SARS-CoV-2 introductory events in Quebec, Canada


The 2019 coronavirus disease (COVID-19) pandemic has spread rapidly across the world, causing more than five million deaths and forcing many countries to adopt costly restrictions that have triggered multiple economic crises. The rapid transmission, the high death rate among at-risk groups and the lack of initial therapies have resulted in social distancing measures, mandatory masks and the closure of public spaces.

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

As mass vaccination programs have begun to bring the disease under control, many countries are still struggling with the logistics of vaccination, and dangerous new variants continue to emerge. Given the persistent threat of the disease, it remains important to understand how outbreaks appear and the pattern of the virus as it enters a new environment. In a study published in Genome medicine, researchers at McGill University studied the number of introductory events in Quebec.

The study

Researchers selected nasopharyngeal swabs positive for COVID-19 from the Laboratoire de santé publique du Québec from the start of the pandemic until June 1st, 2020. In total, they sequenced nearly 3,000 genomes of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All samples found to be positive by PCR tests targeting the E and N genes were randomly selected and sequenced. RNA samples were processed in a 96-well format. Water and extraction buffer blanks were used as negative controls, while commercially available RNA / cDNA / viral cultures were used as positive controls.

The researchers built crude and chronological phylogenomic trees to explore the relationships between genomes. The introductory events in Quebec were determined using a discrete ancestral state reconstruction to infer the non-Quebec and Quebec nodes in the time tree. Among the set of nodes identified, the scientists looked for the most basal and rejected all descendant nodes of other nodes in their set. The parents of the remaining nodes are the non-Quebec transition nodes – where the introductory event took place. While this likely underestimated the number of introductions, most methods of determining these events will be somewhat inaccurate.

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

In total, these genomic sequences cover 5.7% of the reported cases. Until April 1, the average age of cases was around 50, after which it rose to 75 – indicating the spread of the virus in healthcare facilities. Quebec has suffered greatly from COVID-19 outbreaks in healthcare facilities, with more than 500 reporting at least one case.

Most of the COVID-19 introductions in Quebec came from travelers who had entered Europe. While a quarantine was put in place in March, more than 1,500 infected travelers had already returned. Not all of them carried unique strains or strains that had not already been introduced and did not all spread from the traveler.

A total of 615 independent introductory events were discovered. Evidence showed an increase in the viral population until the introduction of restriction measures, with the spread of each independent lineage lagging slightly behind Europe. Many of the introductions to Quebec came after spring break – a popular vacation time for families and college students, especially to and from the United States, which has fallen behind other countries. in the introduction of control measures and had to deal with an increase in the number of cases.

While previous studies had uncovered cryptic introductions before the first official cases were recorded, none were observed in this study. However, most cryptic introductions were discovered in Asia or Europe, so this is not necessarily contradictory. The most successful lines were normally the ones that arrived earlier – they spread the most widely and spawned the most new lines. Other countries have seen similar results, with eight introductions in the UK resulting in lines accounting for around 25% of cases.

Conclusion

The researchers point out that the early spring break is a key factor in the spread of the disease in Quebec – unlike the rest of Canada, Quebec vacationers returned before the quarantine. This resulted in rapid transmission and a much larger first wave than in the rest of Canada. The information scientists have reviewed here could be invaluable to public health decision makers and help plan for future restrictions to help curb the spread of the disease in the future.


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