Evolutionary analysis of SARS-CoV-2 spike protein for its different clades

Abstract

ObjectiveThe spike protein of SARS-CoV-2 has become the main target for antiviral and vaccine development. Despite its relevance, there is scarce information about its evolutionary traces. The aim of this study was to investigate the diversification patterns of the spike for each clade of SARS-CoV-2 through different approaches.MethodsTwo thousand and one hundred sequences representing the seven clades of the SARS-CoV-2 were included. Patterns of genetic diversifications and nucleotide evolutionary rate were estimated for the spike genomic region.ResultsThe haplotype networks showed a star shape, where multiple haplotypes with few nucleotide differences diverge from a common ancestor. Four hundred seventy nine different haplotypes were defined in the seven analyzed clades. The main haplotype, named Hap-1, was the most frequent for clades G (54%), GH (54%), and GR (56%) and a different haplotype (named Hap-252) was the most important for clades L (63.3%), O (39.7%), S (51.7%), and V (70%). The evolutionary rate for the spike protein was estimated as 1.08 x 10−3 nucleotide substitutions/site/year. Moreover, the nucleotide evolutionary rate after nine months of pandemic was similar for each clade.ConclusionsIn conclusion, the present evolutionary analysis is relevant since the spike protein of SARS-CoV-2 is the target for most therapeutic candidates; besides, changes in this protein could have consequences on viral transmission, response to antivirals and efficacy of vaccines. Moreover, the evolutionary characterization of clades improves knowledge of SARS-CoV-2 and deserves to be assessed in more detail since re-infection by different phylogenetic clades has been reported.

Clinical grade ACE2 as a universal agent to block SARS-CoV-2 variants

“…Viral evolution of SARS-CoV-2 has been demonstrated to be focused on the Spike protein which is instrumental for the early steps of viral infection (24, 25) . Many single or compound mutations, especially in the RBD of the viral Spike, have been described and either hypothesized or demonstrated to affect binding to the cell entry receptor ACE2 (see (14) for a review).…”

Population genetics in the early emergence of the Omicron SARS-CoV-2 variant in the provinces of South Africa

“…Genome-wide substitutions per site per year were 2.6x 10 -3 (28-8 substitutions /29903 bases / 0.25 years = 20/29903/0.25 = 0.002675 = 2.6x10 -3 ), which is higher than the previously estimated rate of substitution per site per year of 8.90e-4 [25]. In the spike region, there were 1.15x10 -2 substitutions per site per year (15 -4 substitutions / 3822 sites in the spike region /3 months = 11 / 3822 / 0.25 = 0.0115 = 1.15x10 -2 ), which is higher than the range of 1.06 × 10 -3 and 1.69 × 10 -3 previously reported for this region for sequences from different regions worldwide [26].…”