Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada

Abstract

Background: Between February and June 2021, the initial wild-type strains of SARS-CoV-2 were supplanted in Ontario, Canada, by new variants of concern (VOCs), first those with the N501Y mutation (i.e., Alpha/B1.1.17, Beta/B.1.351 and Gamma/P.1 variants) and then the Delta/B.1.617 variant. The increased transmissibility of these VOCs has been documented, but knowledge about their virulence is limited. We used Ontario's COVID-19 case data to evaluate the virulence of these VOCs compared with non-VOC SARS-CoV-2 strains, as measured by risk of hospitalization, intensive care unit (ICU) admission and death.

Methods: We created a retrospective cohort of people in Ontario who tested positive for SARS-CoV-2 and were screened for VOCs, with dates of test report between Feb. 7 and June 27, 2021. We constructed mixed-effect logistic regression models with hospitalization, ICU admission and death as outcome variables. We adjusted models for age, sex, time, vaccination status, comorbidities and pregnancy status. We included health units as random intercepts.

Results: Our cohort included 212 326 people. Compared with non-VOC SARS-CoV-2 strains, the adjusted elevation in risk associated with N501Y-positive variants was 52% (95% confidence interval [CI] 42%-63%) for hospitalization, 89% (95% CI 67%-117%) for ICU admission and 51% (95% CI 30%-78%) for death. Increased risk with the Delta variant was more pronounced at 108% (95% CI 78%-140%) for hospitalization, 235% (95% CI 160%-331%) for ICU admission and 133% (95% CI 54%-231%) for death.

Interpretation: The increasing virulence of SARS-CoV-2 VOCs will lead to a considerably larger, and more deadly, pandemic than would have occurred in the absence of the emergence of VOCs.

Figure 1:

Flow diagram showing inclusion and exclusion of cases from Ontario’s Case and Contact Management database in construction of the data set used for this study, as well as the schema used to assign variant of concern (VOC) status.

Figure 2:

Trends in SARS-CoV-2 case occurrence and distribution of hospitalizations, intensive care unit (ICU) admission and deaths by variants of concern (VOC) status in Ontario, Canada. (A) Cases of reported SARS-CoV-2 infection by test report date, presented as the 7-day average for cases reported over the study period. (B) Distribution of cases hospitalized for COVID-19, cases admitted to ICU and deaths by VOC status, by week of test report. Cases are coloured by assigned VOC status. Before May 1, 2021, Delta cases were detected only by whole genome sequencing. After May 1, 2021, all screened specimens not identified as an N501Y-positive VOC (N501Y+ VOC) or another variant were classified as probable Delta VOC infections.