138338

Sequence Analysis and Variations in the 5’ UTR genomic regions of Coronaviruses

Article

Last updated: 03 Jan 2025

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Abstract

The 5'UTR genomic regions of coronaviruses were analysed regarding sequence variations, nucleotide constituents, and patterns of evolutionary course. The 5ʹ UTR of the viral genome highly conserved that appeared clearly between the closely related viruses. It possessed variable sites of varied nucleotides.
          The 5'UTRs revealed long highly conserved regions (nt61 to nt107, nt211- nt236, nt262 to nt277). The longest one (nt61 to nt107) possessed nearly half of the core leader sequence (nt 61 to nt93) confirming its existence in viral genomes. The nucleotides composition exhibited favouritism towards AT(U) contents against GC contents which potentially is necessary   for viral origin and replication activity. The length of 5′ UTR varies in studied cronaviruses, ranging from 245 bp (SARS coronavirus BJ01, AY278488.2) to 283 bp (hCoV-19_Chile, gaisd-EPI_ISL_445295). Additionally, the 5' UTR region of Chile, EPI_ISL_445295 isolate included a foremost 18 nucleotides, these are not found in other isolates.
            Phylogenetic analysis of 5' UTR regions using the maximum likelihood method confirmed the close evolutionary distance and origin of betacronoviruses analysed. The most genetic closely isolates to the SARS-CoV-2 Wuhan-Hu-1 is the Bat coronavirus RaTG13. The SARS coronaviruses BJ01 and GD01 displayed the most distant betacronoviruses to SARS-CoV-2 that confirm their early arisen lineage. Finally, phylogenetic clustering in 5' UTR regions for studied betacronoviruses revealed the genetic diversity of betacronoviruses and their high tendency towards frequent genetic mutations and gene recombination. This potentially leads to increased risk of interspecies transmission with viral evolution and accumulation of mutations.

DOI

10.21608/eajbsc.2020.138338

Keywords

Orthocoronavirinae, Coronaviruses, SARS CoV-2, 5’ UTR regions, molecular sequence variations

Authors

First Name

Mohammed

Last Name

EL-Mahdi

MiddleName

Bassyouni M.

Affiliation

Laboratory of Molecular Genetics and Molecular Biology, Zoology Department Faculty of Science, South Valley University, Qena, Egypt

Email

melmahdi@svu.edu.eg

City

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Orcid

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Volume

12

Article Issue

2

Related Issue

15286

Issue Date

2020-12-01

Receive Date

2020-10-25

Publish Date

2020-12-01

Page Start

201

Page End

211

Print ISSN

2090-0767

Online ISSN

2090-083X

Link

https://eajbsc.journals.ekb.eg/article_138338.html

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https://eajbsc.journals.ekb.eg/service?article_code=138338

Order

16

Type

Original Article

Type Code

673

Publication Type

Journal

Publication Title

Egyptian Academic Journal of Biological Sciences. C, Physiology and Molecular Biology

Publication Link

https://eajbsc.journals.ekb.eg/

MainTitle

Sequence Analysis and Variations in the 5’ UTR genomic regions of Coronaviruses

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Article

Created At

22 Jan 2023