Impact of routine asymptomatic screening on COVID-19 incidence in a highly vaccinated university population (preprint)

Background: With the return of in-person classes, an understanding of COVID-19 transmission in vaccinated university campuses is essential. Given the context of high anticipated vaccination rates and other measures, there are outstanding questions of the potential impact of campus-based asymptomatic screening. Methods: We estimated the expected number of cases and hospitalizations in one semester using rates derived for British Columbia (BC), Canada up to September 15th, 2021 and age-standardizing to a University population. To estimate the expected number of secondary cases averted due to routine tests of unvaccinated individuals in a BC post-secondary institution, we used a probabilistic model based on the incidence, vaccination effectiveness, vaccination coverage and R0. We examined multiple scenarios of vaccine coverage, screening frequency, and pre-vaccination R0. Results: For one 12 week semester, the expected number of cases is 67 per 50,000 for 80\% vaccination coverage and 37 per 50,000 for 95\% vaccination coverage. Screening of the unvaccinated population averts an expected 6-16 cases per 50,000 at 80\% decreasing to 1-2 averted cases per 50,000 at 95\% vaccination coverage for weekly to daily screening. Further scenarios can be explored using a web-based application. Interpretation: Routine screening of unvaccinated individuals may be of limited benefit if vaccination coverage is 80\% or greater within a university setting.

Social contacts and transmission of COVID-19 in British Columbia, Canada (preprint)

PurposeClose-contact rates are thought to be a significant driving force behind the dynamics of transmission for many infectious respiratory diseases. Efforts to control such infections typically focus on the practice of strict contact-avoidance measures. Yet, contact rates and their relation to transmission, and the impact of control measures, are seldom quantified. Here, we quantify the response of contact rates, transmission and new cases of COVID-19 to public health contact-restriction orders, and the associations among these three variables, in the Canadian province of British Columbia (BC) and within its two most densely populated regional health authorities: Fraser Health Authority (FHA) and Vancouver Coastal Health Authority (VCHA). MethodsWe obtained time series for self-reported close-contact rates from the BC Mix COVID-19 Survey, new reported cases of COVID-19 from the BC Center for Disease Control, and transmission rates based on dynamic model fits to reported cases. Our study period was from September 13, 2020 to February 19, 2021, during which three public health contact-restriction orders were introduced (October 26, November 7 and November 19, 2020). We used segmented linear regression to quantify impacts of public health orders, Pearson correlation to assess the instantaneous relation between contact rates and transmission, and vector autoregressive modeling to study the lagged relations among the three variables. ResultsOverall, declines in contact rates and transmission occurred concurrently with the announcement of public health orders, whereas declines in new cases showed a reporting delay of roughly two weeks. The impact of the first public health order (October 26, 2020) on contact rates and transmission was more pronounced than that of the other two health orders. Contact rates and transmission on the same day were strongly correlated (correlation coefficients = 0.64, 0.53 and 0.34 for BC, FHA, and VCHA, respectively). Moreover, contact rates were a significant time-series driver of COVID-19 and explained roughly 30% and 18% of the variation in new cases and transmission, respectively. Interestingly, increases in transmission and new cases were followed by reduced rates of contact: overall, average daily cases explained about 10% of the variation in provincial contact rates. ConclusionWe show that close-contact rates were a significant driver of transmission of COVID-19 in British Columbia, Canada and that they varied in response to public health orders. Our results also suggest a possible feedback, by which contact rates respond to recent changes in reported cases. Our findings help to explain and validate the commonly assumed, but rarely measured, response of close contact rates to public health guidelines and their impact on the dynamics of infectious diseases.

Geographical concentration of COVID-19 cases by social determinants of health in 16 large metropolitan areas in Canada - a cross-sectional study (preprint)

Background: There is a growing recognition that strategies to reduce SARS-CoV-2 transmission should be responsive to local transmission dynamics. Studies have revealed inequalities along social determinants of health, but little investigation was conducted surrounding geographic concentration within cities. We quantified social determinants of geographic concentration of COVID-19 cases across sixteen census metropolitan areas (CMA) in four Canadian provinces. Methods: We used surveillance data on confirmed COVID-19 cases at the level of dissemination area. Gini (co-Gini) coefficients were calculated by CMA based on the proportion of the population in ranks of diagnosed cases and each social determinant using census data (income, education, visible minority, recent immigration, suitable housing, and essential workers) and the corresponding share of cases. Heterogeneity was visualized using Lorenz (concentration) curves. Results: Geographic concentration was observed in all CMAs (half of the cumulative cases were concentrated among 21-35% of each city's population): with the greatest geographic heterogeneity in Ontario CMAs (Gini coefficients, 0.32-0.47), followed by British Columbia (0.23-0.36), Manitoba (0.32), and Quebec (0.28-0.37). Cases were disproportionately concentrated in areas with lower income, education attainment, and suitable housing; and higher proportion of visible minorities, recent immigrants, and essential workers. Although a consistent feature across CMAs was concentration by proportion visible minorities, the magnitude of concentration by social determinants varied across CMAs. Interpretation: The feature of geographical concentration of COVID-19 cases was consistent across CMAs, but the pattern by social determinants varied. Geographically-prioritized allocation of resources and services should be tailored to the local drivers of inequalities in transmission in response to SARS-CoV-2's resurgence.

Effectiveness of BNT162b2 and mRNA-1273 COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes in Ontario, Canada (preprint)

Objectives: To estimate the effectiveness of one and two doses of mRNA COVID-19 vaccines against symptomatic infection and severe outcomes. Design: Using a test-negative design study and linked laboratory, vaccination, and health administrative databases, we estimated adjusted vaccine effectiveness (aVE) against symptomatic infection and severe outcomes (hospitalization or death) using multivariable logistic regression. Setting: Ontario, Canada between 14 December 2020 and 19 April 2021. Participants: Community-dwelling adults aged [≥]16 years who were tested for SARS-CoV-2 and had COVID-19 symptoms. Interventions: Pfizer-BioNTech's BNT162b2 or Moderna's mRNA-1273 vaccine. Main outcome measures: Laboratory-confirmed SARS-CoV-2 identified by RT-PCR; hospitalization or death associated with SARS-CoV-2 infection. Results: Among 324,033 symptomatic individuals, 53,270 (16.4%) were positive for SARS-CoV-2 and 21,272 (6.6%) received 1 or more vaccine dose. Among test-positive cases, 2,479 (4.7%) had a severe outcome. aVE against symptomatic infection 14 days or more after receiving only 1 dose was 60% (95%CI, 57 to 64%), increasing from 48% (95%CI, 41 to 54%) at 14-20 days after the first dose to 71% (95%CI, 63 to 78%) at 35-41 days. aVE 7 days or more after receiving 2 doses was 91% (95%CI, 89 to 93%). Against severe outcomes, aVE 14 days or more after receiving 1 dose was 70% (95%CI, 60 to 77%), increasing from 62% (95%CI, 44 to 75%) at 14-20 days to 91% (95%CI, 73 to 97%) at 35 days or more, whereas aVE 7 days or more after receiving 2 doses was 98% (95%CI, 88 to 100%). For adults aged 70 years and older, aVE estimates were lower after receiving 1 dose, but were comparable to younger adults after 28 days. After 2 doses, we observed high aVE against E484K-positive variants. Conclusions: Two doses of BNT162b2 and mRNA-1273 vaccines are highly effective against both symptomatic infection and severe outcomes. Effectiveness is lower after only a single dose, particularly for older adults shortly after the first dose.

Quantifying transmissibility of COVID-19 and impact of intervention within long-term health care facilities (preprint)

Estimates of the basic reproduction number (R0) for Coronavirus disease 2019 (COVID-19) are particularly variable in the context of transmission within locations such as long-term health care (LTHC) facilities. We sought to characterise the heterogeneity of R0 across known outbreaks within these facilities. We used a unique comprehensive dataset of all outbreaks that have occurred within LTHC facilities in British Columbia, Canada. We estimated R0 with a Bayesian hierarchical dynamic model of susceptible, exposed, infected, and recovered individuals, that incorporates heterogeneity of R0 between facilities. We further compared these estimates to those obtained with standard methods that utilize the exponential growth rate and maximum likelihood. The total size of an outbreak varied dramatically, with a range of attack rates of 2%-86%. The Bayesian analysis provides more constrained overall estimates of R0 = 2.83 (90% CrI [credible interval] 0.25-7.19) than standard methods, with a range within facilities of 0.66-10.06. We further estimated that intervention led to 67% (56%-73%) of all cases being averted within the LTHC facilities. Understanding the risks and impact of intervention are essential in planning during the ongoing global pandemic, particularly in high-risk environments such as LTHC facilities.

How much leeway is there to relax COVID-19 control measures? (preprint)

Following successful widespread non-pharmaceutical interventions aiming to control COVID-19, many jurisdictions are moving towards reopening economies and borders. Given that little immunity has developed in most populations, re-establishing higher contact rates within and between populations carries substantial risks. Using a Bayesian epidemiological model, we estimate the leeway to reopen in a range of national and regional jurisdictions that have experienced different COVID-19 epidemics. We estimate the risks associated with different levels of reopening and the likely burden of new cases due to introductions from other jurisdictions. We find widely varying leeway to reopen, high risks of exceeding past peak sizes, and high possible burdens per introduced case per week, up to hundreds in some jurisdictions. We recommend a cautious approach to reopening economies and borders, coupled with strong monitoring for changes in transmission.

Estimating the impact of COVID-19 control measures using a Bayesian model of physical distancing (preprint)

Extensive physical distancing measures are currently the primary intervention against coronavirus disease 2019 (COVID-19) worldwide. It is therefore urgent to estimate the impact such measures are having. We introduce a Bayesian epidemiological model in which a proportion of individuals are willing and able to participate in distancing measures, with the timing of these measures informed by survey data on attitudes to distancing and COVID-19.We fit our model to reported COVID-19 cases in British Columbia, Canada, using an observation model that accounts for both underestimation and the delay between symptom onset and reporting. We estimate the impact that physical distancing (also known as social distancing)has had on the contact rate and examine the projected impact of relaxing distancing measures. We find that distancing has had a strong impact, consistent with declines in reported cases and in hospitalization and intensive care unit numbers. We estimate that approximately 0.78 (0.66-0.89 90% CI) of contacts have been removed for individuals in British Columbia practising physical distancing and that this fraction is above the threshold of 0.45 at which prevalence is expected to grow. However, relaxing distancing measures beyond this threshold re-starts rapid exponential growth. Because the extent of underestimation is unknown, the data are consistent with a wide range in the prevalence of COVID-19 in the population; changes to testing criteria over time introduce additional uncertainty. Our projections indicate that intermittent distancing measures - if sufficiently strong and robustly followed - could control COVID-19 transmission, but that if distancing measures are relaxed too much, the epidemic curve would grow to high prevalence.