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

View ORCID ProfileRahul C. Bhoyar, View ORCID ProfileAbhinav Jain, View ORCID ProfileParas Sehgal, Mohit Kumar Divakar, Disha Sharma, Mohamed Imran, Bani Jolly, Gyan Ranjan, Mercy Rophina, Sumit Sharma, Sanjay Siwach, Kavita Pandhare, Swayamprabha Sahoo, Maheswata Sahoo, Ananya Nayak, Jatindra Nath Mohanty, Jayashankar Das, View ORCID ProfileSudhir Bhandari, Sandeep K Mathur, Anshul Kumar, Rahul Sahlot, Pallavali Rojarani, Juturu Vijaya Lakshmi, Araveti Surekha, Pulala Chandra Sekhar, Shelly Mahajan, View ORCID ProfileShet Masih, Pawan Singh, Vipin Kumar, Blessy Jose, Vidur Mahajan, Vivek Gupta, Rakesh Gupta, Prabhakar Arumugam, Anjali Singh, Ananya Nandy, P.V. Raghavendran, Rakesh Mohan Jha, Anupama Kumari, View ORCID ProfileSheetal Gandotra, Vivek Rao, View ORCID ProfileMohammed Faruq, Sanjeev Kumar, G Betsy Reshma, G Narendra Varma, Shuvra Shekhar Roy, Antara Sengupta, Sabyasachi Chattopadhyay, Khushboo Singhal, Shalini Pradhan, Diksha Jha, Salwa Naushin, Saruchi Wadhwa, Nishu Tyagi, Mukta Poojary, View ORCID ProfileVinod Scaria, View ORCID ProfileSridhar Sivasubbu
doi: https://doi.org/10.1101/2020.08.10.242677
Rahul C. Bhoyar
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
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Abhinav Jain
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Paras Sehgal
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Mohit Kumar Divakar
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Disha Sharma
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
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Mohamed Imran
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Bani Jolly
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Gyan Ranjan
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Mercy Rophina
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Sumit Sharma
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
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Sanjay Siwach
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
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Kavita Pandhare
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
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Swayamprabha Sahoo
3IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India
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Maheswata Sahoo
3IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India
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Ananya Nayak
3IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India
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Jatindra Nath Mohanty
3IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India
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Jayashankar Das
3IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, Odisha 751003, India
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Sudhir Bhandari
4Sawai Man Singh Medical College, Jaipur, Rajasthan 302004, India
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Sandeep K Mathur
4Sawai Man Singh Medical College, Jaipur, Rajasthan 302004, India
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Anshul Kumar
4Sawai Man Singh Medical College, Jaipur, Rajasthan 302004, India
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Rahul Sahlot
4Sawai Man Singh Medical College, Jaipur, Rajasthan 302004, India
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Pallavali Rojarani
5Kurnool Medical College, Kurnool, Andhra Pradesh 518002, India
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Juturu Vijaya Lakshmi
5Kurnool Medical College, Kurnool, Andhra Pradesh 518002, India
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Araveti Surekha
5Kurnool Medical College, Kurnool, Andhra Pradesh 518002, India
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Pulala Chandra Sekhar
5Kurnool Medical College, Kurnool, Andhra Pradesh 518002, India
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Shelly Mahajan
6Center for Advanced Research in Imaging, Neuroscience & Genomics, Ring Road, Defence Colony, Delhi, 110024, India
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Shet Masih
6Center for Advanced Research in Imaging, Neuroscience & Genomics, Ring Road, Defence Colony, Delhi, 110024, India
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Pawan Singh
6Center for Advanced Research in Imaging, Neuroscience & Genomics, Ring Road, Defence Colony, Delhi, 110024, India
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Vipin Kumar
6Center for Advanced Research in Imaging, Neuroscience & Genomics, Ring Road, Defence Colony, Delhi, 110024, India
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Blessy Jose
6Center for Advanced Research in Imaging, Neuroscience & Genomics, Ring Road, Defence Colony, Delhi, 110024, India
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Vidur Mahajan
6Center for Advanced Research in Imaging, Neuroscience & Genomics, Ring Road, Defence Colony, Delhi, 110024, India
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Vivek Gupta
7Government Institute of Medical Sciences, NOIDA, India
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Rakesh Gupta
7Government Institute of Medical Sciences, NOIDA, India
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Prabhakar Arumugam
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Anjali Singh
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Ananya Nandy
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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P.V. Raghavendran
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Rakesh Mohan Jha
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Anupama Kumari
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Sheetal Gandotra
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Vivek Rao
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Mohammed Faruq
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Sanjeev Kumar
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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G Betsy Reshma
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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G Narendra Varma
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
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Shuvra Shekhar Roy
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Antara Sengupta
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Sabyasachi Chattopadhyay
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Khushboo Singhal
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Shalini Pradhan
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
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Diksha Jha
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Salwa Naushin
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Saruchi Wadhwa
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Nishu Tyagi
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Mukta Poojary
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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Vinod Scaria
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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  • For correspondence: s.sivasubbu@igib.res.in vinods@igib.res.in
Sridhar Sivasubbu
1CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
2Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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  • For correspondence: s.sivasubbu@igib.res.in vinods@igib.res.in
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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 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 detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.

Competing Interest Statement

The authors have declared no competing interest.

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High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing
Rahul C. Bhoyar, Abhinav Jain, Paras Sehgal, Mohit Kumar Divakar, Disha Sharma, Mohamed Imran, Bani Jolly, Gyan Ranjan, Mercy Rophina, Sumit Sharma, Sanjay Siwach, Kavita Pandhare, Swayamprabha Sahoo, Maheswata Sahoo, Ananya Nayak, Jatindra Nath Mohanty, Jayashankar Das, Sudhir Bhandari, Sandeep K Mathur, Anshul Kumar, Rahul Sahlot, Pallavali Rojarani, Juturu Vijaya Lakshmi, Araveti Surekha, Pulala Chandra Sekhar, Shelly Mahajan, Shet Masih, Pawan Singh, Vipin Kumar, Blessy Jose, Vidur Mahajan, Vivek Gupta, Rakesh Gupta, Prabhakar Arumugam, Anjali Singh, Ananya Nandy, P.V. Raghavendran, Rakesh Mohan Jha, Anupama Kumari, Sheetal Gandotra, Vivek Rao, Mohammed Faruq, Sanjeev Kumar, G Betsy Reshma, G Narendra Varma, Shuvra Shekhar Roy, Antara Sengupta, Sabyasachi Chattopadhyay, Khushboo Singhal, Shalini Pradhan, Diksha Jha, Salwa Naushin, Saruchi Wadhwa, Nishu Tyagi, Mukta Poojary, Vinod Scaria, Sridhar Sivasubbu
bioRxiv 2020.08.10.242677; doi: https://doi.org/10.1101/2020.08.10.242677
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High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing
Rahul C. Bhoyar, Abhinav Jain, Paras Sehgal, Mohit Kumar Divakar, Disha Sharma, Mohamed Imran, Bani Jolly, Gyan Ranjan, Mercy Rophina, Sumit Sharma, Sanjay Siwach, Kavita Pandhare, Swayamprabha Sahoo, Maheswata Sahoo, Ananya Nayak, Jatindra Nath Mohanty, Jayashankar Das, Sudhir Bhandari, Sandeep K Mathur, Anshul Kumar, Rahul Sahlot, Pallavali Rojarani, Juturu Vijaya Lakshmi, Araveti Surekha, Pulala Chandra Sekhar, Shelly Mahajan, Shet Masih, Pawan Singh, Vipin Kumar, Blessy Jose, Vidur Mahajan, Vivek Gupta, Rakesh Gupta, Prabhakar Arumugam, Anjali Singh, Ananya Nandy, P.V. Raghavendran, Rakesh Mohan Jha, Anupama Kumari, Sheetal Gandotra, Vivek Rao, Mohammed Faruq, Sanjeev Kumar, G Betsy Reshma, G Narendra Varma, Shuvra Shekhar Roy, Antara Sengupta, Sabyasachi Chattopadhyay, Khushboo Singhal, Shalini Pradhan, Diksha Jha, Salwa Naushin, Saruchi Wadhwa, Nishu Tyagi, Mukta Poojary, Vinod Scaria, Sridhar Sivasubbu
bioRxiv 2020.08.10.242677; doi: https://doi.org/10.1101/2020.08.10.242677

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