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

Virology Journal

Mohamed A. Farrag¹  Rauf Bhat¹  Fahad N. Almajhdi¹  Haitham M. Amer² 

[1] Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia;Department of Virology, Faculty of Veterinary Medicine, Cairo University, 12211, Giza, Egypt;

关键词: Human coronaviruses;    Mutation;    Viruses;    Sequence analysis;    Evolution;   

DOI  :  10.1186/s12985-021-01563-7

来源: Springer

【 摘 要 】

BackgroundThe 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.MethodsRNA 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.ResultsSeveral 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.ConclusionsIn 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.

【 授权许可】

CC BY