1
|
Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, Rakshit P, Singh S, Abraham P, Panda S, Team NIC. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms 2021; 9:1542. [PMID: 34361977 PMCID: PMC8307577 DOI: 10.3390/microorganisms9071542] [Citation(s) in RCA: 393] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/12/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of "variants of concern" (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches were undertaken to identify possible new variants and gauge the fitness of the current circulating strains. Phylogenetic analysis revealed that newly identified lineages B.1.617.1 and B.1.617.2 were predominantly circulating. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Further in vitro/in vivo studies would help confirm the phenotypic changes of the mutant strains. Overall, the study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra. Lineage B.1.617.2 has been designated as a VOC delta and B.1.617.1 as a variant of interest kappa, and they are being widely reported in the rest of the country as well as globally. Continuous monitoring of these and emerging variants in India is essential.
Collapse
Affiliation(s)
- Sarah Cherian
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Varsha Potdar
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Santosh Jadhav
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Pragya Yadav
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Nivedita Gupta
- Indian Council of Medical Research, New Delhi 110029, India; (N.G.); (S.P.)
| | - Mousumi Das
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Partha Rakshit
- National Centre for Disease Control, New Delhi 110054, India; (P.R.); (S.S.)
| | - Sujeet Singh
- National Centre for Disease Control, New Delhi 110054, India; (P.R.); (S.S.)
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi 110029, India; (N.G.); (S.P.)
| | | |
Collapse
|
2
|
Potdar V, Cherian SS, Deshpande GR, Ullas PT, Yadav PD, Choudhary ML, Gughe R, Vipat V, Jadhav S, Patil S, Nyayanit D, Majumdar T, Walimbe A, Gaikwad S, Dighe H, Shete-Aich A, Mohandas S, Chowdhury D, Sapkal G, Basu A, Gupta N, Gangakhedkar RR, Giri S, Dar L, Jain A, Malhotra B, Abraham P. Genomic analysis of SARS-CoV-2 strains among Indians returning from Italy, Iran & China, & Italian tourists in India. Indian J Med Res 2020; 151:255-260. [PMID: 32362650 PMCID: PMC7366550 DOI: 10.4103/ijmr.ijmr_1058_20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Varsha Potdar
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sarah S. Cherian
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Gururaj Rao Deshpande
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | | | - Pragya D. Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Manohar Lal Choudhary
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Rohan Gughe
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Veena Vipat
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sheetal Jadhav
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Savita Patil
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Dimpal Nyayanit
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Triparna Majumdar
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Atul Walimbe
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Shivshankar Gaikwad
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Hitesh Dighe
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Anita Shete-Aich
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sreelekshmy Mohandas
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Deepika Chowdhury
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Gajanan Sapkal
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Atanu Basu
- Electron Microscopy & Histopathology Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Nivedita Gupta
- 6Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Raman R. Gangakhedkar
- 6Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Sidhartha Giri
- 6Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Lalit Dar
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Bharati Malhotra
- Department of Microbiology, SMS Medical College, Jaipur 302 004, Rajasthan, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - NIC Team
- National Influenza Centre (NIC) Team: S.D. Bharadwaj, Y. Gurav, S. Tomar, H. Kaushal, M. Lavania, B. Mathapati, K.P. Patil, A. Deoshatwar, V.K. Meena, N. Srivastava, V. Malik, V. Saha, S. Hundekar, H.K. Kengale, A.S. Awhale, A.S. Jagtap, A. Gondhalekar, S. Digraskar, P. Malsane, K.D. Patel, S. Ranshing, N.Y.B. Karthick, M.B. Kakade, S. Ranawade, S. Vaidya, V.N. Autade, S. Bhorekar, S.S. Salve, P.A. Shinde & B. Nimhas
| |
Collapse
|