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

J Med Virol. 2021 Feb;93(2):945-951. doi: 10.1002/jmv.26361. Epub 2020 Aug 13.


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.

Keywords: acute respiratory infection; influenza-like illness; outpatient clinic; phylogenetic tree.

MeSH terms

  • Adolescent
  • Adult
  • Child
  • Child, Preschool
  • Coronavirus Infections / epidemiology*
  • Coronavirus Infections / virology
  • Coronavirus OC43, Human / classification
  • Coronavirus OC43, Human / genetics*
  • Evolution, Molecular
  • Female
  • Genotype*
  • Humans
  • Infant
  • Infant, Newborn
  • Longitudinal Studies
  • Male
  • Middle Aged
  • Phylogeny*
  • RNA, Viral / genetics
  • Recombination, Genetic
  • Sequence Analysis, DNA
  • Spike Glycoprotein, Coronavirus / genetics*
  • Young Adult


  • RNA, Viral
  • Spike Glycoprotein, Coronavirus