Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study

SARS-CoV-2 has become one of the unprecedented global health challenge for human population. Genomic signature studies of SARS-CoV-2 reveals relation between geographical location of the isolates and genetic diversity. The present work is an in silico, cross sectional study aimed to determine the ge...

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Autores principales:	Mohammad Fahad Ullah, Tarig M.S. Alnour, Elmutuz H. Elssaig, Eltayib H. Ahmed-Abakur
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	SARS-CoV-2 Covid 19 BLAST Mutations Nucleotide Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c30e9895a5ba40c2a9df2d7d547a53f0
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spelling	oai:doaj.org-article:c30e9895a5ba40c2a9df2d7d547a53f02021-11-20T04:56:26ZCharacterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study1319-562X10.1016/j.sjbs.2021.07.054https://doaj.org/article/c30e9895a5ba40c2a9df2d7d547a53f02021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1319562X21006379https://doaj.org/toc/1319-562XSARS-CoV-2 has become one of the unprecedented global health challenge for human population. Genomic signature studies of SARS-CoV-2 reveals relation between geographical location of the isolates and genetic diversity. The present work is an in silico, cross sectional study aimed to determine the genetic heterogeneity of SARS-CoV-2 variants isolated in Saudi Arabia compared to the first isolated strain NC_045512 (reference sequence). Each sequence was aligned against the reference sequence using local alignment search tool (NCBI) Nucleotide-BLAST. A total of 58 SARS-CoV-2 genomes were isolated in KSA and retrieved from NCBI. Our study shows that KSA variants demonstrated homology ranging between 99.96 and 99.98 % compared to the reference strain. There are 89 nucleotide changes that have been identified among the KSA variants; the most common nucleotide change was C: T accounting for 50.6% (45/89). These nucleotides changes resulted in 53.9% (48/89) missense mutations and 42.7% (38/89) silent mutations; while the majority of mutations- 48.3% (43/89) occurred in ORF1ab gene. All structural genes displayed mutations; N gene harbored 16.9% (15/89) mutations, S gene displayed 15.7% (14/89) mutations, M gene exhibited 2.2% (2/89) mutations and E gene showed only 1 mutation which was silent. The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5′UTR) which were found in 56 and 55 variants respectively. The Phylogenetic trees showed that SARS-CoV-2 variants isolated in Saudi Arabia clustered together closely.Mohammad Fahad UllahTarig M.S. AlnourElmutuz H. ElssaigEltayib H. Ahmed-AbakurElsevierarticleSARS-CoV-2Covid 19BLASTMutationsNucleotideBiology (General)QH301-705.5ENSaudi Journal of Biological Sciences, Vol 28, Iss 12, Pp 6803-6807 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	SARS-CoV-2 Covid 19 BLAST Mutations Nucleotide Biology (General) QH301-705.5
spellingShingle	SARS-CoV-2 Covid 19 BLAST Mutations Nucleotide Biology (General) QH301-705.5 Mohammad Fahad Ullah Tarig M.S. Alnour Elmutuz H. Elssaig Eltayib H. Ahmed-Abakur Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study
description	SARS-CoV-2 has become one of the unprecedented global health challenge for human population. Genomic signature studies of SARS-CoV-2 reveals relation between geographical location of the isolates and genetic diversity. The present work is an in silico, cross sectional study aimed to determine the genetic heterogeneity of SARS-CoV-2 variants isolated in Saudi Arabia compared to the first isolated strain NC_045512 (reference sequence). Each sequence was aligned against the reference sequence using local alignment search tool (NCBI) Nucleotide-BLAST. A total of 58 SARS-CoV-2 genomes were isolated in KSA and retrieved from NCBI. Our study shows that KSA variants demonstrated homology ranging between 99.96 and 99.98 % compared to the reference strain. There are 89 nucleotide changes that have been identified among the KSA variants; the most common nucleotide change was C: T accounting for 50.6% (45/89). These nucleotides changes resulted in 53.9% (48/89) missense mutations and 42.7% (38/89) silent mutations; while the majority of mutations- 48.3% (43/89) occurred in ORF1ab gene. All structural genes displayed mutations; N gene harbored 16.9% (15/89) mutations, S gene displayed 15.7% (14/89) mutations, M gene exhibited 2.2% (2/89) mutations and E gene showed only 1 mutation which was silent. The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5′UTR) which were found in 56 and 55 variants respectively. The Phylogenetic trees showed that SARS-CoV-2 variants isolated in Saudi Arabia clustered together closely.
format	article
author	Mohammad Fahad Ullah Tarig M.S. Alnour Elmutuz H. Elssaig Eltayib H. Ahmed-Abakur
author_facet	Mohammad Fahad Ullah Tarig M.S. Alnour Elmutuz H. Elssaig Eltayib H. Ahmed-Abakur
author_sort	Mohammad Fahad Ullah
title	Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study
title_short	Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study
title_full	Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study
title_fullStr	Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study
title_full_unstemmed	Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study
title_sort	characterization of altered genomic landscape of sars-cov-2 variants isolated in saudi arabia in a comparative in silico study
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/c30e9895a5ba40c2a9df2d7d547a53f0
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Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study

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