SARS-CoV-2: Evolution and Emergence of New Viral Variants

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent responsible for the coronavirus disease 2019 (COVID-19). The high rate of mutation of this virus is associated with a quick emergence of new viral variants that have been rapidly spreading worldwide. Several mutations have been documented in the receptor-binding domain (RBD) of the viral spike protein that increases the interaction between SARS-CoV-2 and its cellular receptor, the angiotensin-converting enzyme 2 (ACE2). Mutations in the spike can increase the viral spread rate, disease severity, and the ability of the virus to evade either the immune protective responses, monoclonal antibody treatments, or the efficacy of current licensed vaccines. This review aimed to highlight the functional virus classification used by the World Health Organization (WHO), Phylogenetic Assignment of Named Global Outbreak (PANGO), Global Initiative on Sharing All Influenza Data (GISAID), and Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data, the chronological emergence of viral variants of concern (VOCs) and variants of interest (VOIs), the major findings related to the rate of spread, and the mutations in the spike protein that are involved in the evasion of the host immune responses elicited by prior SARS-CoV-2 infections and by the protection induced by vaccination.

Keywords: COVID-19; SARS-CoV-2; immune response; viral variants.

Figure 1

SARS-CoV-2 variants. Timeline that summarizes the emergence of SARS-CoV-2 variants. Classification according to the WHO is shown as well as the lineages of the mutagenic profile. VOC: variants of concern, VOI: variants of interest.

Figure 2

Mutations in Delta and Omicron variants. (A,C) Localization of defined mutations in the S1 domain and RBD of the spike protein of Delta and Omicron SARS-CoV-2 variants. (B,D) Model of mutations associated with the RBD domain (green) of the spike protein in interaction with the ACE2 receptor (red). Amino acid changes occurring more than one hundred times are indicated in blue, amino acids involved in direct interaction with ACE2 or associated with antigenicity are displayed in orange, potential amino acids involved in glycosylation are depicted in magenta, and amino acids inserted or deleted are indicated in cyan. GenBank access for the Delta variant is QWK65230.1 and for Omicron is OM095411.1. Modeling of the RBD domain with ACE2 was evaluated with the CoVsurver mutations app available on GISAID web page [57].