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Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa

Sallam, Malik LU ; Ababneh, Nidaa A. ; Dababseh, Deema ; Bakri, Faris G. and Mahafzah, Azmi (2021) In Heliyon 7(1).
Abstract

Background: Phylogeny construction can help to reveal evolutionary relatedness among molecular sequences. The spike (S) gene of SARS-CoV-2 is the subject of an immune selective pressure which increases the variability in such region. This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Another aim was to analyze the S gene sequences phylogenetically. Methods: The SARS-CoV-2 S gene sequences collected in the MENA were retrieved from the GISAID public database, together with its metadata. Mutation analysis was conducted in Molecular Evolutionary Genetics Analysis software. Phylogenetic... (More)

Background: Phylogeny construction can help to reveal evolutionary relatedness among molecular sequences. The spike (S) gene of SARS-CoV-2 is the subject of an immune selective pressure which increases the variability in such region. This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Another aim was to analyze the S gene sequences phylogenetically. Methods: The SARS-CoV-2 S gene sequences collected in the MENA were retrieved from the GISAID public database, together with its metadata. Mutation analysis was conducted in Molecular Evolutionary Genetics Analysis software. Phylogenetic analysis was done using maximum likelihood (ML) and Bayesian methods. Result: A total of 553 MENA sequences were analyzed and the most frequent S gene mutations included: D614G = 435, Q677H = 8, and V6F = 5. A significant increase in the proportion of D614G was noticed from (63.0%) in February 2020, to (98.5%) in June 2020 (p < 0.001). Two large phylogenetic clusters were identified via ML analysis, which showed an evidence of inter-country mixing of sequences, which dated back to February 8, 2020 and March 15, 2020 (median estimates). The mean evolutionary rate for SARS-CoV-2 was about 6.5 × 10−3 substitutions/site/year based on large clusters' Bayesian analyses. Conclusions: The D614G mutation appeared to be taking over the COVID-19 infections in the MENA. Bayesian analysis suggested that SARS-CoV-2 might have been circulating in MENA earlier than previously reported. Phylogeny; Trend; COVID-19; MENA; Jordan; Oman; Egypt; Iran; Saudi Arabia; Morocco.

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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
COVID-19, Egypt, Iran, Jordan, MENA, Morocco, Oman, Phylogeny, Saudi Arabia, Trend
in
Heliyon
volume
7
issue
1
article number
e06035
publisher
Elsevier
external identifiers
  • scopus:85099614605
  • pmid:33495741
ISSN
2405-8440
DOI
10.1016/j.heliyon.2021.e06035
language
English
LU publication?
yes
id
9e3e91b4-3b5f-46f6-a607-0dd7f1309cc6
date added to LUP
2021-12-23 11:58:48
date last changed
2022-09-25 02:20:55
@article{9e3e91b4-3b5f-46f6-a607-0dd7f1309cc6,
  abstract     = {{<p>Background: Phylogeny construction can help to reveal evolutionary relatedness among molecular sequences. The spike (S) gene of SARS-CoV-2 is the subject of an immune selective pressure which increases the variability in such region. This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Another aim was to analyze the S gene sequences phylogenetically. Methods: The SARS-CoV-2 S gene sequences collected in the MENA were retrieved from the GISAID public database, together with its metadata. Mutation analysis was conducted in Molecular Evolutionary Genetics Analysis software. Phylogenetic analysis was done using maximum likelihood (ML) and Bayesian methods. Result: A total of 553 MENA sequences were analyzed and the most frequent S gene mutations included: D614G = 435, Q677H = 8, and V6F = 5. A significant increase in the proportion of D614G was noticed from (63.0%) in February 2020, to (98.5%) in June 2020 (p &lt; 0.001). Two large phylogenetic clusters were identified via ML analysis, which showed an evidence of inter-country mixing of sequences, which dated back to February 8, 2020 and March 15, 2020 (median estimates). The mean evolutionary rate for SARS-CoV-2 was about 6.5 × 10<sup>−3</sup> substitutions/site/year based on large clusters' Bayesian analyses. Conclusions: The D614G mutation appeared to be taking over the COVID-19 infections in the MENA. Bayesian analysis suggested that SARS-CoV-2 might have been circulating in MENA earlier than previously reported. Phylogeny; Trend; COVID-19; MENA; Jordan; Oman; Egypt; Iran; Saudi Arabia; Morocco.</p>}},
  author       = {{Sallam, Malik and Ababneh, Nidaa A. and Dababseh, Deema and Bakri, Faris G. and Mahafzah, Azmi}},
  issn         = {{2405-8440}},
  keywords     = {{COVID-19; Egypt; Iran; Jordan; MENA; Morocco; Oman; Phylogeny; Saudi Arabia; Trend}},
  language     = {{eng}},
  number       = {{1}},
  publisher    = {{Elsevier}},
  series       = {{Heliyon}},
  title        = {{Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa}},
  url          = {{http://dx.doi.org/10.1016/j.heliyon.2021.e06035}},
  doi          = {{10.1016/j.heliyon.2021.e06035}},
  volume       = {{7}},
  year         = {{2021}},
}