The performance of phenomenological models in providing near-term Canadian case projections in the midst of the COVID-19 pandemic: March - April, 2020

Data-driven mathematical modeling approaches for COVID-19: A survey

In this review, we successively present the methods for phenomenological modeling of the evolution of reported and unreported cases of COVID-19, both in the exponential phase of growth and then in a complete epidemic wave. After the case of an isolated wave, we present the modeling of several successive waves separated by endemic stationary periods. Then, we treat the case of multi-compartmental models without or with age structure. Eventually, we review the literature, based on 260 articles selected in 11 sections, ranging from the medical survey of hospital cases to forecasting the dynamics of new cases in the general population. This review favors the phenomenological approach over the mechanistic approach in the choice of references and provides simulations of the evolution of the number of observed cases of COVID-19 for 10 states (California, China, France, India, Israel, Japan, New York, Peru, Spain and United Kingdom).

A New Paradigm for Pandemic Preparedness

Purpose of Review

Preparing for pandemics requires a degree of interdisciplinary work that is challenging under the current paradigm. This review summarizes the challenges faced by the field of pandemic science and proposes how to address them.

Recent Findings

The structure of current siloed systems of research organizations hinders effective interdisciplinary pandemic research. Moreover, effective pandemic preparedness requires stakeholders in public policy and health to interact and integrate new findings rapidly, relying on a robust, responsive, and productive research domain. Neither of these requirements are well supported under the current system.

Summary

We propose a new paradigm for pandemic preparedness wherein interdisciplinary research and close collaboration with public policy and health practitioners can improve our ability to prevent, detect, and treat pandemics through tighter integration among domains, rapid and accurate integration, and translation of science to public policy, outreach and education, and improved venues and incentives for sustainable and robust interdisciplinary work.

Transmission Characteristics and Predictive Model for Recent Epidemic Waves of COVID-19 Associated With OMICRON Variant in Major Cities in China

Objectives: Waves of epidemics associated with Omicron variant of Coronavirus Disease 2019 (COVID-19) in major cities in China this year have been controlled. It is of great importance to study the transmission characteristics of these cases to support further interventions.

Methods: We simulate the transmission trajectory and analyze the intervention influences of waves associated with Omicron variant in major cities in China using the Suspected-Exposed-Infectious-Removed (SEIR) model. In addition, we propose a model using a function between the maximum daily infections and the duration of the epidemic, calibrated with data from Chinese cities.

Results: An infection period of 5 days and basic reproduction number R0 between 2 and 8.72 are most appropriate for most cases in China. Control measures show a significant impact on reducing R0, and the earlier control measures are implemented, the shorter the epidemic will last. Our proposed model performs well in predicting the duration of the epidemic with an average error of 2.49 days.

Conclusion: Our results show great potential in epidemic model simulation and predicting the end date of the Omicron epidemic effectively and efficiently.

A Model for Highly Fluctuating Spatio-Temporal Infection Data, with Applications to the COVID Epidemic

Spatio-temporal models need to address specific features of spatio-temporal infection data, such as periods of stable infection levels (endemicity), followed by epidemic phases, as well as infection spread from neighbouring areas. In this paper, we consider a mixture-link model for infection counts that allows alternation between epidemic phases (possibly multiple) and stable endemicity, with higher AR1 coefficients in epidemic phases. This is a form of regime-switching, allowing for non-stationarity in infection levels. We adopt a generalised Poisson model appropriate to the infection count data and avoid transformations (e.g., differencing) to alternative metrics, which have been adopted in many studies. We allow for neighbourhood spillover in infection, which is also governed by adaptive regime-switching. Compared to existing models, the observational (in-sample) model is expected to better reflect the balance between epidemic and endemic tendencies, and short-term extrapolations are likely to be improved. Two case study applications involve COVID area-time data, one for 32 London boroughs (and 96 weeks) since the start of the COVID epidemic, the other for a shorter time span focusing on the epidemic phase in 144 areas of Southeast England associated with the Alpha variant. In both applications, the proposed methods produce a better in-sample fit and out-of-sample short term predictions. The spatial dynamic implications are highlighted in the case studies.

A semi-parametric mixed model for short-term projection of daily COVID-19 incidence in Canada

During a pandemic, data are very “noisy” with enormous amounts of local variation in daily counts, compared with any rapid changes in trend. Accurately characterizing the trends and reliable predictions on future trajectories are important for planning and public situation awareness. We describe a semi-parametric statistical model that is used for short-term predictions of daily counts of cases and deaths due to COVID-19 in Canada, which are routinely disseminated to the public by Public Health Agency of Canada. The main focus of the paper is the presentation of the model. Performance indicators of our model are defined and then evaluated through extensive sensitivity analyses. We also compare our model with other commonly used models such as generalizations of logistic models for similar purposes. The proposed model is shown to describe the historical trend very well with excellent ability to predict the short-term trajectory.