Early and ongoing importations of SARS-CoV-2 in Canada

Abstract

AbstractTracking the emergence and spread of SARS-CoV-2 is critical to inform public health interventions. Phylodynamic analyses have quantified SARS-CoV-2 migration on global and local scales1–5, yet they have not been applied to determine transmission dynamics in Canada. We quantified SARS-CoV-2 migration into, within, and out of Canada in the context of COVID-19 travel restrictions. To minimize sampling bias, global sequences were subsampled with probabilities corrected for their countries’ monthly contribution to global new diagnoses. A time-scaled maximum likelihood tree was used to estimate most likely ancestral geographic locations (country or Canadian province), enabling identification of sublineages, defined as introduction events into Canada resulting in domestic transmission. Of 402 Canadian sublineages identified, the majority likely originated from the USA (54%), followed by Russia (7%), India (6%), Italy (6%), and the UK (5%). International introductions were mostly into Ontario (39%) and Quebec (38%). Among Pango lineages6, B.1 was imported at least 191 separate times from 11 different countries. Introduction rates peaked in late March then diminished but were not eliminated following national interventions including restrictions on non-essential travel. We further identified 1,380 singleton importations, international importations that did not result in further sampled transmission, whereby representation of lineages and location were comparable to sublineages. Although proportion of international transmission decreased over time, this coincided with exponential growth of within-province transmission – in fact, total number of sampled transmission events from international or interprovincial sources increased from winter 2020 into spring 2020 in many provinces. Ontario, Quebec, and British Columbia acted as sources of transmission more than recipients, within the caveat of higher sequence representation. We present strong evidence that international introductions and interprovincial transmission of SARS-CoV-2 contributed to the Canadian COVID-19 burden throughout 2020, despite initial reductions mediated by travel restrictions in 2020. More stringent border controls and quarantine measures may have curtailed introductions of SARS-CoV-2 into Canada and may still be warranted.Significance StatementBy analyzing SARS-CoV-2 genomes from Canada in the context of the global pandemic, we illuminate the extent to which the COVID-19 burden in Canada was perpetuated by ongoing international importations and interprovincial transmission throughout 2020. Although travel restrictions enacted in March 2020 reduced the importation rate and proportion of transmission from abroad across all Canadian provinces, SARS-CoV-2 introductions from the USA, India, Russia, and other nations were detectable through the summer and fall of 2020.