Rapid and cost-efficient whole-genome sequencing of SARS-CoV-2, the virus that causes COVID-19, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit allows for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. This primer set results in amplicons that exhibit lower levels of variation in coverage compared to other commonly used primer sets. Using five SARS-CoV-2 patient samples with C_q values between 20 and 31, we show that high-quality genomes can be generated with as few as 10,000 reads (approximately 5 Mbp of sequence data). We also show that mis-classification of barcodes, which may be more likely when using the Oxford Nanopore Rapid Barcode library prep, is unlikely to cause problems in variant calling. This method reduces the time from RNA to genome sequence by more than half compared to the more standard ligation-based Oxford Nanopore library preparation method at considerably lower costs.

中文翻译：

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使用1200 bp平铺扩增子和牛津纳米孔快速条形码技术，对SARS-CoV-2进行快速且廉价的全基因组测序

SARS-CoV-2（引起COVID-19的病毒）的快速且经济高效的全基因组测序对于理解病毒传播动态至关重要。在这里，我们展示了使用一套新的多重引物与牛津纳米孔快速条形码文库试剂盒，可以更快，更简单，更便宜地进行SARS-CoV-2基因组测序。与其他常用引物组相比，该引物组可导致扩增子的覆盖率变异程度较低。使用5个SARS-CoV-2患者样本的C _q值介于20到31之间，我们证明只需10,000次读取（约5 Mbp的序列数据）就可以生成高质量的基因组。我们还表明，条形码的错误分类（使用牛津纳米孔快速条形码库制备方法时更可能发生）不太可能在变量调用中引起问题。与更标准的基于连接的牛津纳米孔文库制备方法相比，该方法将从RNA到基因组序列的时间减少了一半以上，且成本大大降低。