COVID-19

  • 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…

  • Modelling the impact of reopening schools in the UK in early 2021 in the presence of the alpha variant and with roll-out of vaccination against SARS-CoV-2

    Background Following the resurgence of the COVID-19 epidemic in the UK in late 2020 and the emergence of the alpha (also known as B117) variant of the SARS-CoV-2 virus, a third national lockdown was imposed from January 4, 2021. Following the decline of COVID-19 cases over the remainder of January 2021, the question of when…

  • Modelling the potential impact of mask use in schools and society on COVID-19 control in the UK

    As the UK reopened after the first wave of the COVID-19 epidemic, crucial questions emerged around the role for ongoing interventions, including test-trace-isolate (TTI) strategies and mandatory masks. Here we assess the importance of masks in secondary schools by evaluating their impact over September 1–October 23, 2020. We show that, assuming TTI levels from August…

  • Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

    Background The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington. Methods We conducted a phylogenetic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019…

  • Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

    Background The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington. Methods We conducted a molecular epidemiologic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December…

  • Predicting the unpredictable: how fluid COVID-19 policies and restrictions challenge model forecasts

    To retrospectively assess the accuracy of a mathematical modelling study that projected the rate of COVID-19 diagnoses for 72 locations worldwide in 2021, and to identify predictors of model accuracy. Methods Between June and August 2020, an agent-based model was used to project rates of COVID-19 infection incidence and cases diagnosed as positive from 15…

  • Regional comparisons of COVID reporting rates, burden, and mortality age-structure using auxiliary data sources

    We correct common assumptions about COVID burden and disease characteristics in high-income (HIC) versus low- and middle-income (LMIC) countries by augmenting widely-used surveillance data with auxiliary data sources. We constructed an empirically-based model of serological detection rates to quantify COVID reporting rates in national and sub-national locations. From those reporting rates, we estimated relative COVID…

  • Agent-based modeling of COVID-19 outbreaks for New York state, UK and Novosibirsk region

    This paper uses Covasim, an agent-based model (ABM) of COVID-19, to evaluate and scenarios of epidemic spread in New York State (USA), the UK, and the Novosibirsk region (Russia). Epidemiological parameters such as contagiousness (virus transmission rate), initial number of infected people, and probability of being tested depend on the region’s demographic and geographical features,…

  • Regional differences in NPI efficacy and recommendations for Africa

    Non-pharmaceutical interventions (NPIs) remain a key component of COVID response, particularly in low- and middle-income countries (LMICs) where vaccination is limited (Padma, 2021). Much of what we know about NPI efficacy, however, comes from HIC contexts, and this knowledge is not necessarily transferrable to LMICs (Chowdhury et al., 2020). It is well-established that lockdowns have…

  • Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting

    Importance The association between COVID-19 symptoms and SARS-CoV-2 viral levels in children living in the community is not well understood. Objective To characterize symptoms of pediatric COVID-19 in the community and analyze the association between symptoms and SARS-CoV-2 RNA levels, as approximated by cycle threshold (Ct) values, in children and adults. Design, Setting, and Participants…