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

Abstract

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.

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e

“…We constructed time-resolved phylogenies of the OC43 and 229E using publicly accessible sequenced isolates. A cursory look at these trees confirms previous reports that substantial diversity exists within each viral species ( Zhang et al, 2015 ; Komabayashi et al, 2020 ; Lau et al, 2011 ). Additionally, the trees form ladder-like topologies with isolate tips arranged into temporal clusters rather than geographic clusters, indicating a single global population rather than geographically isolated populations of virus.…”

“…Additionally, two genetically distinct groupings (each of which include multiple of the aforementioned eight genotypes) of OC43 viruses have been shown to alternate in prevalence within a Japanese community, meaning that the majority of OC43 infections are caused by one group for about 2–4 years at which point the other group begins to account for the bulk of infections. It has been suggested that antigenic differences between these groups contribute to this epidemic switching ( Komabayashi et al, 2020 ).…”

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E

“…A cursory look at these trees confirms previous reports that substantial diversity exists within each viral species (Y. Zhang et al 2015; Komabayashi et al 2020; Lau et al 2011). Additionally, the trees form ladder-like topologies with isolate tips arranged into temporal clusters rather than geographic clusters, indicating a single global population rather than geographically-isolated populations of virus.…”

“…We constructed time-resolved phylogenies of the OC43 and 229E using publicly accessible sequenced isolates. A cursory look at these trees confirms previous reports that substantial diversity exists within each viral species (Zhang et al 2015; Komabayashi et al 2020; Lau et al 2011). The phylogeny of OC43 bifurcates immediately from the root (Fig.…”

“…Additionally, two genetically distinct groupings (each of which include multiple of the aforementioned 8 genotypes) of OC43 viruses have been shown to alternate in prevalence within a Japanese community, meaning that the majority of OC43 infections are caused by one group for about 2-4 years at which point the other group begins to account for the bulk of infections. It has been suggested that antigenic differences between these groups contribute to this epidemic switching (Komabayashi et al 2020).…”