Journal of Pediatric Perspectives

Evaluation of Mutations in SARS-CoV-2 N and S Genes on the Proteins Stability, Immunogenicity, and Pathogenicity in Iranian Patients from Golestan Province

Bahman Aghcheli; Alireza Tahamtan; Hadi Razavi Nikoo; Zahra Bazi; Mohammad Reza Kalani; Abdolvahab Moradi

Volume 10, Issue 8 , August 2022, , Pages 16486-16497

https://doi.org/10.22038/ijp.2022.64880.4906

Abstract

Background: Natural selection such as mutations is known as a constant process for viral fitness and selective adaptation. Understanding the effects of each mutation, especially on ... Read More Background: Natural selection such as mutations is known as a constant process for viral fitness and selective adaptation. Understanding the effects of each mutation, especially on structural proteins in the viral life cycle, is important in tracking the viruses behavior. Here, we evaluated the effects of mutations in SARS-CoV-2 nucleoprotein (N) and spike (S) genes on the protein stability, immunogenicity, and pathogenicity in Iranian COVID-19 patients from Golestan province. Methods: In this study, 8 SARS-CoV-2 RNA samples were enrolled from referral hospitals in Golestan province. These samples were confirmed using a real-time RT-PCR assay targeting the SARS-CoV-2 nucleoprotein (N) and ORF1ab genes (Pishtazteb, Iran). Next-generation sequencing (NGS) was done on samples and subsequent sequences were retrieved from Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. Structural analysis was performed between wild type (Wuhan accession number: NC_045512.2) and mutant N and S proteins to evaluate their stability, immunogenicity, and pathogenicity via bioinformatics servers such as Dynamut, Prodigy, IEDB, and software’s (Mega XI and Pymol II.V.II visualizer). Results: Amino acid codon changes in N and S proteins show that mutations could alter the translation efficiency. Normal Mode Analysis (NMA) by Dynamut server shows that stability and flexibility are changed by the mutations of these proteins. Immunogenicity analysis indicates the potential effects of some mutations such as P681H, Q675R, L699I, and D3L on immune escape. Interaction complex binding energy and affinity are higher in the mutant type compared to the Wuhan wild type, indicating higher pathogenicity. Conclusion: The results indicate that there are some important mutations in N and S genes that affect the virus behavior in the infectivity. Regarding the sample size limitation and various mutations in SARS-CoV-2 variants, other studies using whole-genome sequencing with larger sample sizes will be required. Therefore, continuous monitoring of the SARS-CoV-2 genome seems important.

Assessment and Molecular Docking of SARS-CoV-2 NSP3 and NSP12 Mutants in Iranian Patients in Golestan Province

Emad Behboudi; Alijan Tabarraei; Alireza Tahamtan; Mohammad Reza Kalani; Abdolvahab Moradi

Volume 10, Issue 7 , July 2022, , Pages 16370-16380

https://doi.org/10.22038/ijp.2022.64007.4862

Abstract

Background: Molecular analysis of SARS-CoV-2 genome is important to predict viral pathogenicity. In addition to transmission, replication is a key factor in pathogenicity of the virus. ... Read More

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Author = Mohammad Reza Kalani

Evaluation of Mutations in SARS-CoV-2 N and S Genes on the Proteins Stability, Immunogenicity, and Pathogenicity in Iranian Patients from Golestan Province

Abstract

Assessment and Molecular Docking of SARS-CoV-2 NSP3 and NSP12 Mutants in Iranian Patients in Golestan Province

Abstract