| Literature DB >> 33596239 |
Rahul C Bhoyar1, Abhinav Jain1,2, Paras Sehgal1,2, Mohit Kumar Divakar1,2, Disha Sharma1, Mohamed Imran1,2, Bani Jolly1,2, Gyan Ranjan1,2, Mercy Rophina1,2, Sumit Sharma1, Sanjay Siwach1, Kavita Pandhare1, Swayamprabha Sahoo3, Maheswata Sahoo3, Ananya Nayak3, Jatindra Nath Mohanty3, Jayashankar Das3, Sudhir Bhandari4, Sandeep K Mathur4, Anshul Kumar4, Rahul Sahlot4, Pallavali Rojarani5, Juturu Vijaya Lakshmi5, Avileli Surekha5, Pulala Chandra Sekhar5, Shelly Mahajan6, Shet Masih6, Pawan Singh6, Vipin Kumar6, Blessy Jose6, Vidur Mahajan6, Vivek Gupta7, Rakesh Gupta7, Prabhakar Arumugam1,2, Anjali Singh1,2, Ananya Nandy1,2, Ragavendran P V1,2, Rakesh Mohan Jha1,2, Anupama Kumari1,2, Sheetal Gandotra1,2, Vivek Rao1,2, Mohammed Faruq1,2, Sanjeev Kumar1,2, Betsy Reshma G1,2, Narendra Varma G1, Shuvra Shekhar Roy1,2, Antara Sengupta1,2, Sabyasachi Chattopadhyay1,2, Khushboo Singhal1,2, Shalini Pradhan1, Diksha Jha1,2, Salwa Naushin1,2, Saruchi Wadhwa1,2, Nishu Tyagi1,2, Mukta Poojary1,2, Vinod Scaria1,2, Sridhar Sivasubbu1,2.
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.Entities:
Year: 2021 PMID： 33596239 DOI： 10.1371/journal.pone.0247115
Source DB: PubMed Journal: PLoS One ISSN： 1932-6203 Impact factor: 3.240