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Open Access 01-12-2021 | Middle Eastern Respiratory Syndrome | Research

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

Authors: Mohamed A. Farrag, Haitham M. Amer, Rauf Bhat, Fahad N. Almajhdi

Published in: Virology Journal | Issue 1/2021

Abstract

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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Title: Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019
Authors: Mohamed A. Farrag
Haitham M. Amer
Rauf Bhat
Fahad N. Almajhdi
Publication date: 01-12-2021
Publisher: BioMed Central
Keywords: Middle Eastern Respiratory Syndrome
Coronavirus
Published in: Virology Journal / Issue 1/2021
Electronic ISSN: 1743-422X
DOI: https://doi.org/10.1186/s12985-021-01563-7

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Abstract

Background

Methods

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Conclusions

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