Ontario is stepping up genomic surveillance in areas where coronavirus infections are trending upward faster than average out of concern that new variants could be accelerating the spread of COVID-19, the province’s head microbiologist says.
Vanessa Allen, chief of microbiology and laboratory science at Public Health Ontario, identified six regional health units where higher infection rates have prompted an increase in the number of samples of the virus selected for genomic sequencing.
“We’re specifically focusing on health units where there’s been rapid growth since December,” Dr. Allen said on Thursday.
The regions include Windsor-Essex – which has lately had the highest increase in new cases provincewide – and Hamilton, Durham, Peel, York and Toronto.
Half a dozen cases of a new variant of the virus that originated in the United Kingdom have turned up in Ontario, more than all other provinces combined. All have been connected directly to recent travel, but the variant could have become established in Canada before it was first recognized in Britain a month ago. A variant from South Africa has not been seen in Canada. Researchers in the U.K. were alerted to the new variant because of an anomalous rise in cases in southeastern England.
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Early evidence suggests both variants are more transmissible versions of the virus, and may increase the reproduction number – the number of new cases that arise from one case of COVID-19 – by 50 per cent. But epidemiologists say many important factors are unknown, including whether the variant affects the period of time over which a case of COVID-19 is contagious.
“That [reproduction number] alone doesn’t tell you everything you want to know about the rate at which it’s going to spread through a population,” said Troy Day, a mathematical biologist at Queen’s University in Kingston.
Dr. Day began building mathematical models of the U.K. variant just before Christmas, and said he became concerned when he realized it shortened the doubling time of cases there from about 40 days to less than two weeks. However, he added, the situation might be significantly different in Canada because of lower population density.
“Assuming the variant gains its advantage through an increased transmission … that advantage is going to be enhanced in high-density populations,” he said.
Dr. Day added that his modelling suggests the impact of a more transmissible variant of the virus in Canada would only just be starting to show up now if it was introduced as far back as October.
So far, there is no indication a new variant is driving the recent numbers in Ontario hot spots. Even so, the ramped up effort to sequence viral genomes can capture only a small subset of all known cases in the community.
Compared with diagnostic testing, which merely indicates whether someone has been exposed to the virus, whole-genome sequencing is laborious and time-consuming. Dr. Allen said that, over the holidays, Public Health Ontario increased its genomic sequencing efforts from about 200 to 350 samples a week. Five other laboratories in Ontario are sequencing samples of the virus. The province has also developed a more rapid test that is sensitive to the U.K. and South African variants to help prioritize samples.
Similar efforts across Canada are also looking where a new variant is thought to be most likely to turn up first. That has put the emphasis on travellers returning from abroad who test positive for COVID-19. The sequencing includes not only those who went to the U.K., but also the United States, where far less genomic sequencing is happening than in Canada and where it is even easier for variants of the virus to circulate undetected.
Catalina Correa-Lopez, who leads a national sequencing collaboration for Genome Canada, said she is concerned new variants could come from people who travel to Latin America, where only a few thousand viral genomes have been sequenced, compared with 30,000 in Canada alone.
According to the Public Health Agency of Canada, the part of the strategy that targets travellers also includes looking back at samples from those who tested positive as long ago as Sept. 1, about the time of the first known appearance of the U.K. variant.
Sequencing capacity is also being directed toward identifying other cases in the community that look out of the ordinary, including those that originated from “superspreader” events, or that may persist longer or cause more severe illness than is typical in cases without an obvious reason such as age or health issues.
Another anomaly could be increased cases among the young, which has been a trend in Ontario in the past few weeks. Dr. Allen said that while samples of the virus found in children are part of the broader surveillance effort, so far there has not been more targeted additional sampling from younger age groups, although this strategy is under discussion.
She added that if community spread of a new variant is found in Ontario or elsewhere in the next few weeks, the public-health efforts to contain it will be the same as those that have been used for many months, primarily aimed at reduced contact between individuals.
“The hope is if we can detect small clusters earlier … we can reinforce that strategy, and the communication of that strategy could be more precise,” she said.
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