International Journal of Pediatrics

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.

Prevalence of Cystic Fibrosis Trans-membrane Conductance Regulator Gene common mutations in children with cystic fibrosis in Isfahan, Iran

Mohsen Reisi; Mahdiyeh Behnam; Seyed Javad Sayedi; Farzaneh Salimi; Pegah Kargar; Mansoor Salehi; Hossein Saneian; Iman Kashani; Roya Kelishadi

Volume 7, Issue 4 , April 2019, , Pages 9333-9339

https://doi.org/10.22038/ijp.2018.36309.3168

Abstract

Background: Cystic fibrosis (CF) is the most common lethal genetic disorder of Cystic Fibrosis Trans-membrane Conductance (CFTR) Regulator gene mutations. We aimed to investigate common ... Read More

Children with Steroid-resistant Nephrotic Syndrome: a Single-Center Study

Rahime Renda; Özlem Aydoğ; Mehmet Bülbül; Evrim Kargın Çakıcı

Volume 4, Issue 1 , January 2016, , Pages 1233-1242

https://doi.org/10.22038/ijp.2016.6315

Abstract

Background and Aim: Steroid-resistant nephrotic syndrome (SRNS) accounts for 10%-20% of all cases of idiopathic nephrotic syndrome. These patients are at risk of developing end-stage ... Read More

Genetic Susceptibility to Transient and Permanent Neonatal Diabetes Mellitus

Masoud Dehghan Tezerjani; Mohammad Yahya Vahidi Mehrjardi; Seyed Mehdi Kalantar; Mohammadreza Dehghani

Volume 3, Issue 6.1 , November 2015, , Pages 1073-1081

https://doi.org/10.22038/ijp.2015.5628

Abstract

Neonatal diabetes mellitus (NDM) is a rare kind of diabetes characterized by hyperglycemia and low levels of insulin. Clinically, it is categorized into two main types: transient NDM ... Read More

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Keywords = mutations

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

Prevalence of Cystic Fibrosis Trans-membrane Conductance Regulator Gene common mutations in children with cystic fibrosis in Isfahan, Iran

Abstract

Children with Steroid-resistant Nephrotic Syndrome: a Single-Center Study

Abstract

Genetic Susceptibility to Transient and Permanent Neonatal Diabetes Mellitus

Abstract