Respiratory Pathogens

  • 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…

  • 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…

  • 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…

  • 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…

  • Examination of scenarios introducing rubella vaccine in the Democratic Republic of the Congo

    Background Rubella vaccine has yet to be introduced into the national immunization schedule of the Democratic Republic of the Congo (DRC); the current burden of congenital rubella syndrome (CRS) is unknown and likely to be high. An important consideration prior to introducing rubella containing vaccine (RCV) is the potential inverse relationship between RCV coverage and…

  • 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…

  • 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…

  • 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…

  • Mathematical modelling of respiratory syncytial virus (RSV) in low- and middle-income countries: a systematic review

    Background Due to high burden of respiratory syncytial virus (RSV) in low- and middle-income countries (LMIC), international funding organizations have prioritized the development of RSV vaccines. Mathematical models of RSV will play an important role in assessing the relative value of these interventions. Our objectives were to provide an overview of the existing RSV modelling…

  • 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 demographic information on age structure and population size; realistic transmission networks in…