SARS-CoV-2 Introductory Events in Quebec, Canada

The Coronavirus disease 2019 (COVID-19) pandemic spread rapidly across the globe, causing over five million deaths and forcing many countries to impose costly restrictions that triggered several economic crises. The rapid transfer, high mortality among vulnerable groups and lack of initial treatments resulted in social distance measures, mandatory face masks and closed public areas.

Study: A small number of early introductions revealed widespread transmission of SARS-CoV-2 in Quebec, Canada.  Image credit: mervas / ShutterstockStudy: A small number of early introductions revealed widespread transmission of SARS-CoV-2 in Quebec, Canada. Image credit: mervas / Shutterstock

While mass vaccination schemes have begun to bring the disease under control, many countries are still struggling with vaccination logistics, and dangerous new variants of concern continue to emerge. Given the continuing threat of the disease, it is still important to understand how outbreaks occur and the pattern of the virus as it enters a new environment. In a study published in Through Medicine, researchers from McGill University have studied the number of introductory events in Quebec.

The study

The researchers selected nasopharyngeal vaccines positive for COVID-19 from the Public Health Laboratory in Quebec from the beginning of the pandemic until June 1.st, 2020. In total, they sequenced nearly 3000 genomes with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All samples that were found to be positive through PCR tests targeting the E and N genes were randomly selected and sequenced. RNA samples were processed in 96-well format. Water and extraction buffer blank were used as the negative control, while commercially available RNA / cDNA / viral culture was used as the positive controls.

The researchers built both raw and time-scaled phylogenetic trees to explore the relationship between the genomes. Introductory events in Quebec were determined using a state-of-the-art ancestral state reconstruction to derive non-Quebec and Quebec nodes in the time tree. Among the identified set of nodes, the researchers searched for the most basic and discarded all nodes that were descendants of other nodes in their set. The parents of the remaining nodes are the transition nodes outside Quebec – where the introductory event took place. Although this probably underestimated the number of introductions, most methods of determining these events will be somewhat inaccurate.

The identified candidates were then cross-checked with travel history data. In the case of a polytomy with several basic Quebec sequences, the shortest branch length was chosen. To determine changes in the viral effective population size and deviation from a standard neutral model, the researchers calculated Tajimas D by randomly sampling 20 consensus sequences every two weeks between February 20, 2020 and June 10, 2020.

In total, these genome sequences cover 5.7% of the reported cases. Until April 1, the average age of the cases was about 50 years old, after which it rose to 75 – indicating the spread of the virus in care facilities. Quebec suffered greatly from COVID-19 outbreaks in care facilities, with over 500 reporting at least one case.

Most introductions of COVID-19 to Quebec were from travelers entering Europe. While a quarantine was put in place in March, over 1,500 infected travelers had already returned. Not all bore unique strains or strains that had not already been introduced and not all spread from the traveler.

A total of 615 independent introductory events were detected. Evidence showed an increasing virus population until restrictions were introduced, with the spread of each independent lineage lagging slightly behind Europe. Many of the introductions in Quebec took place after the spring break – a popular holiday season for both families and college students, especially to and from the United States, which lagged behind other countries in imposing control measures and struggling with rising case numbers.

While previous studies had discovered cryptic introductions before the first official cases were recorded, no one was seen in this study. However, most cryptic introductions have been discovered in Asia or Europe, so this is not necessarily contradictory. The most successful genera were usually those that arrived earliest – they spread the most and gave rise to the most new genera. Other countries have seen similar results, with eight introductions in the UK giving rise to genera that accounted for ~ 25% of cases.

Conclusion

Researchers highlight the early spring break as a key factor in the spread of the disease in Quebec – unlike the rest of Canada, Quebec holidaymakers returned before the quarantine was implemented. This resulted in rapid transmission and a much larger first wave than in the rest of Canada. The information that researchers have examined here may be invaluable to public health politicians and help plan future restrictions to help slow the spread of the disease in the future.

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