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.
【저자키워드】 viruses, Evolution, Mutation, Sequence analysis, human coronaviruses, 【초록키워드】 spike, bioinformatics, sputum, MERS-CoV, RNA, amplification, Characteristics, outbreak, nasopharyngeal, comparison, Clustering, clade, clades, molecular, respiratory, genomic, mutation rate, S gene, Analysis, amino acid changes, strain, Middle East, sequence, ORF1a, selective, MERS-CoV infection, Prevent, human coronavirus, Result, defined, highest, analyzed, required, nine, appear, hospitalized patient, the receptor-binding domain, the S protein, tracheal, ORF4b, amplified fragment, ORF1a/b, 【제목키워드】 MERS-CoV, Saudi Arabia, Analysis,