Evolution of the SARS-CoV-2 pandemic in India

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bat-derived betacoronavirus, that emerged around December 2019. In spite of the lesser genomic diversity of CoVs in general, a steady accumulation of mutations spread over its genome have been noted, resulting in the emergence of several clades and lineages. Majority of these mutations are random and non-functional changes; however a few variants of concern (VOC) and variants of interest (VOI) designated by the WHO since late 2020 have implications to diagnostics, pathogenicity and immune escape. This review discusses the various nomenclatures depicting the SARS-CoV-2 evolution, the designated VOCs and VOIs and the mutations characterizing these variants. The evolution of SARS-CoV-2 in India and the implications to vaccine efficacy and breakthrough infections is also addressed.

Keywords: Evolution; Genome; Mutations; SARS-CoV-2; Variants of concern.

Fig. 1

Genomic organization of SARS-CoV-2. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Fig. 2

The state wise distribution of SARS-CoV-2 (a) and the trend of the clade distribution in India (b).

Fig. 3

Effect of key mutations N501Y, K417N, and E484K on ACE-2 binding. (a) Complex of spike RBD with ACE2. Interacting residues in wild type and mutant strains are shown in (b) and (c), respectively. ACE-2, angiotensin-converting enzyme 2; RBD, receptor-binding domain; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Fig. 4

Neutralization escape of antibodies directed to the ACE2-binding epitopes by substitutions at residue positions 417 & 484. (a) Complex of spike RBD with monoclonal antibody REGN10933. Interacting residues in wild type and mutant strains are shown in (b) and (c), respectively. ACE-2, angiotensin-converting enzyme 2; RBD, receptor-binding domain.