[1] |
Luo HM, Ran L, Meng L, et al. Analysis of epidemiological characteristics of report cases of rotavirus diarrhea in children under 5 years old in China, 2005-2018. Chin J Prev Med, 2020; 54, 181−6. (In Chinese |
[2] |
Adams WR, Kraft LM. Epizootic diarrhea of infant mice: identification of the etiologic agent. Science, 1963; 141, 359−60. doi: 10.1126/science.141.3578.359 |
[3] |
Bishop RF, Davidson GP, Holmes IH, et al. Virus particles in epithelial cells of duodenal mucosa from children with acute non-bacterial gastroenteritis. Lancet, 1973; 2, 1281−3. |
[4] |
Trask SD, McDonald SM, Patton JT. Structural insights into the coupling of virion assembly and rotavirus replication. Nat Rev Microbiol, 2012; 10, 165−77. doi: 10.1038/nrmicro2673 |
[5] |
Hyser JM, Collinson-Pautz MR, Utama B, et al. Rotavirus disrupts calcium homeostasis by NSP4 viroporin activity. mBio, 2010; 1, e00265−10. |
[6] |
Crawford SE, Criglar JM, Liu Z, et al. COPII vesicle transport is required for rotavirus NSP4 interaction with the autophagy protein LC3 II and trafficking to viroplasms. J Virol, 2019; 94, e01341−19. |
[7] |
Offit PA. Rotaviruses: immunological determinants of protection against infection and disease. Adv Virus Res, 1994; 44, 161−202. |
[8] |
Desselberger U, Huppertz HI. Immune responses to rotavirus infection and vaccination and associated correlates of protection. J Infect Dis, 2011; 203, 188−95. doi: 10.1093/infdis/jiq031 |
[9] |
Clarke E, Desselberger U. Correlates of protection against human rotavirus disease and the factors influencing protection in low-income settings. Mucosal Immunol, 2015; 8, 1−17. doi: 10.1038/mi.2014.114 |
[10] |
Feng NG, Lawton JA, Gilbert J, et al. Inhibition of rotavirus replication by a non-neutralizing, rotavirus VP6-specific IgA mAb. J Clin Invest, 2002; 109, 1203−13. doi: 10.1172/JCI14397 |
[11] |
Armah GE, Steele AD, Binka FN, et al. Changing patterns of rotavirus genotypes in ghana: emergence of human rotavirus G9 as a major cause of diarrhea in children. J Clin Microbiol, 2003; 41, 2317−22. doi: 10.1128/JCM.41.6.2317-2322.2003 |
[12] |
Hoshino Y, Jones RW, Kapikian AZ. Serotypic characterization of outer capsid spike protein VP4 of vervet monkey rotavirus SAff11 strain. Arch Virol, 1998; 143, 1233−44. doi: 10.1007/s007050050371 |
[13] |
Gorziglia M, Larralde G, Kapikian AZ, et al. Antigenic relationships among human rotaviruses as determined by outer capsid protein VP4. Proc Natl Acad Sci USA, 1990; 87, 7155−9. doi: 10.1073/pnas.87.18.7155 |
[14] |
Matthijnssens J, Heylen E, Zeller M, et al. Phylodynamic analyses of rotavirus genotypes G9 and G12 underscore their potential for swift global spread. Mol Biol Evol, 2010; 27, 2431−6. doi: 10.1093/molbev/msq137 |
[15] |
Matthijnssens J, Van Ranst M. Genotype constellation and evolution of group A rotaviruses infecting humans. Curr Opin Virol, 2012; 2, 426−33. doi: 10.1016/j.coviro.2012.04.007 |
[16] |
Li K, Lin XD, Huang KY, et al. Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology, 2016; 494, 168−77. doi: 10.1016/j.virol.2016.04.017 |
[17] |
Matthijnssens J, Ciarlet M, Rahman M, et al. Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch Virol, 2008; 153, 1621−9. doi: 10.1007/s00705-008-0155-1 |
[18] |
Matthijnssens J, Ciarlet M, Heiman E, et al. Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J Virol, 2008; 82, 3204−19. doi: 10.1128/JVI.02257-07 |
[19] |
Lovmar L, Fock C, Espinoza F, et al. Microarrays for genotyping human group a rotavirus by multiplex capture and type-specific primer extension. J Clin Microbiol, 2003; 41, 5153−8. doi: 10.1128/JCM.41.11.5153-5158.2003 |
[20] |
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 2013; 30, 772−80. doi: 10.1093/molbev/mst010 |
[21] |
Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis. Nuclc Acids Symp 1999; 95-8. |
[22] |
Nguyen LT, Schmidt HA, von Haeseler A, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol, 2015; 32, 268−74. doi: 10.1093/molbev/msu300 |
[23] |
Website. http://tree.bio.ed.ac.uk/software/Figtree/. [2023-01-11] |
[24] |
Lole KS, Bollinger RC, Paranjape RS, et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol, 1999; 73, 152−60. doi: 10.1128/JVI.73.1.152-160.1999 |
[25] |
Tamura K, Stecher G, Peterson D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol, 2013; 30, 2725−9. doi: 10.1093/molbev/mst197 |
[26] |
Wong EHM, Smith DK, Rabadan R, et al. Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evol Biol, 2010; 10, 253. doi: 10.1186/1471-2148-10-253 |
[27] |
Zhou ZJ, Qiu Y, Pu Y, et al. BioAider: an efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Sustain Cities Soc, 2020; 63, 102466. doi: 10.1016/j.scs.2020.102466 |
[28] |
Gupta R, Brunak S. Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput, 2002; 7, 310−22. |
[29] |
Matthijnssens J, Ciarlet M, McDonald SM, et al. Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol, 2011; 156, 1397−413. doi: 10.1007/s00705-011-1006-z |
[30] |
Shafat Z, Ahmed A, Parvez MK, et al. Sequence to structure analysis of the ORF4 protein from Hepatitis E virus. Bioinformation, 2021; 17, 818−28. doi: 10.6026/97320630017818 |
[31] |
Koch G, Kant A. Binding of antibodies that strongly neutralise infectious bronchitis virus is dependent on the glycosylation of the viral peplomer protein. In: Cavanagh D, Brown TDK. Coronaviruses and their Diseases. Springer. 1990, 143-50. |
[32] |
Smati R, Silim A, Guertin C, et al. Molecular characterization of three new avian infectious bronchitis virus (IBV) strains isolated in Quebec. Virus Genes 2002; 25, 85-93. |
[33] |
Thongprachum A, Khamrin P, Maneekarn N, et al. Epidemiology of gastroenteritis viruses in Japan: prevalence, seasonality, and outbreak. J Med Virol, 2016; 88, 551−70. doi: 10.1002/jmv.24387 |
[34] |
Degiuseppe JI, Reale EA, Stupka JA, et al. Rotavirus epidemiology and surveillance before vaccine introduction in Argentina, 2012-2014. J Med Virol, 2017; 89, 423−8. doi: 10.1002/jmv.24650 |
[35] |
Kilic IH, Ozaslan M, Karsligil T, et al. Investigation of diarrhea agents less than 5 years of age in summer in Gaziantep/Turkey. Pak J Biol Sci, 2007; 10, 2915−9. doi: 10.3923/pjbs.2007.2915.2919 |
[36] |
Estes MK, Cohen J. Rotavirus gene structure and function. Microbiol Rev, 1989; 53, 410−9. doi: 10.1128/mr.53.4.410-449.1989 |
[37] |
Nahar S, Paul SK, Kubayashi N, et al. Electrophoretic patterns of human rotavirus strain prevailing among children. Mymensingh Med J, 2018; 27, 679−84. |
[38] |
Rovida F, Nepita EV, Giardina F, et al. Rotavirus molecular epidemiology in hospitalized patients, northern Italy, 2015-2018. New Microbiol, 2020; 43, 1−5. |
[39] |
Desselberger U, Iturriza-Gómara M, Gray JJ. Rotavirus epidemiology and surveillance. In: Chadwick D, Goode JA. Gastroenteritis Viruses: Novartis Foundation Symposium 238. John Wiley & Sons. 2001, 125-47. |
[40] |
Kota M, Bino S, Delogu R, et al. Epidemiology of rotavirus diarrhoea in Albania. Arch Virol, 2014; 159, 2491−5. doi: 10.1007/s00705-014-2093-4 |
[41] |
Kang YB, Cai Y. Epidemiology and genetic diversity of rotavirus in Kunming, China, in 2015. Intervirology, 2018; 61, 9−13. doi: 10.1159/000489309 |
[42] |
Kang RH, Xun HM, Zhang Y, et al. Impacts of different grades of tropical cyclones on infectious diarrhea in Guangdong, 2005-2011. PLoS One, 2015; 10, e0131423. doi: 10.1371/journal.pone.0131423 |
[43] |
Mohan VR, Karthikeyan R, Babji S, et al. Rotavirus infection and disease in a multisite birth cohort: results from the MAL-ED study. J Infect Dis, 2017; 216, 305−16. doi: 10.1093/infdis/jix199 |
[44] |
Chen YH, Chen F, Zhou T, et al. Prevalence and clinical profile of rotavirus A infection among diarrhoeal children and phylogenetic analysis with vaccine strains in Chengdu, West China, 2009-2014. Trop Med Int Health, 2018; 23, 704−13. doi: 10.1111/tmi.13077 |
[45] |
Kaplon J, Grangier N, Pillet S, et al. Predominance of G9P[8] rotavirus strains throughout France, 2014-2017. Clin Microbiol Infect, 2018; 24, 660.e1-4 |
[46] |
Pérez-Ortín R, Santiso-Bellón C, Vila-Vicent S, et al. Rotavirus symptomatic infection among unvaccinated and vaccinated children in Valencia, Spain. BMC Infect Dis, 2019; 19, 998. doi: 10.1186/s12879-019-4550-x |
[47] |
Azaran A, Makvandi M, Teimoori A, et al. Distribution of rotavirus genotypes ccirculating in Ahvaz, Iran in 2016. Iran Biomed J, 2018; 22, 107−16. |
[48] |
Zhou X, Wang YH, Pang BB, et al. Surveillance of human rotavirus in Wuhan, China (2011-2019): predominance of G9P[8] and emergence of G12. Pathogens, 2020; 9, 810. doi: 10.3390/pathogens9100810 |
[49] |
Li W, Xiang WQ, Li CX, et al. Molecular epidemiology of rotavirus A and adenovirus among children with acute diarrhea in Hangzhou, China. Gut Pathog, 2020; 12, 19. doi: 10.1186/s13099-020-00359-4 |
[50] |
Nan X, Jinyuan W, Yan Z, et al. Epidemiological and clinical studies of rotavirus-induced diarrhea in China from 1994-2013. Hum Vaccin Immunother, 2014; 10, 3672−80. doi: 10.4161/21645515.2014.979691 |
[51] |
Liu N, Xu ZQ, Li DD, et al. Update on the disease burden and circulating strains of rotavirus in China: a systematic review and meta-analysis. Vaccine, 2014; 32, 4369−75. doi: 10.1016/j.vaccine.2014.06.018 |
[52] |
Yu JX, Lai SJ, Geng QB, et al. Prevalence of rotavirus and rapid changes in circulating rotavirus strains among children with acute diarrhea in China, 2009-2015. J Infect, 2019; 78, 66−74. doi: 10.1016/j.jinf.2018.07.004 |
[53] |
Zhao LF, Shi XH, Meng DQ, et al. Prevalence and genotype distribution of group A rotavirus circulating in Shanxi province, China during 2015-2019. BMC Infect Dis, 2021; 21, 94. doi: 10.1186/s12879-021-05795-4 |
[54] |
Desselberger U. Genome rearrangements of rotaviruses. In: Chiba S, Estes MK, Nakata S, et al. Viral Gastroenteritis. Springer. 1996, 37-51. |
[55] |
Santiana M, Ghosh S, Ho BA, et al. Vesicle-cloaked virus clusters are optimal units for inter-organismal viral transmission. Cell Host Microbe 2018; 24, 208-20. e8. |
[56] |
Dóró R, Farkas SL, Martella V, et al. Zoonotic transmission of rotavirus: surveillance and control. Expert Rev Anti Infect Ther, 2015; 13, 1337−50. doi: 10.1586/14787210.2015.1089171 |
[57] |
Hoxie I, Dennehy JJ. Intragenic recombination influences rotavirus diversity and evolution. Virus Evol, 2020; 6, vez059. doi: 10.1093/ve/vez059 |
[58] |
Oki H, Masuda T, Hayashi-Miyamoto M, et al. Genomic diversity and intragenic recombination of species C rotaviruses. J Gen Virol, 2022; 103, 001703. |
[59] |
Jere KC, Mlera L, Page NA, et al. Whole genome analysis of multiple rotavirus strains from a single stool specimen using sequence-independent amplification and 454® pyrosequencing reveals evidence of intergenotype genome segment recombination. Infect Genet Evol, 2011; 11, 2072−82. doi: 10.1016/j.meegid.2011.09.023 |
[60] |
Horie Y, Masamune O, Nakagomi O. Three major alleles of rotavirus NSP4 proteins identified by sequence analysis. J Gen Virol, 1997; 78, 2341−6. doi: 10.1099/0022-1317-78-9-2341 |
[61] |
Ciarlet M, Liprandi F, Conner ME, et al. Species specificity and interspecies relatedness of NSP4 genetic groups by comparative NSP4 sequence analyses of animal rotaviruses. Arch Virol, 2000; 145, 371−83. doi: 10.1007/s007050050029 |
[62] |
Ito H, Sugiyama M, Masubuchi K, et al. Complete nucleotide sequence of a group A avian rotavirus genome and a comparison with its counterparts of mammalian rotaviruses. Virus Res, 2001; 75, 123−38. doi: 10.1016/S0168-1702(01)00234-9 |
[63] |
Kirkwood CD, Palombo EA. Genetic characterization of the rotavirus nonstructural protein, NSP4. Virology, 1997; 236, 258−65. doi: 10.1006/viro.1997.8727 |
[64] |
Pan KY, Deem MW. Quantifying selection and diversity in viruses by entropy methods, with application to the haemagglutinin of H3N2 influenza. J Roy Soc Interface, 2011; 8, 1644−53. doi: 10.1098/rsif.2011.0105 |
[65] |
Wang K, Samudrala R. Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics, 2006; 7, 385. doi: 10.1186/1471-2105-7-385 |
[66] |
Wang Y, Guo X, Li W, et al. Phylogenetic analysis and evolution of feline bocavirus in Anhui Province, eastern China. Comp Immunol Microbiol Infect Dis, 2021; 77, 101676. doi: 10.1016/j.cimid.2021.101676 |
[67] |
Li GR, Ji SL, Zhai XF, et al. Evolutionary and genetic analysis of the VP2 gene of canine parvovirus. BMC Genomics, 2017; 18, 534. doi: 10.1186/s12864-017-3935-8 |
[68] |
Franzo G, Tucciarone CM, Cecchinato M, et al. Canine parvovirus type 2 (CPV-2) and Feline panleukopenia virus (FPV) codon bias analysis reveals a progressive adaptation to the new niche after the host jump. Mol Phylogenet Evol, 2017; 114, 82−92. doi: 10.1016/j.ympev.2017.05.019 |
[69] |
Zhang MD, Zeng CQY, Morris AP, et al. A functional NSP4 enterotoxin peptide secreted from rotavirus-infected cells. J Virol, 2000; 74, 11663−70. doi: 10.1128/JVI.74.24.11663-11670.2000 |
[70] |
Fung TS, Liu DX. Post-translational modifications of coronavirus proteins: roles and function. Future Virol, 2018; 13, 405−30. doi: 10.2217/fvl-2018-0008 |
[71] |
Sadiq A, Bostan N, Yinda KC, et al. Rotavirus: genetics, pathogenesis and vaccine advances. Rev Med Virol, 2018; 28, e2003. doi: 10.1002/rmv.2003 |