Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome

Osong Public Health and Research Perspectives
Jun-Sub KimMyung-Guk Han

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in December 2019 and has been rapidly spreading worldwide. Although the causal relationship among mutations and the features of SARS-CoV-2 such as rapid transmission, pathogenicity, and tropism, remains unclear, our results of genomic mutations in SARS-CoV-2 may help to interpret the interaction between genomic characterization in SARS-CoV-2 and infectivity with the host. A total of 4,254 genomic sequences of SARS-CoV-2 were collected from the Global Initiative on Sharing all Influenza Data (GISAID). Multiple sequence alignment for phylogenetic analysis and comparative genomic approach for mutation analysis were conducted using Molecular Evolutionary Genetics Analysis (MEGA), and an in-house program based on Perl language, respectively. Phylogenetic analysis of SARS-CoV-2 strains indicated that there were 3 major clades including S, V, and G, and 2 subclades (G.1 and G.2). There were 767 types of synonymous and 1,352 types of non-synonymous mutation. ORF1a, ORF1b, S, and N genes were detected at high frequency, whereas ORF7b and E genes exhibited low frequency. In the receptor-binding domain (RBD) of the S gene, 11 non-synonymous mutations wer...Continue Reading

References

Dec 2, 2009·The Journal of Molecular Diagnostics : JMD·Ralph StadhoudersMartin Schutten
Feb 1, 2012·The Journal of Biological Chemistry·Kailang WuFang Li
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Apr 7, 2017·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Yuelong Shu, John McCauley
Feb 7, 2020·Journal of Medical Virology·Carmine Ceraolo, Federico M Giorgi
Feb 23, 2020·Science·Daniel WrappJason S McLellan
Mar 27, 2020·Pathogens·Saif Ur RehmanQingyou Liu
Apr 1, 2020·Nature·Jian ShangFang Li
Apr 15, 2020·Nature Medicine·Kristian G AndersenRobert F Garry

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Citations

Jun 4, 2020·Journal of Medical Virology·A S M Rubayet Ul AlamM Anwar Hossain
Sep 25, 2020·Journal of Medical Virology·Christian Luke D C BaduaPaul Mark B Medina
Sep 22, 2020·Transboundary and Emerging Diseases·Mohammad Shaminur RahmanMohammad Anwar Hossain
Aug 14, 2020·Journal of Virology·Marc C JohnsonDetlef G Ritter
Nov 19, 2020·Transboundary and Emerging Diseases·Fangfeng YuanLeyi Wang
Dec 21, 2020·Briefings in Bioinformatics·Pratik GoswamiVáclav Brázda
Dec 17, 2020·Heliyon·Shweta JakhmolaHem Chandra Jha
Oct 23, 2020·Genomics·Mhamad Abou-HamdanFadi Abdel-Sater
Mar 25, 2021·Scientific Reports·Aysun Urhan, Thomas Abeel
Apr 4, 2021·International Journal of Molecular Sciences·Szu-Wei Huang, Sheng-Fan Wang
Apr 6, 2021·Computational and Structural Biotechnology Journal·Sally Esmail, Wayne R Danter
Jul 6, 2021·Indian Journal of Clinical Biochemistry : IJCB·Sagar DholariyaDigishaben Patel
Aug 14, 2021·Antibody Therapeutics·Marios MejdaniRadhakrishnan Mahadevan
Aug 15, 2021·Virology Journal·Jalen SinghKaren Mossman
Oct 20, 2020·ACS Pharmacology & Translational Science·Aditya K Padhi, Timir Tripathi
Nov 5, 2021·Scientific Reports·Abdel-Rahman N ZekriMohamed Abouelhoda
Dec 8, 2021·Archives of Microbiology·Ananda Vardhan HebbaniVaddi Damodara Reddy

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Methods Mentioned

BETA
GISAID

Software Mentioned

Perl
GISAID
MEGA

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