All ambiguous nucleotides in the alignment analysis were set to N. The ratio of non-N greater than 85% indicated a good fragment assembly in accordance with the manufacturer’s instruction.

    • The complete reference genomes were retrieved from the National Center for Biotechnology Information database (https://www.ncbi.nlm.nih.gov/). Pangolin web tool (https://cov-lineages.org/) was used for the origin of clades. Mattf v7.037 (Kazutaka Katoh, Japan, 2002) and BioEdit v7.0.9.0 (Borland, USA, 2009) were applied to sequence alignment and trimming, respectively. The maximum-likelihood (ML) phylogenetic tree was constructed using IQ-Tree v1.6.12 (Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, et al., USA, 2011). A total of 1,000 bootstrap replicates were used to deduce branch support. The phylogenetic tree was visualized using FigTree v1.4.2 (Andrew Rambaut, UK, 2006) and Adobe Illustrator CS6 (Adobe, USA, 1987). In addition, the Nextclade web tool (https://clades.nextstrain.org) was used for putting up information about nucleotide mutations and amino acid mutations. R v3.6.1 (Ross Ihaka, Robert Gentleman, New Zealand, 1995) was used to calculate the genetic distance of sequences, obtain the homology, and cleanse the mutation data at the nucleotide and amino acid levels.

    • The data were managed using EpiData v3.1 (Jens M. Lauritsen, Mark Myatt, Michael Bruus, DK, 1999). R v3.6.1 (Ross Ihaka, Robert Gentleman, New Zealand, 1995) was used for descriptive analysis and plotting. All the bar graphs were drawn using the GraphPad Prism software v8.0.2 (San Diego, CA, USA, 1992).

      Age variables were expressed using “median {Interquartile range [(IQR): 25%–75%]},” and categorical variables including age group, gender, and NAT results were presented as percentages. A two-tailed P-value of < 0.05 was considered statistically significant throughout the study.

    • A total of 177 patients were included in this study, and their demographic characteristics are shown in Table 1. More than half of the respondents were male (136, 76.84%). A total of 78 individuals (44.07%) were aged 31–40 years, and 6 people were over 61. The minimum age was 16, and the maximum was 85 (median age, 34 years). A total of 123 out of 177 (69.49%) individuals showed positive results for SARS-CoV-2 RNA by the NATs, and among them, 117 cases (95.12%) were sequenced successfully. Exactly 43 patients in our studies (24.29%) were asymptomatic cases (Table 1).

      VariablesPatients (N = 177)
      Age, years
       Median (P25, P75) 34 (31, 45)
      Age group, n (%)
       ≤ 3039 (22.03)
       31–4078 (44.07)
       41–5034 (19.21)
       51–6020 (11.30)
       ≥ 616 (3.39)
      Gender, n (%)
       Female41 (23.16)
       Male136 (76.84)
      NATs results, n (%)
       Positive123 (69.49)
        Sequenced successfully117 (95.12)
        Failed to sequence6 (4.87)
       Negative54 (30.51)
      Clinical classification, n (%) 
       Asymptomatic case43 (24.29)
       Confirmed case134 (75.71)
        Note. NATs, nucleic acid detection

      Table 1.  Demographic information of patients with SARS-CoV-2 infection

    • A total of 117 complete genomes sequences were obtained from this study, and the time and regional distribution through sequence clades are shown in Figure 1. With the sampling dated between June 2020 and May 2021, the time distributions of 177 patients were mainly in May 2021 (65/177, 36.72%), February 2021 (43/177, 24.29%), January 2021 (33/177, 18.64%), and March 2021 (24/177, 13.56%) (Figure 1A), and the time distributions of sequences were primarily in May 2021 (40/117, 34.19%), January 2020 (25/117, 21.37%), February 2020 (24/117, 20.51%), and March 2021 (18/117, 15.38%). The sequence distribution relevant to the timelines was asymmetrical due to the successful epidemic control in China after April 2020 [4]. The sequences from this study were classified into 39 sublineages: A, A.23.1, B.1, B.1.1, B.1.1.157, B.1.1.214, B.1.1.222, B.1.1.228, B.1.1.368, B.1.1.420, B.1.1.7, B.1.170, B.1.177.81, B.1.2, B.1.214.2, B.1.351, B.1.36, B.1.36.16, B.1.36.17, B.1.36.38, B.1.36.22, B.1.402, B.1.413, B.1.427, B.1.429, B.1.438.1, B.1.466.2, B.1.468, B.1.524, B.1.525, B.1.533, B.1.580, B.1.595, B.1.596, B.1.618, B.1.84, C.36, L.3, and P.2, where the clades located were chiefly concentrated on B.1.1.7 (28/117, 23.93%) and B.1.351 (20/117, 17.09%). The lineage distribution included Europe (n = 50), Africa (n = 28), North America (n = 22), Asia (excluding China) (n = 12), China (n = 3), South Africa (n = 1), South America (n = 1), and B.1.1.228 (n = 1) (Figure 1B). The largest diversity of lineages was observed in January 2021, with six lineages, followed by February 2021, with five lineages. European and African lineages mainly appeared in May 2021 (25/117, 21.37% vs. 10/117, 8.55%), the North American lineage emerged in January 2021 (11/117, 9.40%), and that from South America and variant B.1.1.228 materialized in January 2021 (not classified on the Pangolin web tool). China lineages were interspersed in October 2020 and January and February 2021 (Figure 1C).

      Figure 1.  Distribution of imported cases. (A) Time distribution of 177 imported cases during the whole study period (from June 2020 to May 2021); (B) total number of lineages (including those from Europe, Africa, North America, Asia (excluding China), China, and South America and sublineage B.1.1.228) in 117 imported cases; (C) temporal distribution of each lineage in 117 imported cases.

      The regional distribution was chiefly imported from the United States (USA; 13/117, 11.11%), Zambia (8/117, 6.84%), Nigeria (8/117, 6.84%), and the United Arab Emirates (UAE; 6/117, 5.13%). Additionally, the regional distribution included Indonesia (n = 5), Cambodia (n = 5), Tanzania (n = 4), Bangladesh (n = 4). Notably, the UK strains of the European lineage (B.1.1.7 and B.1.36.2) mostly came from Cambodia and Nigeria. The USA strains of the North American lineage (B.1.1.222, B.1.1.368, B.1.2, B.1.402, B.1.427, B.1.429, B.1.580, B.1.595, and B.1.596) were predominantly from the USA. The two patients infected with sublineage B.1.618 (Indian lineage) were asymptomatic and imported from UAE and Mozambique. Sublineage B.1.170, belonging to the European lineage (Egypt and UAE), first appeared in the world on March 19, 2020, but occurred in June 2020 in our study. Sublineage B.1.468 (Asian lineage (Indonesia), a member of the early epidemiological transmission chains, first emerged on February 13, 2020, and was included in our study in July 2020.

    • For this study, a GTR + F + I + G4 nucleotide substitution model, the best-fit model based on the Akaike Information Criterion according to the Bayesian information criterion, was used for the phylogenetic analyses. The virus species in this study clustered in two large groups. Most viral sequences from patients with SARS-CoV-2 infection clustered in the African, North American, and European lineages. The rest of the sublineages were scattered in diverse branches of the phylogenetic tree. The diversity of molecular evolution of SARS-CoV-2 cases imported to Guangdong Province was revealed, which was consistent with the case distribution (left part of Figure 3). In the homology analyses, a comparison of the reference sequences with the sequences of respective samples indicated that the homology among genomic sequences was 99.68%–100%. In addition, the viral genomes from infected patients were consistent with the animal reference sequences, including the Canis lupus family, feline, mink, ferret, Panthera leo, tiger, and Neovison vison (99.76%–99.98%). Moreover, we analyzed the correlations between age, gender, clinical classification, and VOCs, with a statistically significant difference between males and females (P < 0.05, not shown in the table).

      Figure 3.  Maximum-likelihood phylogenetic dendrogram constructed based on Pangolin’s classifications from the 117 sequences and Wuhan-hu-01 in GenBank as a reference sequence. The positions of all missense mutation sites on genes and their distribution, regardless of whether they were published or reported or unpublished and unreported, are revealed in the right part of the graph.

      The mutations in nucleotide that occurred in 117 sequences were found in these loci: S (nt23403), 1a (nt241, 3037), 1b (nt14408), 3a (nt25563), N (nt28881–28883), 8 (nt27972), E (nt26456), and M (nt26735). Position 1a (nt241 and nt3037) exhibited the highest mutation rate, with T substituting for C, followed by nt14408 (position 1b) with C displacing T. At the amino acid level, mutations were discovered in the following sites: S (aa614), 1b (aa314), 1a (aa3676–aa3677), N (aa203–aa205), 3a (aa57), and 8 (aa52). D614G had the highest mutation rate, followed by P314L (Figure 2 and Table 2). Supplementary Table S1 (available in www.besjournal.com) lists all substitutions in the nucleotides and amino acids.

      RegionsNucleotide mutationsAmino acid mutations
      SiteNo.TypeTotal typesTotal frequencySiteNo.TypeTotal typesTotal frequency
      Gene E2645620C→T4247120P→L222
      Gene M2673514C→T2259822I→T710
      Gene N2888149G→A9146220349R→K45278
      2888247G→A20446G→R
      2888347G→C20531T→I
      Gene ORF
      1a241110C→T3451104367750F→L184540
      3037110C→T367650G→S
      1b14408110C→T148465314108P→L74226
      3a2556352G→T461535752Q→H38140
      6272132C→T6922F→M24
      7a275772C→T1011512D→A78
      7b278812C→T6962L→M58
      82797229C→T241855228R→I18151
      9b323R→P912
      Gene S23403114A→G123617614114D→G77544
        Note. Abbreviations: E, envelope protein; M, membrane; N, nucleocapsid protein; ORF, open reading frame; S, spike protein; 1a, 1b, 3a, 6, 7a, 7b, 8, and 9b represent ORFs 1a, 1b, 3a, 6, 7a, 7b, 8, and 9b, respectively.

      Table 2.  The main location of nucleotide or amino acid variant in SARS-CoV-2 patients

      Figure 2.  Frequencies of all mutations on the genome at the nucleotide level.

      Supplementary Tables S2 and S3 (available in www.besjournal.com) show the nonsense and missense mutation distributions in the non-synonymous mutation. Additionally, Supplementary Tables S4 and S5 (available in www.besjournal.com) list the reported amino acid mutation loci on the Global Initiative of Sharing All Influenza Data (GISAID) website (https://www.gisaid.org/) and publications in PubMed (https://pubmed.ncbi.nlm.nih.gov/), respectively. In total, 1,076 nonsense mutations were observed on 476 nucleotide sites in all the analyzed sequences. A total of 2,010 missense mutations were present in 441 loci, and they were largely disseminated in positions ORF 1a and S. The missense mutations were demonstrated in all 12 gene fragments (right part of Figure 3). We also identified some missense mutations that had neither been reported on the GISAID database nor published in PubMed, including position non-S (replacements at five amino acid residue lineages, including those from the North American (sublineage B.1.2): Ile5Val of ORF9b and European lineages (sublineage B.1.214.2: Ala75Val of ORF9b; sublineage B.1.1.7: Met1- and Leu6Met of ORF7b; sublineage B.1.1.7: Met1- and Leu6Met of ORF7b and Arg25Ile of ORF9b), and position S (eight substitution sites, including those in lineages from North America (sublineage B.1.595): Leu226Phe; Europe (sublineage B.1): Tyr248Asn; North America (sublineage B.1.402): Cys1247Arg; Asia (not China) (B.1.618): Tyr145- and His146-; Asia (not China) (B.1.1.25): His66Asp; Africa (sublineage L.3): Gly75Arg, Tyr1155Phe; Africa (sublineage L.3): Tyr1155Phe, whose corresponding coding nucleotide sites were demonstrated as the points marked in red in the right panel of Figure 4.

      Figure 4.  Maximum-likelihood phylogenetic dendrogram. The red dots in the right panel indicate that the missense mutations were not reported and not published.

      NameLineageMissense mutationORF1aORF1bSORF3aEMOEF6ORF7aORF8NORF10
      SARS-CoV-2/
      human/CHN/462/2020
      A.23.1G28878A, A4040G, C8240T, G11230T, G11266T, G11521T, A12759C, G25855C, T28144C, G28167A, G21867T, C22033A, G22661T, G23401T, C23604GA4040G, C8240T, G11230T, G11266T, G11521T, A12759CC22033A, G22661T, G23401T, C23604GG25855CT28144C, G28167A, G21867TG28878A
      SARS-CoV-2/
      human/CHN/464/2020
      B.1.2C28472T, C28869T, G29402T, C1059T, G8083A, C10319T, C14408T, A18424G, C21304T, G25563T, G25907T, C26212T, C27964T, A23403GC1059T, G8083A, C10319TC14408T, A18424G, C21304TA23403GG25563T, G25907T, C26212TC27964TC28472T, C28869T, G29402T
      SARS-CoV-2/
      human/CHN/467/2020
      B.1.1G28881A, G28882A, G28883C, T606C, A6867G, C14408T, G20134A, C25658T, A23403GT606C, A6867GC14408T, G20134AA23403GC25658TG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/469/2020
      B.1.1.368G28881A, G28882A, G28883C, G29402T, C1101T, A1982G, G7145A, C9996T, C14408T, C20104T, G27798T, G22017T, A23403GC1101T, A1982G, G7145A, C9996TC14408T, C20104TG22017T, A23403GG28881A, G28882A, G28883C, G29402T
      SARS-CoV-2/
      human/CHN/471/2020
      B.1G28899T, A1004G, C1911T, G3259T, G7272A, C14408T, G15766T, A18919G, A27545C, A23403GA1004G, C1911T, G3259T, G7272AC14408T, G15766T, A18919GA23403GA27545CG28899T
      SARS-CoV-2/
      human/CHN/475/2020
      B.1.36.38C28854T, T1947C, A8348G, C11109T, C14408T, C16376T, G25563T, A23403GT1947C, A8348G, C11109TC14408T, C16376TA23403GG25563TC28854T
      SARS-CoV-2/
      human/CHN/476/2020
      B.1.1.228C28638A, G28881A, G28882A, G28883C, C815T, C906T, C14408T, A20288G, G25785T, A23403G, C23604AC815T, C906TC14408T, A20288GA23403G, C23604AG25785TC28638A, G28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/477/2020
      B.1.468G28851T, G2891A, C6449T, G10793T, A12498G, C14408T, A16978G, G25563T, G28077T, A23403GG2891A, C6449T, G10793T, A12498GC14408T, A16978GA23403GG25563TG28077TG28851T
      SARS-CoV-2/
      human/CHN/478/2020
      B.1.36.22C28854T, G488A, A10323G, C14408T, G19542T, G25563T, A23403GG488A, A10323GC14408T, G19891TA23403GG25563TC28854T
      SARS-CoV-2/
      human/CHN/482/2020
      B.1.1.413A26741G, G28881A, G28882A, G28883C, G524A, C13684T, G13849T, C14408T, G25647T, G25690T, G21974T, G22992A, A23403G, G24926TG524AC13684T, G13849T, C14408TG21974T, G22992A, A23403G, G24926TG25647T, G25690TA26741GG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/485/2020
      B.1.595C26622T, C28887T, C29366T, C1059T, T2343C, C3411T, C8097T, C10319T, C14408T, G19009T, G25563T, C27964T, C22088T, G22240T, A23403GC1059T, T2343C, C3411T, C8097T, C10319TC14408T, G19009C22088T, G22240T, A23403GG25563TC26622TC27964TC28887T, C29366T
      SARS-CoV-2/
      human/CHN/486/2020
      B.1.595C26622T, C28887T, C29366T, C1059T, T2343C, C3411T, C8097T, C10319T, C14408T, G19009T, G25563T, C27964T, C22088T, G22240T, A23403GC1059T, T2343C, C3411T, C8097T, C10319TC14408T, G19009C22088T, G22240T, A23403GG25563TC26622T, C27964TC28887T, C29366T
      SARS-CoV-2/
      human/CHN/488/2020
      B.1.2C28472T, C28869T, G29402T, C1059T, G8083A, C10319T, C14408T, A18424G, C21304T, G25563T, G25907T, C27964T, A23403GC1059T, G8083A, C10319TC14408T, A18424G, C21304TA23403GG25563T, G25907TC27964TC28472T, C28869T, G29402T
      SARS-CoV-2/
      human/CHN/495/2020
      B.1.36.22C28854T, G488A, A10323G, C14408T, G19542T, C20132T, G25563T, A23403GG488A, A10323GC14408T, G19542TA23403GG25563TC28854T
      SARS-CoV-2/
      human/CHN/496/2020
      B.1.402C28854T, T519A, G524A, C875T, C3093T, G11083T, C13430T, C14408T, C19718T, G25563T, G25660C, A23403G, G25249T, T25301CT519A, G524A, C875T, C3093T, G11083T, C13430TC14408T, C19718TA23403G, G25249T, T25301CG25563T, G25660CC28854T
      SARS-CoV-2/
      human/CHN/499/2020
      B.1.84C28890T, G2885T, A13951G, C14408T, G19117T, A21131G, C25624T, A23403G, G23522AG2885TA13951G, C14408T, G19117T, A21131GA23403G, G23522AC25624TC28890T
      SARS-CoV-2/
      human/CHN/500/2020
      B.1.466.2C28887T, C3768T, C5184T, C14408T, C20389T, G25563T, C22879A, A23403GC3768T, C5184TC14408T, C20389TC22879A, A23403GC28887T
      SARS-CoV-2/
      human/CHN/505/2020
      B.1.438.1G28975T, G29474T, A1154G, C14408T, G25563T, G25677T, A23403G, G23587TA1154GC14408TA23403G, G23587TG25563T, G25677TG28975T, G29474T
      SARS-CoV-2/
      human/CHN/507/2020
      B.1.429C28887T, C1059T, A2406G, A5780G, A12878G, C14408T, G15452T, G17014T, G25563T, G25912A, G21600T, G22018T, T22917G, A23403GC1059T, A2406G, A5780G, A12878GC14408T, G15452T, G17014TG21600T, G22018T, T22917G, A23403GG25563T, G25912AC28887T
      SARS-CoV-2/
      human/CHN/508/2020
      B.1.596C28472T, C28869T, C1059T, C3738T, A5852G, C10319T, C12708T, C14408T, A18424G, G25563T, G25907T, C27964T, A23403G, G25244TC1059T, C3738T, A5852G, C10319T, C12708TC14408T, A18424GA23403G, G25244TG25563T, G25907TC27964TC28472T, C28869T
      SARS-CoV-2/
      human/CHN/509/2020
      B.1.170C28977T, C14408T, C16375A, G16741T, G25563T, A25864G, T27299C, A23403GC14408T, C16375A, G16741A23403GG25563T, A25864GT27299CC28977T
      SARS-CoV-2/
      human/CHN/514/2020
      B.1.468G28851T, G2891A, C6449T, G10793T, A12498G, C14408T, A16978G, G25563T, G28077T, A23403GG2891A, C6449T, G10793T, A12498GC14408T, A16978GA23403GG25563TG28077TG28851T
      SARS-CoV-2/
      human/CHN/516/2020
      B.1.466.2C28887T, C3768T, C5184T, C14408T, C20389T, G25563T, C22879A, A23403GC3768T, C5184TC14408T, C20389TC22879A, A23403GC28887T
      SARS-CoV-2/
      human/CHN/521/2020
      B.1.170C28977T, C14408T, C16375A, G16741T, G25563T, A25864G, T27299C, A23403GC14408T, C16375A, G16741A23403GG25563T, A25864GT27299CC28977T
      SARS-CoV-2/
      human/CHN/525/2020
      B.1.351C26456T, C28887T, C1059T, C3924T, G5230T, A10323G, G11291A, T11296G, C14408T, G25563T, C25904T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, C3924T, G5230T, A10323G, G11291A, T11296GC14408TC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TC28887T
      SARS-CoV-2/
      human/CHN/527/2020
      B.1C1059T, C14408T, G25563T, T22304A, A23403GC1059TC14408TT22304A, A23403GG25563T
      SARS-CoV-2/
      human/CHN/535/2020
      AC28292A, G28878A, A5606G, C6539T, A6610T, G11230T, G15016T, C25487T, G25563T, G28028T, G28178T, C22227T, G22319T, A23403GA5606G, C6539T, A6610T, G11230TG15016TC22227T, G22319T, A23403GC25487T, G25563TG28028T, G28178TC28292A, G28878A
      SARS-CoV-2/
      human/CHN/538/2020
      B.1.177.81C28932T, C10376T, C12119T, C14408T, C25889T, C22227T, A23403GC10376T, C12119TC14408TC22227T, A23403GC25889TC28932T
      SARS-CoV-2/
      human/CHN/542/2020
      B.1C28887T, C14408T, G25563T, G25912A, A23403GC14408TA23403GG25563T, G25912AC28887T
      SARS-CoV-2/
      human/CHN/547/2020
      B.1.36.17C28854T, T1947C, G3431T, C14408T, G19891T, G25563T, C26060T, A23403GT1947C, G3431TC14408T, G19891TA23403GG25563T, C26060TC28854T
      SARS-CoV-2/
      human/CHN/558/2020
      L.3G28881A, G28882A, G28883C, C1601T, G4399T, C8481T, A9453C, C11565T, C14408T, G21785C, T22917G, A23403G, A25026T, G25244TC1601T, G4399T, C8481T, A9453C, C11565TC14408TG21785C, T22917G, A23403G, A25026T, G25244TG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/559/2020
      B.1.1G28881A, G28882A, G28883C, G2229A, C5147T, C14408T, G26063T, A23403GG2229A, C5147TC14408TA23403GG26063TG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/561/2020
      B.1.36.16C28854T, C1878T, G11083T, G11596T, G12188T, C14408T, G25563T, C25883A, G28077T, G22205C, A22396C, A23403GC1878T, G11083T, G11596T, G12188TG22205C, A22396C, A23403GG25563T, C25883AG28077TC28854T
      SARS-CoV-2/
      human/CHN/564/2020
      B.1.36.16C28854T, C1878T, G11083T, G11596T, G12188T, C14408T, G25563T, C25883A, G28077T, G22205C, A22396C, A23403GC1878T, G11083T, G11596T, G12188TG22205C, A22396C, A23403GG25563T, C25883AG28077TC28854T
      SARS-CoV-2/
      human/CHN/566/2020
      AC28292A, G28878A, A5606G, C6539T, G11230T, G15016T, C25487T, G25563T, G28028T, G28178T, C22227T, G22319T, A23403GA5606G, C6539T, G11230TG15016TC22227T, G22319T, A23403GC25487T, G25563TG28028T, G28178TC28292A, G28878A
      SARS-CoV-2/
      human/CHN/571/2020
      B.1.177.81C28932T, C10376T, C12119T, C14408T, C25889T, C22227T, A23403GC10376T, C12119TC14408TC22227T, A23403GC25889TC28932T
      SARS-CoV-2/
      human/CHN/585/2020
      B.1.36.16C28854T, C1878T, G11083T, G11596T, G12188T, C14408T, G25563T, C25883A, G28077T, G22205C, A22396C, A23403GC1878T, G11083T, G11596T, G12188TG22205C, A22396C, A23403GG25563T, C25883AG28077TC28854T
      SARS-CoV-2/
      human/CHN/587/2020
      B.1.427C28887T, C1059T, C4055T, C6151A, G9738C, C9996T, C14408T, C16394T, G17014T, G25563T, G21600T, G22018T, T22917G, A23403GC1059T, C4055T, C6151A, G9738C, C9996TC14408T, C16394T, G17014TG21600T, G22018T, T22917G, A23403GG25563TC28887T
      SARS-CoV-2/
      human/CHN/593/2020
      L.3G28881A, G28882A, G28883C, C1601T, G4399T, C8481T, A9453C, C11565T, C14408T, G28178T, T22917G, A23403G, A25026T, G25244TC1601T, G4399T, C8481T, A9453C, C11565TC14408TT22917G, A23403G, A25026T, G25244TG28178TG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/595/2020
      A.23.1C28278A, G28878A, G28881A, G11230T, G11266T, G11521T, C21058T, T28144C, G28167A, C22033A, G22661T, G23282T, G23401T, G23429T, C23604GG11230T, G11266T, G11521TC21058TC22033A, G22661T, G23282T, G23401T, G23429T, C23604GT28144C, G28167AC28278A, G28878A, G28881A
      SARS-CoV-2/
      human/CHN/596/2020
      B.1G28881A, G28882A, G28883C, G25563T, C25883A, G28077T, G22205C, A22396C, A23403GG22205C, A22396C, A23403GG25563T, C25883AG28077TG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/599/2020
      B.1.1.157G28881A, G28882A, G28883C, C4158T, C5339T, G6986A, T8603C, G11272A, C14408T, A17615G, T17659G, C17678T, G22021T, A23403G, A24952GC4158T, C5339T, G6986A, T8603C, G11272AC14408T, A17615G, T17659G, C17678TG22021T, A23403G, A24952GG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/600/2020
      B.1.351C26456T, C28887T, C1059T, G5230T, C6258T, A10323G, G11291A, T11296G, C14408T, C25546T, G25563T, C25904T, A28254C, A21801C, A22206G, G22813T, G23012A, A23403G, C23664TC1059T, G5230T, C6258T, A10323G, G11291A, T11296GC14408TC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC25546T, G25563T, C25904TC26456TC28887T
      SARS-CoV-2/
      human/CHN/608/2020
      B.1.351C26456T, C28310T, C28887T, C1059T, G5230T, A10323G, G11291A, T11296G, C14408T, G25563T, C25904T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G5230T, A10323G, G11291A, T11296GC14408TC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TC28310T, C28887T
      SARS-CoV-2/
      human/CHN/609/2020
      B.1.2C28472T, C28869T, A29439T, C1059T, C2106T, C5310T, C6312T, C10319T, C14408T, G15766T, A18424G, A18470G, G18538T, C21304T, G25563T, G25907T, T25930C, C27964T, A23403GC1059T, C2106T, C5310T, C6312T, C10319TC14408T, G15766T, A18424G, A18470G, G18538T, C21304TA23403GG25563T, G25907T, T25930CC27964TC28472T, C28869T, A29439T
      SARS-CoV-2/
      human/CHN/610/2020
      B.1.580C26895T, G28842T, G29447T, C1059T, T1791C, C8892T, A10323G, G11417T, C14408T, G18255T, G25563T, A25843G, C23315T, A23403GC1059T, T1791C, C8892T, A10323G, G11417TC14408T, G18255TC23315T, A23403GG25563T, A25843GC26895TG28842T, G29447T
      SARS-CoV-2/
      human/CHN/611/2020
      B.1.524C28854T, C1188T, C1929T, C6312T, C8637T, A10124G, C14408T, C17518T, C21365T, A23403G, C23664TC1188T, C1929T, C6312T, C8637T, A10124GC14408T, C17518T, C21365TA23403G, C23664TC28854T
      SARS-CoV-2/
      human/CHN/613/2020
      B.1.1G28881A, G28882A, G28883C, G28985T, C3411T, G11083T, G11410T, C14408T, C25976T, G26104T, T28251G, C28253T, A28254C, C22879G, A23403GC3411T, G11083T, G11410TC14408TC25976T, G26104TT28251G, C28253T, A28254CG28881A, G28882A, G28883C, G28985T
      SARS-CoV-2/
      human/CHN/623/2020
      B.1.1.214G28881A, G28882A, G28883C, G28975T, C14408T, C18167T, G20560T, G21518T, A23403GC14408T, C18167T, G20560T, G21518TA23403GG28881A, G28882A, G28883C, G28975T
      SARS-CoV-2/
      human/CHN/625/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G7042T, G11291A, T11296G, C14120T, C14408T, C27972T, G28048T, A28095T, A28111G, G22289T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G7042T, G11291A, T11296GC14120T, C14408TG22289T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/626/2020
      A.23.1C28278A, G28878A, G28881A, G11230T, G11266T, G11521T, C21058T, T28144C, G28167A, C22033A, G22661T, G23282T, G23401T, G23429T, C23604GG11230T, G11266T, G11521TC21058TC22033A, G22661T, G23282T, G23401T, G23429T, C23604GT28144C, G28167AC28278A, G28878A, G28881A
      SARS-CoV-2/
      human/CHN/627/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G7042T, G11291A, T11296G, C14120T, C14408T, C27972T, G28048T, A28095T, A28111G, G22289T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G7042T, G11291A, T11296GC14120T, C14408TG22289T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/632/2020
      AG28878A, G11230T, C26042T, G27990T, C28000T, T28144C, G28167A, A23403G, C24149TG11230TA23403G, C24149TC26042TG27990T, C28000T, T28144C, G28167AG28878A
      SARS-CoV-2/
      human/CHN/638/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14120T, C14408T, C19390T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14120T, C14408T, C19390TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/639/2020
      B.1.2A28296G, C28472T, C28869T, C1059T, A2726G, C3966T, C10319T, T11672C, C14408T, G15349A, A18424G, C21304T, G25563T, G25907T, C27964T, C23271T, A23403GC1059T, A2726G, C3966T, C10319T, T11672CC14408T, G15349A, A18424G, C21304TC23271T, A23403GG25563T, G25907TC27964TA28296G, C28472T, C28869T
      SARS-CoV-2/
      human/CHN/642/2020
      B.1.1G28881A, G28882A, G28883C, G3307T, A3336G, T5619C, A5948G, G11417T, C12525T, C14408T, C26060T, A23403G, G23522CG3307T, A3336G, T5619C, A5948G, G11417T, C12525TC14408TA23403G, G23522CC26060TG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/644/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, C6843T, T6954C, G10887A, G11291A, T11296G, C14120T, C14408T, C19390T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, C6843T, T6954C, G10887A, G11291A, T11296GC14120T, C14408T, C19390TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/646/2020
      B.1.351C26456T, C28310T, C28887T, C1059T, G5230T, A10323G, G11291A, T11296G, C14408T, G25563T, C25904T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G5230T, A10323G, G11291A, T11296GC14408TC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TC28310T, C28887T
      SARS-CoV-2/
      human/CHN/649/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3045T, C3267T, C5388A, T6954C, C9344T, G11291A, T11296G, C14408T, C26191T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3045T, C3267T, C5388A, T6954C, C9344T, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC26191TC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/651/2020
      B.1.351C26456T, C28887T, C29259T, T606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, C17999T, C21110T, C25546T, G25563T, C25904T, A28254C, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TT606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296GC14408T, C17999T, C21110TA21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TC25546T, G25563T, C25904TC26456TA28254CC28887TT, C29259T
      SARS-CoV-2/
      human/CHN/652/2020
      B.1.351C26456T, C28887T, T606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, C17999T, C21110T, C25546T, G25563T, C25904T, A28254C, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TT606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296GC14408T, C17999T, C21110TA21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TC25546T, G25563T, C25904TC26456TA28254CC28887T
      SARS-CoV-2/
      human/CHN/655/2020
      B.1.351C26456T, C28887T, C29259T, T606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, C17999T, C21110T, C25546T, G25563T, C25904T, A28254C, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TT606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296GC14408T, C17999T, C21110TA21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TC25546T, G25563T, C25904TC26456TA28254CC28887T, C29259T
      SARS-CoV-2/
      human/CHN/658/2020
      B.1.1.222G28881A, G28882A, G28883C, C11345T, A13498G, C14408T, C25549T, A28254C, G22331A, A23403G, A23756GC11345TA13498G, C14408TG22331A, A23403G, A23756GC25549TA28254CG28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/659/2020
      B.1.351C26456T, C28887T, C1059T, G5230T, A10323G, G11291A, T11296G, C14408T, G25563T, C25904T, T28033C, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G5230T, A10323G, G11291A, T11296GC14408TC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TT28033CC28887T
      SARS-CoV-2/
      human/CHN/666/2020
      B.1A3069G, C8964T, C10341T, G11083T, G11230T, C14408T, G15380T, G19388T, G25621A, C26060T, G28028T, C28227T, A23403G, G23545TA3069G, C8964T, C10341T, G11083T, G11230TC14408T, G15380T, G19388TA23403G, G23545TG25621A, C26060TG28028T, C28227T
      SARS-CoV-2/
      human/CHN/671/2020
      B.1.351C26456T, C28887T, C29358T, C1059T, C5100T, G5230T, A10323G, G11291A, T11296G, C14408T, G25563T, C25904T, G27870T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, C5100T, G5230T, A10323G, G11291A, T11296GC14408TA21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TG27870TC28887T, C29358T
      SARS-CoV-2/
      human/CHN/671/2020 (1)
      B.1.351C26456T, C28887T, C29259T, T606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, G15451A, C17999T, C21110T, C25546T, G25563T, C25904T, A28254C, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TT606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296GC14408T, G15451A, C17999T, C21110TA21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TC25546T, G25563T, C25904TC26456TA28254CC28887T, C29259T
      SARS-CoV-2/
      human/CHN/671/2020 (2)
      B.1.351C26456T, C28887T, T606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, C17999T, C21110T, C25546T, G25563T, C25904T, A28254C, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TT606C, C1059T, G5230T, C9360T, A10323G, G11291A, T11296GC14408T, C17999T, C21110TA21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664TC25546T, G25563T, C25904TC26456TA28254CC28887T
      SARS-CoV-2/
      human/CHN/671/2020 (3)
      B.1.351C26456T, C28887T, C1059T, G1068A, G5230T, C9195A, A10323G, G11291A, T11296G, C14408T, G25563T, C25904T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G1068A, G5230T, C9195A, A10323G, G11291A, T11296GC14408TC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TC28887T
      SARS-CoV-2/
      human/CHN/681/2020
      B.1.1.420C28310T, G28727T, T28862A, G28881A, G28882A, G28883C, C5178T, A11451G, C13694T, C14408T, G25839T, C21614T, T22882G, A23403G, G23593TC5178T, A11451GC13694T, C14408TC21614T, T22882G, A23403G, G23593TG25839TC28310T, G28727T, T28862A, G28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/682/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14120T, C14408T, G18910T, C19390T, C27972T, G28048T, A28095T, A28111G, G23009T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14120T, C14408T, G18910T, C19390TG23009T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/695/2020
      P.2G28628T, G28881A, G28882A, G28883C, G28975T, T10667G, C12053T, C12488T, C14408T, C27972T, G23012A, T23255C, A23403G, G25088TT10667G, C12053T, C12488TC14408TG23012A, T23255C, A23403G, G25088TC27972TG28628T, G28881A, G28882A, G28883C, G28975T
      SARS-CoV-2/
      human/CHN/712/2020
      B.1.36C28854T, T1947C, C7321G, G11417T, G11521T, C14408T, G25543T, G25563T, C25867T, G23120T, A23403G, G23522A, G23593TT1947C, C7321G, G11417T, G11521TC14408TG23120T, A23403G, G23522A, G23593TG25543T, G25563T, C25867TC28854T
      SARS-CoV-2/
      human/CHN/715/2020
      B.1.177.81C28932T, G3971T, C12119T, C14408T, C25844T, C25889T, C22227T, A23403GG3971T, C12119TC14408TC22227T, A23403GC25844T, C25889TC28932T
      SARS-CoV-2/
      human/CHN/719/2020
      B.1.351C26456T, C28887T, C1059T, G5230T, C6285T, A10323G, G11291A, T11296G, C13329T, C14408T, C17999T, C21110T, C25546T, G25563T, C25904T, A28254C, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G5230T, C6285T, A10323G, G11291A, T11296G, C13329TC14408T, C17999T, C21110TA21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC25546T, G25563T, C25904TC26456TA28254CC28887T
      SARS-CoV-2/
      human/CHN/722/2020
      B.1.351C26456T, C28887T, C1059T, G2162A, A4295G, C5100T, G5230T, C5832T, A10323G, G11291A, T11296G, C14408T, G17122T, G25563T, C25904T, C27476T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G2162A, A4295G, C5100T, G5230T, C5832T, A10323G, G11291A, T11296GC14408T, G17122TA21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TC27476TC28887T
      SARS-CoV-2/
      human/CHN/728/2020
      B.1.1.420C28310T, G28727T, T28862A, G28881A, G28882A, G28883C, C5178T, A11451G, C13694T, C14408T, G25839T, C21614T, T22882G, A23403G, G23593TC5178T, A11451GC13694T, C14408TC21614T, T22882G, A23403G, G23593TG25839TC28310T, G28727T, T28862A, G28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/729/2020
      B.1.351C26456T, C28887T, C1059T, G5230T, C6285T, A10323G, G11291A, T11296G, C13329T, C14408T, C17999T, C21110T, C25546T, G25563T, C25904T, A28254C, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G5230T, C6285T, A10323G, G11291A, T11296G, C13329TC14408T, C17999T, C21110TA21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC25546T, G25563T, C25904TC26456TA28254CC28887T
      SARS-CoV-2/
      human/CHN/731/2020
      B.1.177.81C28932T, G3971T, C12119T, C14408T, C25844T, C25889T, C22227T, A23403GG3971T, C12119TC14408TC22227T, A23403GC25844T, C25889TC28932T
      SARS-CoV-2/
      human/CHN/736/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/741/2020
      B.1.429C27145T, C28887T, C1059T, C5907T, C6255T, C6285T, A12878G, C14408T, G17014T, G25563T, A27712G, G21600T, G22018T, T22917G, A23403GC1059T, C5907T, C6255T, C6285T, A12878GC14408TG21600T, G22018T, T22917G, A23403GG25563TC27145TA27712GC28887T
      SARS-CoV-2/
      human/CHN/761/2020
      C.36G28881A, G28882A, G28883C, G28908T, G569A, C936T, C1347T, C1427T, G2249A, C2841T, C4002T, G5180A, C7124T, G9929A, G10097A, T11337C, C12534T, C14408T, G17122T, G17218A, A17743T, G18546T, G27882T, C21597T, T22917G, A23403G, G23593TG569A, C936T, C1347T, C1427T, G2249A, C2841T, C4002T, G5180A, C7124T, G9929A, G10097A, T11337C, C12534TC14408T, G17122T, G17218A, A17743T, G18546TC21597T, T22917G, A23403G, G23593TG27882TG28881A, G28882A, G28883C, G28908T
      SARS-CoV-2/
      human/CHN/762/2020
      B.1.525C26305T, T26767C, C28308G, C28887T, C6285T, G11291A, T11296G, C14407T, C14408T, A21717G, C21762T, G23012A, A23403G, G23593C, T24224CC6285T, G11291A, T11296GC14407T, C14408TA21717G, C21762T, G23012A, A23403G, G23593C, T24224CC26305TT26767CC28308G, C28887T,
      SARS-CoV-2/
      human/CHN/767/2020
      B.1.351C26456T, C28887T, C29358T, C1059T, A3222G, C5100T, G5230T, A10323G, G11291A, T11296G, C14408T, G25563T, C25904T, G27870T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, A3222G, C5100T, G5230T, A10323G, G11291A, T11296GC14408TA21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TC28887T, C29358T
      SARS-CoV-2/
      human/CHN/779/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, G6446C, T6954C, G11291A, T11296G, C14120T, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, G6446C, T6954C, G11291A, T11296GC14120T, C14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/782/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C12789T, G12911A, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296G, C12789T, G12911AC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/786/2020
      B.1.618G27163T, G28325A, G28628T, G28922T, G28975T, A3830G, C4809T, G11083T, G14245A, C14408T, A17066G, C25844T, G27852T, A27979T, G22131A, G23012A, A23403GA3830G, C4809T, G11083TG14245A, C14408T, A17066GG22131A, G23012A, A23403GC25844TG27163TA27979TG28325A, G28628T, G28922T, G28975T
      SARS-CoV-2/
      human/CHN/788/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/789/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/798/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C12789T, G12911A, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296G, C12789T, G12911AC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/803/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, A4707G, C5388A, T6954C, G11291A, T11296G, C13458T, C14408T, A17615G, C27972T, G28048T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, A4707G, C5388A, T6954C, G11291A, T11296G, C13458TC14408T, A17615GA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/804/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, G26152T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CG26152TC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/805/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C2453T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, C16726T, G19613A, C27577T, C27972T, G28048T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC2453T, C3267T, C5388A, T6954C, G11291A, T11296GC14408T, C16726T, G19613AA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27577TC27972T, G28048T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/807/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C12789T, G12911A, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296G, C12789T, G12911AC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/808/2020
      B.1.618G27163T, G28325A, G28628T, G28922T, G28975T, A3830G, C4809T, G11083T, G14245A, C14408T, A17066G, C25844T, G27852T, A27979T, G22131A, G23012A, A23403GA3830G, C4809T, G11083TG14245A, C14408T, A17066GG22131A, G23012A, A23403GC25844TG27163TA27979TG28325A, G28628T, G28922T, G28975T
      SARS-CoV-2/
      human/CHN/809/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, C25844T, C27577T, C27972T, G28048T, A28111G, C21575T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14408TC21575T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC25844TC27577TC27972T, G28048T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/811/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/824/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, G26152T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CG26152TC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/825/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C12789T, G12911A, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296G, C12789T, G12911AC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/834/2020
      B.1.525C26305T, T26767C, C28308G, C28887T, C29274G, C6285T, G11291A, T11296G, C14407T, C14408T, C18457T, A21717G, C21762T, G23012A, A23403G, G23593C, T24224CC6285T, G11291A, T11296GC14407T, C14408T, C18457TA21717G, C21762T, G23012A, A23403G, G23593C, T24224CC26305TT26767CC28308G, C28887T, C29274G
      SARS-CoV-2/
      human/CHN/857/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, C18463T, C25427T, C27503T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, T6954C, G11291A, T11296GC14408T, C18463TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC25427TC27503TC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/859/2020
      B.1C28854T, C843T, G11222T, C14408T, A25590T, C26060T, G21578T, A23403GC843T, G11222TC14408TG21578T, A23403GA25590T, C26060TC28854T
      SARS-CoV-2/
      human/CHN/863/2020
      B.1C28854T, C843T, G11222T, C14408T, A25590T, C26060T, G21578T, A23403GC843T, G11222TC14408TG21578T, A23403GA25590T, C26060TC28854T
      SARS-CoV-2/
      human/CHN/865/2020
      B.1.1.7G28280C, A28281T, T28282A, A28295G, C28695T, G28881A, G28882A, G28883C, C28977T, C2453T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, C27972T, G28048T, A28111G, C21855T, G21974C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC2453T, C3267T, C5388A, T6954C, G11291A, T11296GC14408TC21855T, G21974C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28111GG28280C, A28281T, T28282A, A28295G, C28695T, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/872/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C3177T, C3264T, C3267T, C5388A, T6954C, C7772T, G11291A, T11296G, C14408T, G25691T, C27972T, G28048T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3177T, C3264T, C3267T, C5388A, T6954C, C7772T, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CG25691TC27972T, G28048T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/879/2020
      B.1.351C26456T, C28887T, C1059T, G5230T, A10323G, G11291A, T11296G, C12809T, C14408T, C15925T, G25563T, C25904T, G27463T, A28254C, G21641T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G5230T, A10323G, G11291A, T11296G, C12809TC14408T, C15925TG21641T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TG27463TA28254CC28887T
      SARS-CoV-2/
      human/CHN/888/2020
      B.1.351.3C26456T, C28887T, C1059T, G5230T, C6402T, A8052G, A10323G, G11291A, T11296G, C14408T, A16687G, G25563T, C25904T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G5230T, C6402T, A8052G, A10323G, G11291A, T11296GC14408T, A16687GC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TC28887T
      SARS-CoV-2/
      human/CHN/889/2020
      B.1.1.7G28280C, A28281T, T28282A, G28357T, G28881A, G28882A, G28883C, C28977T, C3177T, C3264T, C3267T, C5388A, T6954C, C7772T, G11291A, T11296G, C14408T, C15857T, G25691T, C27972T, G28048T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3177T, C3264T, C3267T, C5388A, T6954C, C7772T, G11291A, T11296GC14408T, C15857TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CG25691TC27972T, G28048T, A28111GG28280C, A28281T, T28282A, G28357T, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/890/2020
      B.1.214.2G28280C, A28281T, T28282A, C28887T, C1185T, A4457G, C5184T, C5907T, A9204G, A11430G, C12312T, C14408T, G15181T, A15187G, C19975A, C22802A, T22912G, A23403G, C23709TC1185T, A4457G, C5184T, C5907T, A9204G, A11430G, C12312TC14408T, G15349A, A18424G, C21304TC22802A, T22912G, A23403G, C23709TG28280C, A28281T, T28282A, C28887T
      SARS-CoV-2/
      human/CHN/894/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C1218T, G1805A, A2784G, C3267T, C5388A, C5849T, T6954C, G11291A, T11296G, C14408T, C27972T, G28048T, A28095T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, C24237T, T24506G, G24914CC1218T, G1805A, A2784G, C3267T, C5388A, C5849T, T6954C, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, C24237T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/895/2020
      B.1.351.3C26456T, C28887T, C1059T, G2246A, G5230T, C6402T, G6532T, A8052G, A10323G, G11291A, T11296G, C14408T, A16687G, G25563T, C25904T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TC1059T, G2246A, G5230T, C6402T, G6532T, A8052G, A10323G, G11291A, T11296GC14408T, A16687GC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664TG25563T, C25904TC26456TC28887T
      SARS-CoV-2/
      human/CHN/901/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, G28884C, C28977T, C3267T, C5388A, C5907T, T6954C, G11291A, T11296G, C14408T, G18266A, C27972T, G28048T, A28095T, A28111G, C22482T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC3267T, C5388A, C5907T, T6954C, G11291A, T11296GC14408T, G18266AA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC27972T, G28048T, A28095T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, G28884C, C28977T
      SARS-CoV-2/
      human/CHN/904/2020
      B.1.351.3C26456T, C28887T, C1059T, G2246A, G5230T, C6402T, A8052G, A10323G, G11291A, T11296G, C14408T, A16687G, G25563T, C25904T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25352TC1059T, G2246A, G5230T, C6402T, A8052G, A10323G, G11291A, T11296GC14408T, A16687GC21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25352TG25563T, C25904TC26456TC28887T
      SARS-CoV-2/
      human/CHN/911/2020
      B.1.1.25C28290T, G28881A, G28882A, G28883C, A1163T, A1193G, C1473T, A3542G, C4890T, T4974C, C5730T, A6953G, C9693T, A10323G, C14408T, G15406T, C16163T, G17581A, T20407C, T27722C, C21758G, G22205C, G23012A, A23403G, C24795TA1163T, A1193G, C1473T, A3542G, C4890T, T4974C, C5730T, A6953G, C9693T, A10323GC14408T, G15406T, C16163T, G17581A, T20407CC21758G, G22205C, G23012A, A23403G, C24795TT27722CC28290T, G28881A, G28882A, G28883C
      SARS-CoV-2/
      human/CHN/912/2020
      B.1.1.7G28280C, A28281T, T28282A, A28295G, G28881A, G28882A, G28883C, C28977T, C2453T, C3267T, T3882G, C5388A, T6954C, G11291A, T11296G, C14408T, T25502C, C27972T, G28048T, A28111G, C21855T, G21974C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CC2453T, C3267T, T3882G, C5388A, T6954C, G11291A, T11296GC14408TC21855T, G21974C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CT25502CC27972T, G28048T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, G28884C, C28977T
      SARS-CoV-2/
      human/CHN/914/2020
      B.1.1.7G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, T582C, C2003T, C3267T, C5388A, T6954C, G11291A, T11296G, C14408T, A26174G, C27972T, G28048T, A28111G, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CT582C, C2003T, C3267T, C5388A, T6954C, G11291A, T11296GC14408TA23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914CA26174GC27972T, G28048T, A28111GG28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T
      SARS-CoV-2/
      human/CHN/915/2020
      B.1.1T26604C, C28833T, G28881A, G28882A, G28883C, G29527T, C1419T, A3957G, T10721G, C14408T, G17551A, C19274A, G22017T, G23012A, A23403G, G23868TC1419T, A3957G, T10721GC14408T, G17551A, C19274AG22017T, G23012A, A23403G, G23868TT26604CC28833T, G28881A, G28882A, G28883C, G29527T

      Table S3.  Missense mutation distribution of 117 imported cases

      seqNameLineageS protein specific site (compare with nextstrain)
      GISAID reported; PMC publishedGISAID reported;
      PMC unpublished
      No reports
      and publications
      SARS-CoV-2/human/CHN/462/2020A.23.1S: R102I, S: F157L, S: V367F, S: Q613H
      SARS-CoV-2/human/CHN/464/2020B.1.2
      SARS-CoV-2/human/CHN/467/2020B.1.1
      SARS-CoV-2/human/CHN/469/2020B.1.1.368S: W152L
      SARS-CoV-2/human/CHN/471/2020B.1
      SARS-CoV-2/human/CHN/475/2020B.1.36.38
      SARS-CoV-2/human/CHN/476/2020B.1.1.228
      SARS-CoV-2/human/CHN/477/2020B.1.468
      SARS-CoV-2/human/CHN/478/2020B.1.36.22
      SARS-CoV-2/human/CHN/482/2020B.1.1.413S: V1122L
      SARS-CoV-2/human/CHN/485/2020B.1.595S: L176FS: L226F
      SARS-CoV-2/human/CHN/486/2020B.1.595S: L176FS: L226F
      SARS-CoV-2/human/CHN/488/2020B.1.2
      SARS-CoV-2/human/CHN/495/2020B.1.36.22
      SARS-CoV-2/human/CHN/496/2020B.1.402S: M1229IS: C1247R
      SARS-CoV-2/human/CHN/499/2020B.1.84S: E654K
      SARS-CoV-2/human/CHN/500/2020B.1.466.2S: N439K
      SARS-CoV-2/human/CHN/505/2020B.1.438.1S: Q675H
      SARS-CoV-2/human/CHN/507/2020B.1.429
      SARS-CoV-2/human/CHN/508/2020B.1.596S: V1228L
      SARS-CoV-2/human/CHN/509/2020B.1.170
      SARS-CoV-2/human/CHN/514/2020B.1.468
      SARS-CoV-2/human/CHN/516/2020B.1.466.2S: N439K
      SARS-CoV-2/human/CHN/521/2020B.1.170
      SARS-CoV-2/human/CHN/525/2020B.1.351
      SARS-CoV-2/human/CHN/527/2020B.1S: Y248N
      SARS-CoV-2/human/CHN/535/2020AS: A222V, S: D253Y
      SARS-CoV-2/human/CHN/538/2020B.1.177.81S: A222V
      SARS-CoV-2/human/CHN/542/2020B.1
      SARS-CoV-2/human/CHN/547/2020B.1.36.17
      SARS-CoV-2/human/CHN/558/2020L.3S: V1228LS: Y1155F,S: G75R
      SARS-CoV-2/human/CHN/559/2020B.1.1
      SARS-CoV-2/human/CHN/561/2020B.1.36.16S: D215H, S: K278N
      SARS-CoV-2/human/CHN/564/2020B.1.36.16S: D215H, S: K278N
      SARS-CoV-2/human/CHN/566/2020AS: A222V, S: D253Y
      SARS-CoV-2/human/CHN/571/2020B.1.177.81S: A222V
      SARS-CoV-2/human/CHN/585/2020B.1.36.16S: D215H, S: K278N
      SARS-CoV-2/human/CHN/587/2020B.1.427
      SARS-CoV-2/human/CHN/593/2020L.3S: V1228LS: Y1155F
      SARS-CoV-2/human/CHN/595/2020A.23.1S: F157L, S: V367F, S: D574Y, S: Q613H, S: A623S
      SARS-CoV-2/human/CHN/596/2020B.1S: D215H, S: K278N
      SARS-CoV-2/human/CHN/599/2020B.1.1.157S: M153I, S: I1130M
      SARS-CoV-2/human/CHN/600/2020B.1.351
      SARS-CoV-2/human/CHN/608/2020B.1.351
      SARS-CoV-2/human/CHN/609/2020B.1.2
      SARS-CoV-2/human/CHN/610/2020B.1.580S: L585F
      SARS-CoV-2/human/CHN/611/2020B.1.524
      SARS-CoV-2/human/CHN/613/2020B.1.1S: N439K
      SARS-CoV-2/human/CHN/623/2020B.1.1.214
      SARS-CoV-2/human/CHN/625/2020B.1.1.7S: A243S
      SARS-CoV-2/human/CHN/626/2020A.23.1S: F157L, S: V367F, S: D574Y, S: Q613H, S: A623S
      SARS-CoV-2/human/CHN/627/2020B.1.1.7S: A243S
      SARS-CoV-2/human/CHN/632/2020AS: P863S
      SARS-CoV-2/human/CHN/638/2020B.1.1.7
      SARS-CoV-2/human/CHN/639/2020B.1.2S: A570V
      SARS-CoV-2/human/CHN/642/2020B.1.1S: E654Q
      SARS-CoV-2/human/CHN/644/2020B.1.1.7
      SARS-CoV-2/human/CHN/646/2020B.1.351
      SARS-CoV-2/human/CHN/649/2020B.1.1.7
      SARS-CoV-2/human/CHN/651/2020B.1.351S: T478I
      SARS-CoV-2/human/CHN/652/2020B.1.351S: T478I
      SARS-CoV-2/human/CHN/655/2020B.1.351S: T478I
      SARS-CoV-2/human/CHN/658/2020B.1.1.222S: G257S, S: T732A
      SARS-CoV-2/human/CHN/659/2020B.1.351
      SARS-CoV-2/human/CHN/666/2020B.1S: E661D
      SARS-CoV-2/human/CHN/671/2020B.1.351
      SARS-CoV-2/human/CHN/671/2020 (1)B.1.351S: T478I
      SARS-CoV-2/human/CHN/671/2020 (2)B.1.351S: T478I
      SARS-CoV-2/human/CHN/671/2020 (3)B.1.351
      SARS-CoV-2/human/CHN/681/2020B.1.1.420S: N440K
      SARS-CoV-2/human/CHN/682/2020B.1.1.7S: V483F
      SARS-CoV-2/human/CHN/695/2020P.2S: F565L
      SARS-CoV-2/human/CHN/712/2020B.1.36S: A520S, S: E654K
      SARS-CoV-2/human/CHN/715/2020B.1.177.81S: A222V
      SARS-CoV-2/human/CHN/719/2020B.1.351
      SARS-CoV-2/human/CHN/722/2020B.1.351
      SARS-CoV-2/human/CHN/728/2020B.1.1.420S: N440K
      SARS-CoV-2/human/CHN/729/2020B.1.351
      SARS-CoV-2/human/CHN/731/2020B.1.177.81S: A222V
      SARS-CoV-2/human/CHN/736/2020B.1.1.7
      SARS-CoV-2/human/CHN/741/2020B.1.429
      SARS-CoV-2/human/CHN/761/2020C.36S: S12F
      SARS-CoV-2/human/CHN/762/2020B.1.525
      SARS-CoV-2/human/CHN/767/2020B.1.351
      SARS-CoV-2/human/CHN/779/2020B.1.1.7
      SARS-CoV-2/human/CHN/782/2020B.1.1.7
      SARS-CoV-2/human/CHN/786/2020B.1.618S: R190KS: H145-,S: Y146-
      SARS-CoV-2/human/CHN/788/2020B.1.1.7
      SARS-CoV-2/human/CHN/789/2020B.1.1.7
      SARS-CoV-2/human/CHN/798/2020B.1.1.7
      SARS-CoV-2/human/CHN/803/2020B.1.1.7
      SARS-CoV-2/human/CHN/804/2020B.1.1.7
      SARS-CoV-2/human/CHN/805/2020B.1.1.7
      SARS-CoV-2/human/CHN/807/2020B.1.1.7
      SARS-CoV-2/human/CHN/808/2020B.1.618S: R190KS: H146-,S: Y145-
      SARS-CoV-2/human/CHN/809/2020B.1.1.7
      SARS-CoV-2/human/CHN/811/2020B.1.1.7
      SARS-CoV-2/human/CHN/824/2020B.1.1.7
      SARS-CoV-2/human/CHN/825/2020B.1.1.7
      SARS-CoV-2/human/CHN/834/2020B.1.525
      SARS-CoV-2/human/CHN/857/2020B.1.1.7
      SARS-CoV-2/human/CHN/859/2020B.1S: V6F
      SARS-CoV-2/human/CHN/863/2020B.1S: V6F
      SARS-CoV-2/human/CHN/865/2020B.1.1.7S: S98F, S: D138H
      SARS-CoV-2/human/CHN/872/2020B.1.1.7
      SARS-CoV-2/human/CHN/879/2020B.1.351S: A27S
      SARS-CoV-2/human/CHN/888/2020B.1.351.3
      SARS-CoV-2/human/CHN/889/2020B.1.1.7
      SARS-CoV-2/human/CHN/890/2020B.1.214.2S: Q414K, S: N450K
      SARS-CoV-2/human/CHN/894/2020B.1.1.7S: A892V
      SARS-CoV-2/human/CHN/895/2020B.1.351.3
      SARS-CoV-2/human/CHN/901/2020B.1.1.7S: T307I
      SARS-CoV-2/human/CHN/904/2020B.1.351.3S: V1264L
      SARS-CoV-2/human/CHN/911/2020B.1.1.25S: D215H, S: A1078VS: H66D
      SARS-CoV-2/human/CHN/912/2020B.1.1.7S: S98F, S: D138H
      SARS-CoV-2/human/CHN/914/2020B.1.1.7
      SARS-CoV-2/human/CHN/915/2020B.1.1S: W152L, S: G769V

      Table S4.  PMC publication of S protein specific ectopic sites in 117 patients

      NameLineageSpecific mutation except S protein (compare with nextstrain)
      GISAID reported; PMC publishedGISAID reported; PMC unpublishedNo reports
      and publications
      SARS-CoV-2/
      human/CHN/462/2020
      A.23.1ORF1a: I1259V, ORF1a: D4165A
      SARS-CoV-2/
      human/CHN/464/2020
      B.1.2ORF3a: P274S
      SARS-CoV-2/
      human/CHN/467/2020
      B.1.1ORF1a: N2201S, ORF1b: V2223I
      SARS-CoV-2/
      human/CHN/469/2020
      B.1.1.368ORF1a: I573V
      SARS-CoV-2/
      human/CHN/471/2020
      B.1ORF1a: K247E, ORF1a: S549F,
      ORF1a: R2336K, ORF7a: D51A
      SARS-CoV-2/
      human/CHN/475/2020
      B.1.36.38ORF1a: S2695G
      SARS-CoV-2/
      human/CHN/476/2020
      B.1.1.228ORF1a: T214I
      SARS-CoV-2/
      human/CHN/477/2020
      B.1.468ORF1a: N4078S, ORF1b: R1171G
      SARS-CoV-2/
      human/CHN/478/2020
      B.1.36.22ORF1a: D75N
      SARS-CoV-2/
      human/CHN/482/2020
      B.1.1.413M: I73M,ORF1a: E87K,
      ORF1b: H73Y, ORF1b: G128C
      SARS-CoV-2/
      human/CHN/485/2020
      B.1.595M: L34F,ORF1a: I693T, ORF1a: T2611I
      SARS-CoV-2/
      human/CHN/486/2020
      B.1.595M: L34F,ORF1a: I693T, ORF1a: T2611I
      SARS-CoV-2/
      human/CHN/488/2020
      B.1.2
      SARS-CoV-2/
      human/CHN/495/2020
      B.1.36.22ORF1a: D75N
      SARS-CoV-2/
      human/CHN/496/2020
      B.1.402ORF1a: M85K, ORF1a: E87K,
      ORF1a: P943L, ORF1a: P4389S, ORF3a: V90L
      SARS-CoV-2/
      human/CHN/499/2020
      B.1.84ORF1a: V874F, ORF1b: I162V
      SARS-CoV-2/
      human/CHN/500/2020
      B.1.466.2
      SARS-CoV-2/
      human/CHN/505/2020
      B.1.438.1
      SARS-CoV-2/
      human/CHN/507/2020
      B.1.429
      SARS-CoV-2/
      human/CHN/508/2020
      B.1.596ORF1a: A4148V
      SARS-CoV-2/
      human/CHN/509/2020
      B.1.170ORF1b: P970T, ORF1b: V1092F
      SARS-CoV-2/
      human/CHN/514/2020
      B.1.468ORF1a: N4078S, ORF1b: R1171G
      SARS-CoV-2/
      human/CHN/516/2020
      B.1.466.2
      SARS-CoV-2/
      human/CHN/521/2020
      B.1.170ORF1b: P970T, ORF1b: V1092F
      SARS-CoV-2/
      human/CHN/525/2020
      B.1.351ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/527/2020
      B.1
      SARS-CoV-2/
      human/CHN/535/2020
      AORF1a: K1781E, ORF1a: R2115S,
      ORF1b: A517S
      SARS-CoV-2/
      human/CHN/538/2020
      B.1.177.81
      SARS-CoV-2/
      human/CHN/542/2020
      B.1
      SARS-CoV-2/
      human/CHN/547/2020
      B.1.36.17
      SARS-CoV-2/
      human/CHN/558/2020
      L.3
      SARS-CoV-2/
      human/CHN/559/2020
      B.1.1ORF1a: R1628C
      SARS-CoV-2/
      human/CHN/561/2020
      B.1.36.16ORF3a: T164N
      SARS-CoV-2/
      human/CHN/564/2020
      B.1.36.16ORF3a: T164N
      SARS-CoV-2/
      human/CHN/566/2020
      AORF1a: K1781E, ORF1b: A517S
      SARS-CoV-2/
      human/CHN/571/2020
      B.1.177.81
      SARS-CoV-2/
      human/CHN/585/2020
      B.1.36.16ORF3a: T164N
      SARS-CoV-2/
      human/CHN/587/2020
      B.1.427ORF1a: H1264Y, ORF1a: D1962E
      SARS-CoV-2/
      human/CHN/593/2020
      L.3
      SARS-CoV-2/
      human/CHN/595/2020
      A.23.1
      SARS-CoV-2/
      human/CHN/596/2020
      B.1ORF3a: T164N
      SARS-CoV-2/
      human/CHN/599/2020
      B.1.1.157ORF1a: G2241S, ORF1b: F1398V
      SARS-CoV-2/
      human/CHN/600/2020
      B.1.351ORF3a: L52FORF1a: T1998I, ORF1a: G3676S,
      ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/608/2020
      B.1.351ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/609/2020
      B.1.2ORF1b: D1668G
      SARS-CoV-2/
      human/CHN/610/2020
      B.1.580N: V392L, ORF1a: T2876I, ORF3a: T151A
      SARS-CoV-2/
      human/CHN/611/2020
      B.1.524ORF1a: S308L, ORF1a: A555V, ORF1a: T2791I, ORF1a: T3287A, ORF1b: P2633L
      SARS-CoV-2/
      human/CHN/613/2020
      B.1.1ORF1a: L3715F, ORF3a: S195F
      SARS-CoV-2/
      human/CHN/623/2020
      B.1.1.214
      SARS-CoV-2/
      human/CHN/625/2020
      B.1.1.7ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/626/2020
      A.23.1
      SARS-CoV-2/
      human/CHN/627/2020
      B.1.1.7ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/632/2020
      AORF3a: T217I, ORF8: P36LORF8: V33F
      SARS-CoV-2/
      human/CHN/638/2020
      B.1.1.7ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/639/2020
      B.1.2N: N8S,ORF1a: T821A,
      ORF1a: Y3803H, ORF1b: V628I
      ORF9b: I5V
      SARS-CoV-2/
      human/CHN/642/2020
      B.1.1ORF1a: M1014IORF1a: E1024G, ORF1a: K1895E
      SARS-CoV-2/
      human/CHN/644/2020
      B.1.1.7ORF1a: G3541E, ORF1a: G3676S,
      ORF1a: F3677L, ORF7b: F13-
      SARS-CoV-2/
      human/CHN/646/2020
      B.1.351ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/649/2020
      B.1.1.7ORF3a: P267SORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/651/2020
      B.1.351N: T329M, ORF3a: L52FORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/652/2020
      B.1.351ORF3a: L52FORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/655/2020
      B.1.351N: T329M, ORF3a: L52FORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/658/2020
      B.1.1.222ORF1b: T11A
      SARS-CoV-2/
      human/CHN/659/2020
      B.1.351ORF1a: G3676S, ORF1a: F3677L,
      ORF8: I47T
      SARS-CoV-2/
      human/CHN/666/2020
      B.1ORF1b: S1974I, ORF8: H112Y
      SARS-CoV-2/
      human/CHN/671/2020
      B.1.351ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/671/2020 (1)
      B.1.351N: T329M, ORF3a: L52FORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/671/2020 (2)
      B.1.351ORF3a: L52FORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/671/2020 (3)
      B.1.351ORF1a: T2977K, ORF1a: G3676S,
      ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/681/2020
      B.1.1.420
      SARS-CoV-2/
      human/CHN/682/2020
      B.1.1.7ORF1a: G3676S, ORF1a: F3677L,
      ORF1b: D1815Y
      SARS-CoV-2/
      human/CHN/695/2020
      P.2
      SARS-CoV-2/
      human/CHN/712/2020
      B.1.36ORF3a: A51SORF1a: S2352R
      SARS-CoV-2/
      human/CHN/715/2020
      B.1.177.81ORF1a: V1236F
      SARS-CoV-2/
      human/CHN/719/2020
      B.1.351ORF3a: L52FORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/722/2020
      B.1.351ORF1a: E633K, ORF1a: T1344A, ORF1a: S1856F, ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/728/2020
      B.1.1.420
      SARS-CoV-2/
      human/CHN/729/2020
      B.1.351ORF3a: L52FORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/731/2020
      B.1.177.81ORF1a: V1236F
      SARS-CoV-2/
      human/CHN/736/2020
      B.1.1.7ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/741/2020
      B.1.429M: T208IORF7a: I107V
      SARS-CoV-2/
      human/CHN/761/2020
      C.36ORF1a: G662R, ORF1a: K1230E
      SARS-CoV-2/
      human/CHN/762/2020
      B.1.525ORF6: M1-ORF1a: G3676S, ORF1a: F3677L,
      ORF1b: P314F, ORF6: F2M
      SARS-CoV-2/
      human/CHN/767/2020
      B.1.351ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/779/2020
      B.1.1.7ORF1a: V2061L, ORF1a: G3676S,
      ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/782/2020
      B.1.1.7ORF1a: G3676S, ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/786/2020
      B.1.618M: S214I,N: G18S, ORF1a: S1515FN: A217S,ORF1a: S1189G, ORF1b: D260N,ORF8: Q29L
      SARS-CoV-2/
      human/CHN/788/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/789/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/798/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/803/2020
      B.1.1.7ORF1a: D1481G,ORF1a: G3676S,
      ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/804/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/805/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L,
      ORF1b: R2049K
      SARS-CoV-2/
      human/CHN/807/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/808/2020
      B.1.618M: S214I,N: G18S,
      ORF1a: S1515F
      N: A217S,ORF1a: S1189G,
      ORF1b: D260N,ORF8: Q29L
      SARS-CoV-2/
      human/CHN/809/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/811/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/824/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/825/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/834/2020
      B.1.525ORF6: M1-N: T334R,ORF1a: G3676S, ORF1a:
      F3677L,ORF1b: P314F, ORF6: F2M
      SARS-CoV-2/
      human/CHN/857/2020
      B.1.1.7ORF1a: G3676S,ORF1a: F3677L,
      ORF1b: P1666S,ORF3a: T12I
      SARS-CoV-2/
      human/CHN/859/2020
      B.1ORF3a: K66N
      SARS-CoV-2/
      human/CHN/863/2020
      B.1ORF3a: K66N
      SARS-CoV-2/
      human/CHN/865/2020
      B.1.1.7N: N8DORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/872/2020
      B.1.1.7ORF3a: G100VORF1a: T1000I,ORF1a: G3676S,
      ORF1a: F3677L
      ORF7b: L6M,ORF7b: M1-
      SARS-CoV-2/
      human/CHN/879/2020
      B.1.351ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/888/2020
      B.1.351.3ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/889/2020
      B.1.1.7ORF3a: G100VORF1a: T1000I,ORF1a: G3676S,
      ORF1a: F3677L,N: Q28H
      ORF7b: L6M,ORF9b:
      R25I, ORF7b: M1-
      SARS-CoV-2/
      human/CHN/890/2020
      B.1.214.2ORF1b: A572SORF9b: A75V
      SARS-CoV-2/
      human/CHN/894/2020
      B.1.1.7ORF1a: G514R,ORF1a: N840S,
      ORF1a: G3676S,ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/895/2020
      B.1.351.3ORF1a: G661S,ORF1a: G3676S,
      ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/901/2020
      B.1.1.7N: G204P,ORF1a: G3676S,
      ORF1a: F3677L,ORF1b: R1600H
      SARS-CoV-2/
      human/CHN/904/2020
      B.1.351.3ORF1a: G661S,ORF1a: G3676S,
      ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/911/2020
      B.1.1.25ORF7a: I110TORF1a: N310D,ORF1a: T1093A,
      ORF1a: V1570A,ORF1a: I2230V, ORF1b: F2314L
      SARS-CoV-2/
      human/CHN/912/2020
      B.1.1.7N: N8D,ORF1a: I1206S,ORF1a: G3676S,
      ORF1a: F3677L
      SARS-CoV-2/
      human/CHN/914/2020
      B.1.1.7ORF1a: V106A,ORF1a: L580F,
      ORF1a: G3676S,ORF1a: F3677L, ORF3a: E261G
      SARS-CoV-2/
      human/CHN/915/2020
      B.1.1ORF1a: K1231R,ORF1a: F3486V

      Table S5.  PMC publication of non-S protein specific ectopic sites in 117 patients

    • We narrated the complete sequences of 117 patients with SARS-CoV-2 infection from the Guangzhou Eighth People’s Hospital, Guangdong, China, during the whole study period (June 2020 to May 2021). Based on our basic description and phylogenetic analysis of imported cases, the median age of patients in this study was younger than that of patients in earlier studies [5-7], and we noticed a close identity between the genome of the respondents and animal reference sequences [including Canis lupus family, feline, mink, ferret, Panthera leo, tiger, and Neovison vison (99.76%–99.98%)]. Similar findings were described previously in other studies (homology between rhinolophine, bat, pangolin, and human) [8-11]. New variants with several critical mutations, such as B.1.1.7, B.1.351, B.1.617, and P.1, to which the available vaccines or potential drugs may be ineffective, emerged in 2021 [12-14]. The B.1.617 variant rapidly spread to India and several countries in the world. In this study, the Indian lineage we found was sublineage B.1.618 and not the B.1.617.2 variant that was first detected and caused a pandemic in India [15]. This variant was first isolated and sequenced in Guangzhou in May 2021 [16]. Sublineages B.1.17 and B.1.351 were considered to be the main variants. They had been affiliated with the increased transmissibility of COVID-19 epidemiology and virulence, changes in clinical disease presentation, and reduced effectiveness of available vaccines and therapeutics [17,18]. In addition, we discovered the B.1.427/B.1.429, P.2, and B.1.525 variants in our studied cases. They caused community transmission or multiple clusters of COVID-19, which should arouse our attention [19-22]. Previous studies showed that D614G endowed a replication advantage to SARS-CoV-2 by increasing the feasibility of human-to-human transmission [23-25]. Given the limitations of epidemiological and clinical data, with a conservative interpretation method, we can only discover the D614G in the spike protein that presented the highest mutation density, presenting another limitation of our research.

      According to current studies, the ORF7b gene of SARS-CoV-2 with a procaspase-3 cleavage activity has a prerequisite role in viral replication[17,26]. It potentially impedes certain cellular processes that dominate several common symptoms of SARS-CoV-2 infection, such as leucine zipper formation and epithelial cell–cell adhesion, which may contribute to heart-rate disorders [26-28]. The ORF9b of SARS-CoV-2, encoding a 97-amino acid protein on the mitochondrial membrane, was located within the nucleocapsid gene (N gene) [27]. Previous studies revealed that SARS-CoV-2 ORF9b, as an accessory protein, inhibits innate immunity by targeting mitochondria. It can potentially suppress the antiviral response of infected cells and regulate the host immune response by suppressing type I interferon synthesis [29-31]. Among the various missense mutations in the 117 sequences, we disclosed some missense mutations in several sublineages (such as B.1, B.1.1.25, B.1.1.7, B.1.2, B.1.214.2, B.1.402, B.1.595, B.1.618, and L3) of partial lineages, including those from North America, Europe, Asia (excluding China), and Africa. They had neither been reported in the GISAID database nor published on PubMed and included five amino acid substitutions of the non-S positions and eight substitution sites in the S position. Given our lack of access to the information on clinical symptoms and dissemination chain in patients infected with the corresponding sublineages, we cannot prove whether these novel mutations contribute to its pathological functions (like serious symptoms: loss of speech or mobility, or confusion), spread, or adaptation to particular surroundings, including the age, pre-existing medical conditions, and living environment of the host. Our findings nevertheless provide important resources for tracking SARS-CoV-2 single-nucleotide variations, lineages, and clades in the imported cases of Southern China.

    • These imported cases in Guangdong, China, were identified, sequenced, and characterized epidemiologically and genetically, portraying the current studies on the molecular evolution of SARS-CoV-2. The descriptive epidemiology approaches demonstrated the distribution of this virus. Our phylogenetic and homology analyses increased the awareness of the detailed description of this virus. Based on the results of our viral sequence analysis, sublineage diversity and high homology at the amino acid level were present in the imported cases in Guangdong. This finding confirmed the result of a previous study reporting that SARS-CoV-2 exhibited genetic diversity over time[32]. All our results provide an important step in the search for viral variants with reduced pathogenicity or without potential pathogenicity.

    • No potential conflicts of interest were disclosed. LIANG Dan performed the experiment, drew figures, wrote the manuscript, analyzed phylogenetic relationships, completed statistical tables, and interpreted the results. WANG Tao experimented and undertook fragment assembly. ZHANG Guan Ting and LIANG Yu Feng were in charge of data analysis and statistics and performed the literature search and the experiment. HONG Wen Shan and LI An An performed the experiment and recorded the results. LI Jia Jiao, GUAN Da Wei, DENG Xiao Ling, CHEN Feng Juan, PAN Xing Fei, and LEI Chun Liang were responsible for collecting samples and collating the basic information about patients. WANG Li and CHEN Meng Lin gave advice on the diagrams in this manuscript. JIA Hong Ling was in charge of editing the English text of a draft of this manuscript. KE Chang Wen designed the whole study framework and took responsibility for the integrity and accuracy of the data.

    • The authors declare no conflict of interest.

    • The authors wish to thank Dr. LI Peng (Chinese PLA Center for Disease Control and Prevention, Beijing 510030, China) for his guidance on the diagrams in our manuscript.

      seqNameLineageSubstitutionsaaSubstitutions
      SARS-CoV-2/
      human/CHN/462/2021
      A.23.1A4040G, C4573T, C8240T, C8782T, C10747T, G11230T, G11266T, G11521T, A12759C, C16575T, C17745T, G21867T, C22000T, C22033A, G22661T, G23401T, C23604G, T24097C, G25855C, T28144C, G28167A, G28378C, G28878A, G29742AN: S202N, ORF1a: I1259V, ORF1a: H2659Y, ORF1a: M3655I, ORF1a: L3667F, ORF1a: M3752I, ORF1a: D4165A, ORF3a: D155H, ORF8: L84S, ORF8: E92K, ORF9b: R32P, S: R102I, S: F157L, S: V367F, S: Q613H, S: P681R
      SARS-CoV-2/
      human/CHN/464/2021
      B.1.2C241T, C1059T, C3037T, C3796T, G8083A, C10319T, C14408T, C14805T, A18424G, C21304T, A23403G, G25563T, G25907T, C26212T, C27964T, C28472T, C28869T, G29402T, G29736TN: P67S, N: P199L, N: D377Y, ORF1a: T265I, ORF1a: M2606I, ORF1a: L3352F, ORF1b: P314L, ORF1b: N1653D, ORF1b: R2613C, ORF3a: Q57H, ORF3a: G172V, ORF3a: P274S, ORF8: S24L, S: D614G
      SARS-CoV-2/
      human/CHN/467/2021
      B.1.1C241T, T606C, C3037T, C5806T, A6867G, C14408T, G20134A, T21640C, A23403G, C25156T, C25658T, G28881A, G28882A, G28883CN: R203K, N: G204R, ORF1a: I114T, ORF1a: N2201S, ORF1b: P314L, ORF1b: V2223I, ORF3a: T89I, S: D614G
      SARS-CoV-2/
      human/CHN/469/2021
      B.1.1.368C241T, C1101T, A1982G, C3037T, G7145A, C9996T, C14408T, C20104T, C21216T, G22017T, A23403G, G27798T, G28881A, G28882A, G28883C, G29402T, T29583CN: R203K, N: G204R, N: D377Y, ORF1a: S279F, ORF1a: I573V, ORF1a: G2294S, ORF1a: S3244L, ORF1b: P314L, ORF1b: L2213F, ORF7b: A15S, S: W152L, S: D614G
      SARS-CoV-2/
      human/CHN/471/2021
      B.1C241T, G529T, A1004G, C1420T, C1911T, C3037T, G3259T, G7272A, C10582T, T14073C, C14408T, C15324T, G15766T, A18919G, C23029T, A23403G, A27545C, G28899T, G29688TN: R209I, ORF1a: K247E, ORF1a: S549F, ORF1a: Q998H, ORF1a: R2336K, ORF1b: P314L, ORF1b: V767L, ORF1b: I1818V, ORF7a: D51A, S: D614G
      SARS-CoV-2/
      human/CHN/475/2021
      B.1.36.38C241T, T586C, T1947C, C3037T, C7006T, A8348G, A9925G, C11109T, C14408T, C16332T, C16376T, C18877T, C22444T, G22918T, A23403G, G25563T, C26735T, C28854TN: S194L, ORF1a: V561A, ORF1a: S2695G, ORF1a: A3615V, ORF1b: P314L, ORF1b: P970L, ORF3a: Q57H, S: D614G
      SARS-CoV-2/
      human/CHN/476/2021
      B.1.1.228C241T, C815T, C906T, C3037T, T4579A, C5144T, C6310T, C14408T, C15222T, A20288G, C21721T, A23403G, C23604A, G25785T, G26262T, C26894T, C28638A, G28881A, G28882A, G28883CN: P122H, N: R203K, N: G204R, ORF1a: R184C, ORF1a: T214I, ORF1b: P314L, ORF1b: E2274G, ORF3a: W131C, S: D614G, S: P681H
      SARS-CoV-2/
      human/CHN/477/2021
      B.1.468C241T, G2891A, C3037T, C6449T, C7471T, A8026G, G10793T, A12498G, C14408T, A16978G, C18877T, C22444T, A23403G, G25563T, C26735T, C27219T, G28077T, G28851TN: S193I, ORF1a: A876T, ORF1a: L2062F, ORF1a: V3510F, ORF1a: N4078S, ORF1b: P314L, ORF1b: R1171G, ORF3a: Q57H, ORF8: V62L, S: D614G
      SARS-CoV-2/
      human/CHN/478/2021
      B.1.36.22C241T, G488A, C3037T, A10323G, G10396T, C14408T, C18877T, G19542T, C22444T, A23403G, C23683T, G25563T, C25584T, C26735T, C28854T, G29543TN: S194L, ORF1a: D75N, ORF1a: K3353R, ORF1b: P314L, ORF1b: M2025I, ORF3a: Q57H, S: D614G
      SARS-CoV-2/
      human/CHN/482/2021
      B.1.1.413C44T, C241T, G524A, A604G, C3037T, C12076T, C13684T, G13849T, C14408T, G21974T, G22992A, A23403G, G24926T, G25647T, G25690T, A26741G, C28291T, G28881A, G28882A, G28883C, C29311TM: I73M, N: R203K, N: G204R, ORF1a: E87K, ORF1b: H73Y, ORF1b: G128C, ORF1b: P314L, ORF3a: L85F, ORF3a: G100C, ORF8: K68E, ORF9b: P3L, S: D138Y, S: S477N, S: D614G, S: V1122L
      SARS-CoV-2/
      human/CHN/485/2021
      B.1.595C241T, C1059T, T2343C, C3037T, C3411T, C6310T, T6394C, C8097T, C10319T, A12421T, C14408T, G19009T, C22088T, G22240T, A23403G, G25563T, C26622T, C27964T, C28887T, C29366TM: L34F, N: T205I, N: P365S, ORF1a: T265I, ORF1a: I693T, ORF1a: A1049V, ORF1a: T2611I, ORF1a: L3352F, ORF1b: P314L, ORF1b: D1848Y, ORF3a: Q57H, ORF8: S24L, S: L176F, S: L226F, S: D614G
      SARS-CoV-2/
      human/CHN/486/2021
      B.1.595C241T, C1059T, T2343C, C3037T, C3411T, C6310T, T6394C, C8097T, C10319T, A12421T, C14408T, G19009T, C22088T, G22240T, A23403G, G25563T, C26622T, C27964T, C28887T, C29366TM: L34F, N: T205I, N: P365S, ORF1a: T265I, ORF1a: I693T, ORF1a: A1049V, ORF1a: T2611I, ORF1a: L3352F, ORF1b: P314L, ORF1b: D1848Y, ORF3a: Q57H, ORF8: S24L, S: L176F, S: L226F, S: D614G
      SARS-CoV-2/
      human/CHN/488/2021
      B.1.2C241T, C1059T, C3037T, C3796T, G8083A, C10319T, C14408T, C14805T, A18424G, C21304T, C22450T, A23403G, G25563T, G25907T, C27964T, C28472T, C28869T, G29402T, G29736TN: P67S, N: P199L, N: D377Y, ORF1a: T265I, ORF1a: M2606I, ORF1a: L3352F, ORF1b: P314L, ORF1b: N1653D, ORF1b: R2613C, ORF3a: Q57H, ORF3a: G172V, ORF8: S24L, S: D614G
      SARS-CoV-2/
      human/CHN/495/2021
      B.1.36.22C241T, G488A, C3037T, A10323G, G10396T, C14408T, C18877T, G19542T, C20132T, C22444T, A23403G, C23683T, G25563T, C25584T, C26735T, C28854T, G29543TN: S194L, ORF1a: D75N, ORF1a: K3353R, ORF1b: P314L, ORF1b: M2025I, ORF1b: A2222V, ORF3a: Q57H, S: D614G
      SARS-CoV-2/
      human/CHN/496/2021
      B.1.402C241T, C478T, T519A, G524A, C875T, C2416T, C3037T, C3093T, C7735T, A11023G, G11083T, C13430T, C14408T, T14643C, C16767T, C19718T, A23403G, C24418T, A24862T, G25249T, T25301C, G25563T, G25660C, C28854TN: S194L, ORF1a: M85K, ORF1a: E87K, ORF1a: L204F, ORF1a: P943L, ORF1a: L3606F, ORF1a: P4389S, ORF1b: P314L, ORF1b: T2084I, ORF3a: Q57H, ORF3a: V90L, S: D614G, S: M1229I, S: C1247R
      SARS-CoV-2/
      human/CHN/499/2021
      B.1.84C241T, T814G, G2885T, C3037T, G4300T, T6130C, C7267T, A12577G, A13951G, C14408T, C15324T, G19117T, A21131G, A23403G, G23522A, T23797C, C25624T, C28890T, T29656A, T29832CN: S206F, ORF1a: V874F, ORF1b: I162V, ORF1b: P314L, ORF1b: A1884S, ORF1b: Q2555R, ORF3a: H78Y, S: D614G, S: E654K
      SARS-CoV-2/
      human/CHN/500/2021
      B.1.466.2C241T, C3037T, C3768T, C5184T, C14408T, C18877T, C20389T, C22879A, A23403G, G25563T, C26735T, C28887TN: T205I, ORF1a: T1168I, ORF1a: P1640L, ORF1b: P314L, ORF1b: R2308C, ORF3a: Q57H, S: N439K, S: D614G
      SARS-CoV-2/
      human/CHN/505/2021
      B.1.438.1C241T, A1154G, C3037T, C8152T, C10702T, A12121G, C14408T, C18877T, A23403G, G23587T, G25563T, G25677T, A28272G, G28975T, G29474TN: M234I, N: D401Y, ORF1a: M297V, ORF1b: P314L, ORF3a: Q57H, ORF3a: L95F, S: D614G, S: Q675H
      SARS-CoV-2/human/CHN/507/2021B.1.429C241T, C1059T, C2395T, A2406G, T2597C, C3037T, A5780G, C7528T, A12878G, C14408T, G15452T, C16338T, G17014T, G21600T, G22018T, T22917G, A23403G, T24349C, G25563T, G25912A, C26681T, C27889T, G27890T, A28272T, C28887T, C29362TN: T205I, ORF1a: T265I, ORF1a: K714R, ORF1a: I1839V, ORF1a: I4205V, ORF1b: P314L, ORF1b: G662V, ORF1b: D1183Y, ORF3a: Q57H, ORF3a: G174S, S: S13I, S: W152C, S: L452R, S: D614G
      SARS-CoV-2/
      human/CHN/508/2021
      B.1.596C241T, C829T, C1059T, C1627T, T1927A, C3037T, C3738T, A5852G, C10319T, C12708T, C14408T, A18424G, A23403G, G25244T, C25521T, G25563T, G25907T, T27336A, C27964T, C28472T, C28869TN: P67S, N: P199L, ORF1a: T265I, ORF1a: P1158L, ORF1a: I1863V, ORF1a: L3352F, ORF1a: A4148V, ORF1b: P314L, ORF1b: N1653D, ORF3a: Q57H, ORF3a: G172V, ORF8: S24L, S: D614G, S: V1228L
      SARS-CoV-2/
      human/CHN/509/2021
      B.1.170T41C, C241T, C3037T, C5833T, C10207T, T11525C, T12811C, C14408T, C14925T, C16375A, G16741T, C18501T, C18877T, A23403G, C23533T, G25563T, A25864G, T27299C, T28229C, C28977T, T29233CN: S235F, ORF1b: P314L, ORF1b: P970T, ORF1b: V1092F, ORF3a: Q57H, ORF3a: I158V, ORF6: I33T, S: D614G
      SARS-CoV-2/
      human/CHN/514/2021
      B.1.468C241T, G2891A, C3037T, C6449T, C7471T, A8026G, G10793T, A12498G, C14408T, A16978G, C18877T, C22444T, A23403G, G25563T, C26735T, C27219T, G28077T, G28851TN: S193I, ORF1a: A876T, ORF1a: L2062F, ORF1a: V3510F, ORF1a: N4078S, ORF1b: P314L, ORF1b: R1171G, ORF3a: Q57H, ORF8: V62L, S: D614G
      SARS-CoV-2/
      human/CHN/516/2021
      B.1.466.2C241T, C3037T, C3768T, C5184T, C14408T, C18877T, C20389T, C22879A, A23403G, G25563T, C26735T, C28887TN: T205I, ORF1a: T1168I, ORF1a: P1640L, ORF1b: P314L, ORF1b: R2308C, ORF3a: Q57H, S: N439K, S: D614G
      SARS-CoV-2/
      human/CHN/521/2021
      B.1.170T41C, C241T, C3037T, C5833T, C10207T, T11525C, T12811C, C14408T, C14925T, C16375A, G16741T, C18501T, C18877T, A23403G, C23533T, G25563T, A25864G, T27299C, T28229C, C28977T, T29233CN: S235F, ORF1b: P314L, ORF1b: P970T, ORF1b: V1092F, ORF3a: Q57H, ORF3a: I158V, ORF6: I33T, S: D614G
      SARS-CoV-2/
      human/CHN/525/2021
      B.1.351G174T, C241T, C1059T, A2692T, C3037T, C3817T, C3924T, G5230T, A10323G, G11291A, T11296G, C14408T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25904T, C26456T, C26894T, C28253T, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: P1220L, ORF1a: K1655N, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: Q57H, ORF3a: S171L, S: L18F, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/527/2021
      B.1C241T, C1059T, C3037T, C14408T, T22304A, A23403G, G25563TORF1a: T265I, ORF1b: P314L, ORF3a: Q57H, S: Y248N, S: D614G
      SARS-CoV-2/
      human/CHN/535/2021
      AA5606G, C6539T, A6610T, T8215C, C8782T, C9223T, C9226T, G11230T, A11746G, G15016T, T17136C, C17439T, C18171T, C22227T, G22319T, A23403G, T24736C, C25487T, G25563T, A26019T, G28028T, G28178T, C28292A, G28878A, C29272T, G29742AN: Q7K, N: S202N, ORF1a: K1781E, ORF1a: H2092Y, ORF1a: R2115S, ORF1a: M3655I, ORF1b: A517S, ORF3a: T32I, ORF3a: Q57H, ORF8: W45C, ORF8: L95F, S: A222V, S: D253Y, S: D614G
      SARS-CoV-2/
      human/CHN/538/2021
      B.1.177.81C241T, T445C, C2638A, C3037T, C6286T, C10376T, C12119T, C14408T, A21222T, G21255C, C22227T, A23403G, C25889T, C26801G, C27944T, C28932T, G29645TN: A220V, ORF1a: P3371S, ORF1a: P3952S, ORF1b: P314L, ORF3a: S166L, S: A222V, S: D614G
      SARS-CoV-2/
      human/CHN/542/2021
      B.1C241T, C3037T, C14408T, A23403G, G25563T, G25912A, C26681T, C28887TN: T205I, ORF1b: P314L, ORF3a: Q57H, ORF3a: G174S, S: D614G
      SARS-CoV-2/
      human/CHN/547/2021
      B.1.36.17C241T, T1947C, C3037T, G3431T, T5653C, C5654T, G5950A, G8179T, T8593C, C11674T, C14408T, C18877T, G19891T, A20289G, C22444T, A23403G, G25563T, C26060T, C26735T, C28854T, C29555TN: S194L, ORF1a: V561A, ORF1a: V1056L, ORF1b: P314L, ORF1b: D2142Y, ORF3a: Q57H, ORF3a: T223I, S: D614G
      SARS-CoV-2/
      human/CHN/558/2021
      L.3C241T, C1601T, C3037T, G4399T, C4543T, G8179T, C8481T, A9453C, C11565T, C12406T, C14408T, C19170T, C19269T, G19509A, T20376C, G21785C, T22917G, A23403G, T24850G, A25026T, G25244T, G26918T, A26927G, G28881A, G28882A, G28883CN: R203K, N: G204R, ORF1a: L446F, ORF1a: M1378I, ORF1a: P2739L, ORF1a: Y3063S, ORF1a: P3767L, ORF1b: P314L, S: G75R, S: L452R, S: D614G, S: Y1155F, S: V1228L
      SARS-CoV-2/
      human/CHN/559/2021
      B.1.1C241T, G2229A, A2923G, C3037T, A4870G, C5147T, C10834T, C12400T, C14408T, A23403G, G25644T, G26063T, G28881A, G28882A, G28883CN: R203K, N: G204R, ORF1a: C655Y, ORF1a: R1628C, ORF1b: P314L, ORF3a: G224V, S: D614G
      SARS-CoV-2/
      human/CHN/561/2021
      B.1.36.16C241T, C1594T, C1878T, C3037T, T7480C, T10099C, G11083T, G11596T, G12188T, A13012T, C14408T, G16377A, G18756T, C18877T, G22205C, A22396C, C22444T, A23403G, G25494T, G25563T, C25883A, C26735T, G28077T, C28854TN: S194L, ORF1a: S538L, ORF1a: L3606F, ORF1a: Q3777H, ORF1a: V3975F, ORF1b: P314L, ORF3a: Q57H, ORF3a: T164N, ORF8: V62L, S: D215H, S: K278N, S: D614G
      SARS-CoV-2/
      human/CHN/564/2021
      B.1.36.16C241T, C1594T, C1878T, C3037T, T7480C, T10099C, G11083T, G11596T, G12188T, A13012T, C14408T, G16377A, G18756T, C18877T, G22205C, A22396C, C22444T, A23403G, G25494T, G25563T, C25883A, C26735T, G28077T, C28854TN: S194L, ORF1a: S538L, ORF1a: L3606F, ORF1a: Q3777H, ORF1a: V3975F, ORF1b: P314L, ORF3a: Q57H, ORF3a: T164N, ORF8: V62L, S: D215H, S: K278N, S: D614G
      SARS-CoV-2/
      human/CHN/566/2021
      AA5606G, C6539T, T8215C, C8782T, C9223T, C9226T, G11230T, A11746G, G15016T, T17136C, C17439T, C18171T, C22227T, G22319T, A23403G, T24736C, C25487T, G25563T, A26019T, G28028T, G28178T, C28292A, G28878A, C29272T, G29742AN: Q7K, N: S202N, ORF1a: K1781E, ORF1a: H2092Y, ORF1a: M3655I, ORF1b: A517S, ORF3a: T32I, ORF3a: Q57H, ORF8: W45C, ORF8: L95F, S: A222V, S: D253Y, S: D614G
      SARS-CoV-2/
      human/CHN/571/2021
      B.1.177.81C241T, T445C, C2638A, C3037T, C6286T, C10376T, C12119T, C14408T, A21222T, G21255C, C22227T, A23403G, C25889T, C26801G, C27944T, C28932T, G29645TN: A220V, ORF1a: P3371S, ORF1a: P3952S, ORF1b: P314L, ORF3a: S166L, S: A222V, S: D614G
      SARS-CoV-2/
      human/CHN/585/2021
      B.1.36.16C241T, C1594T, C1878T, C3037T, T7480C, T10099C, G11083T, G11596T, G12188T, A13012T, C14408T, G16377A, G18756T, C18877T, G22205C, A22396C, C22444T, A23403G, G25494T, G25563T, C25883A, C26735T, G28077T, C28854TN: S194L, ORF1a: S538L, ORF1a: L3606F, ORF1a: Q3777H, ORF1a: V3975F, ORF1b: P314L, ORF3a: Q57H, ORF3a: T164N, ORF8: V62L, S: D215H, S: K278N, S: D614G
      SARS-CoV-2/
      human/CHN/587/2021
      B.1.427C241T, C1059T, C3037T, C4055T, C6151A, G9738C, C9996T, G13713A, C14408T, C16394T, G17014T, G21600T, G22018T, G22468T, T22917G, A23403G, G25563T, C26681T, A28272T, C28887T, C29362T, C29509TN: T205I, ORF1a: T265I, ORF1a: H1264Y, ORF1a: D1962E, ORF1a: S3158T, ORF1a: S3244L, ORF1b: P314L, ORF1b: P976L, ORF1b: D1183Y, ORF3a: Q57H, S: S13I, S: W152C, S: L452R, S: D614G
      SARS-CoV-2/
      human/CHN/593/2021
      L.3C241T, C1601T, C3037T, G4399T, C4543T, G8179T, C8481T, C8692T, A9453C, C11565T, C12406T, C14408T, C19170T, C19269T, G19509A, T22917G, A23403G, A25026T, G25244T, A26927G, G28178T, G28881A, G28882A, G28883CN: R203K, N: G204R, ORF1a: L446F, ORF1a: M1378I, ORF1a: P2739L, ORF1a: Y3063S, ORF1a: P3767L, ORF1b: P314L, ORF8: L95F, S: L452R, S: D614G, S: Y1155F, S: V1228L
      SARS-CoV-2/
      human/CHN/595/2021
      A.23.1C337T, C2695T, C4573T, C8782T, C10747T, G11230T, G11266T, G11521T, C16575T, C17745T, C20325T, C21058T, C22000T, C22033A, G22661T, G23282T, G23401T, G23429T, C23604G, T24097C, T28144C, G28167A, C28278A, G28378C, G28878A, G28881A, C29200T, G29254A, G29742AN: S2Y, N: S202N, N: R203K, ORF1a: M3655I, ORF1a: L3667F, ORF1a: M3752I, ORF1b: P2531S, ORF8: L84S, ORF8: E92K, ORF9b: R32P, S: F157L, S: V367F, S: D574Y, S: Q613H, S: A623S, S: P681R
      SARS-CoV-2/
      human/CHN/596/2021
      B.1T4579A, C5144T, C6310T, C16575T, C17745T, G22205C, A22396C, C22444T, A23403G, G25494T, G25563T, C25883A, C26735T, G28077T, G28881A, G28882A, G28883CN: R203K, N: G204R, ORF3a: Q57H, ORF3a: T164N, ORF8: V62L, S: D215H, S: K278N, S: D614G
      SARS-CoV-2/
      human/CHN/599/2021
      B.1.1.157C241T, C3037T, C4158T, C5339T, C6145T, G6986A, T8603C, G11272A, C13378T, C14408T, A17615G, T17659G, C17678T, G22021T, A23403G, A24952G, G28881A, G28882A, G28883CN: R203K, N: G204R, ORF1a: A1298V, ORF1a: P1692S, ORF1a: G2241S, ORF1a: F2780L, ORF1a: M3669I, ORF1b: P314L, ORF1b: K1383R, ORF1b: F1398V, ORF1b: T1404M, S: M153I, S: D614G, S: I1130M
      SARS-CoV-2/
      human/CHN/600/2021
      B.1.351T52C, G174T, C241T, C1059T, C3037T, G5230T, C6258T, A10323G, G11291A, T11296G, C14408T, A14463G, T18342A, C19803T, A21801C, A22206G, G22813T, G23012A, A23403G, C23664T, C25546T, G25563T, C25904T, C26456T, C27059T, C28253T, A28254C, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: K1655N, ORF1a: T1998I, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: L52F, ORF3a: Q57H, ORF3a: S171L, ORF8: I121L, S: D80A, S: D215G, S: K417N, S: E484K, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/608/2021
      B.1.351G174T, C241T, C1059T, A2692T, C3037T, C4276T, G5230T, A10323G, G11291A, T11296G, C14408T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25904T, C26456T, C28253T, C28310T, C28887TE: P71L, N: P13S, N: T205I, ORF1a: T265I, ORF1a: K1655N, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: Q57H, ORF3a: S171L, S: L18F, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/609/2021
      B.1.2C241T, C1059T, T1927C, C2106T, C3037T, C5310T, C6312T, C10319T, C14408T, G15766T, A18424G, A18470G, G18538T, C20133T, C21219T, C21304T, A22255T, A23403G, G25563T, G25907T, T25930C, C27964T, C28472T, C28869T, A29439TN: P67S, N: P199L, N: Q389L, ORF1a: T265I, ORF1a: T614I, ORF1a: T1682I, ORF1a: T2016I, ORF1a: L3352F, ORF1b: P314L, ORF1b: V767L, ORF1b: N1653D, ORF1b: D1668G, ORF1b: V1691L, ORF1b: R2613C, ORF3a: Q57H, ORF3a: G172V, ORF3a: S180P, ORF8: S24L, S: D614G
      SARS-CoV-2/
      human/CHN/610/2021
      B.1.580C241T, C1059T, T1791C, C3037T, C6997T, C8892T, A10323G, G11417T, C14408T, G18255T, G20679T, C23315T, A23403G, G25563T, A25843G, C26895T, G28842T, G29447TM: H125Y, N: S190I, N: V392L, ORF1a: T265I, ORF1a: F509S, ORF1a: T2876I, ORF1a: K3353R, ORF1a: V3718F, ORF1b: P314L, ORF1b: M1596I, ORF3a: Q57H, ORF3a: T151A, S: L585F, S: D614G
      SARS-CoV-2/
      human/CHN/611/2021
      B.1.524C241T, C1188T, C1929T, C3037T, C5869T, C6312T, C8637T, A10124G, C14408T, C17518T, C21365T, C21516T, C21622A, A23403G, C23664T, A28133T, C28854T, C29272T, G29751TN: S194L, ORF1a: S308L, ORF1a: A555V, ORF1a: T2016I, ORF1a: T2791I, ORF1a: T3287A, ORF1b: P314L, ORF1b: L1351F, ORF1b: P2633L, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/613/2021
      B.1.1C241T, C3037T, C3411T, G11083T, T11218C, G11410T, C14408T, C22879G, A23403G, C23929T, G24928T, C25976T, G26104T, C26894T, C27889T, T28251G, C28253T, A28254C, G28881A, G28882A, G28883C, G28985TN: R203K, N: G204R, N: G238C, ORF1a: A1049V, ORF1a: L3606F, ORF1a: L3715F, ORF1b: P314L, ORF3a: S195F, ORF3a: D238Y, ORF8: F120V, ORF8: I121L, S: N439K, S: D614G
      SARS-CoV-2/
      human/CHN/623/2021
      B.1.1.214C241T, C313T, C3037T, C5365T, C8917T, C12049T, C14408T, C18167T, G20560T, C20703T, G21518T, A23403G, C26735T, G28881A, G28882A, G28883C, G28975T, C29679T, C29784TN: R203K, N: G204R, N: M234I, ORF1b: P314L, ORF1b: P1567L, ORF1b: V2365F, ORF1b: R2684I, S: D614G
      SARS-CoV-2/
      human/CHN/625/2021
      B.1.1.7C241T, C913T, C2110T, C3037T, C3267T, C5388A, C5986T, T6954C, G7042T, G11291A, T11296G, C14120T, C14408T, C14676T, C15279T, T16176C, G22289T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: M2259I, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P218L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: A243S, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/626/2021
      A.23.1C337T, C2695T, C4573T, C8782T, C10747T, G11230T, G11266T, G11521T, C16575T, C17745T, C20325T, C21058T, C22000T, C22033A, G22661T, G23282T, G23401T, G23429T, C23604G, T24097C, T28144C, G28167A, C28278A, G28378C, G28878A, G28881A, G29742AN: S2Y, N: S202N, N: R203K, ORF1a: M3655I, ORF1a: L3667F, ORF1a: M3752I, ORF1b: P2531S, ORF8: L84S, ORF8: E92K, ORF9b: R32P, S: F157L, S: V367F, S: D574Y, S: Q613H, S: A623S, S: P681R
      SARS-CoV-2/
      human/CHN/627/2021
      B.1.1.7C241T, C913T, C2110T, C3037T, C3267T, C5388A, C5986T, T6954C, G7042T, G11291A, T11296G, C14120T, C14408T, C14676T, C15279T, T16176C, G22289T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: M2259I, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P218L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: A243S, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/632/2021
      AG922A, C8782T, T11077C, G11230T, A16227G, A23403G, A24067G, C24149T, C26042T, G27990T, C28000T, T28144C, G28167A, G28878A, G29742AN: S202N, ORF1a: M3655I, ORF3a: T217I, ORF8: V33F, ORF8: P36L, ORF8: L84S, ORF8: E92K, S: D614G, S: P863S
      SARS-CoV-2/
      human/CHN/638/2021
      B.1.1.7C241T, C913T, C2110T, C3037T, C3267T, C5388A, C5986T, T6954C, T7984C, C10747T, G11291A, T11296G, C14120T, C14408T, C14676T, C15279T, T16176C, C19390T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P218L, ORF1b: P314L, ORF1b: P1975S, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/639/2021
      B.1.2C241T, C1059T, A2726G, C3037T, C3966T, T6025C, C10319T, T11672C, C12784T, C14408T, G15349A, A18424G, C21304T, C23271T, A23403G, C23758T, G25563T, G25907T, C27964T, A28296G, C28472T, C28869TN: N8S, N: P67S, N: P199L, ORF1a: T265I, ORF1a: T821A, ORF1a: A1234V, ORF1a: L3352F, ORF1a: Y3803H, ORF1b: P314L, ORF1b: V628I, ORF1b: N1653D, ORF1b: R2613C, ORF3a: Q57H, ORF3a: G172V, ORF8: S24L, ORF9b: I5V, S: A570V, S: D614G
      SARS-CoV-2/
      human/CHN/642/2021
      B.1.1C241T, C3037T, G3307T, A3336G, T5619C, A5948G, C10279T, G11417T, C12115T, C12525T, C14408T, T22925C, A23403G, G23522C, C24023T, C26060T, C26469T, G28881A, G28882A, G28883CN: R203K, N: G204R, ORF1a: M1014I, ORF1a: E1024G, ORF1a: I1785T, ORF1a: K1895E, ORF1a: V3718F, ORF1a: T4087I, ORF1b: P314L, ORF3a: T223I, S: D614G, S: E654Q
      SARS-CoV-2/
      human/CHN/644/2021
      B.1.1.7C241T, C913T, C2110T, C3037T, C3267T, C5388A, C5986T, C6843T, T6954C, T7984C, G10887A, G11291A, T11296G, C14120T, C14408T, C14676T, C15279T, T16176C, C19390T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: S2193F, ORF1a: I2230T, ORF1a: G3541E, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P218L, ORF1b: P314L, ORF1b: P1975S, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/646/2021
      B.1.351G160T, G174T, C241T, C1059T, A2692T, C3037T, C4276T, G5230T, A10323G, G11291A, T11296G, C14408T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25904T, C26456T, C28253T, C28310T, C28887TE: P71L, N: P13S, N: T205I, ORF1a: T265I, ORF1a: K1655N, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: Q57H, ORF3a: S171L, S: L18F, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/649/2021
      B.1.1.7C241T, C913T, C3037T, C3045T, C3267T, C5388A, C5986T, T6954C, C9344T, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, A23063T, C23271A, A23403G, C23604A, C23709T, C24109T, T24506G, G24914C, C26191T, G26828A, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: P927L, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: L3027F, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: P267S, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/651/2021
      B.1.351G174T, C241T, T606C, C1059T, C3037T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, C17999T, C19803T, C21110T, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664T, C25546T, G25563T, C25904T, C26456T, C27059T, C28253T, A28254C, C28887T, C29259TE: P71L, N: T205I, N: T329M, ORF1a: I114T, ORF1a: T265I, ORF1a: K1655N, ORF1a: T3032I, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: T1511I, ORF1b: T2548I, ORF3a: L52F, ORF3a: Q57H, ORF3a: S171L, ORF8: I121L, S: D80A, S: D215G, S: K417N, S: T478I, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/652/2021
      B.1.351G174T, C241T, T606C, C1059T, C3037T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, C17999T, C19803T, C21110T, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664T, C25546T, G25563T, C25904T, C26456T, C27059T, C28253T, A28254C, C28887TE: P71L, N: T205I, ORF1a: I114T, ORF1a: T265I, ORF1a: K1655N, ORF1a: T3032I, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: T1511I, ORF1b: T2548I, ORF3a: L52F, ORF3a: Q57H, ORF3a: S171L, ORF8: I121L, S: D80A, S: D215G, S: K417N, S: T478I, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/655/2021
      B.1.351G174T, C241T, T606C, C1059T, C3037T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, C17999T, C19803T, C21110T, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664T, C25546T, G25563T, C25904T, C26456T, C27059T, C28253T, A28254C, C28887T, C29259TE: P71L, N: T205I, N: T329M, ORF1a: I114T, ORF1a: T265I, ORF1a: K1655N, ORF1a: T3032I, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: T1511I, ORF1b: T2548I, ORF3a: L52F, ORF3a: Q57H, ORF3a: S171L, ORF8: I121L, S: D80A, S: D215G, S: K417N, S: T478I, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/658/2021
      B.1.1.222C241T, C3037T, T3295C, C10165T, C11345T, A13498G, C14408T, C17586T, T19839C, G22331A, A23403G, A23756G, C25549T, C28253T, A28254C, G28881A, G28882A, G28883CN: R203K, N: G204R, ORF1a: L3694F, ORF1b: T11A, ORF1b: P314L, ORF3a: L53F, ORF8: I121L, S: G257S, S: D614G, S: T732A
      SARS-CoV-2/
      human/CHN/659/2021
      B.1.351G174T, C241T, C1059T, A2692T, C3037T, G5230T, A10323G, G11291A, T11296G, C14408T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, G25650A, C25904T, C26456T, C26645T, T28033C, C28253T, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: K1655N, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: Q57H, ORF3a: S171L, ORF8: I47T, S: L18F, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/666/2021
      B.1C241T, C3037T, A3069G, C5884T, C8964T, C10341T, G11083T, G11230T, C14408T, G15380T, G16197A, T18144C, G19388T, C21646T, A23403G, G23545T, G25621A, C26060T, T27908C, G28028T, C28227TORF1a: D935G, ORF1a: S2900L, ORF1a: P3359L, ORF1a: L3606F, ORF1a: M3655I, ORF1b: P314L, ORF1b: S638I, ORF1b: S1974I, ORF3a: V77I, ORF3a: T223I, ORF8: W45C, ORF8: H112Y, S: D614G, S: E661D
      SARS-CoV-2/
      human/CHN/671/2021
      B.1.351G174T, C241T, C1059T, A2692T, C3037T, C5100T, G5230T, A10323G, G11291A, T11296G, C14408T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25904T, C26456T, G27870T, C28253T, C28887T, C29358TE: P71L, N: T205I, N: T362I, ORF1a: T265I, ORF1a: S1612L, ORF1a: K1655N, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: Q57H, ORF3a: S171L, ORF7b: E39*, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/672/2021
      B.1.351G174T, C241T, T606C, C1059T, C3037T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, G15451A, C17999T, C19803T, C21110T, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664T, C25546T, G25563T, C25904T, C26456T, C27059T, C28253T, A28254C, C28887T, C29259TE: P71L, N: T205I, N: T329M, ORF1a: I114T, ORF1a: T265I, ORF1a: K1655N, ORF1a: T3032I, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: G662S, ORF1b: T1511I, ORF1b: T2548I, ORF3a: L52F, ORF3a: Q57H, ORF3a: S171L, ORF8: I121L, S: D80A, S: D215G, S: K417N, S: T478I, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/676/2021
      B.1.351G174T, C241T, T606C, C1059T, C3037T, G5230T, C9360T, A10323G, G11291A, T11296G, C14408T, C17999T, C19803T, C21110T, A21801C, A22206G, G22813T, C22995T, G23012A, A23063T, A23403G, C23664T, C25546T, G25563T, C25904T, C26456T, C27059T, C28253T, A28254C, C28887TE: P71L, N: T205I, ORF1a: I114T, ORF1a: T265I, ORF1a: K1655N, ORF1a: T3032I, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: T1511I, ORF1b: T2548I, ORF3a: L52F, ORF3a: Q57H, ORF3a: S171L, ORF8: I121L, S: D80A, S: D215G, S: K417N, S: T478I, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/678/2021
      B.1.351G174T, C241T, C1059T, G1068A, A2692T, C3037T, G5230T, C8290T, C9195A, A10323G, G11291A, T11296G, C14408T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25904T, C26456T, C26645T, C28253T, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: G268E, ORF1a: K1655N, ORF1a: T2977K, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: Q57H, ORF3a: S171L, S: L18F, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/681/2021
      B.1.1.420G61A, C241T, T847C, C3037T, G3994T, C5178T, C5548T, C5842T, A10258G, A11451G, C12115T, C13694T, C14408T, G16710A, C16767T, T18132C, C18138T, C19884T, C21614T, T22882G, A23403G, G23593T, A24373G, G25839T, C28310T, G28727T, T28862A, G28881A, G28882A, G28883CN: P13S, N: A152S, N: S197T, N: R203K, N: G204R, ORF1a: T1638I, ORF1a: Q3729R, ORF1b: T76I, ORF1b: P314L, ORF3a: W149C, S: L18F, S: N440K, S: D614G, S: Q677H
      SARS-CoV-2/
      human/CHN/682/2021
      B.1.1.7C241T, C913T, C2110T, G2539A, C3037T, C3267T, C5388A, C5986T, T6954C, T7984C, G11291A, T11296G, C14120T, C14408T, C14676T, C15279T, T16176C, G18910T, C19390T, G23009T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P218L, ORF1b: P314L, ORF1b: D1815Y, ORF1b: P1975S, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: V483F, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/695/2021
      P.2C100T, C241T, C3037T, T10667G, C11824T, C12053T, C12488T, A12964G, C14408T, G23012A, T23255C, A23403G, G25088T, C27972T, C28253T, G28628T, G28881A, G28882A, G28883C, G28975T, C29754TN: A119S, N: R203K, N: G204R, N: M234I, ORF1a: L3468V, ORF1a: L3930F, ORF1a: P4075S, ORF1b: P314L, ORF8: Q27*, S: E484K, S: F565L, S: D614G, S: V1176F
      SARS-CoV-2/
      human/CHN/712/2021
      B.1.36G174T, C241T, T1947C, C3037T, C7321G, C9163T, G11417T, G11521T, C14408T, C16111T, C18744T, C18877T, C19186T, C22444T, G23120T, A23403G, G23522A, G23593T, G25543T, G25563T, C25867T, C26735T, C27213T, A27690G, C28854T, G29179T, C29614TN: S194L, ORF1a: V561A, ORF1a: S2352R, ORF1a: V3718F, ORF1a: M3752I, ORF1b: P314L, ORF3a: A51S, ORF3a: Q57H, ORF3a: P159S, S: A520S, S: D614G, S: E654K, S: Q677H
      SARS-CoV-2/
      human/CHN/715/2021
      B.1.177.81C241T, T445C, C3037T, G3971T, C6286T, C10228T, C12119T, C14408T, A21222T, G21255C, C22227T, A23403G, T23407C, C25844T, C25889T, C26801G, C27944T, C28932T, G29645TN: A220V, ORF1a: V1236F, ORF1a: P3952S, ORF1b: P314L, ORF3a: T151I, ORF3a: S166L, S: A222V, S: D614G
      SARS-CoV-2/
      human/CHN/719/2021
      B.1.351G174T, C241T, C1059T, C3037T, G5230T, C6285T, A10323G, G11291A, T11296G, C13329T, C14408T, C17999T, C19803T, C21110T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, C25546T, G25563T, C25904T, C26456T, C27059T, C27128T, C27998T, C28253T, A28254C, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: K1655N, ORF1a: T2007I, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1a: T4355I, ORF1b: P314L, ORF1b: T1511I, ORF1b: T2548I, ORF3a: L52F, ORF3a: Q57H, ORF3a: S171L, ORF8: I121L, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/722/2021
      B.1.351G174T, A231G, C241T, C1059T, G2162A, A2692T, C3037T, A4295G, C5100T, G5230T, C5832T, A10323G, G11291A, T11296G, C14408T, G17122T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25904T, C26456T, C27476T, G28001C, C28253T, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: E633K, ORF1a: T1344A, ORF1a: S1612L, ORF1a: K1655N, ORF1a: S1856F, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: A1219S, ORF3a: Q57H, ORF3a: S171L, ORF7a: T28I, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/728/2021
      B.1.1.420G61A, C241T, T847C, C3037T, G3994T, C5178T, C5548T, C5842T, A10258G, A11451G, C12115T, C13694T, C14408T, G16710A, C16767T, T18132C, C18138T, C19884T, C21614T, T22882G, A23403G, G23593T, A24373G, G25839T, C28310T, G28727T, T28862A, G28881A, G28882A, G28883CN: P13S, N: A152S, N: S197T, N: R203K, N: G204R, ORF1a: T1638I, ORF1a: Q3729R, ORF1b: T76I, ORF1b: P314L, ORF3a: W149C, S: L18F, S: N440K, S: D614G, S: Q677H
      SARS-CoV-2/
      human/CHN/729/2021
      B.1.351G174T, C241T, C1059T, C3037T, G5230T, C6285T, A10323G, G11291A, T11296G, C13329T, C14408T, C17999T, C19803T, C21110T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, C25546T, G25563T, C25904T, C26456T, C27059T, C27128T, C27998T, C28253T, A28254C, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: K1655N, ORF1a: T2007I, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1a: T4355I, ORF1b: P314L, ORF1b: T1511I, ORF1b: T2548I, ORF3a: L52F, ORF3a: Q57H, ORF3a: S171L, ORF8: I121L, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/731/2021
      B.1.177.81C241T, T445C, C3037T, G3971T, C6286T, C10228T, C12119T, C14408T, A21222T, G21255C, C22227T, A23403G, T23407C, C25844T, C25889T, C26801G, C27944T, C28932T, G29645TN: A220V, ORF1a: V1236F, ORF1a: P3952S, ORF1b: P314L, ORF3a: T151I, ORF3a: S166L, S: A222V, S: D614G
      SARS-CoV-2/
      human/CHN/736/2021
      B.1.1.7C241T, C913T, C1825T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, C17862T, A23063T, C23271A, A23403G, C23604A, C23709T, C24109T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C29585TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/741/2021
      B.1.429C241T, C1059T, C2395T, T2597C, C3037T, C5907T, C6255T, C6285T, C7081T, C8947T, G10051A, C12100T, A12878G, C14408T, G17014T, G19419A, G21600T, G22018T, T22917G, A23403G, T24349C, G25563T, C26681T, C27145T, A27712G, G27890T, A28272T, C28887T, C29203T, C29218T, C29362TM: T208I, N: T205I, ORF1a: T265I, ORF1a: T1881I, ORF1a: A1997V, ORF1a: T2007I, ORF1a: I4205V, ORF1b: P314L, ORF1b: D1183Y, ORF3a: Q57H, ORF7a: I107V, S: S13I, S: W152C, S: L452R, S: D614G
      SARS-CoV-2/
      human/CHN/761/2021
      C.36C241T, G569A, C936T, C1347T, C1427T, G2249A, C2841T, C3037T, C4002T, C4586T, G5180A, C7124T, G9929A, G10097A, T11337C, G12163A, C12534T, C13536T, C14408T, G17122T, G17218A, A17743T, C17766T, G18546T, C21597T, T22917G, A23329G, A23403G, G23593T, C23731T, G27882T, G28881A, G28882A, G28883C, G28908TN: R203K, N: G204R, N: G212V, ORF1a: E102K, ORF1a: T224I, ORF1a: P361L, ORF1a: H388Y, ORF1a: G662R, ORF1a: A859V, ORF1a: K1230E, ORF1a: T1246I, ORF1a: D1639N, ORF1a: P2287S, ORF1a: D3222N, ORF1a: G3278S, ORF1a: L3691S, ORF1a: T4090I, ORF1b: P314L, ORF1b: A1219S, ORF1b: D1251N, ORF1b: N1426Y, ORF1b: M1693I, ORF7b: A43S, S: S12F, S: L452R, S: D614G, S: Q677H
      SARS-CoV-2/
      human/CHN/762/2021
      B.1.525C241T, C1498T, A1807G, G2659A, C3037T, C6285T, T8593C, C9565T, G11291A, T11296G, C14407T, C14408T, C18171T, A20724G, A21717G, C21762T, G23012A, A23403G, G23593C, T24224C, C24748T, C26305T, T26767C, C28308G, A28699G, C28887T, G29543TE: L21F, M: I82T, N: S2M, N: D3Y, N: A12G, N: T205I, ORF1a: T2007I, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314F, ORF6: F2M, ORF9b: H9D, S: Q52R, S: A67V, S: E484K, S: D614G, S: Q677H, S: F888L
      SARS-CoV-2/
      human/CHN/767/2021
      B.1.351G174T, C241T, C1059T, A2692T, C3037T, A3222G, C5100T, G5230T, A10323G, G11291A, T11296G, C14408T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25904T, C26456T, G27870T, C28253T, C28887T, C29358TE: P71L, N: T205I, N: T362I, ORF1a: T265I, ORF1a: Q986R, ORF1a: S1612L, ORF1a: K1655N, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: Q57H, ORF3a: S171L, ORF7b: E39*, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/779/2021
      B.1.1.7C241T, C913T, C2110T, C3037T, C3267T, C5388A, C5986T, G6446C, T6954C, C10252T, G11291A, T11296G, C14120T, C14408T, C14676T, C15279T, T16176C, T20409C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, G27014T, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, A29248CN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: V2061L, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P218L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/782/2021
      B.1.1.7C241T, C913T, T2734C, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C12789T, G12911A, C14408T, C14676T, T15096C, C15279T, T16176C, C18486T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, C28846T, G28881A, G28882A, G28883C, C28977T, T29804AN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1a: T4175I, ORF1a: V4216I, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/786/2021
      B.1.618G105T, C241T, C853T, C1684T, C3037T, A3830G, C4809T, T5263C, G11083T, C11950T, T13114C, G14245A, C14408T, A17066G, G22131A, G23012A, A23403G, C23644T, T25084C, C25844T, C26885T, G26909T, G27163T, G27852T, A27979T, G28325A, G28628T, G28922T, G28975TM: S214I, N: G18S, N: A119S, N: A217S, N: M234I, ORF1a: S1189G, ORF1a: S1515F, ORF1a: L3606F, ORF1b: D260N, ORF1b: P314L, ORF1b: Y1200C, ORF3a: T151I, ORF7b: E33*, ORF8: Q29L, S: R190K, S: E484K, S: D614G
      SARS-CoV-2/
      human/CHN/788/2021
      B.1.1.7C241T, C913T, C1825T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, C17862T, A23063T, C23271A, A23403G, C23604A, C23709T, C24109T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C29585TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/789/2021
      B.1.1.7C241T, C913T, C1825T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, C17862T, A23063T, C23271A, A23403G, C23604A, C23709T, C24109T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C29585TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/798/2021
      B.1.1.7C241T, C913T, T2734C, C3037T, C3267T, C5388A, C5497T, C5986T, T6954C, G11291A, T11296G, C12789T, G12911A, C14408T, C14676T, T15096C, C15279T, T16176C, C18486T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, C28846T, G28881A, G28882A, G28883C, C28977T, T29804AN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1a: T4175I, ORF1a: V4216I, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/803/2021
      B.1.1.7C241T, C913T, C3037T, C3267T, A4707G, C5388A, C5986T, T6954C, C9661T, G11291A, T11296G, C13458T, C14408T, C14676T, C15279T, T16176C, A17615G, C21742T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, T27531C, C27972T, G28048T, A28111G, C28253T, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: D1481G, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1a: S4398L, ORF1b: P314L, ORF1b: K1383R, ORF8: Q27*, ORF8: R52I, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/804/2021
      B.1.1.7C241T, C913T, C1825T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, C17862T, A23063T, C23271A, A23403G, C23604A, C23709T, C24109T, T24506G, G24914C, G26152T, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C29585TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: G254*, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/805/2021
      B.1.1.7C241T, C913T, C2453T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, C15279T, T16176C, C16726T, G19613A, T22159C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27294T, C27577T, C27972T, G28048T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: L730F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: H1087Y, ORF1b: R2049K, ORF7a: Q62*, ORF8: Q27*, ORF8: R52I, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/807/2021
      B.1.1.7C241T, C913T, T2734C, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C12789T, G12911A, C14408T, C14676T, T15096C, C15279T, T16176C, C18486T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, C28846T, G28881A, G28882A, G28883C, C28977T, T29804AN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1a: T4175I, ORF1a: V4216I, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/808/2021
      B.1.618G105T, C241T, C853T, C1684T, C3037T, A3830G, C4809T, T5263C, G11083T, C11950T, T13114C, G14245A, C14408T, A17066G, G22131A, G23012A, A23403G, C23644T, T25084C, C25844T, C26885T, G26909T, G27163T, G27852T, A27979T, G28325A, G28628T, G28922T, G28975TM: S214I, N: G18S, N: A119S, N: A217S, N: M234I, ORF1a: S1189G, ORF1a: S1515F, ORF1a: L3606F, ORF1b: D260N, ORF1b: P314L, ORF1b: Y1200C, ORF3a: T151I, ORF7b: E33*, ORF8: Q29L, S: R190K, S: E484K, S: D614G
      SARS-CoV-2/
      human/CHN/809/2021
      B.1.1.7C241T, C913T, C3037T, C3267T, C5388A, C5986T, T6954C, C8950T, G11291A, T11296G, C14408T, C14676T, A15033T, C15279T, T16176C, C19524T, C21234T, C21575T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C25844T, C27577T, C27972T, G28048T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, T29524CN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: T151I, ORF7a: Q62*, ORF8: Q27*, ORF8: R52I, ORF8: Y73C, S: L5F, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/811/2021
      B.1.1.7C241T, C913T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, C14724T, T15096C, C15279T, T16176C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, A29209TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/824/2021
      B.1.1.7C241T, C913T, C1825T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, C17862T, A23063T, C23271A, A23403G, C23604A, C23709T, C24109T, T24506G, G24914C, G26152T, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, C29585TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: G254*, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/825/2021
      B.1.1.7C241T, C913T, T2734C, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C12789T, G12911A, C14408T, C14676T, T15096C, C15279T, T16176C, C18486T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, C28846T, G28881A, G28882A, G28883C, C28977T, T29804AN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1a: T4175I, ORF1a: V4216I, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/834/2021
      B.1.525C241T, C1498T, A1807G, G2659A, C3037T, C6285T, T8593C, C9565T, G11291A, T11296G, C14407T, C14408T, C18171T, C18457T, A20724G, A21717G, C21762T, G23012A, A23403G, G23593C, T24224C, C24370T, C24748T, C26305T, T26767C, C28308G, A28699G, C28887T, C29274G, G29543T, T29804AE: L21F, M: I82T, N: S2M, N: D3Y, N: A12G, N: T205I, N: T334R, ORF1a: T2007I, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314F, ORF1b: P1664S, ORF6: F2M, ORF9b: H9D, S: Q52R, S: A67V, S: E484K, S: D614G, S: Q677H, S: F888L
      SARS-CoV-2/
      human/CHN/857/2021
      B.1.1.7C241T, C913T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, C16323T, C18463T, A23063T, C23271A, A23403G, C23604A, C23709T, C24109T, T24506G, G24914C, C25427T, C27503T, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: P1666S, ORF3a: T12I, ORF7a: S37F, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/859/2021
      B.1C241T, C292T, C843T, T1537C, C3037T, G11222T, C14408T, A20268G, G21123T, G21578T, A23403G, A25590T, C26060T, C26873T, C27881T, C28854T, G29449T, T29524C, C29738TN: S194L, ORF1a: P193L, ORF1a: V3653F, ORF1b: P314L, ORF3a: K66N, ORF3a: T223I, S: V6F, S: D614G
      SARS-CoV-2/
      human/CHN/863/2021
      B.1C241T, C292T, C843T, T1537C, C3037T, G11222T, C14408T, A20268G, G21123T, G21578T, A23403G, A25590T, C26060T, C26873T, C27881T, C28854T, G29449T, T29524C, C29738TN: S194L, ORF1a: P193L, ORF1a: V3653F, ORF1b: P314L, ORF3a: K66N, ORF3a: T223I, S: V6F, S: D614G
      SARS-CoV-2/
      human/CHN/865/2021
      B.1.1.7C241T, C913T, C2453T, C2644T, C3037T, C3267T, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, C15279T, T16176C, C19602T, C21855T, G21974C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28111G, G28280C, A28281T, T28282A, A28295G, C28695T, G28881A, G28882A, G28883C, C28977TN: D3L, N: N8D, N: T141I, N: R203K, N: G204R, N: S235F, ORF1a: L730F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: Y73C, S: S98F, S: D138H, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/872/2021
      B.1.1.7C241T, C913T, C3037T, C3177T, C3264T, C3267T, C5388A, C5986T, T6954C, C7772T, C7844T, G11291A, T11296G, C14408T, C14676T, C15279T, T16176C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, G25691T, C27972T, G28048T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: P971L, ORF1a: T1000I, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: L2503F, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: G100V, ORF7b: L6M, ORF8: Q27*, ORF8: R52I, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/879/2021
      B.1.351G174T, C241T, C1059T, C3037T, T4213C, G5230T, A10323G, G11291A, T11296G, C11812A, C12809T, C14408T, C15925T, T17970C, G21641T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, T23449G, C23664T, A23764T, G25563T, C25904T, C26456T, G27463T, C28253T, A28254C, T28642C, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: K1655N, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1a: L4182F, ORF1b: P314L, ORF1b: L820F, ORF3a: Q57H, ORF3a: S171L, ORF7a: V24F, ORF8: I121L, S: A27S, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/888/2021
      B.1.351.3G174T, C241T, C1059T, A2692T, C3037T, G5230T, C6402T, T7624C, A8052G, A10323G, G10396T, C10615T, G11291A, T11296G, C14408T, A16687G, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25603T, C25904T, C26456T, C28253T, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: K1655N, ORF1a: P2046L, ORF1a: N2596S, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: I1074V, ORF3a: Q57H, ORF3a: S171L, S: L18F, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/889/2021
      B.1.1.7C241T, C913T, C3037T, C3177T, C3264T, C3267T, C5388A, C5986T, T6954C, C7772T, C7844T, G11291A, T11296G, C14408T, C14676T, C15279T, C15857T, T16176C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, G25691T, C27972T, G28048T, A28111G, G28280C, A28281T, T28282A, G28357T, G28881A, G28882A, G28883C, C28977TN: D3L, N: Q28H, N: R203K, N: G204R, N: S235F, ORF1a: P971L, ORF1a: T1000I, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: L2503F, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: T797I, ORF3a: G100V, ORF7b: L6M, ORF8: Q27*, ORF8: R52I, ORF8: Y73C, ORF9b: R25I, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/890/2021
      B.1.214.2C241T, C1185T, C3037T, A4457G, C4891T, C5184T, C5907T, A9204G, C11224T, A11430G, C12312T, C14408T, G15181T, A15187G, C15324T, C19975A, C21811T, C22802A, T22912G, A23403G, C23709T, T27576C, C27800T, G28280C, A28281T, T28282A, C28507T, C28846T, C28887T, C29730TN: D3L, N: T205I, ORF1a: A307V, ORF1a: I1398V, ORF1a: P1640L, ORF1a: T1881I, ORF1a: D2980G, ORF1a: Y3722C, ORF1a: A4016V, ORF1b: P314L, ORF1b: A572S, ORF1b: R574G, ORF1b: L2170I, ORF9b: A75V, S: Q414K, S: N450K, S: D614G, S: T716I
      SARS-CoV-2/
      human/CHN/894/2021
      B.1.1.7C241T, C913T, C1218T, G1805A, A2784G, C3037T, C3267T, C5388A, C5849T, C5986T, G6421T, T6954C, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, A18000G, A23063T, C23271A, A23403G, C23604A, C23709T, C24237T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, C28977T, T29377A, G29449T, C29686TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: S318L, ORF1a: G514R, ORF1a: N840S, ORF1a: T1001I, ORF1a: A1708D, ORF1a: P1862S, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: A892V, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/895/2021
      B.1.351.3G174T, C241T, C1059T, G2246A, A2692T, C3037T, G5230T, C6402T, G6532T, T7624C, A8052G, A10323G, G10396T, C10615T, G11291A, T11296G, C12974T, C14408T, A16687G, C21411T, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25563T, C25904T, C26456T, C28253T, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: G661S, ORF1a: K1655N, ORF1a: P2046L, ORF1a: E2089D, ORF1a: N2596S, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: I1074V, ORF3a: Q57H, ORF3a: S171L, S: L18F, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V
      SARS-CoV-2/
      human/CHN/901/2021
      B.1.1.7C241T, C913T, C2701T, C3037T, C3267T, C5388A, C5907T, C5944T, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, T15096C, C15279T, T16176C, G18266A, T21763C, C22482T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28095T, A28111G, G28280C, A28281T, T28282A, G28881A, G28882A, G28883C, G28884C, C28977TN: D3L, N: R203K, N: G204P, N: S235F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: T1881I, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: R1600H, ORF8: Q27*, ORF8: R52I, ORF8: K68*, ORF8: Y73C, S: T307I, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/904/2021
      B.1.351.3G174T, C241T, C1059T, G2246A, A2692T, C3037T, G5230T, C6402T, T7624C, A8052G, A10323G, G10396T, C10615T, G11291A, T11296G, C14408T, A16687G, C21614T, A21801C, A22206G, G22813T, G23012A, A23063T, A23403G, C23664T, G25352T, G25563T, C25904T, C26456T, C28253T, C28887TE: P71L, N: T205I, ORF1a: T265I, ORF1a: G661S, ORF1a: K1655N, ORF1a: P2046L, ORF1a: N2596S, ORF1a: K3353R, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF1b: I1074V, ORF3a: Q57H, ORF3a: S171L, S: L18F, S: D80A, S: D215G, S: K417N, S: E484K, S: N501Y, S: D614G, S: A701V, S: V1264L
      SARS-CoV-2/
      human/CHN/911/2021
      B.1.1.25C106T, C241T, A1163T, A1193G, C1473T, C3037T, G3250A, A3542G, C4890T, T4974C, C5730T, A6953G, T9022C, C9693T, A10323G, C11620T, C12754T, C14408T, G15406T, C16163T, G17581A, T20407C, C21758G, G22205C, T22342A, G23012A, A23403G, C24795T, A27270G, T27722C, C28290T, G28321A, G28881A, G28882A, G28883CN: P6L, N: R203K, N: G204R, ORF1a: I300F, ORF1a: N310D, ORF1a: T403I, ORF1a: T1093A, ORF1a: T1542I, ORF1a: V1570A, ORF1a: T1822I, ORF1a: I2230V, ORF1a: A3143V, ORF1a: K3353R, ORF1b: P314L, ORF1b: A647S, ORF1b: T899I, ORF1b: V1372I, ORF1b: F2314L, ORF7a: I110T, ORF9b: P3S, ORF9b: R13H, S: H66D, S: D215H, S: E484K, S: D614G, S: A1078V
      SARS-CoV-2/
      human/CHN/912/2021
      B.1.1.7C241T, C913T, C1102T, C2453T, C3037T, C3267T, T3882G, C5388A, C5986T, T6954C, G11291A, T11296G, C14408T, C14676T, C15279T, C15852T, T16176C, C21855T, G21974C, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, T25502C, C27972T, G28048T, A28111G, G28280C, A28281T, T28282A, A28295G, G28881A, G28882A, G28883C, C28977TN: D3L, N: N8D, N: R203K, N: G204R, N: S235F, ORF1a: L730F, ORF1a: T1001I, ORF1a: I1206S, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: I37T, ORF8: Q27*, ORF8: R52I, ORF8: Y73C, S: S98F, S: D138H, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/914/2021
      B.1.1.7C241T, C274T, T582C, C913T, C2003T, C3037T, C3267T, C5388A, C5986T, T6954C, C9857T, G11291A, T11296G, C14408T, C14676T, C15279T, T16176C, A23063T, C23271A, A23403G, C23604A, C23709T, T24143C, T24506G, G24914C, A26174G, A26981C, C27972T, G28048T, A28111G, G28280C, A28281T, T28282A, C28531T, G28881A, G28882A, G28883C, C28977TN: D3L, N: R203K, N: G204R, N: S235F, ORF1a: V106A, ORF1a: L580F, ORF1a: T1001I, ORF1a: A1708D, ORF1a: I2230T, ORF1a: G3676S, ORF1a: F3677L, ORF1b: P314L, ORF3a: E261G, ORF8: Q27*, ORF8: R52I, ORF8: Y73C, ORF9b: T83I, S: N501Y, S: A570D, S: D614G, S: P681H, S: T716I, S: S982A, S: D1118H
      SARS-CoV-2/
      human/CHN/915/2021
      B.1.1C241T, G529T, C829T, C1419T, T1834C, C3037T, A3957G, C5192T, T10721G, C14340T, C14408T, G16377T, G17551A, C18877T, A19167G, C19274A, T19839C, G22017T, G23012A, A23403G, G23868T, T26076C, T26604C, C27213T, C28606T, C28833T, G28881A, G28882A, G28883C, G29422A, G29527T, G29745TM: F28L, N: S187L, N: R203K, N: G204R, N: Q418H, ORF1a: A385V, ORF1a: K1231R, ORF1a: F3486V, ORF1b: P314L, ORF1b: G1362R, ORF1b: P1936H, S: W152L, S: E484K, S: D614G, S: G769V

      Table S1.  Mutations distribution of 117 imported cases

      seqNameLineageNonsense mutationORF1aORF1bSORF3aEMOEF6ORF7aORF8NORF10
      SARS-CoV-2/
      human/CHN/462/2020
      A.23.1C4573T, C8782T, C10747T, C16575T, C17745T, C22000T, T24097C, G28378C, G29742AC4573T, C8782T, C10747TC16575T,
      C17745T
      C22000T,
      T24097C
      G28378C
      SARS-CoV-2/
      human/CHN/464/2020
      B.1.2C241T, C3037T, C3796T, C14805T, G29736TC3037T, C3796TC14805T
      SARS-CoV-2/
      human/CHN/467/2020
      B.1.1C241T, C3037T, C5806T, T21640C, C25156TC3037T, C5806TT21640C, C25156T
      SARS-CoV-2/
      human/CHN/469/2020
      B.1.1.368C241T, C3037T, C21216T, T29583CC3037TC21216TT29583C
      SARS-CoV-2/
      human/CHN/471/2020
      B.1C241T, G529T, C1420T, C3037T, C10582T, T14073C, C15324T, C23029T, G29688TG529T, C1420T, C3037T, C10582TT14073C, C15324TC23029T
      SARS-CoV-2/
      human/CHN/475/2020
      B.1.36.38C241T, T586C, C3037T, C7006T, A9925G, C16332T, C18877T, C22444T, G22918T, C26735TT586C, C3037T, C7006T, A9925GC16332T, C18877TC22444T, G22918TC26735T
      SARS-CoV-2/
      human/CHN/476/2020
      B.1.1.228C241T, C3037T, T4579A, C5144T, C6310T, C15222T, C21721T, G26262T, C26894TC3037T, T4579A, C5144T, C6310TC15222TC21721TG26262T26894T
      SARS-CoV-2/
      human/CHN/477/2020
      B.1.468C241T, C3037T, C7471T, A8026G, C18877T, C22444T, C26735T, C27219TC3037T, C7471T, A8026GC18877TC22444TC26735TC27219T
      SARS-CoV-2/
      human/CHN/478/2020
      B.1.36.22C241T, C3037T, G10396T, C18877T, C22444T, C23683T, C25584T, C26735T, G29543TC3037T, G10396TC18877TC22444T, C23683TC25584TC26735T
      SARS-CoV-2/
      human/CHN/482/2020
      B.1.1.413C44T, C241T, A604G, C3037T, C12076T, C28291T, C29311TA604G, C3037T, C12076TC28291T, C29311T
      SARS-CoV-2/
      human/CHN/485/2020
      B.1.595C241T, C3037T, C6310T, T6394C, A12421TC3037T, C6310T, T6394C, A12421T
      SARS-CoV-2/
      human/CHN/486/2020
      B.1.595C241T, C3037T, C6310T, T6394C, A12421TC3037T, C6310T, T6394C, A12421T
      SARS-CoV-2/
      human/CHN/488/2020
      B.1.2C241T, C3037T, C3796T, C14805T, C22450T, G29736TC3037T, C3796TC14805TC22450T
      SARS-CoV-2/
      human/CHN/495/2020
      B.1.36.22C241T, C3037T, G10396T, C18877T, C22444T, C23683T, C25584T, C26735T, G29543TC3037T, G10396TC18877TC22444T, C23683TC25584TC26735T
      SARS-CoV-2/
      human/CHN/496/2020
      B.1.402C241T, C478T, C2416T, C3037T, C7735T, A11023G, T14643C, C16767T, C24418T, A24862TC478T, C2416T, C3037T, C7735T, A11023GT14643C, C16767T, C24418T, A24862T
      SARS-CoV-2/
      human/CHN/499/2020
      B.1.84C241T, T814G, C3037T, G4300T, T6130C, C7267T, A12577G, C15324T, T23797C, T29656A, T29832CT814G, C3037T, G4300T, T6130C, C7267T, A12577GC15324TT23797CT29656A
      SARS-CoV-2/
      human/CHN/500/2020
      B.1.466.2C241T, C3037T, C18877T, C26735TC3037TC18877TC26735T
      SARS-CoV-2/
      human/CHN/505/2020
      B.1.438.1C241T, C3037T, C8152T, C10702T, A12121G, C18877T, A28272GC3037T, C8152T, C10702T, A12121GC18877T
      SARS-CoV-2/
      human/CHN/507/2020
      B.1.429C241T, C2395T, T2597C, C3037T, C7528T, C16338T, T24349C, C26681T, C27889T, G27890T, A28272T, C29362TC3037T, C7528TC16338TT24349CC26681TC29362T
      SARS-CoV-2/
      human/CHN/508/2020
      B.1.596C241T, C829T, C1627T, T1927A, C3037T, C25521T, T27336AC829T, C1627T, T1927A, C3037TC25521TT27336A
      SARS-CoV-2/
      human/CHN/509/2020
      B.1.170T41C, C241T, C3037T, C5833T, C10207T, T11525C, T12811C, C14925T, C18501T, C18877T, C23533T, T28229C, T29233CC3037T, C5833T, C10207T, T11525C, T12811CC14925T, C18501T, C18877TC23533TT28229CT29233C
      SARS-CoV-2/
      human/CHN/514/2020
      B.1.468C241T, C3037T, C7471T, A8026G, C18877T, C22444T, C26735T, C27219TC3037T, C7471T, A8026GC18877TC22444TC26735TC27219T
      SARS-CoV-2/
      human/CHN/516/2020
      B.1.466.2C241T, C3037T, C18877T, C26735TC3037TC18877TC26735T
      SARS-CoV-2/
      human/CHN/521/2020
      B.1.170T41C, C241T, C3037T, C5833T, C10207T, T11525C, T12811C, C14925T, C18501T, C18877T, C23533T, T28229C, T29233CC3037T, C5833T, C10207T, T11525C, T12811CC14925T, C18501T, C18877TC23533TT28229CT29233C
      SARS-CoV-2/
      human/CHN/525/2020
      B.1.351G174T, C241T, A2692T, C3037T, C3817T, C26894T, C28253TA2692T, C3037T, C3817TC26894TC28253T
      SARS-CoV-2/
      human/CHN/527/2020
      B.1C241T, C3037TC3037T
      SARS-CoV-2/
      human/CHN/535/2020
      AT8215C, C8782T, C9223T, C9226T, A11746G, T17136C, C17439T, C18171T, T24736C, A26019T, C29272T, G29742AT8215C, C8782T, C9223T, C9226T, A11746GT17136C, C17439T, C18171TT24736CA26019TC29272T
      SARS-CoV-2/
      human/CHN/538/2020
      B.1.177.81C241T, T445C, C2638A, C3037T, C6286T, A21222T, G21255C, C26801G, C27944T, G29645TT445C, C2638A, C3037T, C6286TA21222T, G21255CC26801GC27944TG29645T
      SARS-CoV-2/
      human/CHN/542/2020
      B.1C241T, C3037T, C26681TC3037TC26681T
      SARS-CoV-2/
      human/CHN/547/2020
      B.1.36.17C241T, C3037T, T5653C, C5654T, G5950A, G8179T, T8593C, C11674T, C18877T, A20289G, C22444T, C26735T, C29555TC3037T, T5653C, C5654T, G5950A, G8179T, T8593C, C11674TC18877T, A20289GC22444TC26735TC29555T
      SARS-CoV-2/
      human/CHN/558/2020
      L.3C241T, C3037T, C4543T, G8179T, C12406T, C19170T, C19269T, G19509A, T20376C, T24850G, G26918T, A26927GC3037T, C4543T, G8179T, C12406TC19170T, C19269T, G19509A, T20376CT24850GG26918T, A26927G
      SARS-CoV-2/
      human/CHN/559/2020
      B.1.1C241T, A2923G, C3037T, A4870G, C10834T, C12400T, G25644TA2923G, C3037T, A4870G, C10834T, C12400TG25644T
      SARS-CoV-2/
      human/CHN/561/2020
      B.1.36.16C241T, C1594T, C3037T, T7480C, T10099C, A13012T, G16377A, G18756T, C18877T, C22444T, G25494T, C26735TC1594T, C3037T, T7480C, T10099C, A13012TG16377A, G18756T, C18877TC22444TG25494TC26735T
      SARS-CoV-2/
      human/CHN/564/2020
      B.1.36.16C241T, C1594T, C3037T, T7480C, T10099C, A13012T, G16377A, G18756T, C18877T, C22444T, G25494T, C26735TC1594T, C3037T, T7480C, T10099C, A13012TG16377A, G18756T, C18877TC22444TG25494TC26735T
      SARS-CoV-2/
      human/CHN/566/2020
      AT8215C, C8782T, C9223T, C9226T, A11746G, T17136C, C17439T, C18171T, T24736C, A26019T, C29272T, G29742AT8215C, C8782T, C9223T, C9226T, A11746GT17136C, C17439T, C18171TT24736CA26019TC29272T
      SARS-CoV-2/
      human/CHN/571/2020
      B.1.177.81C241T, T445C, C2638A, C3037T, C6286T, A21222T, G21255C, C26801G, C27944T, G29645TT445C, C2638A, C3037T, C6286TA21222T, G21255CC26801GC27944TG29645T
      SARS-CoV-2/
      human/CHN/585/2020
      B.1.36.16C241T, C1594T, C3037T, T7480C, T10099C, A13012T, G16377A, G18756T, C18877T, C22444T, G25494T, C26735TC1594T, C3037T, T7480C, T10099C, A13012TG16377A, G18756T, C18877TC22444TG25494TC26735T
      SARS-CoV-2/
      human/CHN/587/2020
      B.1.427C241T, C3037T, G13713A, G22468T, C26681T, A28272T, C29362T, C29509TC3037T, C5869TG13713AG22468TC26681TC29362T, C29509T
      SARS-CoV-2/
      human/CHN/593/2020
      L.3C241T, C3037T, C4543T, G8179T, C8692T, C12406T, C19170T, C19269T, G19509A, A26927GC3037T, C4543T, G8179T, C8692T, C12406TC19170T, C19269T, G19509AA26927G
      SARS-CoV-2/
      human/CHN/595/2020
      A.23.1C337T, C2695T, C4573T, C8782T, C10747T, C16575T, C17745T, C20325T, C22000T, T24097C, G28378C, C29200T, G29254A, G29742AC337T, C2695T, C4573T, C8782T, C10747TC16575T, C17745T, C20325TT24097CG28378C, C29200T, G29254A
      SARS-CoV-2/
      human/CHN/596/2020
      B.1T4579A, C5144T, C6310T, C16575T, C17745T, C22444T, G25494T, C26735TT4579A, C5144T, C6310TC16575T, C17745TC22444TG25494TC26735T
      SARS-CoV-2/
      human/CHN/599/2020
      B.1.1.157C241T, C3037T, C6145T, C13378TC3037T, C6145TC13378T
      SARS-CoV-2/
      human/CHN/600/2020
      B.1.351T52C, G174T, C241T, C3037T, A14463G, T18342A, C19803T, C27059T, C28253TC3037TA14463G, T18342A, C19803TC27059TC28253T
      SARS-CoV-2/
      human/CHN/608/2020
      B.1.351G174T, C241T, A2692T, C3037T, C4276T, C28253TA2692T, C3037T, C4276TC28253T
      SARS-CoV-2/
      human/CHN/609/2020
      B.1.2C241T, T1927C, C3037T, C20133T, C21219T, A22255TT1927C, C3037TC20133T, C21219T
      SARS-CoV-2/
      human/CHN/610/2020
      B.1.580C241T, C3037T, C6997T, G20679TC3037T, C6997TG20679T
      SARS-CoV-2/
      human/CHN/611/2020
      B.1.524C241T, C3037T, C5869T, C21516T, C21622A, A28133T, C29272T, G29751TC3037T, C5869TC21516T, C21622AA28133TG29751T
      SARS-CoV-2/
      human/CHN/613/2020
      B.1.1C241T, C3037T, T11218C, C23929T, G24928T, C26894T, C27889TC3037T, T11218CC23929T, G24928TC26894T
      SARS-CoV-2/
      human/CHN/623/2020
      B.1.1.214C241T, C313T, C3037T, C5365T, C8917T, C12049T, C20703T, C26735T, C29679T, C29784TC313T, C3037T, C5365T, C8917T, C12049TC12049T, C20703TC26735T
      SARS-CoV-2/
      human/CHN/625/2020
      B.1.1.7C241T, C913T, C2110T, C3037T, C5986T, C14676T, C15279T, T16176CC913T, C2110T, C3037T, C5986TC14676T, C15279T, T16176C
      SARS-CoV-2/
      human/CHN/626/2020
      A.23.1C337T, C2695T, C4573T, C8782T, C10747T, C16575T, C17745T, C20325T, C22000T, T24097C, G28378C, G29742AC337T, C2695T, C4573T, C8782T, C10747TC16575T, C17745T, C20325TC22000T, T24097CG28378C
      SARS-CoV-2/
      human/CHN/627/2020
      B.1.1.7C241T, C913T, C2110T, C3037T, C5986T, C14676T, C15279T, T16176CC913T, C2110T, C3037T, C5986TC14676T, C15279T, T16176C
      SARS-CoV-2/
      human/CHN/632/2020
      AG922A, C8782T, T11077C, A16227G, A24067G, G29742AG922A, C8782T, T11077CA16227GA24067G
      SARS-CoV-2/
      human/CHN/638/2020
      B.1.1.7C241T, C913T, C2110T, C3037T, C5986T, T7984C, C10747T, C14676T, C15279T, T16176CC913T, C2110T, C3037T, C5986T, T7984C, C10747TC14676T, C15279T, T16176C
      SARS-CoV-2/
      human/CHN/639/2020
      B.1.2C241T, C3037T, T6025C, C12784T, C23758TC3037T, T6025C, C12784TC23758T
      SARS-CoV-2/
      human/CHN/642/2020
      B.1.1C241T, C3037T, C10279T, C12115T, T22925C, C24023T, C26469TC3037T, C10279T, C12115TT22925C, C24023TC26469T
      SARS-CoV-2/
      human/CHN/644/2020
      B.1.1.7C241T, C913T, C2110T, C3037T, C5986T, T7984C, C14676T, C15279T, T16176CC913T, C2110T, C3037T, C5986T, T7984CC14676T, C15279T, T16176C
      SARS-CoV-2/
      human/CHN/646/2020
      B.1.351G160T, G174T, C241T, A2692T, C3037T, C4276T, C28253TA2692T, C3037T, C4276TC28253T
      SARS-CoV-2/
      human/CHN/649/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C24109T, G26828AC913T, C3037T, C5986T, C14676T, T15096C, C15279T, T16176CC24109TG26828A
      SARS-CoV-2/
      human/CHN/651/2020
      B.1.351G174T, C241T, C3037T, C19803T, C27059T, C28253TC3037TC19803TC27059TC28253T
      SARS-CoV-2/
      human/CHN/652/2020
      B.1.351G174T, C241T, C3037T, C19803T, C27059T, C28253TC3037TC19803TC27059TC28253T
      SARS-CoV-2/
      human/CHN/655/2020
      B.1.351G174T, C241T, C3037T, C19803T, C27059T, C28253TC3037TC19803TC27059TC28253T
      SARS-CoV-2/
      human/CHN/658/2020
      B.1.1.222C241T, C3037T, T3295C, C10165T, C17586T, T19839C, C28253TC3037T, T3295C, C10165TC17586T, T19839CC28253T
      SARS-CoV-2/
      human/CHN/659/2020
      B.1.351G174T, C241T, A2692T, C3037T, G25650A, C26645T, C28253TA2692T, C3037TG25650AC26645TC28253T
      SARS-CoV-2/
      human/CHN/666/2020
      B.1C241T, C3037T, C5884T, G16197A, T18144C, C21646T, T27908CC3037T, C5884TG16197A, T18144CT27908C
      SARS-CoV-2/
      human/CHN/671/2020
      B.1.351G174T, C241T, A2692T, C3037T, C28253TA2692T, C3037TC28253T
      SARS-CoV-2/
      human/CHN/671/2020 (1)
      B.1.351G174T, C241T, C3037T, C19803T, C27059T, C28253TC3037TC19803TC27059TC28253T
      SARS-CoV-2/
      human/CHN/671/2020 (2)
      B.1.351G174T, C241T, C3037T, C19803T, C27059T, C28253TC3037TC19803TC27059TC28253T
      SARS-CoV-2/
      human/CHN/671/2020 (3)
      B.1.351G174T, C241T, A2692T, C3037T, C8290T, C26645T, C28253TA2692T, C3037T, C8290TC26645TC28253T
      SARS-CoV-2/
      human/CHN/681/2020
      B.1.1.420G61A, C241T, T847C, C3037T, G3994T, C5548T, C5842T, A10258G, C12115T, G16710A, C16767T, T18132C, C18138T, C19884T, A24373GT847C, C3037T, G3994T, C5548T, C5842T, A10258G, C12115TG16710A, C16767T, T18132C, C18138T, C19884TA24373G
      SARS-CoV-2/
      human/CHN/682/2020
      B.1.1.7C241T, C913T, C2110T, G2539A, C3037T, C5986T, T7984C, C14676T, C15279T, T16176CC913T, C2110T, G2539A, C3037T, C5986T, T7984CC14676T, C15279T, T16176C
      SARS-CoV-2/
      human/CHN/695/2020
      P.2C100T, C241T, C3037T, C11824T, A12964G, C28253T, C29754TC3037T, C11824T, A12964GC28253TC29754T
      SARS-CoV-2/
      human/CHN/712/2020
      B.1.36G174T, C241T, C3037T, C9163T, C16111T, C18744T, C18877T, C19186T, C22444T, C26735T, C27213T, A27690G, G29179T, C29614TC3037T, C9163TC16111T, C18744T, C18877T, C19186TC22444TC26735TC27213TA27690GG29179TC29614T
      SARS-CoV-2/
      human/CHN/715/2020
      B.1.177.81C241T, T445C, C3037T, C6286T, C10228T, A21222T, G21255C, T23407C, C26801G, C27944T, G29645TT445C, C3037T, C6286T, C10228TA21222T, G21255CT23407CC26801GC27944TG29645T
      SARS-CoV-2/
      human/CHN/719/2020
      B.1.351G174T, C241T, C3037T, C19803T, C27059T, C27128T, C27998T, C28253TC3037TC19803TC27059T, C27128TC27998T, C28253T
      SARS-CoV-2/
      human/CHN/722/2020
      B.1.351G174T, A231G, C241T, A2692T, C3037T, G28001C, C28253TA2692T, C3037TG28001C, C28253T
      SARS-CoV-2/
      human/CHN/728/2020
      B.1.1.420G61A, C241T, T847C, C3037T, G3994T, C5548T, C5842T, A10258G, C12115T, G16710A, C16767T, T18132C, C18138T, C19884T, A24373GT847C, C3037T, G3994T, C5548T, C5842T, A10258G, C12115TG16710A, C16767T, T18132C, C18138T, C19884TA24373G
      SARS-CoV-2/
      human/CHN/729/2020
      B.1.351G174T, C241T, C3037T, C19803T, C27059T, C27128T, C27998T, C28253TC3037TC19803TC27059T, C27128TC27998T, C28253T
      SARS-CoV-2/
      human/CHN/731/2020
      B.1.177.81C241T, T445C, C3037T, C6286T, C10228T, A21222T, G21255C, T23407C, C26801G, C27944T, G29645TT445C, C3037T, C6286T, C10228TA21222T, G21255CT23407CC26801GC27944TG29645T
      SARS-CoV-2/
      human/CHN/736/2020
      B.1.1.7C241T, C913T, C1825T, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C17862T, C24109T, C29585TC913T, C1825T, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C17862TC24109TC29585T
      SARS-CoV-2/
      human/CHN/741/2020
      B.1.429C241T, C2395T, T2597C, C3037T, C7081T, C8947T, G10051A, C12100T, G19419A, T24349C, C26681T, G27890T, A28272T, C29203T, C29218T, C29362TC3037T, C7081T, C8947T, G10051A, C12100TG19419AT24349CC26681TC29203T, C29218T, C29362T
      SARS-CoV-2/
      human/CHN/761/2020
      C.36C241T, C3037T, C4586T, G12163A, C13536T, C17766T, A23329G, C23731TC3037T, C4586T, G12163AC13536T, C17766TA23329G, C23731T
      SARS-CoV-2/
      human/CHN/762/2020
      B.1.525C241T, C1498T, A1807G, G2659A, C3037T, T8593C, C9565T, C18171T, A20724G, C24748T, A28699G, G29543TC1498T, A1807G, G2659A, C3037T, T8593C, C9565TC18171T, A20724GC24748TA28699G
      SARS-CoV-2/
      human/CHN/767/2020
      B.1.351G174T, C241T, A2692T, C3037T, C28253TA2692T, C3037TC28253T
      SARS-CoV-2/
      human/CHN/779/2020
      B.1.1.7C241T, C913T, C2110T, C3037T, C5986T, C10252T, C14676T, C15279T, T16176C, T20409C, G27014T, A29248CC913T, C2110T, C3037T, C5986T, C10252TC14676T, C15279T, T16176C, T20409CG27014TA29248C
      SARS-CoV-2/
      human/CHN/782/2020
      B.1.1.7C241T, C913T, T2734C, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C18486T, C28846T, T29804AC913T, T2734C, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C18486TC28846TT29804A
      SARS-CoV-2/
      human/CHN/786/2020
      B.1.618G105T, C241T, C853T, C1684T, C3037T, T5263C, C11950T, T13114C, C23644T, T25084C, C26885T, G26909TC853T, C1684T, C3037T, T5263C, C11950T, T13114CC23644T, T25084CC26885T, G26909T
      SARS-CoV-2/
      human/CHN/788/2020
      B.1.1.7C241T, C913T, C1825T, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C17862T, C24109T, C29585TC913T, C1825T, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C17862TC24109TC29585T
      SARS-CoV-2/
      human/CHN/789/2020
      B.1.1.7C241T, C913T, C1825T, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C17862T, C24109T, C29585TC913T, C1825T, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C17862TC24109TC29585T
      SARS-CoV-2/
      human/CHN/798/2020
      B.1.1.7C241T, C913T, T2734C, C3037T, C5497T, C5986T, C14676T, T15096C, C15279T, T16176C, C18486T, C28846T, T29804AC913T, T2734C, C3037T, C5497T, C5986TC14676T, T15096C, C15279T, T16176C, C18486TC28846TT29804A
      SARS-CoV-2/
      human/CHN/803/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, C9661T, C14676T, C15279T, T16176C, C21742T, T27531C, C28253TC913T, C3037T, C5986T, C9661TC14676T, C15279T, T16176CC21742TT27531CC28253T
      SARS-CoV-2/
      human/CHN/804/2020
      B.1.1.7C241T, C913T, C1825T, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C17862T, C24109T, C29585TC913T, C1825T, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C17862TC24109TC29585T
      SARS-CoV-2/
      human/CHN/805/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, C14676T, C15279T, T16176C, T22159C, C27294TC913T, C3037T, C5986TC14676T, C15279T, T16176CT22159CC27294T
      SARS-CoV-2/
      human/CHN/807/2020
      B.1.1.7C241T, C913T, T2734C, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C18486T, C28846T, T29804AC913T, T2734C, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C18486TC28846T
      SARS-CoV-2/
      human/CHN/808/2020
      B.1.618G105T, C241T, C853T, C1684T, C3037T, T5263C, C11950T, T13114C, C23644T, T25084C, C26885T, G26909TC853T, C1684T, C3037T, T5263C, C11950T, T13114CC23644T, T25084CC26885T, G26909T
      SARS-CoV-2/
      human/CHN/809/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, C8950T, C14676T, A15033T, C15279T, T16176C, C19524T, C21234T, T29524CC913T, C3037T, C5986T, C8950TC14676T, A15033T, C15279T, T16176C, C19524T, C21234TT29524C
      SARS-CoV-2/
      human/CHN/811/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, C14676T, C14724T, T15096C, C15279T, T16176C, A29209TC913T, C3037T, C5986TC14676T, C14724T, T15096C, C15279T, T16176CA29209T
      SARS-CoV-2/
      human/CHN/824/2020
      B.1.1.7C241T, C913T, C1825T, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C17862T, C24109T, C29585TC913T, C1825T, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C17862TC24109TC29585T
      SARS-CoV-2/
      human/CHN/825/2020
      B.1.1.7C241T, C913T, T2734C, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C18486T, C28846T, T29804AC913T, T2734C, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C18486TC28846T
      SARS-CoV-2/
      human/CHN/834/2020
      B.1.525C241T, C1498T, A1807G, G2659A, C3037T, T8593C, C9565T, C18171T, A20724G, C24370T, C24748T, A28699G, G29543T, T29804AC1498T, A1807G, G2659A, C3037T, T8593C, C9565TC18171T, A20724GC24370T, C24748TA28699G
      SARS-CoV-2/
      human/CHN/857/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, C14676T, T15096C, C15279T, T16176C, C16323T, C24109TC913T, C3037T, C5986TC14676T, T15096C, C15279T, T16176C, C16323TC24109T
      SARS-CoV-2/
      human/CHN/859/2020
      B.1C241T, C292T, T1537C, C3037T, A20268G, G21123T, C26873T, C27881T, G29449T, T29524C, C29738TC292T, T1537C, C3037TA20268G, G21123TC26873TG29449T, T29524C
      SARS-CoV-2/
      human/CHN/863/2020
      B.1C241T, C292T, T1537C, C3037T, A20268G, G21123T, C26873T, C27881T, G29449T, T29524C, C29738TC292T, T1537C, C3037TA20268G, G21123TC26873TG29449T, T29524C
      SARS-CoV-2/
      human/CHN/865/2020
      B.1.1.7C241T, C913T, C2644T, C3037T, C5986T, C14676T, C15279T, T16176C, C19602TC913T, C2644T, C3037T, C5986TC14676T, C15279T, T16176C, C19602T
      SARS-CoV-2/
      human/CHN/872/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, C7844T, C14676T, C15279T, T16176CC913T, C3037T, C5986T, C7844TC14676T, C15279T, T16176C
      SARS-CoV-2/
      human/CHN/879/2020
      B.1.351G174T, C241T, C3037T, T4213C, C11812A, T17970C, T23449G, A23764T, C28253T, T28642CC3037T, T4213C, C11812AT17970CT23449G, A23764TC28253TT28642C
      SARS-CoV-2/
      human/CHN/888/2020
      B.1.351.3G174T, C241T, A2692T, C3037T, T7624C, G10396T, C10615T, C25603T, C28253TA2692T, C3037T, T7624C, G10396T, C10615TC25603TC28253T
      SARS-CoV-2/
      human/CHN/889/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, C7844T, C14676T, C15279T, T16176CC913T, C3037T, C5986T, C7844TC14676T, C15279T, T16176C
      SARS-CoV-2/
      human/CHN/890/2020
      B.1.214.2C241T, C3037T, C4891T, C11224T, C15324T, C21811T, T27576C, C27800T, C28507T, C28846T, C29730TC3037T, C4891T, C11224T, C15324TC21811TT27576CC28507T, C28846T
      SARS-CoV-2/
      human/CHN/894/2020
      B.1.1.7C241T, C913T, C3037T, C5986T, G6421T, C14676T, T15096C, C15279T, T16176C, A18000G, T29377A, G29449T, C29686TC913T, C3037T, C5986T, G6421TC14676T, T15096C, C15279T, T16176C, A18000GT29377A, G29449T, C29686T
      SARS-CoV-2/
      human/CHN/895/2020
      B.1.351.3G174T, C241T, A2692T, C3037T, T7624C, G10396T, C10615T, C12974T, C21411T, C28253TA2692T, C3037T, T7624C, G10396T, C10615T, C12974TC21411TC28253T
      SARS-CoV-2/
      human/CHN/901/2020
      B.1.1.7C241T, C913T, C2701T, C3037T, C5944T, C5986T, C14676T, T15096C, C15279T, T16176C, T21763CC913T, C2701T, C3037T, C5944T, C5986TC14676T, T15096C, C15279T, T16176CT21763C
      SARS-CoV-2/
      human/CHN/904/2020
      B.1.351.3G174T, C241T, A2692T, C3037T, T7624C, G10396T, C10615T, C28253TA2692T, C3037T, T7624C, G10396T, C10615TC28253T
      SARS-CoV-2/
      human/CHN/911/2020
      B.1.1.25C106T, C241T, C3037T, G3250A, T9022C, C11620T, C12754T, T22342A, A27270G, G28321AC3037T, G3250A, T9022C, C11620T, C12754TT22342AA27270GG28321A
      SARS-CoV-2/
      human/CHN/912/2020
      B.1.1.7C241T, C913T, C1102T, C3037T, C5986T, C14676T, C15279T, C15852T, T16176CC913T, C1102T, C3037T, C5986TC14676T, C15279T, C15852T, T16176C
      SARS-CoV-2/
      human/CHN/914/2020
      B.1.1.7C241T, C274T, C913T, C3037T, C5986T, C9857T, C14676T, C15279T, T16176C, T24143C, A26981C, C28531TC274T, C913T, C3037T, C5986T, C9857TC14676T, C15279T, T16176CT24143CA26981CC28531T
      SARS-CoV-2/
      human/CHN/915/2020
      B.1.1C241T, G529T, C829T, T1834C, C3037T, C5192T, C14340T, G16377T, C18877T, A19167G, T19839C, T26076C, C27213T, C28606T, G29422A, G29745TG529T, C829T, T1834C, C3037T, C5192TC14340T, G16377T, C18877T, A19167G, T19839CT26076CC27213TC28606T, G29422A

      Table S2.  Nonsense mutation distribution of 117 imported cases

Reference (32)
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