Abstract
Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients and one inpatient health facility (HF). Ninety-two patient samples tested HCoV-OC43 positive and forty (43.5%) were successfully sequenced in spike (S) gene region (2,864 long, ∼70%). Phylogenetic analysis confirmed co-circulation of two distinct HCoV-OC43 clades that closely clustered with genotype G (n = 34, 85%) and genotype H (n = 6, 15%) reference strains. Local viruses within the same clade displayed low genetic diversity yielding identical sequences in multiple HF. Furthermore, the newly sequenced Kenyan viruses showed close phylogenetic relationship to other contemporaneous sampled strains (2015–16) including those originating from distant places (e.g. USA and China). Using a genetic similarity threshold of 99.1 per cent at nucleotide level, the HCoV-OC43 strains sampled globally between 1967 and 2019 fell into nine sequence clusters. Notably, some of these clusters appeared to have become extinct, or occurred only sporadically in a few geographical areas while others persisted globally for multiple years. In conclusion, we found that HCoV-OC43 strains spread rapidly both locally and across the globe with limited genetic evolution in the spike gene. Full-genome sequences that are spatio-temporally representative are required to advance understanding of the transmission pathways of this important human respiratory pathogen.
Highlights
Coronaviruses (CoVs) infect a variety of mammalian and avian species resulting in diverse disease outcomes ranging from asymptomatic infection to severe and potentially fatal respiratory and gastrointestinal disease (Cui, Li, and Shi 2019)
Participants were recruited between December 2015 and June 2016 during two separate surveillance studies of acute respiratory illness (ARI) within the County targeting: 1, children
We investigated the global phylogenetic context and potential origins of HCoV-OC43 detected in Kilifi, by co-analysis of the Kilifi data with spike sequence data deposited in GenBank
Summary
Coronaviruses (CoVs) infect a variety of mammalian and avian species resulting in diverse disease outcomes ranging from asymptomatic infection to severe and potentially fatal respiratory and gastrointestinal disease (Cui, Li, and Shi 2019). Using serology and sequence phylogenetics, CoVs are classified into four distinct genera within which seven members that infect humans have been identified (Su et al 2016; Chen, Liu, and Guo 2020; ICTV 2020). Four of these members: HCoV-NL63, HCoV-229E, HCoV-OC43, HCoVHKU1 are endemic HCoVs in humans and cause regular seasonal infections (Su et al 2016; Corman et al 2018; Cui, Li, and Shi 2019). There are no licenced vaccines against HCoVs there are candidate vaccines in development undergoing field trials (Modjarrad et al 2019; Schindewolf and Menachery 2019)
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