Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: Parameter estimates, identifiability, sensitivity and the eclipse phase profile.

Within-host SARS-CoV-2 modelling studies have been published throughout the COVID-19 pandemic. These studies contain highly variable numbers of individuals and capture varying timescales of pathogen dynamics; some studies capture the time of disease onset, the peak viral load and subsequent heterogeneity in clearance dynamics across individuals, while others capture late-time post-peak dynamics. In this study, we curate multiple previously published SARS-CoV-2 viral load data sets, fit these data with a consistent modelling approach, and estimate the variability of in-host parameters including the basic reproduction number, R0, as well as the best-fit eclipse phase profile. We find that fitted dynamics can be highly variable across data sets, and highly variable within data sets, particularly when key components of the dynamic trajectories (e.g. peak viral load) are not represented in the data. Further, we investigated the role of the eclipse phase time distribution in fitting SARS-CoV-2 viral load data. By varying the shape parameter of an Erlang distribution, we demonstrate that models with either no eclipse phase, or with an exponentially-distributed eclipse phase, offer significantly worse fits to these data, whereas models with less dispersion around the mean eclipse time (shape parameter two or more) offered the best fits to the available data across all data sets used in this work. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".

COVID-19 Vaccination and Healthcare Demand.

One of the driving concerns during any epidemic is the strain on the healthcare system. As we have seen many times over the globe with the COVID-19 pandemic, hospitals and ICUs can quickly become overwhelmed by cases. While strict periods of public health mitigation have certainly helped decrease incidence and thus healthcare demand, vaccination is the only clear long-term solution. In this paper, we develop a two-module model to forecast the effects of relaxation of non-pharmaceutical intervention and vaccine uptake on daily incidence, and the cascade effects on healthcare demand. The first module is a simple epidemiological model which incorporates non-pharmaceutical intervention, the relaxation of such measures and vaccination campaigns to predict caseloads into the Fall of 2021. This module is then fed into a healthcare module which can forecast the number of doctor visits, the number of occupied hospital beds, number of occupied ICU beds and any excess demand of these. From this module, we can also estimate the length of stay of individuals in ICU. For model verification and forecasting, we use the four most populous Canadian provinces as a case study.

Integrated vaccination and non-pharmaceutical interventions based strategies in Ontario, Canada, as a case study: a mathematical modelling study.

Recently, two coronavirus disease 2019 (COVID-19) vaccine products have been authorized in Canada. It is of crucial importance to model an integrated/combined package of non-pharmaceutical (physical/social distancing) and pharmaceutical (immunization) public health control measures. A modified epidemiological, compartmental SIR model was used and fit to the cumulative COVID-19 case data for the province of Ontario, Canada, from 8 September 2020 to 8 December 2020. Different vaccine roll-out strategies were simulated until 75% of the population was vaccinated, including a no-vaccination scenario. We compete these vaccination strategies with relaxation of non-pharmaceutical interventions. Non-pharmaceutical interventions were supposed to remain enforced and began to be relaxed on 31 January, 31 March or 1 May 2021. Based on projections from the data and long-term extrapolation of scenarios, relaxing the public health measures implemented by re-opening too early would cause any benefits of vaccination to be lost by increasing case numbers, increasing the effective reproduction number above 1 and thus increasing the risk of localized outbreaks. If relaxation is, instead, delayed and 75% of the Ontarian population gets vaccinated by the end of the year, re-opening can occur with very little risk. Relaxing non-pharmaceutical interventions by re-opening and vaccine deployment is a careful balancing act. Our combination of model projections from data and simulation of different strategies and scenarios, can equip local public health decision- and policy-makers with projections concerning the COVID-19 epidemiological trend, helping them in the decision-making process.

A simple model for fitting mild, severe, and known cases during an epidemic with an application to the current SARS-CoV-2 pandemic.

One of the major difficulties with modelling an ongoing epidemic is that often data is limited or incomplete, making it hard to estimate key epidemic parameters and outcomes (e.g. attack rate, peak time, reporting rate, reproduction number). In the current study, we present a model for data-fitting limited infection case data which provides estimates for important epidemiological parameters and outcomes. The model can also provide reasonable short-term (one month) projections. We apply the model to the current and ongoing COVID-19 outbreak in Canada both at the national and provincial/territorial level.