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.

Association of SARS-COV-2 Cycle Threshold Values with Clinical and Epidemiological Features of Children and Adolescents in Iran

Mohammad Ebrahim Ghamarchehreh; Hasan Ashoori; Farnaz Vahidian; Behnaz Shabani Fouladi; Dorsa Safari; Bita Najafian

Volume 10, Issue 6 , June 2022, , Pages 16174-16181

https://doi.org/10.22038/ijp.2022.61977.4753

Abstract

Background: The associations between the epidemiological, clinical, and serological features of coronavirus disease 2019 (COVID-19) and the nasopharyngeal viral load have not, yet, ... Read More

Coronavirus Disease 2019 in Patients with Thalassemia; Emerging Challenges

Mozhgan Hashemieh; Fariba Shirvani

Volume 9, Issue 7 , July 2021, , Pages 13895-13903

https://doi.org/10.22038/ijp.2020.53675.4254

Abstract

BackgroundThe World Health Organization (WHO) has announced that severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) outbreak is a public health emergency requiring international ... Read More

The Accuracy of Enzyme-Linked Immunosorbent Assay in the Diagnosis of COVID-19 in Iranian Children

Vahid Tarmahi; Mohammadreza Afghan; Sina Raeisi; Hamid Reza Yousefi Nodeh; Mona Tamaddon; Fatemeh Moahamadzadeh; Nader Mohammadzadeh; Zakiyeh Ebadi

Volume 9, Issue 7 , July 2021, , Pages 13937-13945

https://doi.org/10.22038/ijp.2020.54348.4299

Abstract

BackgroundThe present study aimed to evaluate the accuracy of enzyme-linked immunosorbent assay (ELISA) compared to the real-time reverse transcription-polymerase chain reaction (rRT-PCR) ... Read More

COVID-19 Associated Thrombocytopenia in Children: An Emerging Issue

Mozhgan Hashemieh; Shahrzad Tabatabaee; Mitra Radfar; Parnian Fahim

Volume 9, Issue 6 , June 2021, , Pages 13635-13642

https://doi.org/10.22038/ijp.2020.52364.4162

Abstract

Thrombocytopenia is a risk factor for increased mortality and morbidity during the Coronavirus Disease 2019 (COVID-19). In patients with COVID-19, the mechanisms lead to thrombocytopenia ... Read More

Preventive Strategies for Cancer Patients during COVID-19 Pandemic: A Review

Mozhgan Hashemieh

Volume 9, Issue 2 , February 2021, , Pages 12981-12987

https://doi.org/10.22038/ijp.2020.51220.4069

Abstract

Immunosuppressed children with cancer remain a vulnerable group for acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ... Read More

Hematologic Parameters of COVID – 19: A Review on Alteration of Hematologic Laboratory Findings

Mozhgan Hashemieh

Volume 8, Issue 9 , September 2020, , Pages 11921-11929

https://doi.org/10.22038/ijp.2020.50620.4024

Abstract

Corona virus 2019 (COVID –19) is a public health emergency and according to the recent statistic of World Health Organization (WHO), this novel virus has infected all continents. ... Read More

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Keywords = SARS-CoV-2

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

Association of SARS-COV-2 Cycle Threshold Values with Clinical and Epidemiological Features of Children and Adolescents in Iran

Abstract

Coronavirus Disease 2019 in Patients with Thalassemia; Emerging Challenges

Abstract

The Accuracy of Enzyme-Linked Immunosorbent Assay in the Diagnosis of COVID-19 in Iranian Children

Abstract

COVID-19 Associated Thrombocytopenia in Children: An Emerging Issue

Abstract

Preventive Strategies for Cancer Patients during COVID-19 Pandemic: A Review

Abstract

Hematologic Parameters of COVID – 19: A Review on Alteration of Hematologic Laboratory Findings

Abstract