Statisticians in action: Highlighting COVID-19 research in Canada

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Given the unprecedented and worldwide challenge of COVID-19, the Biostatistics Section is showcasing the many ways that statisticians are involved in COVID-19 research. From clinical trials to Indigenous health, impact on teaching to spatial modelling, local applications to international projects, our expertise is vast and we are leading the way! A small “sample” of these exciting projects is included below.

1. McGill University researchers Dr. Nicole Basta and Dr. Erica Moodie are delighted to share a new initiative that they recently launched: https://covid19.trackvaccines.org/! Researchers around the globe are working to develop safe and effective COVID-19 vaccines as soon as possible. The big question is “how long will it really take?” Our team collates and curates COVID-19 vaccine clinical trial data from multiple sources to track vaccine candidates designed specifically to prevent COVID-19 once they are part of a registered clinical trial. On the website, viewers can hover over our COVID-19 vaccine tracker map to find out how many trials are ongoing in each country. Our COVID-19 vaccine tracker page uses an innovative card-based system, which displays the name, primary developer/sponsor, highest phase of clinical trial underway, and more. Finally, users can find information on how vaccines work or submit a question. Information and content are updated regularly, so check back often!

2. A team co-led by Dr. Michael Rotondi (York University), Dr. Janet Smylie (St. Michael’s Hospital, Toronto), and Cheryllee Bourgeois (Seventh Generation Midwives Toronto) received $395,460 from the Canadian Institutes of Health Research (CIHR) to estimate the rate of COVID-19 transmission for Indigenous peoples in cities. Their team will use information from the Our Health Counts studies, population-based health research studies co-led by Indigenous communities using respondent-driven sampling and social networks, in Toronto, London, and Thunder Bay. The Our Health Counts studies will be linked to the provincial COVID-19 database at the Institute for Clinical Evaluative Sciences (IC/ES) to actively monitor prevalence and incidence of COVID-19 in urban Indigenous communities. While estimators of prevalence for respondent-driven sampling are well defined, estimation of incidence and multivariable models for respondent-driven sampling studies remain an area of ongoing methodological research. In partnership with Indigenous community health service providers, their research team will produce statistically valid and representative information regarding the burden of COVID-19 and its rate of spread through these urban Indigenous communities.

3. Professors Grace Y. Yi and Wenqing He co-lead a team at the University of Western Ontario to work on various research projects on COVID-19. One project entitled “Can the reported COVID-19 data tell us the truth?” was funded by the Rapid Response Program COVID-19 of the Canadian Statistical Sciences Institute (CANSSI). The research results on multiple topics produced from the team members and their collaborators are posted at the COVID-19 Canada website, https://covid-19 canada.uwo.ca/. This website, developed by the team, provides a timely view and understanding of the evolving pandemic in Canada with a real time interactive web-based platform. The website highlights data visualization of the daily development of COVID-19 in Canada and forecasts future trends derived from different statistical predictive models. In addition, the website lists a variety of public data sources for researchers and industry professionals to have quick access to COVID-19 data. Selected news updates on COVID-19 can also be found on this website.

4. Professor Robert Platt is collaborating with Dr. Kristian Filion’s team at McGill University on a population-based study of the association between use of anticoagulants and COVID-19-related outcomes. Although the COVID-19 pandemic is a global public health crisis, there are currently few known treatments. Emerging evidence suggests abnormal blood clotting may occur among COVID-19 patients, and this clotting is associated with worse prognosis and decreased survival. It is hypothesized that the body’s immune system may be responding to the SARS-CoV-2 infection by activating a series of reactions that promote coagulation. Anticoagulants may therefore provide beneficial effects among patients with COVID-19. Funded by the McGill Interdisciplinary Initiative in Infection and Immunity, Dr. Filion and his team are working with collaborators at Sungkyunkwan University in South Korea to examine the effectiveness of anticoagulants at improving COVID-19-related outcomes using the Korean Nationwide Healthcare Database. Results for this ongoing study are expected later this year. 

5. Dr. Rob Deardon (University of Calgary) has been working on a number of COVID-19 projects. One involves a collaboration with researchers both at Calgary and at the Guru Angad Dev Veterinary and Animal Sciences University, modelling and analyzing Indian COVID-19 data. This collaboration has resulted in a publication in Transboundary & Emerging Diseases, which looks at the effect of lockdown measures on the disease’s effective reproductive number at state level. A second project, with visiting PhD student, Zeyi Liu, has involved using machine learning classification methods to provide for quick methods of inference for fitting spatial meta-population models to data from multiple cities. The model they developed allows for road-distance based transmission between cities, differentiates within-city and between-city spread, and allows for both reporting delays and underreporting. The method has been applied to data from Wuhan, China and surrounding cities in Hubei province, and a paper is currently submitted.

6. The rapid spread of COVID-19 around the world has created an urgent need for more knowledge about its epidemiology, symptoms, and treatment. In particular, there is a need to determine symptoms and signs that can be used to recommend screening or self-isolation to an individual. Since patients with mild symptoms are important sources of transmission of COVID-19, it is necessary to not only identify non-specific symptoms (fever, cough, and shortness of breath) but also specific symptoms (anosmia, myalgia, and abdominal pain) to curb the future spread of COVID-19. Dr. Braden O’Neill, Dr. Sheila Dunn, and Sumeet Kalia (North York General and Women’s College Hospitals, Toronto) hypothesize that if anosmia is a highly prevalent symptom associated with COVID-19 infection, its occurrence could be a useful tool to promote self-isolation and reduce the transmission of disease. In addition to the estimation of appropriate diagnostic metrics, this study will rely on the use of shrinkage estimators based on lasso regression to determine the symptoms with the most predictability for positive COVID-19 cases.

7. Melanie Poulin-Costello (Roche Canada) and her colleagues are exploring the serious effects of COVID-19 in clinical trials. The COVID-19 pandemic has adversely affected overall patient care including access to care, access to diagnostics, and in-clinic treatment regimes. Statisticians are faced with unprecedented challenges in the conduct of clinical trials and analysis as enrollment has significantly slowed down and as COVID-19 generates missing data from both patients in quarantine and those too vulnerable to attend a scheduled visit. Both the FDA and EMA released guidances in June 2020 to address clinical trials during COVID-19. Statistics in Biopharmaceutical Research had a special issue dedicated to the impact of COVID-19 on clinical trials. The statistical aspects include safety concerns for patients with COVID-19, amendments to clinical trial protocols and analysis plans, missing data effects on the primary analysis, and in particular, the definition of estimands. Statisticians play an important role in maintaining the integrity of clinical trials in the context of COVID-19.

8. The 2020 theme for CANSSI’s Rapid Response Program is COVID-19. This program is designed to support CANSSI members who can provide critical research support on a rapidly emerging problem important to society on a provincial, national, and/or international scale. The focus is on applied research that has strong potential to have an immediate impact. The program supports graduate students and/or postdoctoral fellows, as well as the costs of data acquisition. Budgets for a project are typically \$5,000–\$7,000 for a duration of two to four months. This year, CANSSI is excited to support these nine projects in this priority research area:

a) Estimating the Number of Hidden COVID-19 Cases, led by Laura Cowen, Junling Ma, and Pauline van de Driessche (UVic)
b) Perfectionnement de l’estimation des matrices de contacts sociaux pour la modélisation de l’épidémie de COVID-19 au Canada, led by Alexandre Bureau and Mark Bresson (ULaval) and Mélanie Drolet (Centre de recherche du CHU de Québec)
c) Host Genetics for SARS-CoV-2 Severity and Infection: Power and Control, led by Lloyd Elliott (SFU)
d) Statistical Methods for COVID-19 Mortality Forecasting at the Small-Area Level, led by Jeffrey Rosenthal and Patrick Brown (UofT)
e) Investigating Exposure and Host Genetic Risk Factors in Studies of COVID-19, led by Lei Sun and Lisa Strug (UofT)
f) Nouvelles tables de mortalité 2020 du Québec prenant en compte l’excès de mortalité dû à la COVID-19 et à ses effets indirects, led by Louis Doray, Jean-François Angers, and Nadine Ouellette (UdeM)
g) Can the Reported COVID-19 Data Tell us the Truth? led by Grace Yi and Wenqing He (WesternU)
h) Modelling and Visualization of the COVID-19 Outbreak in Canadian Long-Term Care Homes, led by John Braun and Ngan Lyle (UBC-O) and Patrick Brown (UofT)
i) Detecting Anomalies in COVID-19 Indicators, led by Daniel McDonald (UBC)

Full funded project details are available at: http://www.canssi.ca/news-events/projects-from-canssis-rapid-response-program-covid-19/

9. Through our current national funding from the Canadian Statistical Sciences Institute—Collaborative Research Team (CANSSI-CRT), we have been working on spatial modelling of infectious diseases to enhance our knowledge on geographical patterns of infectious diseases to ultimately improve the health of Canadians. Our national collaborative research team members are from five Canadian provinces: Dr. Rhonda Rosychuk from University of Alberta; Dr. Rob Deardon from University of Calgary; Dr. Mahmoud Torabi from University of Manitoba; Dr. Charmaine Dean from University of Waterloo; Dr. Eris Rees from University of Montreal; Dr. Cindy Feng from Dalhousie University. Due to the recent emergence of COVID-19 pandemic, we recently received two additional research grants from NSERC Alliance and Research Manitoba to advance mathematical/statistical modelling techniques to project COVID-19 cases and also to evaluate possible interventions. In particular, our research goal is to better understand the spread of COVID-19 in Canada using sophisticated modelling approaches to be able to predict the needs of the Canadian healthcare system and plan for interventions.

10. In their upcoming book chapter in COVID-19 and EducationDr. Carolyn Augusta and Dr. Robert D. E. Henderson (University of Saskatchewan) examine strategies for reducing academic misconduct in online courses, including when the instructor must move a course from in-person to online and when an online course is developed intentionally. Courses that would not traditionally have been developed for web-based learning are now being retrofitted to accommodate restrictions introduced by the COVID-19 pandemic, which may introduce additional challenges when it comes to ensuring academic integrity. Beyond discussing plagiarism, we consider subscription-based resources which may enable cheating on a broader scale. We review the motivation behind many instances of academic dishonesty and suggest methods for mitigation. We emphasize the need for promoting honesty and not just preventing dishonesty. We address the question: As an instructor, how can I prevent academic misconduct to the best of my ability in an online environment during a pandemic?

In addition, Dr. Carolyn Augusta (University of Saskatchewan), Dr. Robert D.E. Henderson (University of Saskatchewan), Dr. Rob Deardon (University of Calgary), and Dr. Graham Taylor (University of Guelph) are applying a compartmental infectious disease model for COVID-19 in the province of Saskatchewan. We estimate the model parameters using publicly available case data with a Bayesian optimization approach. In addition, we examine the effects of physical distancing and suggest approaches to minimize future outbreaks, using cumulative hospital and ICU admission counts per day to aid in fitting. This approach is helpful in cases of rare event data and serves as an example, which could be adapted to other jurisdictions.

For more information on the statistical challenges in COVID-19 research, be sure to keep an eye out for the upcoming Canadian Journal of Statistics Special Issue: COVID-19: Statisticians in Action. We’re looking forward to the results of these exciting projects! Stay well, take care and we hope to see everyone again soon!

 

By Michael Rotondi (York University)

Monday, November 2, 2020

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