Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010–2017: Two groups based on spike gene appear one after another

• Published in: Journal of medical virology Vol. 93; no. 2; pp. 945 - 951
• Main Authors: Komabayashi, Kenichi, Matoba, Yohei, Tanaka, Shizuka, Seto, Junji, Aoki, Yoko, Ikeda, Tatsuya, Shimotai, Yoshitaka, Matsuzaki, Yoko, Itagaki, Tsutomu, Mizuta, Katsumi
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.02.2021
• Subjects: acute respiratory infection; Adolescent; Adult; Child; Child, Preschool; Clusters; Coronaviridae; Coronavirus Infections - epidemiology; Coronavirus Infections - virology; Coronavirus OC43, Human - classification; Coronavirus OC43, Human - genetics; Coronaviruses; Epidemics; Epidemiology; Evolution, Molecular; Female; Genotype; Genotype & phenotype; Genotypes; Humans; Infant; Infant, Newborn; influenza‐like illness; Longitudinal Studies; Male; Middle Aged; outpatient clinic; phylogenetic tree; Phylogenetics; Phylogeny; Recombination; Recombination, Genetic; RNA, Viral - genetics; S gene; Sequence Analysis, DNA; Spike Glycoprotein, Coronavirus - genetics; Spikes; Strains (organisms); Virology; Young Adult; Japan; phylogenetic tree; outpatient clinic; acute respiratory infection; influenza-like illness
• ISSN: 0146-6615; 1096-9071; 1096-9071
• DOI: 10.1002/jmv.26361

Human coronavirus OC43 (HCoV‐OC43) is divided into genotypes A to H based on genetic recombination including the spike (S) gene. To investigate the longitudinal transition of the phylogenetic feature of the HCoV‐OC43 S gene in a community, phylogenetic analysis of the S1 region of the S gene was conducted using 208 strains detected in Yamagata during 2010 to 2017 with reference strains of the genotype. The S1 sequences were divisible into four groups: A to D. All Yamagata strains belonged to either group B or group D. In group B, 46 (90.2%) out of 51 Yamagata strains were clustered with those of genotype E reference strains (cluster E). In group D, 28 (17.8%) and 122 (77.7%) out of 157 Yamagata strains were clustered, respectively, with genotype F and genotype G reference strains. In cluster G, 28 strains formed a distinct cluster. Monthly distributions of HCoV‐OC43 in Yamagata in 2010 to 2017 revealed that group B and group D appeared one after another. In group B, the cluster E strains were prevalent recurrently. In conclusion, epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups: group B showed a recurrent epidemic of strains belonging to a single phylogenetic cluster and group D showed epidemic strains belonging to multiple clusters. Highlights Longitudinal transition of the phylogenetic feature of the HCoV‐OC43 spike gene in a community. Epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups.