Speaker
Description
The emergence of SARS-CoV-2 has renewed interest in how coronaviruses evolve and transition to endemic circulation. The four seasonal human coronaviruses (hCoVs) 229E, NL63, OC43 and HKU1, differ in terms of their estimated times of emergence, receptor usage patterns and genome content. While they are frequently grouped clinically, these differences beg the question as to whether the evolution and epidemiology of these viruses is similarly distinct. Using a publicly available background dataset, as well as 1033 genomes sequenced from 2012 to 2022 in Slovenia, we sought to compare the rates and patterns of substitution and recombination across the hCoVs. We describe the distribution of recombination breakpoints across hCoVs, and the variation in persistence of recombinant lineages across the viruses. While some breakpoints are shared across hCoVs, others are specific to a given virus. We also characterise the extent of selection present within the spike gene, with increased substitutions in the receptor-binding domain typical of antigenic drift observed for 229E and OC43, but not NL63. Our results illustrate the complexity and variety among the four seasonal coronaviruses, with implications for our understanding of coronavirus evolution and the potential routes to endemicity.
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