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High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.

ABSTRACT: 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.

SUBMITTER: Bhoyar RC 

PROVIDER: S-EPMC7888613 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.

Bhoyar Rahul C RC   Jain Abhinav A   Sehgal Paras P   Divakar Mohit Kumar MK   Sharma Disha D   Imran Mohamed M   Jolly Bani B   Ranjan Gyan G   Rophina Mercy M   Sharma Sumit S   Siwach Sanjay S   Pandhare Kavita K   Sahoo Swayamprabha S   Sahoo Maheswata M   Nayak Ananya A   Mohanty Jatindra Nath JN   Das Jayashankar J   Bhandari Sudhir S   Mathur Sandeep K SK   Kumar Anshul A   Sahlot Rahul R   Rojarani Pallavali P   Lakshmi Juturu Vijaya JV   Surekha Avileli A   Sekhar Pulala Chandra PC   Mahajan Shelly S   Masih Shet S   Singh Pawan P   Kumar Vipin V   Jose Blessy B   Mahajan Vidur V   Gupta Vivek V   Gupta Rakesh R   Arumugam Prabhakar P   Singh Anjali A   Nandy Ananya A   P V Ragavendran R   Jha Rakesh Mohan RM   Kumari Anupama A   Gandotra Sheetal S   Rao Vivek V   Faruq Mohammed M   Kumar Sanjeev S   Reshma G Betsy B   Varma G Narendra N   Roy Shuvra Shekhar SS   Sengupta Antara A   Chattopadhyay Sabyasachi S   Singhal Khushboo K   Pradhan Shalini S   Jha Diksha D   Naushin Salwa S   Wadhwa Saruchi S   Tyagi Nishu N   Poojary Mukta M   Scaria Vinod V   Sivasubbu Sridhar S  

PloS one 20210217 2

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  ...[more]

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