Teasing apart the differential impact of variants of concern on COVID-19 severity and health inequities: a population-based genomic epidemiological investigation in Ontario and British Columbia.

As the COVID-19 pandemic turns the one year mark, the causative agent of this disease, SARS-CoV-2 is presenting the Canadian population with new challenges: variants of concern (VoCs), which are mutated strains with undesirable characteristics such as enhanced ability to transmit. VoCs threaten the public health gains obtained via various control measures and may even boost a new trajectory for the pandemic and worsen health inequities. There is early evidence suggesting that these variants may also have deleterious clinical impacts by increasing the disease severity, but these studies used surveillance data alone, and were challenged by potential biases such as the inability to account for factors like chronic health conditions that could act as confounders, and different time periods of comparison - most studies compared severity from VoCs now with cases from a few months ago. Therefore there is urgency in fully understanding the extent of their virulence with population based approaches that can limit these biases. To this end, we propose to use genomic and population-level clinical data on all cases of COVID-19 in two provinces where VoCs were first detected, British Columbia and Ontario, and to fully investigate each of the circulating variant, namely B.1.1.7, B.1.351 and P.1; as well as the role of specific mutations with severity, such as time to clinical deterioration, hospitalizations, need for intensive care, and mortality. We will then estimate the extent to which VoCs may amplify inequities in health outcomes among the most affected communities, such as those living in congregate settings, essential workers, and multigenerational and dense households. The goal of this collaboration is to leverage extensive scientific and methodological expertise, large population-level data and laboratory diagnostic tests, and thousands of genomic sequences to support efficient and proactive public health and health system response to this ever evolving pathogen.