Prevalence and genetic characterization of human coronaviruses in southern Thailand from July 2009 to January 2011.

Suwannakarn, Kamol; Chieochansin, Thaweesak; Vichiwattana, Preeyaporn; Korkong, Sumeth; Theamboonlers, Apiradee; Poovorawan, Yong

Emergence of viruses belonging to the coronavirus family has been widespread in the past, causing respiratory infections in humans, such as severe acute respiratory syndrome (SARS). This study investigated the prevalence of human coronavirus (HCoV) and characterized the molecular viral genetics. We collected 1,254 samples from patients diagnosed with respiratory infection in southern Thailand from July 2009 to January 2011 and screened for HCoV by RT-PCR and genotyped by BLAST analysis of nsp12 gene. Phylogenetic analysis was performed based on S gene sequences. Thirty-five of 1,254 samples were positive for HCoV. Viral genotyping revealed 4 genotypes with HCoV-OC43 being the predominant genotype. Viral prevalence and genotype distribution were not in accordance with seasonal distribution. Phylogenetic analysis and deduced amino acid sequences of the S gene showed amino acid variations in each genotype. The S gene sequence of HCoV-OC43 genotype indicated that it resulted from recombination between subgenotypes B and C. Viral genetics analysis disclosed genetic variations of HCoV and additionally, it can provide information suitable for monitoring and prevention of the emergence and re-emergence of various types of coronavirus.