Respiratory Pathogens

  • 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,…

  • Optima TB: a tool to help optimally allocate tuberculosis spending

    Approximately 85% of tuberculosis (TB) related deaths occur in low- and middle-income countries where health resources are scarce. Effective priority setting is required to maximise the impact of limited budgets. The Optima TB tool has been developed to support analytical capacity and inform evidence-based priority setting processes for TB health benefits package design. This paper…

  • 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…

  • 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…

  • Controlling COVID-19 via test-trace-quarantine

    Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures. However, these interventions have had enormous societal and economic costs. Here, we demonstrate the feasibility of an alternative control strategy, test-trace-quarantine: routine testing of primarily symptomatic individuals, tracing and testing their known contacts, and placing their contacts in quarantine.…

  • 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…

  • Covasim: an agent-based model of COVID-19 dynamics and interventions

    The COVID-19 pandemic has created an urgent need for models that can project epidemic trends, explore intervention scenarios, and estimate resource needs. Here we describe the methodology of Covasim (COVID-19 Agent-based Simulator), an open-source model developed to help address these questions. Covasim includes country-specific demographic information on age structure and population size; realistic transmission networks…

  • Potential Impacts of Mass Nutritional Supplementation on Dynamics of Measles: A Simulation Study

    The bidirectional interaction between undernutrition and infection can be devastating to child health. Nutritional deficiencies stunt growth, impair immunity, increase susceptibility to both infection and more severe outcomes from common infections. Simultaneously, infections compound undernutrition by increasing metabolic demand, reducing food intake, and impairing nutrient absorption. Treatment of acute malnutrition (wasting) can reverse at least…

  • 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…

  • Cell phone mobility data and manifold learning: Insights into population behavior during the COVID-19 pandemic

    As COVID-19 cases resurge in the United States, understanding the complex interplay between human behavior, disease transmission, and non-pharmaceutical interventions during the pandemic could provide valuable insights to focus future public health efforts. Cell-phone mobility data offers a modern measurement instrument to investigate human mobility and behavior at an unprecedented scale. We investigate mobility data…