Respiratory Pathogens

  • Vaccine-preventable diseases

    Vaccines are one of the most effective public health interventions, and an accelerating pace of innovation in vaccine development promises to deliver a broadening range of novel or improved vaccines in coming years. Despite this, there are many challenges facing control efforts for vaccine-preventable diseases (VPD). Coverage of basic childhood vaccines through routine healthcare systems…

  • Estimating the Impact of Vaccination Campaigns on Measles Transmission in Somalia

    Somalia is a complex and fragile setting with a demonstrated potential for disruptive, high-burden measles outbreaks. In response, since 2018, Somalian authorities have partnered with UNICEF and the WHO to implement measles vaccination campaigns across the country. In this paper, we create a Somalia-specific model of measles transmission based on a comprehensive epidemiological dataset including…

  • The changing health impact of vaccines in the COVID-19 pandemic: a modeling study

    Much of the world’s population had already been infected with COVID-19 by the time the Omicron variant emerged at the end of 2021, but the scale of the Omicron wave was larger than any that had come before or has happened since, and it left a global imprinting of immunity that changed the COVID-19 landscape.…

  • Modeling COVID-19 vaccination strategies in LMICs considering uncertainty in viral evolution and immunity

    Vaccines against the SARS-CoV-2 virus were developed in record time, but their distribution has been highly unequal. With demand saturating in high-income countries, many low- and middle-income countries (LMIC) finally have an opportunity to acquire COVID-19 vaccines. But the pandemic has taken its toll, and a majority of LMIC populations have partial immunity to COVID-19…

  • Risk of sustained SARS‑CoV‑2 transmission in Queensland, Australia

    We used an agent-based model Covasim to assess the risk of sustained community transmission of SARSCoV-2/COVID-19 in Queensland (Australia) in the presence of high-transmission variants of the virus. The model was calibrated using the demographics, policies, and interventions implemented in the state. Then, using the calibrated model, we simulated possible epidemic trajectories that could eventuate…

  • A modeling approach for estimating dynamic measles case detection rates

    The main idea in this paper is that the age associated with reported measles cases can be used to estimate the number of undetected measles infections. Somewhat surprisingly, even with age only to the nearest year, estimates of underreporting can be generated at the much faster, 2 week time-scale associated with measles transmission. I describe…

  • Feasibility of measles and rubella vaccination programmes for disease elimination: a modelling study

    Background Marked reductions in the incidence of measles and rubella have been observed since the widespread use of the measles and rubella vaccines. Although no global goal for measles eradication has been established, all six WHO regions have set measles elimination targets. However, a gap remains between current control levels and elimination targets, as shown…

  • 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,…

  • Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

    Background Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11…

  • Modeling anticipated changes in numbers of SARS-CoV-2 infections within communities due to immunization campaigns

    Background: As SARS-CoV-2 spread in early 2020, uncertainty about the scope, duration, and impact of the unfolding outbreaks caused numerous countries to interrupt many routine activities, including health services. Because immunization is an essential health service, modeling changes in SARS-CoV-2 infections among communities and health workers due to different vaccination activities was undertaken to understand…