doi: 10.3967/bes2017.097
Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer
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Abstract:
Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. -
Key words:
- Nanopore sequencing /
- MinION /
- Enterovirus /
- Single molecule sequencing /
- Viral genome sequencing
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Figure 1. The workflow of Nanopore sequencing of the single sample and multiple samples. The EV71 and CA16 genomes were amplified using the RT-PCR protocol established by the National Polio Laboratory of China. A total of 4-10 individual PCRs using overlapping primers were carried out for amplicon preparation. Amplicons were quantified and homogenized before pooling together. Multiple samples were barcoded. The detailed process of the library preparation and MinION sequencing is described in the main text.
Figure 2. The read distribution at eight different time points during EV71 sequencing. The total sequencing run time for EV71 was about 19 h. The curves in different colors represent the length distribution of 4, 000 reads generated in the 5th, 160th, 320th, 480th, 640th, 800th, 960th, and 1, 080th min of sequencing, respectively. Every spot in the scatter plot represented one read (4, 000 for each plot) and Y axis represented the length of reads.
Figure 3. EV71 genome coverage. Sequence coverage profiles for EV71 plotted using the total data generated from the beginning of the sequencing to three different time points. (A) The data generated in the first min after MinION started running. (B) The data generated in the first 14 min, when the identity of the consensus sequence reached 99% compared to the Sanger reference sequence. (C) The data generated in the total run time of 19 h.
Figure 4. The accuracy of Nanopore sequencing of the single EV71 sample and multiple CA16 samples. (A) For the single-sample sequencing of EV71, the consensus sequence from the first generated FASTQ file showed 98.5% identity with the Sanger reference sequence. It took 14 min to reach 99% identity, and 82 min to reach 100% identity. (B) For the multiple-sample sequencing of CA16, the consensus sequences showed an average 96.11% (94.12%-97.33%) identity with the Sanger reference sequence. It took an average of 17 min (range 4-36 min) to reach 99% identity, and 153 min (19-330 min) to reach 100% identity for the 10 samples.
Figure 5. The relationship between the number of reads and the sequencing time. Using a brand-new flow cell, about 1, 060, 000 reads were generated during 6 h of sequencing, which means the MinION could generate about 3, 000 reads per min. But the change of curve slope indicated that the sequencing rate declined with time, which might be due to the loss of hundreds of active pores on running for several hours. This figure was plotted according to the generation of FASTQ files, which means the basecalling rate was also considered. The data curves for FASTQ and FAST5 files are almost identical to each other (data not shown).
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