A study on the transmission of COVID-19 variants to and across Canada shows that international travel restrictions were an important intervention to reduce or slow the spread, according to a report published today in eLife.
The results suggest that reducing the number of virus imports that can cause domestic outbreaks in a country through dynamic travel bans gives governments more time to prepare for a new variant – through more testing, contact tracing and vaccination programs.
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 widely used 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 contain the virus.
Large-scale SARS-CoV-2 genomic epidemiological analyzes in Canada have so far been limited to an early epidemic study in Quebec. We wanted to flesh out this study with a nationwide analysis for the first and second COVID-19 wave. We also wanted to evaluate the impact of international travel restrictions in March 2020 on international imports of the virus and understand why the virus persisted through 2021.”
Angela McLaughlin, lead author, research assistant at the British Columbia Center for Excellence in HIV/AIDS, and a PhD candidate in Bioinformatics, University of British Columbia, Canada
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 geographic origin of the viruses. From this, they identified more than 2,260 introductions of new variants into Canada, including 680 sublines – viruses that were introduced from other countries and then circulated within the Canadian population. They also identified 1,582 loners – viruses that were introduced that did not appear to be spreading among the Canadian population.
Just when travel restrictions were introduced in April 2020, the import rate reached its peak (58.5 sublines per week), including 31.8 from the US and 31.2 imported into Quebec only. Two weeks after the travel restrictions came into effect, the total import rate of sublines had fallen 3.4 times and within four weeks it had fallen 10.3 times.
However, despite these reductions, new virus variants were introduced at a low level until August 2020, when there was a small spike in cases leading up to the second wave. This suggests that wild-type sublines introduced in the summer, when prevalence and immunity were low, contributed to the highest rate of COVID-19 cases in the second wave. This in turn implies that even a low level of continued virus import of similar transmissible variants can contribute to viral persistence. In mid-October, travel restrictions were further eased, and import tariffs recovered quickly, contributing to the second wave.
By categorizing transmission sources as within county, between county, US and other international sources, the team was able to see where the new virus entry came from. They found that most introductions of the first virus (January to July 2020) came from the US, followed by Russia, Italy, India, Spain and the UK, and were mainly imported to Quebec and Ontario. In the second wave (August 2020 to the end of February 2021), the origin of new sublines was still dominated by the US, with increased relative contributions from India, UK, Asia, Europe and Africa.
That the US was a major contributor to COVID-19 cases in 2020 was not unforeseen by the authors, given the high COVID-19 prevalence in 2020 and the long land border shared between the two countries. Even when international arrivals in Canada fell by 77.8% between 2019 and 2020, the number of truck drivers and crew members (air, ship and train) only decreased by 24.8% and accounted for almost half of all international arrivals after April 2020 While essential key players supporting the supply chain, these arrivals may have inadvertently enabled additional imports from the US – suggesting this is an area where better public health measures, such as contact tracing and rapid testing, could have prevented the movement of new variants. .
“These analyzes shed light on the natural epidemiological history of SARS-CoV-2 in the context of public health interventions and demonstrate 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 Center for Excellence in HIV/AIDS and Assistant Professor in the Department of Medicine, University of British Columbia. “Broad and long-term restrictions against non-essential international travel are not necessarily an advisable policy in light of the economic impact. However, our analysis suggests that rapid and strict travel bans to places with a high frequency of a new variant of care, or an outbreak of an entirely new virus, which has not yet been identified domestically, should be seriously considered to reduce the likelihood of multiple, simultaneous outbreaks and overwhelming health care systems.”
McLaughlin, A., et al. (2022) Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada. eLife. doi.org/10.7554/eLife.73896.