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Article

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India

1
ICMR-National Institute of Virology, Pune 411001, India
2
Indian Council of Medical Research, New Delhi 110029, India
3
National Centre for Disease Control, New Delhi 110054, India
*
Author to whom correspondence should be addressed.
Equal authorship.
Prachi Jagtap, Bhagyashri Kasabe, Ujjaini Shah, Tripti Sanjeev, Gayatri Divekar, Kalpita Korabu, Sunil Shelkande, Pooja Shinde, Sayed Zakiuddin, Veena Vipat, Sheetal Jadhav, Krutika Iyengar, Vinita Malik, Sonali Bhorekar, Abhinendra Kumar, Rima Sahay, Anita Shete, Manoharlal Choudhary from National Influenza Center (NIC).
Academic Editor: Mark E. Obrenovich
Received: 1 May 2021 / Revised: 12 June 2021 / Accepted: 1 July 2021 / Published: 20 July 2021
(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)
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. View Full-Text
Keywords: SARS-CoV-2; India; Maharashtra; evolution; second wave; whole genomes; B.1.617.1; B.1.617.2; modeling SARS-CoV-2; India; Maharashtra; evolution; second wave; whole genomes; B.1.617.1; B.1.617.2; modeling
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MDPI and ACS Style

Cherian, S.; Potdar, V.; Jadhav, S.; Yadav, P.; Gupta, N.; Das, M.; Rakshit, P.; Singh, S.; Abraham, P.; Panda, S.; Team, N. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms 2021, 9, 1542. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071542

AMA Style

Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, Rakshit P, Singh S, Abraham P, Panda S, Team N. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms. 2021; 9(7):1542. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071542

Chicago/Turabian Style

Cherian, Sarah, Varsha Potdar, Santosh Jadhav, Pragya Yadav, Nivedita Gupta, Mousumi Das, Partha Rakshit, Sujeet Singh, Priya Abraham, Samiran Panda, and NIC Team. 2021. "SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India" Microorganisms 9, no. 7: 1542. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071542

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