tetano
Editor, Senior Moderator
Virol J
. 2021 Apr 30;18(1):90.
doi: 10.1186/s12985-021-01563-7.
Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012-2019
Mohamed A Farrag[SUP] 1 [/SUP], Haitham M Amer[SUP] 2 [/SUP], Rauf Bhat[SUP] 1 [/SUP], Fahad N Almajhdi[SUP] 3 [/SUP]
Affiliations
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.
Keywords: Evolution; Human coronaviruses; Mutation; Sequence analysis; Viruses.
. 2021 Apr 30;18(1):90.
doi: 10.1186/s12985-021-01563-7.
Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012-2019
Mohamed A Farrag[SUP] 1 [/SUP], Haitham M Amer[SUP] 2 [/SUP], Rauf Bhat[SUP] 1 [/SUP], Fahad N Almajhdi[SUP] 3 [/SUP]
Affiliations
- PMID: 33931099
- DOI: 10.1186/s12985-021-01563-7
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.
Keywords: Evolution; Human coronaviruses; Mutation; Sequence analysis; Viruses.