High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.
High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.
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DOI：
10.1371/journal.pone.0247115
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Sivasubbu S
中科院分区：
文献类型：
--
作者：
Bhoyar RC;Jain A;Sehgal P;Divakar MK;Sharma D;Imran M;Jolly B;Ranjan G;Rophina M;Sharma S;Siwach S;Pandhare K;Sahoo S;Sahoo M;Nayak A;Mohanty JN;Das J;Bhandari S;Mathur SK;Kumar A;Sahlot R;Rojarani P;Lakshmi JV;Surekha A;Sekhar PC;Mahajan S;Masih S;Singh P;Kumar V;Jose B;Mahajan V;Gupta V;Gupta R;Arumugam P;Singh A;Nandy A;P V R;Jha RM;Kumari A;Gandotra S;Rao V;Faruq M;Kumar S;Reshma G B;Varma G N;Roy SS;Sengupta A;Chattopadhyay S;Singhal K;Pradhan S;Jha D;Naushin S;Wadhwa S;Tyagi N;Poojary M;Scaria V;Sivasubbu S
2019年冠状病毒病(新冠肺炎)作为一种影响全球数百万人的全球大流行迅速出现，需要采用敏感和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，该协议包括多重PCR、条形码和样本测序，用于高通量检测和破译SARS-CoV-2的遗传流行病学。我们对752份重复的临床样本使用了该方法，总计1536份样本可以在NovaSeq 6000上的单个S4测序流式细胞上进行测序。我们的分析表明，技术副本之间的高度一致性，以及COVIDSeq和RT-PCR方法之间检测SARS-CoV-2的高度一致性。深入分析发现，COVIDSeq在6个样本中高置信度检测到SARS-CoV-2，而RT-PCR检测为阴性。此外，该方法还检测到21份SARS-CoV-2样本和16份SARS-CoV-2泛阳性样本，表明COVIDSeq可作为确证试验。测序方法还使人们能够深入了解SARS-CoV-2样本的进化和遗传流行病学。样品共分成3个支系。本研究首次在印度报道了B.1.112和B.1.99两个谱系。这项研究还揭示了1143个独特的单核苷酸变异，并增加了总共73个首次发现的新变异。据我们所知，这是COVIDSeq方法用于SARS-CoV-2检测和遗传流行病学的第一份报告。我们的分析表明，COVIDSeq可能是一种潜在的高灵敏度检测SARS-CoV-2的方法，另外一个优点是使SARS-CoV-2的遗传流行病学成为可能。
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 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 the genetic epidemiology of SARS-CoV-2.
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DOI：
10.15585/mmwr.mm6911e1
发表时间：
2020-03-20
期刊：
MMWR. Morbidity and mortality weekly report
影响因子：
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影响因子：
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作者：
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