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

Abstract

Tracking 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 scales, 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 lineages, 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.

Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

“…This study found that the intensity of international travel predicted the spread of SARS-CoV-2 with the introduction of new viral variants, and it estimated that more than half of the lineages that were spreading in late summer 2020 had been newly introduced to countries since mid-June 2020. Such importations into countries of SARS-CoV-2 variants and their impact on the pattern of incidence of SARS-CoV-2 cases have also been reported in other studies (McLaughlin et al, 2021). This sharply confirms what we described as early as at the beginning of September 2020 (Colson et al, 2020b) with the emergence of seven new SARS-CoV-2 variants including one ] for which we had already found a source (Colson et al, 2021c).…”

Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics

“…This study found that the intensity of international travel predicted the spread of SARS-CoV-2 with the introduction of new viral variants, and it estimated that more than half of the lineages that were spreading in late summer 2020 had been newly introduced to countries since mid-June 2020. Such importations into countries of SARS-CoV-2 variants and their impact on the pattern of incidence of SARS-CoV-2 cases have also been reported in other studies (31). This sharply confirms what we described as early as at the beginning of September 2020 (2) with the emergence of seven new SARS-CoV-2 including one (Marseille-1) for which we had already found a source (3).…”

A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities

“…We note that for the Canadian cities studied here, the vaccination coverage was either null or low during the study period. We model SARS-CoV-2as a single-strain pathogen which is an oversimplification of reality, given the numerous variants circulating in Canada since late 2020 McLaughlin et al (2021) . However, it is not clear how (or if) multi-variants modelling would affect our results, given that the difference of viral shedding (respiratory and faecal) between variants is still not fully understood Kidd et al, 2021 , Kissler et al, 2021 .Because of ordinary differential equations, this model is not well adapted to either small communities or very low prevalence settings.…”