Extensive SARS-CoV-2 testing reveals BA.1/BA.2 asymptomatic rates and underreporting in school children (preprint)

Case underreporting during the COVID-19 pandemic has been a major challenge to the planning and evaluation of public health responses. Inconsistent underreporting can undermine effective risk assessment due to high uncertainty in predicted future scenarios. Underreporting rates have been particularly high among children and youth, given that asymptomatic school children were often considered a less vulnerable population. In January 2022, the Canadian province of Newfoundland and Labrador (NL) was experiencing an Omicron variant outbreak (BA.1/BA.2 subvariants) and public health officials recommended that all students returning to elementary, junior high, and high schools (~59,452 students) complete two rapid antigen tests (RATs) to be performed three days apart. To estimate the prevalence of SARS-CoV-2, we asked parents and guardians to report the results of the RATs completed by K-12 students using an online survey, and to specify the students' school level and if students with positive RAT results had symptoms. When comparing the survey responses with the number of cases and tests reported by the NL testing system, we found that 1 out of every 4.3 (3.1-5.3) positive households were captured by provincial case count, with 5.1% positivity estimated from the RAT results, and 1.2% positivity reported by the provincial testing system. The survey data indicate that a higher percentage of SARS-CoV-2 cases were found in elementary schools, with 62.9% of positive cases (95% CI: 44.3%, 83.0%) reported from elementary school students, and the remaining 37.1% (95% CI: 22.7%, 52.9%) reported from junior high and high school students. Asymptomatic infections were 59.8% of the positive cases, with no significant difference between asymptomatic rates in elementary schools (60.8%) or in junior high and high schools (58.1%). Given the low survey participation rate (3.5%), our results may suffer from sample selection biases, and should be interpreted with caution. Nonetheless, our estimate of the underreporting ratio is consistent with ratios calculated from serology data, and our study provides insights into infection prevalence and asymptomatic infections in school children, a currently understudied population.

Pandemic modelling for regions implementing an elimination strategy (preprint)

During the COVID-19 pandemic, some countries, such as Australia, China, Iceland, New Zealand, Thailand and Vietnam, successfully implemented an elimination strategy. Until June 2021, Atlantic Canada and Canada's territories had also experienced prolonged periods with few SARS-CoV-2 community cases. Such regions had a need for epidemiological models that could assess the risk of SARS-CoV-2 outbreaks, but most existing frameworks are applicable to regions where SARS-CoV-2 is spreading in the community, and so it was necessary to adapt existing frameworks to meet this need. We distinguish between infections that are travel-related and those that occur in the community, and find that in Newfoundland and Labrador (NL), Nova Scotia, and Prince Edward Island the mean percentage of daily cases that were travel-related was 80% or greater (July 1, 2020 -- May 31, 2021). We show that by December 24, 2021, the daily probability of an Omicron variant community outbreak establishing in NL was near one, and nearly twice as high as the previous high, which occurred in September 2021 when the Delta variant was dominant. We evaluate how vaccination and new variants might affect hypothetical future outbreaks in Mt. Pearl, NL. Our modelling framework can be used to evaluate alternative plans to relax public health restrictions when high levels of vaccination are achieved in regions that have implemented an elimination strategy.

Downsizing of contact tracing during COVID-19 vaccine roll-out (preprint)

Contact tracing is a key component of successful management of COVID-19. Contacts of infected individuals are asked to quarantine, which can significantly slow down (or prevent) community spread. Contact tracing is particularly effective when infections are detected quickly (e.g., through rapid testing), when contacts are traced with high probability, when the initial number of cases is low, and when social distancing and border restrictions are in place. However, the magnitude of the individual contribution of these factors in reducing epidemic spread and the impact of vaccination in determining contact tracing outputs is not fully understood. We present a delayed differential equation model to investigate how vaccine roll-out and the relaxation of social distancing requirements affect contact tracing practises. We provide an analytical criteria to determine the minimal contact tracing efficiency (defined as the the probability of identifying and quarantining contacts of symptomatic individuals) required to keep an outbreak under control, with respect to the contact rate and vaccination status of the population. Additionally, we consider how delays in outbreak detection and increased case importation rates affect the number of contacts to be traced daily. We show that in vaccinated communities a lower contact tracing efficiency is required to avoid uncontrolled epidemic spread, and delayed outbreak detection and relaxation of border restrictions do not lead to a significantly higher risk of overwhelming contact tracing. We find that investing in testing programs, rather than increasing the contact tracing capacity, has a larger impact in determining whether an outbreak will be controllable. This is because early detection activates contact tracing, which will slow, and eventually reverse exponential growth, while the contact tracing capacity is a threshold that will easily become overwhelmed if exponential growth is not curbed. Finally, we evaluate quarantine effectiveness during vaccine roll-out, by considering the proportion of people that will develop an infection while in isolation in relation to the vaccination status of the population and for different viral variants. We show that quarantine effectiveness decreases with increasing proportion of fully vaccinated individuals, and increases in the presence of more transmissible variants. These results suggest that a cost-effective approach during vaccine roll-out is to establish different quarantine rules for vaccinated and unvaccinated individuals, where rules should depend on viral transmissibility. Altogether, our study provides quantitative information for contact tracing downsizing during vaccine roll-out, to guide COVID-19 exit strategies.