TY - JOUR
T1 - Highlight of potential impact of new viral genotypes of SARS-CoV-2 on vaccines and anti-viral therapeutics
AU - Ghorbani, Abozar
AU - Samarfard, Samira
AU - Jajarmi, Maziar
AU - Bagheri, Mahboube
AU - Karbanowicz, Thomas P.
AU - Afsharifar, Alireza
AU - Eskandari, Mohammad Hadi
AU - Niazi, Ali
AU - Izadpanah, Keramatollah
N1 - Publisher Copyright:
© 2022
PY - 2022/3
Y1 - 2022/3
N2 - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of the coronavirus disease (COVID-19) pandemic, has infected millions of people globally. Genetic variation and selective pressures lead to the accumulation of single nucleotide polymorphism (SNP) within the viral genome that may affect virulence, transmission rate, viral recognition and the efficacy of prophylactic and interventional measures. To address these concerns at the genomic level, we assessed the phylogeny and SNPs of the SARS-CoV-2 mutant population collected to date in Iran in relation to globally reported variants. Phylogenetic analysis of mutant strains revealed the occurrence of the variants known as B.1.1.7 (Alpha), B.1.525 (Eta), and B.1.617 (Delta) that appear to have delineated independently in Iran. SNP analysis of the Iranian sequences revealed that the mutations were predominantly positioned within the S protein-coding region, with most SNPs localizing to the S1 subunit. Seventeen S1-localizing SNPs occurred in the RNA binding domain that interacts with ACE2 of the host cell. Importantly, many of these SNPs are predicted to influence the binding of antibodies and anti-viral therapeutics, indicating that the adaptive host response appears to be imposing a selective pressure that is driving the evolution of the virus in this closed population through enhancing virulence. The SNPs detected within these mutant cohorts are addressed with respect to current prophylactic measures and therapeutic interventions.
AB - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of the coronavirus disease (COVID-19) pandemic, has infected millions of people globally. Genetic variation and selective pressures lead to the accumulation of single nucleotide polymorphism (SNP) within the viral genome that may affect virulence, transmission rate, viral recognition and the efficacy of prophylactic and interventional measures. To address these concerns at the genomic level, we assessed the phylogeny and SNPs of the SARS-CoV-2 mutant population collected to date in Iran in relation to globally reported variants. Phylogenetic analysis of mutant strains revealed the occurrence of the variants known as B.1.1.7 (Alpha), B.1.525 (Eta), and B.1.617 (Delta) that appear to have delineated independently in Iran. SNP analysis of the Iranian sequences revealed that the mutations were predominantly positioned within the S protein-coding region, with most SNPs localizing to the S1 subunit. Seventeen S1-localizing SNPs occurred in the RNA binding domain that interacts with ACE2 of the host cell. Importantly, many of these SNPs are predicted to influence the binding of antibodies and anti-viral therapeutics, indicating that the adaptive host response appears to be imposing a selective pressure that is driving the evolution of the virus in this closed population through enhancing virulence. The SNPs detected within these mutant cohorts are addressed with respect to current prophylactic measures and therapeutic interventions.
KW - Antiviral drugs
KW - Bioinformatics
KW - Mutation detection
KW - Phylogenetic analysis
KW - SARS-CoV-2
KW - Viral vaccines
UR - http://www.scopus.com/inward/record.url?scp=85123900403&partnerID=8YFLogxK
U2 - 10.1016/j.genrep.2022.101537
DO - 10.1016/j.genrep.2022.101537
M3 - Article
AN - SCOPUS:85123900403
SN - 2452-0144
VL - 26
JO - Gene Reports
JF - Gene Reports
M1 - 101537
ER -