Epidemics

Article	Citations
Data pipelines in a public health emergency: The human in the machine	101
Seasonality as a driver of pH1N12009 influenza vaccination campaign impact	74
Modelling the COVID-19 pandemic: Focusing on the case of Greece	42
Collaborative forecasting of influenza-like illness in Italy: The Influcast experience	42
A prospective real-time transfer learning approach to estimate influenza hospitalizations with limited data	41
Accounting for historical injustices in mathematical models of infectious disease transmission: An analytic overview	30
Modeling the population-level impact of treatment on COVID-19 disease and SARS-CoV-2 transmission	27
Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies	26
Asymptomatic but infectious – The silent driver of pathogen transmission. A pragmatic review	25
Supporting LGBTQ+ epidemiologists in the UK during research-related travel and international collaboration	24
Contribution and quality of mathematical modeling evidence in World Health Organization guidelines: A systematic review	23
A method to estimate the serial interval distribution under partially-sampled data	23
A phenomenological approach to predicting tuberculosis cases with an assessment of measurement errors	22
Age-time-specific transmission of hand-foot-and-mouth disease enterovirus serotypes in Vietnam: A catalytic model with maternal immunity	22
Education data needs and challenges for building back from COVID-19	22
Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19	21
Ensemble	21
Estimating the impact of test–trace–isolate–quarantine systems on SARS-CoV-2 transmission in Australia	20
Mumps epidemic dynamics in the United States before vaccination (1923–1932)	20
The impact of household size on measles transmission: A long-term perspective	20
Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter	19
The triple epidemics of arboviruses in Feira de Santana, Brazilian Northeast: Epidemiological characteristics and diffusion patterns	18
Epidemiological characteristics and transmissibility of HPV infection: A long-term retrospective study in Hokkien Golden Triangle, China, 2013–2021	18
The effective reproductive number: Modeling and prediction with application to the multi-wave Covid-19 pandemic	18
Inference for a spatio-temporal model with partial spatial data: African horse sickness virus in Morocco	18

Mathematical modeling of COVID-19 in British Columbia: An age-structured model with time-dependent contact rates	17
Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling	17
Modelling: Understanding pandemics and how to control them	17
A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities	16
A model for reconstructing trends and distribution in age at first sex from multiple household surveys with reporting biases	16
Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak	16
Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data	15
A binary prototype for time-series surveillance and intervention	14
Wastewater-based surveillance for influenza and respiratory syncytial virus: Insights from a 21-month study in Oklahoma	14
First wave of SARS-CoV-2 in Santiago Chile: Seroprevalence, asymptomatic infection and infection fatality rate	14
Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study	14
Ceasing sampling at wastewater treatment plants where viral dynamics are most predictable	14
Optimizing spatial distribution of wastewater-based epidemiology to advance health equity	13
Modelling the dynamics of SARS-CoV-2 during the first 14 days of infection	13
Projecting the population-level impact of norovirus vaccines	13
Complex model calibration through emulation, a worked example for a stochastic epidemic model	13
The effects of HIV self-testing on HIV incidence and awareness of status among men who have sex with men in the United States: Insights from a novel compartmental model	13
Investigating the impact of edge weight selection on the pig trade network topology	13
Learning associations of COVID-19 hospitalizations with wastewater viral signals by Markov modulated models	13
Estimating COVID-19 cases and deaths prevented by non-pharmaceutical interventions, and the impact of individual actions: A retrospective model-based analysis	13
A Cluster-Aggregate-Pool (CAP) ensemble algorithm for improved forecast performance of influenza-like illness	13
Sequential Monte Carlo Squared for online inference in stochastic epidemic models	13
Public health impact of the U.S. Scenario Modeling Hub	13
A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data	12
Retrospective modelling of the disease and mortality burden of the 1918–1920 influenza pandemic in Zurich, Switzerland	12
Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks	12
Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer	12
Preface of the African swine fever modelling challenge special issue	12
Variation in pneumococcal invasiveness metrics is driven by serotype carriage duration and initial risk of disease	12
RAMPVIS: Answering the challenges of building visualisation capabilities for large-scale emergency responses	12
Agent-based modeling of the COVID-19 pandemic in Florida	11
Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example	11
Verifying infectious disease scenario planning for geographically diverse populations	11
Considering waning immunity to better explain dengue dynamics	11
SARS-CoV-2 transmission patterns in educational settings during the Alpha wave in Reggio-Emilia, Italy	11
Modelling lymphatic filariasis elimination in American Samoa: GEOFIL predicts need for new targets and six rounds of mass drug administration	11
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey	10
Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland	10
The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs)	10
Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number	10
Machine learning approaches for real-time ZIP code and county-level estimation of state-wide infectious disease hospitalizations using local health system data	10
Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening	10
Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva	10
Bayesian monitoring of COVID-19 in Sweden	10
A country-specific model of COVID-19 vaccination coverage needed for herd immunity in adult only or population wide vaccination programme	10
Coughs, colds and “freshers’ flu” survey in the University of Cambridge, 2007–2008	9
Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data	9
Lives saved by public health restrictions over the Victorian COVID-19 Delta variant epidemic wave, Aug-Nov 2021	9
Does spatial information improve forecasting of influenza-like illness?	9
Reconstructing the first COVID-19 pandemic wave with minimal data in England	9

In the shadow of privacy: Overlooked ethical concerns in COVID-19 digital epidemiology	9
Explaining the stable coexistence of drug-resistant and -susceptible pathogens: the resistance acquisition purifying selection model	9
The bridge between two worlds: Global South researchers' journeys through Global North academic training and beyond	8
The impact of reactive case detection on malaria transmission in Zanzibar in the presence of human mobility	8
Dose response for Salmonella Typhimurium and Enteritidis and other nontyphoid enteric salmonellae	8
Challenges for modelling interventions for future pandemics	8
Nationally representative social contact patterns among U.S. adults, August 2020-April 2021	8
Malaria temporal dynamic clustering for surveillance and intervention planning	8
A case for ongoing structural support to maximise infectious disease modelling efficiency for future public health emergencies: A modelling perspective	8
Modeling the transmission of antibiotic-resistant Enterobacterales in the community: A systematic review	8
Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design	8
COVID-19 in Scottish care homes: A metapopulation model of spread among residents and staff	8
A combination of probabilistic and mechanistic approaches for predicting the spread of African swine fever on Merry Island	8
Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries	8
Infectious disease dynamics and restrictions on social gathering size	7
Modeling the impact of different PrEP targeting strategies combined with a clinic-based HIV-1 nucleic acid testing intervention in Kenya	7
Enhancing seasonal influenza projections: A mechanistic metapopulation model for long-term scenario planning	7
Estimation of the probability of epidemic fade-out from multiple outbreak data	7
Determinants of RSV epidemiology following suppression through pandemic contact restrictions	7
Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States	7
A comparison of COVID-19 outbreaks across US Combined Statistical Areas using new methods for estimating	7
Inferring transmission routes for foot-and-mouth disease virus within a cattle herd using approximate Bayesian computation	7
Impact of COVID-19 control measures on respiratory syncytial virus and hand-foot-and-mouth disease transmission in Hong Kong and South Korea	7
Trypanosoma cruzi infection in dogs along the US-Mexico border: R changes with vector species composition	6
Robust phylodynamic inference and model specification for HIV transmission dynamics	6
Acquisition and clearance dynamics of Campylobacter spp. in children in low- and middle-income countries	6
Inference of epidemic dynamics in the COVID-19 era and beyond	6
Density forecasting of conjunctivitis burden using high-dimensional environmental time series data	6
Environmental drivers of Ixodes ricinus tick population dynamics: Mechanistic modelling using longitudinal field surveys and climate data	6
Social contact patterns following the COVID-19 pandemic: a snapshot of post-pandemic behaviour from the CoMix study	6
COVSIM: A stochastic agent-based COVID-19 SIMulation model for North Carolina	6
Small area population denominators for improved disease surveillance and response	6
Modelling how face masks and symptoms-based quarantine synergistically and cost-effectively reduce SARS-CoV-2 transmission in Bangladesh	6
SIR… or MADAM? The impact of privilege on careers in epidemic modelling	6
Testing a simple and frugal model of health protective behaviour in epidemic times	6
Unveiling ecological/evolutionary insights in HIV viral load dynamics: Allowing random slopes to observe correlational changes to CpG-contents and other molecular and clinical predictors	6
An optimized geo-hierarchical ensemble model to forecast hospitalizations from respiratory viruses in the United States	6
Forecasting SARS-CoV-2 epidemic dynamic in Poland with the pDyn agent-based model	6
An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study	6
Small area population denominators for improved disease surveillance and response	6
Recalibrating the notion of modelling for policymaking during pandemics	6
A deep learning approach for enhancing pandemic prediction: A retrospective evaluation of transformer neural networks and multi-source data fusion for infectious disease forecasting	6
A novel method to jointly estimate transmission rate and decay rate parameters in environmental transmission models	6
The impact of inaccurate assumptions about antibody test accuracy on the parametrisation and results of infectious disease models of epidemics	6
Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach	6
Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology	5
Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021	5
Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections	5
Optimal capacity sharing for global genomic surveillance	5
When do we need multiple infectious disease models? Agreement between projection rank and magnitude in a multi-model setting	5
Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study	5
Timeliness of reporting of SARS-CoV-2 seroprevalence results and their utility for infectious disease surveillance	5
Association between meteorological factors and the epidemics of influenza (sub)types in a subtropical basin of Southwest China	5
Impact of vaccine effectiveness and coverage on preventing large mumps outbreaks on college campuses: Implications for vaccination strategy	5
Accounting for the geometry of the respiratory tract in viral infections	5
Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys	5
Gaps in mobility data and implications for modelling epidemic spread: A scoping review and simulation study	5
Contents	5
Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages	5
Data needs for better surveillance and response to infectious disease threats	5
Symptom-based vs asymptomatic testing for controlling SARS-CoV-2 transmission in low- and middle-income countries: A modelling analysis	5
Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility	5
Publisher's note	4
Modelling the dynamics of infection, waning of immunity and re-infection with the Omicron variant of SARS-CoV-2 in Aotearoa New Zealand	4
The African swine fever modelling challenge: Objectives, model description and synthetic data generation	4
The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave	4
Data needs for integrated economic-epidemiological models of pandemic mitigation policies	4
Impact of intensified control on visceral leishmaniasis in a highly-endemic district of Bihar, India: an interrupted time series analysis	4
Optimizing age specific strategies of vaccination for prevention of cytomegalovirus infection in the US using agent-based simulation	4
Investigating the impact of non-pharmaceutical interventions (NPIs) on post-pandemic Respiratory Syncytial Virus (RSV) hospitalisations and seasonality in Wales, UK	4
Improving policy-oriented agent-based modeling with history matching: A case study	4
Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates	4
Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis	4
Nowcasting and forecasting the 2022 U.S. mpox outbreak: Support for public health decision making and lessons learned	4
Transmission dynamics of Norovirus GII and Enterovirus in Switzerland during the COVID-19 pandemic (2021–2022) as evidenced in wastewater	4
Integrating macroeconomic and public health impacts in social planning policies for pandemic response	4
On the contact tracing for COVID-19: A simulation study	4
Complementary roles of wild boar and red deer to animal tuberculosis maintenance in multi-host communities	4
Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern	4
The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy	4

Spatially targeted digital chest radiography to reduce tuberculosis in high-burden settings: A study of adaptive decision making	4
Challenges of integrating economics into epidemiological analysis of and policy responses to emerging infectious diseases	4
The challenges of data in future pandemics	4
flepiMoP: The evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic	4
Chimeric Forecasting: An experiment to leverage human judgment to improve forecasts of infectious disease using simulated surveillance data	4
Association between pertussis vaccination coverage and other sociodemographic factors and pertussis incidence using surveillance data	4
The aquaculture disease network model (AquaNet-Mod): A simulation model to evaluate disease spread and controls for the salmonid industry in England and Wales	4