Pandemics and Outbreaks

Susceptibility of zero community transmission regimes to new variants of SARS-CoV-2: a modelling study of Queensland

Objectives To assess the risk of sustained community transmission of SARS-CoV-2/COVID-19 in Queensland (Australia) in the presence of high-transmission variants of the virus. Design We used an agent-based model Covasim and the demographics, policies, and interventions implemented in the state. Using the calibrated model we simulated possible epidemic trajectories that could eventuate due to leakage…
The changing value of vaccines in the COVID-19 pandemic

The Omicron wave has left a global imprinting of immunity which changes the COVID landscape. In this study, we simulate six hypothetical variants emerging over the next year and evaluate the impact of existing and improved vaccines. We base our study on South Africa’s infection- and vaccination-derived immunity. Our findings illustrate that variant-chasing vaccines will…
Impact of SARS-CoV-2 Gamma lineage introduction and COVID-19 vaccination on the epidemiological landscape of a Brazilian city

Background: The emergence of the Brazilian variant of concern, Gamma lineage (P.1), impacted the epidemiological profile of COVID-19 cases due to its higher transmissibility rate and immune evasion ability. Methods: We sequenced 305 SARS-CoV-2 whole-genomes and performed phylogenetic analyses to identify introduction events and the circulating lineages. Additionally, we use epidemiological data of COVID-19 cases,…
Estimating and mitigating the risk of COVID-19 epidemic rebound associated with reopening of international borders in Vietnam: a modelling study

Background Vietnam has emerged as one of the world’s leading success stories in responding to COVID-19. After a prolonged period of little to no transmission, there was an outbreak of unknown source in July, 2020, in the Da Nang region, but the outbreak was quickly suppressed. We aimed to use epidemiological, behavioural, demographic, and policy…
Evaluating COVID-19 reporting data in the context of testing strategies across 31 LMICs

Background COVID-19 case counts are the predominant measure used to track epidemiological dynamics and inform policy decision-making. Case counts, however, are influenced by testing rates and strategies, which have varied over time and space. A method to consistently interpret COVID-19 case counts in the context of other surveillance data is needed, especially for data-limited settings…
Evaluating COVID-19 reporting data in the context of testing strategies across 31 low- and middle-income countries

Background The case count for coronavirus disease 2019 (COVID-19) is the predominant measure used to track epidemiological dynamics and inform policy decision-making. Case counts, however, are influenced by testing rates and strategies, which have varied over time and space. A method to interpret COVID-19 case counts consistently in the context of other surveillance data is…
Modelling the impact of reducing control measures on the COVID-19 pandemic in a low transmission setting

Objectives: To assess the risks associated with relaxing coronavirus disease 2019 (COVID‐19)‐related physical distancing restrictions and lockdown policies during a period of low viral transmission. Design: Network‐based viral transmission risks in households, schools, workplaces, and a variety of community spaces and activities were simulated in an agent‐based model, Covasim. Setting: The model was calibrated for…
Insights into population behavior during the COVID-19 pandemic from cell phone mobility data and manifold learning

Understanding the complex interplay between human behavior, disease transmission and non-pharmaceutical interventions during the COVID-19 pandemic could provide valuable insights with which to focus future public health efforts. Cell phone mobility data offer a modern measurement instrument to investigate human mobility and behavior at an unprecedented scale. We investigate aggregated and anonymized mobility data, which…
Chapter 10 – Mathematical modeling as a tool for policy decision making: Applications to the COVID-19 pandemic

The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of mathematical modeling in advising scientific bodies and informing public policy making. Modeling allows a flexible theoretical framework to be developed in which different scenarios around spread of diseases and strategies to prevent it can be explored. This work brings together perspectives on mathematical modeling of…
Mechanistic modeling of SARS-CoV-2 immune memory, variants, and vaccines

Early waves of the SARS-CoV-2 pandemic were driven by importation events and subsequent policy responses. However, epidemic dynamics in 2021 are largely driven by the spread of more transmissible and/or immune-evading variants, which in turn are countered by vaccination programs. Here we describe updates to the methodology of Covasim (COVID-19 Agent-based Simulator) to account for…