Exploring dynamics of emergence and spread of SARS-CoV-2 variants of concern

In a recent study posted to the medRxiv* preprint server, researchers evaluated the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Canada.

Study: Emergence and Spread of SARS-CoV-2 Variants of Concern in Canada: a Retrospective Analysis from Clinical and Wastewater Data. Image Credit: PHOTOCREO Michal Bednarek/Shutterstock

Wastewater-based epidemiology (WBE) can ascertain the proportion of viral RNA by applying polymerase chain reaction (PCR) or sequencing techniques. WBE helps inform the public and health officials about coronavirus disease 2019 (COVID-19) outbreaks and trends. As such, clinical and wastewater surveillance data can be leveraged to improve estimates of VOC prevalence.

About the study

In the present study, researchers retrospectively analyzed the dynamics of SARS-CoV-2 VOC emergence and spread using clinical and wastewater data in Canada. The Public Health Agency of Canada (PHAC) records clinical COVID-19 case data. Some entries have data on the infecting SARS-CoV-2 variant/lineage determined by genome sequencing or screening via a discriminatory assay.

The PHAC, Statistics Canada, and the National Microbiology Laboratory (NML) initiated a pilot program in October 2020 to test for SARS-CoV-2 in wastewater specimens collected twice/thrice a week 15 from sewage treatment plants in multiple cities, including Edmonton, Montreal, Vancouver, Halifax, and Toronto. Besides, wastewater sampling was performed five times a week from three plants in Winnipeg.

Samples from these cities were shipped to NML for quantitative PCR (qPCR) analysis. In addition, the researchers included qPCR data on wastewater sampled three times a week from Saskatoon by the University of Saskatchewan. The NML and the University of Saskatchewan quantified the proportion of VOCs in wastewater. The authors focused on four SARS-CoV-2 VOCs (Alpha, Gamma, Delta, and Omicron) in this study.

Using PHAC records, VOC-infected clinical cases were identified, and confidence intervals (CIs) for the proportions of each variant were computed. To compute the growth rate, the authors assumed that time-dependent proportions of SARS-CoV-2 VOCs followed a logistic growth model during each wave. A similar logistic growth model with a hierarchical structure was applied to aggregate province-level clinical surveillance data into national estimates.

VOC proportions measured in wastewater were the percentages of variant alleles detected by assays. Due to limited data, wastewater data were not used to derive CIs or fit logistic models. Therefore, the growth rate of each variant was assessed using clinical data alone. Nevertheless, VOC proportions in wastewater were compared to those from clinical surveillance to assess similarities.

Findings

Results from the following provinces with large sample sizes were reported – Alberta, British Columbia, Manitoba, Newfoundland and Labrador, Ontario, Quebec, and Saskatchewan. The authors observed similar trends in SARS-CoV-2 VOC proportions across all provinces in clinical and wastewater data. In the Summer of 2021, Alpha, Gamma, and Delta VOCs likely cocirculated in Alberta, Saskatchewan, and British Columbia.

SARS-CoV-2 VOC transitions appeared faster in Quebec and Ontario. The proportion of unidentified VOCs in clinical data in each province was less than 80%, except during the early alpha wave and post-July 2021 in Manitoba and Quebec. The proportions of SARS-CoV-2 VOCs in wastewater exhibited trends similar to those measured by clinical surveillance, particularly for the Omicron variant.

The Gamma VOC significantly circulated only in British Columbia, whereas the other three VOCs of interest circulated in all provinces. The Delta VOC spread at similar speeds across provinces, with Newfoundland and Labrador being the only outlier, likely due to the small sample size. Likewise, the Omicron VOC spread at a similar rate in provinces. SARS-CoV-2 Delta became predominant within four months.

Contrastingly, the Omicron VOC was the major circulating variant within a month. Posterior estimates suggested that the Alpha, Delta, and Omicron VOCs were spread throughout Canada by early January 2021, July 2021, and January 2022, respectively. In contrast, the national maximum proportion of the Gamma variant, which failed to spread throughout Canada, was approximately 25%.

Conclusions

To summarize, the study reported the spread of SARS-CoV-2 Alpha, Gamma, Delta, and Omicron VOCs in seven provinces in Canada using wastewater and clinical surveillance data. The researchers observed synchrony in SARS-CoV-2 VOC introduction across jurisdictions with similar speeds for each variant. This was remarkable, given the differences between provinces in implementing public health measures for COVID-19 management.

SARS-CoV-2 Gamma and Delta, which harbor few mutations, required four months to become the dominant variant. By contrast, the Omicron variant, which carries several novel mutations, became predominant in less than a month. Overall, WBE can complement clinical surveillance and serve as a viable indicator of SARS-CoV-2 VOC circulation in communities.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

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