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Yadav PD, Nyayanit DA, Majumdar T, Patil S, Kaur H, Gupta N, Shete AM, Pandit P, Kumar A, Aggarwal N, Narayan J, Vijay N, Kalawat U, Sugunan AP, Munivenkatappa A, Sharma T, Devi S, Majumdar T, Jaryal S, Bakshi R, Joshi Y, Sahay R, Shastri J, Singh M, Kumar M, Rawat V, Dutta S, Yadav S, Krishnasamy K, Raut S, Biswas D, Borkakoty B, Verma S, Rani S, Deval H, Patel D, Turuk J, Malhotra B, Fomda B, Nag V, Jain A, Bhargava A, Potdar V, Cherian S, Abraham P, Gopal A, Panda S, Bhargava B. An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Viruses 2021; 13:v13050925. [PMID: 34067745 PMCID: PMC8156686 DOI: 10.3390/v13050925] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022] Open
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.
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Affiliation(s)
- Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Harmanmeet Kaur
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Nivedita Gupta
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
- Correspondence:
| | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Priyanka Pandit
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Neeraj Aggarwal
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Jitendra Narayan
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Neetu Vijay
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Usha Kalawat
- Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, India;
| | | | | | - Tara Sharma
- VRDL Sikkim Government College of Nursing, Gangtok 737101, India;
| | - Sulochna Devi
- Regional Institute of Medical Sciences IMPHAL, Imphal 795004, India;
| | - Tapan Majumdar
- Government Medical College, Agartala, Tripura 799006, India;
| | - Subhash Jaryal
- Dr. Rajendra Prasad Government Medical College, (H.P.), Kangra 176001, India;
| | | | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Rima Sahay
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Jayanti Shastri
- Kasturba Hospital for Infectious Diseases, Mumbai 400034, India;
| | - Mini Singh
- Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India;
| | - Manoj Kumar
- Rajendra Institute of Medical Sciences, Ranchi 834009, India;
| | - Vinita Rawat
- Government Medical College, Haldwani 263129, India;
| | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases, Kolkata 700010, India;
| | - Sarita Yadav
- Bhagat Phool Singh Government Medical College, Sonipat 131305, India;
| | - Kaveri Krishnasamy
- King Institute of Preventive Medicine & Research, Chennai 600032, India;
| | - Sharmila Raut
- Indira Gandhi Government Medical College & Hospital, Nagpur 440018, India;
| | - Debasis Biswas
- All India Institute of Medical Sciences, Bhopal 462020, India;
| | | | - Santwana Verma
- Indira Gandhi Medical College & Hospital, Shimla 171001, India;
| | - Sudha Rani
- Osmania Medical College, Hyderabad 500095, India;
| | - Hirawati Deval
- Regional Medical Research Center Gorakhpur, Gorakhpur 273013, India;
| | - Disha Patel
- B.J. Medical College, Ahmedabad 380016, India;
| | | | | | - Bashir Fomda
- Sher-I-Kashmir Institute of Medical Sciences, Srinagar 190011, India;
| | | | - Amita Jain
- Department of Microbiology, King George’s Medical University, Lucknow 226003, India;
| | - Anudita Bhargava
- All India Institute of Medical Sciences, Raipur, Raipur 492099, India;
| | - Varsha Potdar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Sarah Cherian
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Anjani Gopal
- Indian Institute of Science Education and Research, Pune 411008, India;
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Balram Bhargava
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
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