Iranian Journal of Pathology

Comparative Analysis of 198 SARS-CoV-2 Genomes from Iran and West Asia, February 2020 to December 2021

Document Type : Original Research

Authors

saman karami 1
Marziyeh Mojbafan 1, 2
Ramin Mazaheri Nezhad Fard 3

1 Department of Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Science, Tehran, Iran

2 Department of Medical Genetics, Ali-Asghar Children's Hospital, Tehran, Iran

3 Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran

https://doi.org/10.30699/ijp.2023.557658.2935
Abstract
Background & Objective: Coronavirus disease 2019 (COVID‐19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a worldwide pandemic. The first case of COVID‐19 was reported from Wuhan in the Hubei Province of China in December 2019; however, the disease's origin is still mysterious. Whole-genome sequence analysis is essential for monitoring the spread of infectious diseases as well as studying the pathogenesis and evolution of viruses. In this study, analysis of 198 fully sequenced genomes from Iran and West Asia was carried out to study mutations, phylogeny, amino acid changes, clades, and lineages of these genomes as well as comparison of these sequences with those of reference Wuhan genome of NC_045512.2.
Methods: In total, 198 completely sequenced genome data from Iran and West Asia were collected from GenBank. Mutation detection was carried out using a trial version of CLC Genomics Workbench v.21.0 (QIAGEN, Germany). Online tools such as GISAID Mutations App and Pangolin were used for further analysis of the results.
Results: In this study, several unique mutation sites were identified in the Iranian genomes (n = 8); positions 1397 G>A and 29742 G>T were the most frequent changes in more than 85% of the Iranian genomes. Mutation rate, mutation per sequence, and transition versus transversion for the Iranian genomes included 4.73, 14.14, and 1.6, respectively. Generally, C>T alteration was the most common substitution in all the sequences.
Conclusion: The ORF1ab, N, and S were the genes with the most changes. The current data can help researchers predict future epidemics and establish better strategies to control viral pandemics.

Keywords

COVID‐19
Comparative genomics
Genome sequencing
Pandemic, SARS-CoV-2

Subjects

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Iranian Journal of Pathology
Volume 18, Issue 3
Summer 2023
Pages 289-298

  • Receive Date 19 July 2022
  • Revise Date 23 December 2022
  • Accept Date 15 June 2023

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