Variant analysis of SARS-CoV-2 genomes

Abstract

Objective To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods Between 1 February and 1 May 2020, we downloaded 10 022 SARS CoV-2 genomes from four databases. The genomes were from infected patients in 68 countries. We identified variants by extracting pairwise alignment to the reference genome NC_045512, using the EMBOSS needle. Nucleotide variants in the coding regions were converted to corresponding encoded amino acid residues. For clade analysis, we used the open source software Bayesian evolutionary analysis by sampling trees, version 2.5. Findings We identified 5775 distinct genome variants, including 2969 missense mutations, 1965 synonymous mutations, 484 mutations in the non-coding regions, 142 non-coding deletions, 100 in-frame deletions, 66 non-coding insertions, 36 stop-gained variants, 11 frameshift deletions and two in-frame insertions. The most common variants were the synonymous 3037C > T (6334 samples), P4715L in the open reading frame 1ab (6319 samples) and D614G in the spike protein (6294 samples). We identified six major clades, (that is, basal, D614G, L84S, L3606F, D448del and G392D) and 14 subclades. Regarding the base changes, the C > T mutation was the most common with 1670 distinct variants. Conclusion We found that several variants of the SARS-CoV-2 genome exist and that the D614G clade has become the most common variant since December 2019. The evolutionary analysis indicated structured transmission, with the possibility of multiple introductions into the population.

Genomic characterization of a novel SARS-CoV-2

“…In this study, we worked to find the extent of molecular variation between the recently sequenced genomes of SARS-CoV-2. Numerous investigations have depicted that ORFs and ACE2 genes play a key role during novel coronavirus disease (Koyama et al, 2020;Kirchdoerfer and Ward, 2019;Van der Meer et al, 1998;Wan et al, 2020). So in our study, 156 total variants were found and 116 unique variants (Tables 1 and 2).…”

“…This area of ORF1ab is the most important factor among coronaviruses (Wan et al, 2020). Many researchers found the relationship between ORFs with COVID-19 i.e.8782C > T(ORF1ab) and 28144T > C (ORF8) are available among genomic databases (Kirchdoerfer and Ward, 2019;Koyama et al, 2020). Hence, it will be clinically significant to break down the biological function of the particular protein ORF1ab in SARS-CoV-2.…”

“…A total motif VLVVL (amino corrosive 75-79) has been found in SARS-CoV orf8b which was appeared to trigger intracellular stress pathways and enact NOD-like receptor family pyrin region containing-3 (NLRP3) (Shi et al, 2019). Moreover, multiple arrangements with different coronavirus ORF8 sequences propose that L84 related to 28144T > C (L84S) isn't preserved (Koyama et al, 2020). Thusly, it will be critical to examine the biological function of the particular protein (orf8) in SARS-CoV-2.…”

“…Koyama et al depicted that COVID-19 is ORF10 which doesn't have any comparative proteins in the NCBI repository. This one of a kind protein can be used to distinguish the infection more rapidly than PCR based strategies (Koyama et al, 2020), but the further characterization of this protein is strongly required.…”

“…NC_045512 genome sequence was used for reference and the genomic coordinate in this study is based on this reference genome (Lu et al, 2020). Therefore, genomic coordinates must be adjusted to compare with previous studies (Koyama et al, 2020) Each genome was first aligned to NC_045512 using the EMBOSS needle with a default gap penalty of 10 and an extension penalty of 0.5. Then, differences in comparison with NC_045512 were extracted to create variants (Tables 1 & 2) (Rice et al, 2000).…”