Comparative phylogenetic analysis of SARS-CoV-2 spike protein—possibility effect on virus spillover

Abstract

Coronavirus disease 2019 has developed into a dramatic pandemic with tremendous global impact. The receptor-binding motif (RBM) region of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to host angiotensin-converting enzyme 2 (ACE2) receptors for infection. As ACE2 receptors are highly conserved within vertebrate species, SARS-CoV-2 can infect significant animal species as well as human populations. An analysis of SARS-CoV-2 genotypes isolated from human and significant animal species was conducted to compare and identify mutation and adaptation patterns across different animal species. The phylogenetic data revealed seven distinct phylogenetic clades with no significant relationship between the clades and geographical locations. A high rate of variation within SARS-CoV-2 mink isolates implies that mink populations were infected before human populations. Positions of most single-nucleotide polymorphisms (SNPs) within the spike (S) protein of SARS-CoV-2 genotypes from the different hosts are mostly accumulated in the RBM region and highlight the pronounced accumulation of variants with mutations in the RBM region in comparison with other variants. These SNPs play a crucial role in viral transmission and pathogenicity and are keys in identifying other animal species as potential intermediate hosts of SARS-CoV-2. The possible roles in the emergence of new viral strains and the possible implications of these changes, in compromising vaccine effectiveness, deserve urgent considerations.

Network for network concept offers new insights into host- SARS-CoV-2 protein interactions and potential novel targets for developing antiviral drugs

“…The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) the causal agent of a zoonotic disease called COVID-19 infected more than 422 M people including 5.8 M deaths as of February 2022 [ 1 , 2 ]. Despite the widespread vaccination against the disease, the global number of new cases increased sharply due to the attenuation of the vaccine-induced immunity over time and the emergence of new variants [ 1 , [3] , [4] , [5] ].…”

Highlight of potential impact of new viral genotypes of SARS-CoV-2 on vaccines and anti-viral therapeutics

“…Gamma parameter for site rates was calculated and our data showed that gamma parameter for S protein is higher than the whole-viral genome; thus more positive selective pressure is on S protein and this may be related to selection pressure exerted by the adaptive immune response ( Table 3 ) ( Gelman et al, 2020 ). SNPs of SARS-CoV-2 naturally exist in the population ( Ghorbani et al, 2020a ) or accumulate in a new variant when the virus circulates in different hosts ( Ghorbani et al, 2021 )but their frequency is related to positive selection by mAbs and vaccines ( Gelman et al, 2020 ).…”

Study on Sequence Mutation and Molecular Dynamics Simulation of D614G SARS-CoV-2 Spike Protein in Indonesia

“…Classi cation of SARS-CoV-2 Clades and Construction of the Phylogenetic Tree Phylogenic construction was made in Mega-X from previous alignment results, using the Neighbor-Joining (NJ) Bootstrap 1000 replication method (Gaffar et al 2021;Ghorbani et al 2021;Tabibzadeh et al 2020) from 18 random high coverage sequences from Indonesian representative for each type of GISAID clade, as well as Wuhan-Hu-1 as a reference. Then, the sequences were also analyzed for the type of PANGOLIN variant, as well as the status of the variant using the COG-UK web application (https://pangolin.cog-uk.io/) (O'Toole 2021; Rambaut et al 2020).…”