A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada.
| Title: | A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada. |
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| Authors: | Murall CL; McGill Genome Centre, Montreal, QC, Canada.; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.; Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada.; Fournier E; Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada.; Galvez JH; McGill Genome Centre, Montreal, QC, Canada.; Canadian Center for Computational Genomics, Montreal, QC, Canada.; N'Guessan A; Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada.; Reiling SJ; McGill Genome Centre, Montreal, QC, Canada.; Department of Human Genetics, McGill University, Montreal, QC, Canada.; Quirion PO; McGill Genome Centre, Montreal, QC, Canada.; Canadian Center for Computational Genomics, Montreal, QC, Canada.; Calcul Québec, Montreal, QC, Canada.; Naderi S; McGill Genome Centre, Montreal, QC, Canada.; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.; Roy AM; McGill Genome Centre, Montreal, QC, Canada.; Department of Human Genetics, McGill University, Montreal, QC, Canada.; Chen SH; McGill Genome Centre, Montreal, QC, Canada.; Department of Human Genetics, McGill University, Montreal, QC, Canada.; Stretenowich P; McGill Genome Centre, Montreal, QC, Canada.; Canadian Center for Computational Genomics, Montreal, QC, Canada.; Bourgey M; McGill Genome Centre, Montreal, QC, Canada.; Canadian Center for Computational Genomics, Montreal, QC, Canada.; Bujold D; McGill Genome Centre, Montreal, QC, Canada.; Canadian Center for Computational Genomics, Montreal, QC, Canada.; Gregoire R; McGill Genome Centre, Montreal, QC, Canada.; Canadian Center for Computational Genomics, Montreal, QC, Canada.; Lepage P; McGill Genome Centre, Montreal, QC, Canada.; St-Cyr J; McGill Genome Centre, Montreal, QC, Canada.; Willet P; McGill Genome Centre, Montreal, QC, Canada.; Dion R; Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada.; Ecole de santé publique, Université de Montréal, Montreal, QC, Canada.; Charest H; Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada.; Lathrop M; McGill Genome Centre, Montreal, QC, Canada.; Department of Human Genetics, McGill University, Montreal, QC, Canada.; Roger M; Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada.; Département de Microbiologie, infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.; Bourque G; McGill Genome Centre, Montreal, QC, Canada.; Canadian Center for Computational Genomics, Montreal, QC, Canada.; Department of Human Genetics, McGill University, Montreal, QC, Canada.; Ragoussis J; McGill Genome Centre, Montreal, QC, Canada.; Department of Human Genetics, McGill University, Montreal, QC, Canada.; Department of Bioengineering, McGill University, Montreal, QC, Canada.; Shapiro BJ; McGill Genome Centre, Montreal, QC, Canada. jesse.shapiro@mcgill.ca.; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada. jesse.shapiro@mcgill.ca.; Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada. jesse.shapiro@mcgill.ca.; Moreira S; Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Montreal, QC, Canada. |
| Source: | Genome medicine [Genome Med] 2021 Oct 28; Vol. 13 (1), pp. 169. Date of Electronic Publication: 2021 Oct 28. |
| Publication Type: | Journal Article; Research Support, Non-U.S. Gov't |
| Language: | English |
| Journal Info: | Publisher: BioMed Central Country of Publication: England NLM ID: 101475844 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-994X (Electronic) Linking ISSN: 1756994X NLM ISO Abbreviation: Genome Med Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [London] : BioMed Central |
| MeSH Terms: | COVID-19/*transmission; COVID-19/epidemiology ; COVID-19/virology ; Canada/epidemiology ; Europe/epidemiology ; Quebec/epidemiology ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Genome, Viral ; Humans ; Molecular Epidemiology ; Pandemics ; Phylogeny ; Public Health ; Travel |
| Abstract: | Background: Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province.; Methods: Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec. We report 2921 high-quality SARS-CoV-2 genomes in the context of > 12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatiotemporal spread of the virus.; Results: Conservatively, we estimated approximately 600 independent introduction events, the majority of which happened from spring break until 2 weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (> 50 sequenced cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and "snowbird" destinations, most of the introductions were inferred to have originated from Europe via the Americas. Once introduced into Québec, viral lineage sizes were overdispersed, with a few lineages giving rise to most infections. Consistent with founder effects, the earliest lineages to arrive tended to spread most successfully. Fewer than 100 viral introductions arrived during spring break, of which 7-12 led to the largest transmission lineages of the first wave (accounting for 52-75% of all sequenced infections). These successful transmission lineages dispersed widely across the province. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travellers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order.; Conclusions: Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.; (© 2021. The Author(s).) |
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| Entry Date(s): | Date Created: 20211028 Date Completed: 20211102 Latest Revision: 20211102 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC8550813 |
| DOI: | 10.1186/s13073-021-00986-9 |
| PMID: | 34706766 |
| Database: | MEDLINE |
Journal Article; Research Support, Non-U.S. Gov't