Genomic epidemiology and evolutionary dynamics of COVID-19 and other emerging corona viruses [Added supplement: COVID-19 Variant Supplement]

Emergence of the 2019 coronavirus (SARS-CoV-2) has highlighted the severe impact emerging zoonotic pathogens have on human health, the global economy, and health service delivery. Phylogenetic analyses of SARS-CoV-2 genomic sequences improve our understanding of host reservoir species, assess the potential for transmission to humans, and illuminate evolutionary dynamics relative to other viruses in Coronaviridae, informing response to current and future epidemics. We will study the genomic evolution of SARS-CoV-2 to investigate if particular motifs are under selection for increased virulence and immune evasion. We will compare SARS-CoV-2 with genomes of other zoonotic coronaviruses to elucidate common genomic features associated with virulence, host switching, and human-to-human transmission. We will also evaluate spatiotemporal transmission patterns of SARS-CoV-2 across different populations using Bayesian phylogeographic analyses. Such analyses allow identification of spatially and temporally structured, clinical and epidemiological parameters such as the basic reproduction number, period of infectiousness, and true viral prevalence over time within different populations. We will also elucidate the reservoir host species of SARS-CoV-2 in concert with collaborators from the Chinese Centre for Disease Control as well as other Canadian researchers by probing unique environmental samples as well as both novel and existing datasets available for coronaviruses. Phylogenetic co-speciation analysis will explore whether coronaviruses are more likely to jump between phylogenetically proximate host species allowing development of a predictive framework to anticipate future zoonotic events. We will identify genomic factors of SARS-CoV-2 associated with virulence, estimate vital epidemiological parameters, and illuminate potential reservoir species. With the Chinese CDC, we will help focus the response, control and elimination of the current, and future, coronavirus outbreaks.