Respiratory Pathogens

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…
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…
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.…
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…
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…
Modelling the impact of reopening schools in early 2021 in the presence of the new SARS-CoV-2 variant in the UK

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 and…