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|Link Efficacy of a “stay-at-home” policy on SARS-CoV-2 transmission in Toronto, Canada: a mathematical modelling study|
Author: Pei Yuan, Juan Li, Elena Aruffo, Evgenia Gatov, Qi Li, Tingting Zheng, Nicholas H. Ogden, Beate Sander, Jane Heffernan, Sarah Collier, Yi Tan, Jun Li, Julien Arino, Jacques Bélair, James Watmough, Jude Dzevela Kong, Iain Moyles, Huaiping Zhu
Publication date: 19 April 2022
Publication info: cmaj OPEN, April 19, 2022 10 (2) E367-E378
Cited by: David Price 7:07 PM 21 September 2022 GMT
|Excerpt / Summary|
Background: Globally, nonpharmaceutical interventions for COVID-19, including stay-at-home policies, limitations on gatherings and closure of public spaces, are being lifted. We explored the effect of lifting a stay-at-home policy on virus resurgence under different conditions.
Methods: Using confirmed case data from Toronto, Canada, between Feb. 24 and June 24, 2020, we ran a compartmental model with household structure to simulate the impact of the stay-at-home policy considering different levels of compliance. We estimated threshold values for the maximum number of contacts, probability of transmission and testing rates required for the safe reopening of the community.
Results: After the implementation of the stay-at-home policy, the contact rate outside the household fell by 39% (from 11.58 daily contacts to 7.11). The effective reproductive number decreased from 3.56 (95% confidence interval [CI] 3.02–4.14) on Mar. 12 to 0.84 (95% CI 0.79–0.89) on May 6. Strong adherence to stay-at-home policies appeared to prevent SARS-CoV-2 resurgence, but extending the duration of stay-at-home policies beyond 2 months had little added effect on cumulative cases (25 958 for 65 days of a stay-at-home policy and 23 461 for 95 days, by July 2, 2020) and deaths (1404 for 65 days and 1353 for 95 days). To avoid a resurgence, the average number of contacts per person per day should be kept below 9, with strict nonpharmaceutical interventions in place.
Interpretation: Our study demonstrates that the stay-at-home policy implemented in Toronto in March 2020 had a substantial impact on mitigating the spread of SARS-CoV-2. In the context of the early pandemic, before the emergence of variants of concern, reopening schools and workplaces was possible only with other nonpharmaceutical interventions in place.
Nonpharmaceutical interventions for COVID-19, including stay-at-home policies, isolation of cases and contact tracing, as well as physical distancing, handwashing and use of protective equipment such as face masks, are effective mitigation strategies for preventing virus spread.1–4 Many studies investigating SARS-CoV-2 transmission and nonpharmaceutical interventions point to the importance of within- and between-household transmission. 5–8 Although stay-at-home policies can help curb spread of SARS-CoV-2 in the community by reducing contacts outside the household,8 they can increase contacts among family members, leading to higher risk within the household, 9 with secondary infection rates in households shown to be as high as 30%–52.7%.5,10 Furthermore, prolonged periods of stay-at-home policies may not be practical because of the essential operations of society, and may directly or indirectly harm the economy and the physical and mental health of individuals.11,12 Therefore, it is important to assess the optimal length of policy implementation for preventing virus resurgence.
During the epidemic, stay-at-home policies have been used to mitigate virus spread. The proportion of people staying at home is a paramount factor for evaluating the effectiveness of this policy implementation. For example, symptomatic individuals, those who tested positive for SARS-CoV-2 infection, and traced contacts are more likely to remain in the home through self-isolation or quarantine than uninfected or asymptomatic individuals. 13 Hence, rates of testing, diagnosis, isolation of cases, contact tracing and quarantine of contacts, as well as public compliance with stay-at-home policies, are essential factors for determining virus transmission and the likelihood of epidemic resurgence after the lifting of restrictive closures.1 To allow for this level of complexity, we developed a household-based transmission model to capture differences in policy uptake behaviour using confirmed case data from Toronto, Canada.
Throughout the pandemic, Canadian provinces and territories have implemented restrictive closures of businesses, schools, workplaces and public spaces to reduce the number of contacts in the population and prevent further virus spread, with these restrictions lifted and reinstituted at various times.14 On Mar. 17, 2020, Ontario declared a state of emergency, with directives including stay-at-home policies.15
We aimed to evaluate the effect of the stay-at-home policy issued in March 2020 on the transmission of SARS-CoV-2 in Toronto, accounting for average household size, the degree of adherence to the stay-at-home policy, and the length of policy implementation. Additionally, on the basis of the average family size and local epidemic data, we estimated the basic reproduction number (R0) and effective reproduction number (Rt) and investigated potential thresholds for the number of contacts, testing rates and use of nonpharmaceutical interventions that would be optimal for mitigating the epidemic. Hence, we conducted simulations of dynamic population behaviour under different reopening and adherence scenarios, to compare different public health strategies in hopes of adding those evaluations to the scientific literature.
|Link Projections of the transmission of the Omicron variant for Toronto, Ontario, and Canada using surveillance data following recent changes in testing policies|
Author: Pei Yuan, Elena Aruffo, Yi Tan, Liu Yang, Nicholas H. Ogden, Aamir Fazil, Huaiping Zhu
Publication date: 12 April 2022
Publication info: Infectious Disease Modelling, Volume 7, Issue 2, June 2022, Pages 83-93, ISSN 2468-0427
Cited by: David Price 7:12 PM 21 September 2022 GMT
|Excerpt / Summary|
At the end of 2021, with the rapid escalation of COVID19 cases due to the Omicron variant, testing centers in Canada were overwhelmed. To alleviate the pressure on the PCR testing capacity, many provinces implemented new strategies that promote self testing and adjust the eligibility for PCR tests, making the count of new cases underreported. We designed a novel compartmental model which captures the new testing guidelines, social behaviours, booster vaccines campaign and features of the newest variant Omicron. To better describe the testing eligibility, we considered the population divided into high risk and non-high-risk settings. The model is calibrated using data from January 1 to February 9, 2022, on cases and severe outcomes in Canada, the province of Ontario and City of Toronto. We conduct analyses on the impact of PCR testing capacity, self testing, different levels of reopening and vaccination coverage on cases and severe outcomes. Our results show that the total number of cases in Canada, Ontario and Toronto are 2.34 (95%CI: 1.22–3.38), 2.20 (95%CI: 1.15–3.72), and 1.97(95%CI: 1.13–3.41), times larger than reported cases, respectively. The current testing strategy is efficient if partial restrictions, such as limited capacity in public spaces, are implemented. Allowing more people to have access to PCR reduces the daily cases and severe outcomes; however, if PCR test capacity is insufficient, then it is important to promote self testing. Also, we found that reopening to a pre-pandemic level will lead to a resurgence of the infections, peaking in late March or April 2022. Vaccination and adherence to isolation protocols are important supports to the testing policies to mitigate any possible spread of the virus.
|Link School and community reopening during the COVID-19 pandemic: a mathematical modelling study|
Author: Pei Yuan, Elena Aruffo, Evgenia Gatov, Yi Tan, Qi Li, Nick Ogden, Sarah Collier, Bouchra Nasri, Iain Moyles, Huaiping Zhu
Publication date: 2 February 2022
Publication info: R. Soc. open sci.9211883211883
Cited by: David Price 7:17 PM 21 September 2022 GMT
|Excerpt / Summary|
Operating schools safely during the COVID-19 pandemic requires a balance between health risks and the need for in-person learning. Using demographic and epidemiological data between 31 July and 23 November 2020 from Toronto, Canada, we developed a compartmental transmission model with age, household and setting structure to study the impact of schools reopening in September 2020. The model simulates transmission in the home, community and schools, accounting for differences in infectiousness between adults and children, and accounting for work-from-home and virtual learning. While we found a slight increase in infections among adults (2.2%) and children (4.5%) within the first eight weeks of school reopening, transmission in schools was not the key driver of the virus resurgence in autumn 2020. Rather, it was community spread that determined the outbreak trajectory, primarily due to increases in contact rates among adults in the community after school reopening. Analyses of cross-infection among households, communities and schools revealed that home transmission is crucial for epidemic progression and safely operating schools, while the degree of in-person attendance has a larger impact than other control measures in schools. This study suggests that safe school reopening requires the strict maintenance of public health measures in the community.
|Link Agent-based epidemiological modeling of COVID-19 in localized environments|
Author: P. Ciunkiewicz, W. Brooke, M. Rogers, S. Yanushkevich
Publication date: 15 March 2022
Publication info: Computers in Biology and Medicine, Volume 144, May 2022, 105396
Cited by: David Price 7:23 PM 21 September 2022 GMT
|Excerpt / Summary|
Epidemiological modeling is used, under certain assumptions, to represent the spread of a disease within a population. Information generated by these models can then be applied to inform public health practices and mitigate risk. To provide useful and actionable preparedness information to administrators and policy makers, epidemiological models must be formulated to model highly localized environments such as office buildings, campuses, or long-term care facilities. In this paper, a highly configurable agent-based simulation (ABS) framework designed for localized environments is proposed. This ABS provides information about risk and the effects of both pharmacological and non-pharmacological interventions, as well as detailed control over the rapidly evolving epidemiological characteristics of COVID-19. Simulation results can inform decisions made by facility administrators and be used as inputs for a complementary decision support system. The application of our ABS to our research lab environment as a proof of concept demonstrates the configurability and insights achievable with this form of modeling, with future work focused on extensibility and integration with decision support.
|Link When host populations move north, but disease moves south: counter-intuitive impacts of climate warming on disease spread|
Author: E. Joe Moran, Maria Martignoni, Nicolas Lecomte, Patrick Leighton, Amy Hurford
Publication date: 7 March 2022
Publication info: Preprint Under Revision at Theoretical Ecology, Version 1
posted 7 March 2022
Cited by: David Price 7:26 PM 21 September 2022 GMT
|Excerpt / Summary|
Empirical observations and mathematical models show that climate warming can lead to the northern (or, more generally, poleward) spread of host species ranges and their corresponding diseases. Here, we explore an unexpected possibility whereby climate warming induces disease spread in the opposite direction to the directional shift in the host species range. To test our hypothesis, we formulate a reaction-diffusion equation model with a Susceptible-Infected (SI) epidemiological structure for two host species, both susceptible to a disease, but spatially isolated due to distinct thermal niches, and where prior to climate warming the disease is endemic in the northern species only. Previous theoretical results show that species’ distributions can lag behind species’ thermal niches when climate warming occurs. As such, we find that climate warming, by shifting both species' niches forward, may increase the overlap between northern and southern host species ranges, due to the northern species lagging behind its thermal tolerance limit, thus facilitating a southern disease spread. As our model is general, our findings may apply to viral, bacterial, and prion diseases that do not have thermal tolerance limits and are inextricably linked to their hosts’ distributions, such as the spread of rabies from arctic to red foxes.
|Link An environmental scan of one health preparedness and response: the case of the Covid-19 pandemic in Rwanda|
Author: Gloria Igihozo, Phaedra Henley, Arne Ruckert, Charles Karangwa, Richard Habimana, Rosine Manishimwe, Leandre Ishema, Hélène Carabin, Mary E. Wiktorowicz, Ronald Labonté
Publication date: 16 January 2022
Publication info: One Health Outlook, Volume 4, Article number: 2 (2022)
Cited by: David Price 7:30 PM 21 September 2022 GMT
|Excerpt / Summary|
Background: Over the past decade, 70% of new and re-emerging infectious disease outbreaks in East Africa have originated from the Congo Basin where Rwanda is located. To respond to these increasing risks of disastrous outbreaks, the government began integrating One Health (OH) into its infectious disease response systems in 2011 to strengthen its preparedness and contain outbreaks. The strong performance of Rwanda in responding to the on-going COVID-19 pandemic makes it an excellent example to understand how the structure and principles of OH were applied during this unprecedented situation.
Methods: A rapid environmental scan of published and grey literature was conducted between August and December 2020, to assess Rwanda’s OH structure and its response to the COVID-19 pandemic. In total, 132 documents including official government documents, published research, newspaper articles, and policies were analysed using thematic analysis.
Results: Rwanda’s OH structure consists of multidisciplinary teams from sectors responsible for human, animal, and environmental health. The country has developed OH strategic plans and policies outlining its response to zoonotic infections, integrated OH into university curricula to develop a OH workforce, developed multidisciplinary rapid response teams, and created decentralized laboratories in the animal and human health sectors to strengthen surveillance. To address COVID-19, the country created a preparedness and response plan before its onset, and a multisectoral joint task force was set up to coordinate the response to the pandemic. By leveraging its OH structure, Rwanda was able to rapidly implement a OH-informed response to COVID-19.
Conclusion: Rwanda’s integration of OH into its response systems to infectious diseases and to COVID-19 demonstrates the importance of applying OH principles into the governance of infectious diseases at all levels. Rwanda exemplifies how preparedness and response to outbreaks and pandemics can be strengthened through multisectoral collaboration mechanisms. We do expect limitations in our findings due to the rapid nature of our environmental scan meant to inform the COVID-19 policy response and would encourage a full situational analysis of OH in Rwanda’s Coronavirus response.
|Link Beyond Zoonoses in One Health: Non-communicable Diseases Across the Animal Kingdom|
Author: B. Natterson-Horowitz, Marion Desmarchelier, Andrea Sylvia Winkler, Hélène Carabin
Publication date: 26 January 2022
Publication info: Front. Public Health, 26 January 2022
Cited by: David Price 7:33 PM 21 September 2022 GMT
|Excerpt / Summary|
Greater than 70% of all human deaths are due to non-communicable diseases (NCDs) (1). Increasingly environmental exposures, from air pollution, second-hand smoke, heavy metals, phthalates, pesticides, and endocrine disrupting chemicals, have been linked to a range of NCDs including many cancers, cardiopulmonary diseases, congenital abnormalities and other pathologies (2). Many of the same environmental effects that elevate disease risk in humans, also do so in other species. In fact, the smaller size of many non-human animals, shorter lifespans and their greater exposure to environmental hazards may accelerate the natural history of pathology (2). Between domestication, urbanization and increased land use, the line demarcating “human” and “animal” environments is increasingly blurred and health professionals have an opportunity to turn to animal models to address human health. For instance, surveillance for NCDs in other species has the potential to alert human health professionals to environmental hazards before the emergence of pathology in human populations (2). The importance of animal sentinels in detecting and combating communicable diseases has been made strikingly clear over the past decades (3) as well as by the recent COVID-19 pandemic. The high percentage of communicable diseases with zoonotic origins reveals the need for broad surveillance of wild and domestic animal populations that may carry pathogens that can infect in humans (4). However, despite increased awareness of and resources for surveillance of animal sentinels with zoonotic diseases, far fewer resources have been directed toward surveillance of animal populations for NCDs (5) and widespread reforms addressing the connection between human, animal and environmental health remain elusive. Here, we briefly present examples of NCDs in non-human animals that derive from shared environmental sources to emphasize the utility and need for species-spanning NCD surveillance (Figure 1)…
|Link Epidemic Spreading in Trajectory Networks|
Author: Tilemachos Pechlivanoglou, Jing Li, Jialin Sun, Farzaneh Heidari, Manos Papagelis
Publication date: 28 February 2022
Publication info: Big Data Research, Volume 27, 28 February 2022, 100275
Cited by: David Price 7:37 PM 21 September 2022 GMT
|Excerpt / Summary|
Epidemics of infectious diseases, such as the one caused by the rapid spread of the coronavirus disease 2019 (COVID-19), have tested the world's more advanced health systems and have caused an enormous societal and economic damage. The mechanism of contagion is well understood. As people move around, over time, they regularly engage in social interactions. The spatiotemporal network representing these interactions constitutes the backbone on which an epidemic spreads, causing outbreaks. At the same time, advanced technological responses have claimed some success in controlling the epidemic based on digital contact tracing technologies. Motivated by these observations, we design, develop and evaluate a stochastic agent-based model of epidemic spreading in spatiotemporal networks informed by mobility data of individuals (trajectories). The model focuses on individual variation in mobility patterns that affects the degree of exposure to the disease. Understanding the role that individual nodes play in the process of disease spreading through network effects is fundamental as it allows to (i) assess the risk of infection of individuals, (ii) assess the size of a disease outbreak due to specific individuals, and (iii) assess targeted intervention strategies that aim to control the epidemic spreading. We perform a comprehensive analysis of the model employing COVID-19 as a use case. The results indicate that simple individual-based intervention strategies that exhibit significant network effects can effectively control the spread of an epidemic. We have also demonstrated that targeted interventions can outperform generic intervention strategies. Overall, our work provides an evidence-based data-driven model to support decision making and inform public policy regarding intervention strategies for containing or mitigating the epidemic spread.
|Link Effectiveness of non-pharmaceutical interventions to reduce SARS-CoV-2 transmission in Canada and their association with COVID-19 hospitalisation rates|
Author: Rees EE, Avery BP, Carabin H, Carson CA, Champredon D, Dougherty B, Nasri BR, Ogden NH.
Publication date: October 2022
Publication info: Can Commun Dis Rep 2022;48(10):438–48, The Public Health Agency of Canada, Issue: Volume 48-10, October 2022: Equity, Diversity and Inclusion in Public Health, Date published: October 2022, ISSN: 1481-8531
Cited by: David Price 7:43 PM 21 September 2022 GMT
|Excerpt / Summary|
Background: Non-pharmaceutical interventions (NPIs) aim to reduce the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections mostly by limiting contacts between people where virus transmission can occur. However, NPIs limit social interactions and have negative impacts on economic, physical, mental and social well-being. It is, therefore, important to assess the impact of NPIs on reducing the number of coronavirus disease 2019 (COVID-19) cases and hospitalizations to justify their use.
Methods: Dynamic regression models accounting for autocorrelation in time series data were used with data from six Canadian provinces (British Columbia, Alberta, Saskatchewan, Manitoba, Ontario, Québec) to assess 1) the effect of NPIs (measured using a stringency index) on SARS-CoV-2 transmission (measured by the effective reproduction number), and 2) the effect of the number of hospitalized COVID-19 patients on the stringency index.
Results: Increasing stringency index was associated with a statistically significant decrease in the transmission of SARS-CoV-2 in Alberta, Saskatchewan, Manitoba, Ontario and Québec. The effect of stringency on transmission was time-lagged in all of these provinces except for Ontario. In all provinces except for Saskatchewan, increasing hospitalization rates were associated with a statistically significant increase in the stringency index. The effect of hospitalization on stringency was time-lagged.
Conclusion: These results suggest that NPIs have been effective in Canadian provinces, and that their implementation has been, in part, a response to increasing hospitalization rates of COVID-19 patients.
|Link Risk of COVID-19 variant importation - How useful are travel control measures?|
Author: Julien Arino, Pierre-Yves Boëlle, Evan Milliken, Stéphanie Portet
Publication date: 22 July 2021
Publication info: Infectious Disease Modelling, Volume 6, 2021, Pages 875-897
Cited by: David Price 7:47 PM 21 September 2022 GMT
|Excerpt / Summary|
We consider models for the importation of a new variant COVID-19 strain in a location already seeing propagation of a resident variant. By distinguishing contaminations generated by imported cases from those originating in the community, we are able to evaluate the contribution of importations to the dynamics of the disease in a community. We find that after an initial seeding, the role of importations becomes marginal compared to that of community-based propagation. We also evaluate the role of two travel control measures, quarantine and travel interruptions. We conclude that quarantine is an efficacious way of lowering importation rates, while travel interruptions have the potential to delay the consequences of importations but need to be applied within a very tight time window following the initial emergence of the variant.