ArticleeLife2022
Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- SAASI: Sampling Aware Ancestral State Inference.Nature communications · 2026Article
- Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024.Communications medicine · 2026Article
- Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden.Virus evolution · 2025Article
- Mathematical modelling for pandemic preparedness in Canada: Learning from COVID-19.Canada communicable disease report = Releve des maladies transmissibles au Canada · 2024Article
- In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences.PLoS computational biology · 2024Article
- The influence of cross-border mobility on the COVID-19 epidemic in Nordic countries.PLoS computational biology · 2024Article
- How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort.Microbiology spectrum · 2024Article
- phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things).PeerJ · 2024Article
- Extracellular acyl-CoA-binding protein as an independent biomarker of COVID-19 disease severity.Frontiers in immunology · 2024Article
- Article
- Bloodstream Infections in Intensive Care Unit during Four Consecutive SARS-CoV-2 Pandemic Waves.Antibiotics (Basel, Switzerland) · 2023Article
- Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India.Scientific reports · 2023Article
- A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India.Journal of infection and public health · 2023Article
- Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru.Nature communications · 2023Article
- Article
- The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.Microbial genomics · 2023Article
- Distribution and Current State of Molecular Genetic Characterization in Pathogenic Free-Living Amoebae.Pathogens (Basel, Switzerland) · 2022Review
- Leveraging artificial intelligence to optimize COVID-19 robust spread and vaccination roll-out strategies in Southern Africa.Frontiers in artificial intelligence · 2022Article
- Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics.Frontiers in microbiology · 2021Article
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8 authors.
Funding
Abstract
Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2021. Maximum likelihood phylogenetic trees were used to infer viruses' geographic origins, enabling identification of 2263 (95% confidence interval: 2159-2366) introductions, including 680 (658-703) Canadian sublineages, which are international introductions resulting in sampled Canadian descendants, and 1582 (1501-1663) singletons, introductions with no sampled descendants. Of the sublineages seeded during the first wave, 49% (46-52%) originated from the USA and were primarily introduced into Quebec (39%) and Ontario (36%), while in the second wave, the USA was still the predominant source (43%), alongside a larger contribution from India (16%) and the UK (7%). Following implementation of restrictions on the entry of foreign nationals on 21 March 2020, importations declined from 58.5 (50.4-66.5) sublineages per week to 10.3-fold (8.3-15.0) lower within 4 weeks. Despite the drastic reduction in viral importations following travel restrictions, newly seeded sublineages in summer and fall 2020 contributed to the persistence of COVID-19 cases in the second wave, highlighting the importance of sustained interventions to reduce transmission. Importations rebounded further in November, bringing newly emergent variants of concern (VOCs). By the end of February 2021, there had been an estimated 30 (19-41) B.1.1.7 sublineages imported into Canada, which increasingly displaced previously circulating sublineages by the end of the second wave.Although viral importations are nearly inevitable when global prevalence is high, with fewer importations there are fewer opportunities for novel variants to spark outbreaks or outcompete previously circulating lineages.
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