A study of COVID-19 variant transmission into and across Canada shows that international travel restrictions were a key intervention for reducing or slowing spread, according to a report published today in eLife.
The results suggest that reducing the number of virus importations that can spark domestic outbreaks within a country through dynamic travel bans allows governments more time to prepare for a new variant – by ramping up testing, contact tracing and vaccination programmes.
The COVID-19 pandemic has highlighted the importance of genomic epidemiology – that is, genetic sequencing of SARS-CoV-2 samples from different regions and times – to understand the origin and movement of virus variants internationally, especially variants of concern or interest. These methods have been used widely in the UK, US, Brazil, New Zealand and Europe, and have illustrated the variation in epidemic dynamics between countries that took different public health approaches to containing the virus.
“Large-scale SARS-CoV-2 genomic epidemiology analyses in Canada have so far been limited to a study on the early epidemic within Quebec,” says lead author Angela McLaughlin, Research Assistant at the British Columbia Centre for Excellence in HIV/AIDS, and a PhD candidate in Bioinformatics, University of British Columbia, Canada. “We wanted to elaborate on this research with a national-scale analysis for the first and second COVID-19 waves. We also wanted to evaluate the impact of international travel restrictions in March 2020 on international importations of the virus and to understand why the virus persisted into 2021.”
The team used available sequence data from Canadian COVID-19 cases and data on the prevalence of circulating variants in other countries to estimate the viruses’ geographical origins. From this, they identified more than 2,260 introductions of new variants into Canada, including 680 sublineages – viruses introduced from other countries that went on to circulate within the Canadian population. They also identified 1,582 singletons – viruses introduced that did not appear to spread within the Canadian population.
Just as travel restrictions were introduced in April 2020, the importation rate reached its maximum (58.5 sublineages per week), including 31.8 from the US and 31.2 introduced solely into Quebec. Two weeks after travel restrictions took effect, the overall sublineage importation rate had dropped 3.4-fold and within four weeks had dropped 10.3-fold.
Despite these reductions, however, new virus variants continued to be introduced at a low level until August 2020 when there was a small spike in cases leading into the second wave. This suggests that wildtype sublineages introduced in the summer when prevalence and immunity were low contributed the highest proportion of COVID-19 cases in the second wave. In turn, this implies that even a low level of ongoing virus importations of similarly transmissible variants can contribute to viral persistence. By mid-October, travel restrictions were relaxed further, and importation rates rebounded quickly and contributed to the second wave.
By categorising transmission sources as within-province, between province, the US and other international sources, the team could see where the new virus importations were originating. They found that most first-wave virus introductions (January to July 2020) came from the US, followed by Russia, Italy, India, Spain and the UK, and were primarily imported into Quebec and Ontario. In the second wave (August 2020 to end February 2021), the origin of new sublineages was still dominated by the US, with increased relative contributions from India, the UK, Asia, Europe and Africa.
That the US was a large contributor of COVID-19 cases in 2020 was not unanticipated by the authors, given its high COVID-19 prevalence throughout 2020 and the long land border shared between the two countries. Even when international arrivals into Canada declined by 77.8% from 2019 to 2020, the number of truck drivers and crew members (air, ship and train) only declined by 24.8%, and accounted for almost half of all international arrivals after April 2020. Although essential key workers supporting the supply chain, these arrivals may have inadvertently facilitated additional importations from the US – suggesting this is one area where better public health measures, such as contact tracing and rapid testing, could have helped prevent the movement of new variants.
“These analyses shed light on the natural epidemiological history of SARS-CoV-2 in the context of public health interventions and show how sublineage-based genomic surveillance can be used to identify gaps in a country’s epidemic response,” concludes senior author Jeffrey Joy, Research Scientist at the British Columbia Centre for Excellence in HIV/AIDS and Assistant Professor at the Department of Medicine, University of British Columbia. “Broad and longstanding restrictions against non-essential international travel is not necessarily an advisable policy in light of economic impacts. However, our analysis suggests that swift and stringent travel bans towards localities harbouring a high frequency of a new variant of concern, or an outbreak of an entirely new virus, not yet identified domestically, should be seriously considered to reduce the probability of seeding multiple, simultaneous outbreaks and overwhelming healthcare systems.”
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About the British Columbia Centre for Excellence in HIV/AIDS
The BC Centre for Excellence in HIV/AIDS (BC-CfE) is Canada’s largest HIV/AIDS research, treatment and education facility – nationally and internationally recognised as an innovative world leader in combating HIV/AIDS and related diseases. The made-in-BC Treatment as Prevention® strategy (TasP®), pioneered by BC-CfE and supported by UNAIDS since 2011, inspired the ambitious global target for HIV treatment – known as the 90-90-90 Target – to end AIDS as a pandemic by 2030. The BC-CfE is applying TasP® to therapeutic areas beyond HIV/AIDS, including viral hepatitis and addiction, to promote Targeted Disease Elimination® as a means to contribute to healthcare sustainability. The BC-CfE works in close collaboration with key stakeholders, including government, health authorities, healthcare providers, academics, and the community to decrease the health burden of HIV/AIDS, hepatitis C and addictions across Canada and around the world.
Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada
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