Viruses accrue small amounts of genetic variation over time. By sequencing the virus, we can see this variation and use it to understand where an individual virus likely came from and how it is moving through a population. This helps public health teams to estimate how many cases are due to local transmission as opposed to imported cases. In this proposal, we will establish ways to use virus sequences to understand transmission in a high-resolution way that is not possible with epidemiological or virus sequence data alone. To do this, we will combine viral sequences with epidemiological data in new ways, establishing high-resolution pictures of transmission. We will operationalize the use of these combined datasets for real-time COVID19 public health use in BC.
Year: 2020
Mapping Social Epidemiology of British Columbia: COVID19 Pandemic and Psycho Social and Occupational Well-being of Frontline Health-care Workers in BC
Insights in to Psycho-social wellbeing of health care workers during the COVID19 outbreak is crucial for health equity policy making. Untreated guilt, anxiety and depression among frontline health-care workers (FHCWs) often lead to resignations, poor work performance and burnout. Locating systems approaches in social epidemiologic research, we investigate the COVID19 phenomena and the wellbeing of FHCWs in the home care and Long-term Care Facilities (LTCFs) in BC. By capturing spatial, temporal and social determinants of COVID19 pandemic intersecting race, culture and working conditions of FHCWs, we build an agent-based model and identify complex behavior patterns that influence the quality of care and self-care strategies and to prevent high burdens of illness in key populations in BC.
Preventing and Mitigating the Impacts of COVID-19 Among Im/migrants in British Columbia: Rapid Mixed-Methods Data to Inform Policy and Programmes.
In BC, migrants make up >25% of residents and are overrepresented in crucial roles as essential workers (eg, temporary foreign workers), yet may be disproportionately impacted by COVID-19 and face barriers to healthcare access. Despite purported shifts to ‘universal’ coverage for COVID-related care, many im/migrants report severe ongoing inequities, including gaps in healthcare coverage, unsafe living/working conditions, and confusion about how changes are put in practice. Rapid transition to virtual service delivery may also compound inequities due to language or technology barriers. We will use health system data and interviews to understand migrants’ experiences with COVID-19 related care and health services coverage to ensure “no one is left behind” in the COVID-19 response and beyond.
Managing the risks of future BC COVID-19 outbreaks using mathematical and statistical modelling
Cases of COVID-19 have gone undetected, likely causing future waves. The aim of our research is to develop mathematical and statistical tools for the early detection of future BC COVID-19 waves, and to evaluate control strategies for a future wave. A key component is the estimation of unreported cases and the probability of transmission in high-risk subgroups (such as the elderly and homeless). Our mathematical model will determine disease spread and testing policies interactions. We will then identify early detection strategies for future waves. To track the patterns of individual behaviours and evaluate intervention strategies, we will develop a computer simulation model. With other provinces facing the same problems, our tools can be applied to the national pandemic.
End of Award Update: June 2022
Most exciting outputs
The most exciting development from this project is a model to estimate hidden (e.g. asymptomatic or untested and unconfirmed) COVID-19 cases based on public case, recovery, death count data. We applied this model to the Northern Health Region for the first 30 weeks of the pandemic and found that:
- Actual cases were 2.5 to 6.25 times higher than the number of detected cases.
- Detection rate depends on the number of tests (confirming the intuition that more testing helps find the positive cases).
- Community spread rate changes with every BC recovery plan phase (increased control measures reduces community spread, increased travel/reducing restrictions increases spread).
A second development is our theoretical investigation into the effect of contact tracing through a novel mathematical model. The reproduction number (the average number of new infections coming from a single COVID-19 positive case) decreases as contact tracing efforts increase. This is because cases that are found through contact tracing will often isolate. However, when there is a large transmission rate, contact tracing alone may not control the infection. Thus, additional public health measures to decrease transmission are required for contact tracing to be effective. Further, increased testing rate increases the effectiveness of contact tracing.
The Island Health team has made great strides studying outcomes of control measures through agent-based mathematical models to simulate real world scenarios. The team has also been working on profiling contact events between COVID-19 cases and other patients or healthcare workers while accessing or providing service. This provided another method of contact tracing within Island Health service locations.
Impact so far
Our methods and tools are in place for the next pandemic (including open source R code available online). Dr. Cowen was interviewed by the CBC in November 2021, making the public aware of the issue of hidden case counts in the Northern Health Authority region of B.C. This interview came just as case counts began to increase in the region with the Delta wave.
Potential influence
The work done to estimate hidden populations can be done with new variants, different regions, and across the country. The tools that have been developed for Island Health specifically in relation to pandemic response, can and have been adapted to provide actionable insights into other public health crises (i.e. opioid) and pressing operational challenges (e.g. pressure on emergency departments).
Next steps
Our research is part of an ongoing program to improve population models, and we are continuing to apply our methods to a broad range of problems. We have continued our research on developing statistical models for count data and have drafted a manuscript for a Canada-wide model of COVID-19. Similarly, we are just finishing up drafting an article on the mathematical models that consider contact tracing. These include:
- Parker, MRP, J Cao, LLE Cowen, LT Elliot, J Ma. Multi-site disease analytics with applications to estimating the extent of COVID-19 in Canada.
- Bednarski, S, LLE Cowen, J Ma, T Philippsen, P van den Driessche, M Wang. A Network SIR Contact Tracing Model for Randomly Mixed Populations.
PhD student Matthew Parker has plans to present the Canada-wide modelling work at several conferences this summer and Dr. Cowen has been invited to present the work at the International Chinese Statistical Association Canadian Chapter in Banff.
MSc student Viet Dao is developing a statistical model based on Island Health lab testing data to provide another method of estimating hidden cases. Dr. Cowen is in the process of hiring a post-doc funded by NSERC EIDM and a UVic Aspirations 2030 Fellowship to continue this work, deploying it to all of BC. Dr. Cowen has hired a second post-doc funded by the Canadian Statistical Sciences Institute to develop models using Island Health’s data to estimate the homeless population and study the number of COVID-19 cases within this population.
Useful links
- Under-reporting of COVID-19 in the Northern Health Authority region of British Columbia (Canadian Journal of Statistics, November 2021)
The Cedar Project: Preparing for Culturally-Safe, Trauma Informed COVID-19 Response Among Urban Indigenous People Who Use Drugs in BC
Indigenous people who use drugs in BC are facing two public health emergencies: COVID-19 and the ongoing overdose crisis. One likely creates additional risk for the other. On one hand, COVID-19 and its response may affect access to clean smoking/injection equipment, safe supply of illicit drugs, income, and health and social services. Pandemic fears and restrictions may also impact mental wellbeing. On the other hand, substance use may increase COVID-19 risk through sharing smoking/injection equipment; barriers to physical distancing; and housing instability. Our study assesses impact of COVID-19 and the pandemic response, as well as its domino effects, among Indigenous people who use drugs. The study will inform a culturally-safe, trauma informed response for this population.
Population-based Study of Coronavirus Antibody Cross-Reactivity to Inform SARS-CoV-2 Seroprevalence Surveys, Severity Profiles, and Vaccine Strategies
Most people have had one or more colds due to seasonal coronaviruses (CoV) with the number of prior infections increasing with age. SARS-CoV-2 entered the human population in late 2019, causing the COVID-19 pandemic. Before that no one had immunity yet older males are at higher risk of severe COVID-19 illness. One explanation is that prior antibodies to seasonal CoVs may enhance SARS-CoV-2 risk through a process called antibody dependent enhancement. To assess that hypothesis we first need to know if seasonal CoV antibodies interact with SARS-CoV-2, how common those antibodies are, and if older men have more of them. We will develop a pan-CoV assay to compare prevalence of all human CoVs by age and sex. Findings will inform SARS-CoV-2 sero-surveys, severity profiles and vaccine strategies.
“Blind Spots”: People in Prison and Precarious Housing During COVID-19
Prisons and substandard housing pose serious risks to individuals and communities during the COVID-19 pandemic. Limits on physical distancing are associated with disease outbreaks in shelters, camps, and prisons. The high prevalence of pre-existing illness in the settings places people at risk for medical complications. This project will generate evidence of ways to reduce the spread and impact of COVID-19 by analysing hospitalizations among people who were in custody or inadequate housing during the first wave of COVID-19 in BC. The project will also develop recommendations on the use of mandatory testing. The project team is drawn from established networks of researchers, decision-makers, service providers, and people who have experienced homelessness and time in custody.
Quantitative Isotype Profiling and Dynamics of SARS-CoV-2 Infections: Next-Generation Serology
We are making a blood test that will tell us a lot of information about the body’s response to the COVID-19, including whether a person is likely to get really sick or will easily fight off the virus. The blood test is will be easy to take, using only a drop of blood from the tip of the finger. The test is run using cutting-edge technology so that we can test a lot of people, at low cost, while getting the right results. The test will help prevent people from getting severely sick from COVID-19 by letting doctors know BEFORE things get worse that their patient may need additional care to help fight off the virus. For our citizens most at risk, like the elderly and those with other medical conditions, the results can be used to direct resources and support where they are needed most.
Informing the COVID-19 Response for Vancouver’s Urban Indigenous Population Using Community-driven Methods and Big Data Analytics
COVID-19 poses a significant threat to Urban Indigenous populations. To identify gaps and improve the response, Vancouver Coastal Health Aboriginal Health will use a community-driven approach to examine patient data collected within Vancouver health centres using the Vancouver Community Analytics Tool (VCAT), along with the advice of key urban Indigenous community organizations and stakeholders. Analyzed data will be used to develop an extensive data profile of Indigenous peoples who access care in the Vancouver region, including COVID-19 risk, comorbidities, and impacts to health service access. We will review the current Urban Indigenous COVID-19 response in Vancouver with existing networks to develop recommendations for BC that are driven by and for the Urban Indigenous community.
Accelerating SARS-CoV-2 Seroprevalence Surveys through Dried Blood Spots (ASSESS-DBS)
Phase 4 of BC’s Restart Plan requires community immunity but seroprevalence studies of people who are street entrenched, in prison, or live in remote or rural communities is challenging. The most accurate serology tests are lab-based Enzyme-Linked Immuno Assays (EIAs) that use blood drawn from veins, but with people who are not engaged into care, or who have collapsed veins due injection drug use or obesity, it’s not a viable option. Point-of-care tests (PoCT) that use blood collected through finger prick (like a glucose test) seems to offer a solution but these tests lack specificity and therefore can’t provide an accurate picture. We propose evaluating dried blood spot (DBS) which seems to offer the accuracy of EIAs and the ease of collection of a PoCT to determine BC seroprevalence.