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1. An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India

Author

Pragya D. Yadav, Dimpal A. Nyayanit, Triparna Majumdar, Savita Patil, Harmanmeet Kaur, Nivedita Gupta, Anita M. Shete, Priyanka Pandit, Abhinendra Kumar, Neeraj Aggarwal, Jitendra Narayan, Neetu Vijay, Usha Kalawat, Attayur P. Sugunan, Ashok Munivenkatappa, Tara Sharma, Sulochna Devi, Tapan Majumdar, Subhash Jaryal, Rupinder Bakshi, Yash Joshi, Rima Sahay, Jayanti Shastri, Mini Singh, Manoj Kumar, Vinita Rawat, Shanta Dutta, Sarita Yadav, Kaveri Krishnasamy, Sharmila Raut, Debasis Biswas, Biswajyoti Borkakoty, Santwana Verma, Sudha Rani, Hirawati Deval, Disha Patel, Jyotirmayee Turuk, Bharti Malhotra, Bashir Fomda, Vijaylakshmi Nag, Amita Jain, Anudita Bhargava, Varsha Potdar, Sarah Cherian, Priya Abraham, Anjani Gopal, Samiran Panda, and Balram Bhargava

Subjects
SARS-CoV-2, epidemiology, NGS, clades, India, Microbiology, QR1-502
Abstract

The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the ‘GH’ clade, whereas the southern part reported the ‘GR’, with a few exceptions. These sequences also revealed the presence of single independent mutations—E484Q and N440K—from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January–August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.

Published
2021
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2. An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India

Author

Sudha Rani, Yash Joshi, Subhash Chand Jaryal, Balram Bhargava, Triparna Majumdar, Anjani Gopal, Tara Sharma, Sharmila Raut, Bharti Malhotra, Bashir Ahmad Fomda, Anudita Bhargava, Neetu Vijay, Rupinder Bakshi, Biswajyoti Borkakoty, Tapan Majumdar, Usha Kalawat, Anita M. Shete, Manoj Kumar, Shanta Dutta, Nivedita Gupta, Sulochna Devi, Dimpal A Nyayanit, Mini P Singh, Harmanmeet Kaur, Rima R Sahay, Disha Patel, Pragya D Yadav, Attayur P. Sugunan, Kaveri Krishnasamy, Abhinendra Kumar, Vinita Rawat, Priya Abraham, Hirawati Deval, Sarita Yadav, Jayanti Shastri, Debasis Biswas, Jitendra Narayan, Amita Jain, Ashok Munivenkatappa, Vijaylakshmi Nag, Priyanka Pandit, Jyotirmayee Turuk, Sarah S. Cherian, Samiran Panda, Varsha Potdar, Savita Patil, Neeraj Aggarwal, and Santwana Verma

Subjects
0301 basic medicine, Adult, Male, medicine.medical_specialty, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, Zoology, India, Genome, Viral, Biology, Microbiology, Virus, Article, 03 medical and health sciences, Phylogenetics, Virology, Epidemiology, medicine, Humans, Clade, Phylogeny, SARS-CoV-2, clades, COVID-19, High-Throughput Nucleotide Sequencing, Genomics, Middle Aged, QR1-502, Phylogeography, 030104 developmental biology, Infectious Diseases, Viral evolution, NGS, Mutation, Female, epidemiology, Host adaptation, Early phase
Abstract

The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the ‘GH’ clade, whereas the southern part reported the ‘GR’, with a few exceptions. These sequences also revealed the presence of single independent mutations—E484Q and N440K—from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January–August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.

Published
2021

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