The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.

中文翻译：

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使用COVIDSeq下一代测序技术对SARS-CoV-2进行高通量检测和遗传流行病学

冠状病毒疾病2019（COVID-19）作为影响全球数百万个人的全球性流行病的迅速出现，已经需要灵敏且高通量的方法来诊断，监测和确定SARS-CoV-2的遗传流行病学。在本研究中，我们使用了COVIDSeq协议，该协议涉及多重PCR，条形码编码和样品测序，以进行高通量检测和破译SARS-CoV-2的遗传流行病学。我们对752个重复样本的临床样本使用了该方法，总共可以在NovaSeq 6000的单个S4测序流动池上对1536个样本进行测序。我们的分析表明，技术重复样本与SARS检测的高度一致性-COVIDSeq和RT-PCR方法之间的-CoV-2。深入分析发现总共有六个样品，其中COVIDSeq以高可信度检测到SARS-CoV-2，在RT-PCR中为阴性。此外，该检测方法还可以检测21份样品和16份样品中的SARS-CoV-2，这些样品分别被归类为结论性和泛Sarbeco阳性，这表明COVIDSeq可以用作确认性测试。测序方法还可以洞察SARS-CoV-2样品的进化和遗传流行病学。样本共分为3个进化枝。这项研究首次在印度报道了两个血统B.1.112和B.1.99。这项研究还揭示了1,143个独特的单核苷酸变体，并首次添加了总共73个新颖的变体。据我们所知，这是用于SARS-CoV-2的检测和遗传流行病学的COVIDSeq方法的首次报告。我们的分析表明，COVIDSeq可能是用于检测SARS-CoV-2的潜在高灵敏度检测方法，具有使SARS-CoV-2进行遗传流行病学的其他优势。