Genetic drift in the genome of SARS COV-2 and its global health concern

Abstract

The outbreak of the current coronavirus disease (COVID-19) occurred in late 2019 and quickly spread all over the world. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to a genetically diverse group that mutates continuously leading to the emergence of multiple variants. Although a few antiviral agents and anti-inflammatory medicines are available, thousands of individuals have passed away due to emergence of new viral variants. Thus, proper surveillance of the SARS-CoV-2 genome is needed for the rapid identification of developing mutations over time, which are of the major concern if they occur specifically in the surface spike proteins of the virus (neutralizing analyte). This article reviews the potential mutations acquired by the SARS-CoV2 since the pandemic began and their significant impact on the neutralizing efficiency of vaccines and validity of the diagnostic assays.

Keywords: COVID-19; SARS-CoV-2; genetics; mutation; serodiagnosis; vaccination; variants.

Figure 1

Schematic description of morphology and genome of SARS‐CoV‐2.(A) Virus is covered with S, M, and E protein. Inside phospholipid bilayers, the RNA is encompassed by the N‐protein that is phosphorylated. (B) There are 29903 nucleotide bases and they contain 5′‐UTR, ORF1a, and b that encodes 16 nonstructural proteins, 4 structural genes encoding S, M, N, and E proteins, 6 genes that code for ORF3a, 6, 7a, 7b, 8, and 10 accessory proteins, along with the 3′‐UTR. The vertical red lines with circles having the same color on the genome indicate the position of 17 high‐frequency mutations and co‐mutations. ORF, open reading frame; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2; UTR, untranslated region

Figure 2

Phylogenetic supertree illustrated the evolution of SARS‐CoV‐2 by using a protein source. MRP (Matrix representation with parsimony) pseudo‐sequence supertree is constructed by using source phylogenetic trees for phylogenetic analysis of nine SARS‐CoV‐2 along with 5 SARS‐CoV, 2 MERS‐CoV, and 11 bat coronaviruses as outgroups. MAFFT (Multiple Alignment using Fast Fourier Transform) is used for the alignment of amino acid sequences and phylip file was formed by Clustal W. MRP supertree is constructed by using published supertree software Clann (version 4.2.4). By using PhyML program, ML (Maximum likelihood) phylogenies were utilized to construct source phylogenetic trees based with 100 bootstrap replications. FigTree v1.4.4 software is used for visualization of the phylogenetic tree. In the MRP pseudo‐sequence supertree, SARS‐CoV‐2 is placed on one main branch while SARS‐CoV and MERS‐CoV belonged to another main branch. Particularly, MRP supertree analysis disputed RaTG13 bat coronavirus as the last common ancestor of SARS‐CoV‐2. MERS‐CoV, Middle East Respiratory Syndrome Coronavirus; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2

Figure 3

Frequencies of seven clades by Global initiative on sharing all influenza data (GISAID) nomenclature. ACE‐2, angiotensin‐converting enzyme‐2; β‐CoV, betacoronavirus; COVID‐19, coronavirus disease 2019; GISAID, Global initiative on sharing all influenza data; MAFFT, Multiple Alignment using Fast Fourier Transform; MERS‐CoV, Middle East Respiratory Syndrome Coronavirus; ML, maximum likelihood; MRP, matrix representation with parsimony; nsp: nonstructural proteins; ORFs, open reading frames; RBD, receptor binding domain; RdRp, RNA‐dependent RNA polymerase; SARS‐Cov‐2, severe acute respiratory syndrome coronavirus 2; S protein, spike protein; UTR, untranslated region