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Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019

BACKGROUND: The Middle East Respiratory Syndrome-related Coronavirus (MERS-CoV) continues to exist in the Middle East sporadically. Thorough investigations of the evolution of human coronaviruses (HCoVs) are urgently required. In the current study, we studied amplified fragments of ORF1a/b, Spike (S...

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Autores principales: Farrag, Mohamed A., Amer, Haitham M., Bhat, Rauf, Almajhdi, Fahad N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085657/
https://www.ncbi.nlm.nih.gov/pubmed/33931099
http://dx.doi.org/10.1186/s12985-021-01563-7
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author Farrag, Mohamed A.
Amer, Haitham M.
Bhat, Rauf
Almajhdi, Fahad N.
author_facet Farrag, Mohamed A.
Amer, Haitham M.
Bhat, Rauf
Almajhdi, Fahad N.
author_sort Farrag, Mohamed A.
collection PubMed
description BACKGROUND: The Middle East Respiratory Syndrome-related Coronavirus (MERS-CoV) continues to exist in the Middle East sporadically. Thorough investigations of the evolution of human coronaviruses (HCoVs) are urgently required. In the current study, we studied amplified fragments of ORF1a/b, Spike (S) gene, ORF3/4a, and ORF4b of four human MERS-CoV strains for tracking the evolution of MERS-CoV over time. METHODS: RNA isolated from nasopharyngeal aspirate, sputum, and tracheal swabs/aspirates from hospitalized patients with suspected MERS-CoV infection were analyzed for amplification of nine variable genomic fragments. Sequence comparisons were done using different bioinformatics tools available. RESULTS: Several mutations were identified in ORF1a/b, ORF3/4a and ORF4b, with the highest mutation rates in the S gene. Five codons; 4 in ORF1a and 1 in the S gene, were found to be under selective pressure. Characteristic amino acid changes, potentially hosted and year specific were defined across the S protein and in the receptor-binding domain Phylogenetic analysis using S gene sequence revealed clustering of MERS-CoV strains into three main clades, A, B and C with subdivision of with clade B into B1 to B4. CONCLUSIONS: In conclusion, MERS-CoV appears to continuously evolve. It is recommended that the molecular and pathobiological characteristics of future MERS-CoV strains should be analyzed on regular basis to prevent potential future outbreaks at early phases.
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spelling pubmed-80856572021-04-30 Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019 Farrag, Mohamed A. Amer, Haitham M. Bhat, Rauf Almajhdi, Fahad N. Virol J Research BACKGROUND: The Middle East Respiratory Syndrome-related Coronavirus (MERS-CoV) continues to exist in the Middle East sporadically. Thorough investigations of the evolution of human coronaviruses (HCoVs) are urgently required. In the current study, we studied amplified fragments of ORF1a/b, Spike (S) gene, ORF3/4a, and ORF4b of four human MERS-CoV strains for tracking the evolution of MERS-CoV over time. METHODS: RNA isolated from nasopharyngeal aspirate, sputum, and tracheal swabs/aspirates from hospitalized patients with suspected MERS-CoV infection were analyzed for amplification of nine variable genomic fragments. Sequence comparisons were done using different bioinformatics tools available. RESULTS: Several mutations were identified in ORF1a/b, ORF3/4a and ORF4b, with the highest mutation rates in the S gene. Five codons; 4 in ORF1a and 1 in the S gene, were found to be under selective pressure. Characteristic amino acid changes, potentially hosted and year specific were defined across the S protein and in the receptor-binding domain Phylogenetic analysis using S gene sequence revealed clustering of MERS-CoV strains into three main clades, A, B and C with subdivision of with clade B into B1 to B4. CONCLUSIONS: In conclusion, MERS-CoV appears to continuously evolve. It is recommended that the molecular and pathobiological characteristics of future MERS-CoV strains should be analyzed on regular basis to prevent potential future outbreaks at early phases. BioMed Central 2021-04-30 /pmc/articles/PMC8085657/ /pubmed/33931099 http://dx.doi.org/10.1186/s12985-021-01563-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Farrag, Mohamed A.
Amer, Haitham M.
Bhat, Rauf
Almajhdi, Fahad N.
Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019
title Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019
title_full Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019
title_fullStr Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019
title_full_unstemmed Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019
title_short Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019
title_sort sequence and phylogentic analysis of mers-cov in saudi arabia, 2012–2019
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085657/
https://www.ncbi.nlm.nih.gov/pubmed/33931099
http://dx.doi.org/10.1186/s12985-021-01563-7
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