Steven Riley
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View article: First- and second-order social contact network structure in southern China
First- and second-order social contact network structure in southern China Open
The contact network structure resulting from social interaction between people is a key aspect of epidemic dynamics and control. While many studies have measured first-order network characteristics such as degree, measuring higher order pr…
View article: Cost-effectiveness of geographically targeted versus ring vaccination campaigns in response to an outbreak of Ebola Virus Disease
Cost-effectiveness of geographically targeted versus ring vaccination campaigns in response to an outbreak of Ebola Virus Disease Open
For response to an outbreak of Ebola Virus Disease (EVD), the World Health Organisation (WHO) guidelines recommend vaccination of any contacts and contacts-of-contacts of identified EVD cases, also known as ring vaccination. However this s…
View article: Polymyxin B lethality requires energy-dependent outer membrane disruption
Polymyxin B lethality requires energy-dependent outer membrane disruption Open
Polymyxin antibiotics target lipopolysaccharide (LPS) in both membranes of the bacterial cell envelope, leading to bacterial killing through a mechanism that remains poorly understood. Here, we demonstrate that metabolic activity is essent…
View article: Forecasting COVID-19, influenza, and RSV hospitalizations over winter 2023–4 in England
Forecasting COVID-19, influenza, and RSV hospitalizations over winter 2023–4 in England Open
Background Seasonal respiratory viruses cause substantial pressure on healthcare systems, particularly over winter. System managers can mitigate the impact on patient care when they anticipate hospital admissions due to these viruses. Hosp…
View article: Strategies to Increase Response Rate and Reduce Nonresponse Bias in Population Health Research: Analysis of a Series of Randomized Controlled Experiments during a Large COVID-19 Study
Strategies to Increase Response Rate and Reduce Nonresponse Bias in Population Health Research: Analysis of a Series of Randomized Controlled Experiments during a Large COVID-19 Study Open
Background High response rates are needed in population-based studies, as nonresponse reduces effective sample size and bias affects accuracy and decreases the generalizability of the study findings. Objective We tested different strategie…
View article: Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course
Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course Open
Humans experience many influenza infections over their lives, resulting in complex and varied immunological histories. Although experimental and quantitative analyses have improved our understanding of the immunological processes defining …
View article: Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course
Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course Open
Humans experience many influenza infections over their lives, resulting in complex and varied immunological histories. Although experimental and quantitative analyses have improved our understanding of the immunological processes defining …
View article: Public reporting guidelines for outbreak data: Enabling accountability for effective outbreak response by developing standards for transparency and uniformity
Public reporting guidelines for outbreak data: Enabling accountability for effective outbreak response by developing standards for transparency and uniformity Open
Currently, there are few standards for what essential information about an infectious disease outbreak should be reported to the public and when. The content and timeliness of public reporting (e.g. situation reports) is at the discretion …
View article: Forecasting COVID-19, Influenza and RSV hospitalisations over winter 2023/24 in England
Forecasting COVID-19, Influenza and RSV hospitalisations over winter 2023/24 in England Open
Seasonal respiratory viruses cause substantial pressure on healthcare systems, particularly over winter. System managers can mitigate the impact on patient care when they anticipate hospital admissions due to these viruses. Hospitalisation…
View article: Infectious disease surveillance needs for the United States: lessons from Covid-19
Infectious disease surveillance needs for the United States: lessons from Covid-19 Open
The COVID-19 pandemic has highlighted the need to upgrade systems for infectious disease surveillance and forecasting and modeling of the spread of infection, both of which inform evidence-based public health guidance and policies. Here, w…
View article: Evaluating Large Language Models for Public Health Classification and Extraction Tasks
Evaluating Large Language Models for Public Health Classification and Extraction Tasks Open
Advances in Large Language Models (LLMs) have led to significant interest in their potential to support human experts across a range of domains, including public health. In this work we present automated evaluations of LLMs for public heal…
View article: Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England
Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England Open
Mathematical modelling has played an important role in offering informed advice during the COVID-19 pandemic. In England, a cross government and academia collaboration generated medium-term projections (MTPs) of possible epidemic trajector…
View article: Location-specific patterns of exposure to recent pre-pandemic strains of influenza A in southern China
Location-specific patterns of exposure to recent pre-pandemic strains of influenza A in southern China Open
Variation in influenza incidence between locations is commonly observed on large spatial scales. It is unclear whether such variation occurs on smaller spatial scales and whether it is the result of heterogeneities in population demographi…
View article: An open source tool to infer epidemiological and immunological dynamics from serological data: Serosolver
An open source tool to infer epidemiological and immunological dynamics from serological data: Serosolver Open
We present a flexible, open source R package designed to obtain biological and epidemiological insights from serological datasets. Characterising past exposures for multi-strain pathogens poses a specific statistical challenge: observed an…
View article: Using serological measures to estimate influenza incidence in the presence of secular trends in exposure and immuno-modulation of antibody response
Using serological measures to estimate influenza incidence in the presence of secular trends in exposure and immuno-modulation of antibody response Open
Background: Influenza infection is often measured by a fourfold antibody titer increase over an influenza season (ie seroconversion). However, this approach may fail when influenza seasons are less distinct as it does not account for trans…
View article: Estimating the Life Course of Influenza A(H3N2) Antibody Responses from Cross-Sectional Data
Estimating the Life Course of Influenza A(H3N2) Antibody Responses from Cross-Sectional Data Open
The immunity of a host population against specific influenza A strains can influence a number of important biological processes, from the emergence of new virus strains to the effectiveness of vaccination programmes. However, the developme…
View article: Close encounters of the infectious kind: Methods to measure social mixing behaviour
Close encounters of the infectious kind: Methods to measure social mixing behaviour Open
A central tenet of close-contact or respiratory infection epidemiology is that infection patterns within human populations are related to underlying patterns of social interaction. Until recently, few researchers had attempted to quantify …
View article: Modeling infectious disease dynamics in the complex landscape of global health
Modeling infectious disease dynamics in the complex landscape of global health Open
Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of inte…
View article: Differential mobility and local variation in infection attack rate
Differential mobility and local variation in infection attack rate Open
Infectious disease transmission in animals is an inherently spatial process in which a host's home location and their social mixing patterns are important, with the mixing of infectious individuals often different to that of susceptible in…
View article: A comparison of hemagglutination inhibition and neutralization assays for characterizing immunity to seasonal influenza A
A comparison of hemagglutination inhibition and neutralization assays for characterizing immunity to seasonal influenza A Open
Background: Serum antibody to influenza can be used to identify past exposure and measure current immune status. The two most common methods for measuring this are the hemagglutination inhibition assay (HI) and the viral neutralization ass…
View article: Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course
Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course Open
Humans experience many influenza infections over their lives, resulting in complex and varied immunological histories. Although experimental and quantitative analyses have improved our understanding of the immunological processes defining …
View article: Differences between the true reproduction number and the apparent reproduction number of an epidemic time series
Differences between the true reproduction number and the apparent reproduction number of an epidemic time series Open
The time-varying reproduction number R(t) measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely know…
View article: Key Challenges for Respiratory Virus Surveillance while Transitioning out of Acute Phase of COVID-19 Pandemic
Key Challenges for Respiratory Virus Surveillance while Transitioning out of Acute Phase of COVID-19 Pandemic Open
To support the ongoing management of viral respiratory diseases while transitioning out of the acute phase of the COVID-19 pandemic, many countries are moving toward an integrated model of surveillance for SARS-CoV-2, influenza virus, and …
View article: Forecasting influenza incidence as an ordinal variable using machine learning
Forecasting influenza incidence as an ordinal variable using machine learning Open
Background : Many mechanisms contribute to the variation in the incidence of influenza disease, such as strain evolution, the waning of immunity and changes in social mixing. Although machine learning methods have been developed for forec…
View article: Epidemiological impact of a large number of false negative SARS-CoV-2 test results in South West England during September and October 2021
Epidemiological impact of a large number of false negative SARS-CoV-2 test results in South West England during September and October 2021 Open
During September and October 2021, a substantial number of Polymerase Chain Reaction (PCR) tests in England processed at a single laboratory were incorrectly reported as negative. We estimate the number of false negative test results issue…
View article: Infectious disease surveillance needs for the United States: lessons from COVID-19
Infectious disease surveillance needs for the United States: lessons from COVID-19 Open
The COVID-19 pandemic has highlighted the need to upgrade systems for infectious disease surveillance and forecasting and modeling of the spread of infection, both of which inform evidence-based public health guidance and policies. Here, w…