Epidemics

Article	Citations
Data pipelines in a public health emergency: The human in the machine	108
Seasonality as a driver of pH1N12009 influenza vaccination campaign impact	45
Accounting for historical injustices in mathematical models of infectious disease transmission: An analytic overview	35
Modelling the COVID-19 pandemic: Focusing on the case of Greece	31
Modeling the population-level impact of treatment on COVID-19 disease and SARS-CoV-2 transmission	31
Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies	29
Collaborative forecasting of influenza-like illness in Italy: The Influcast experience	28
A prospective real-time transfer learning approach to estimate influenza hospitalizations with limited data	28
Contribution and quality of mathematical modeling evidence in World Health Organization guidelines: A systematic review	27
Sequential federated analysis of early outbreak data applied to incubation period estimation	27
Asymptomatic but infectious – The silent driver of pathogen transmission. A pragmatic review	27
Spatio-temporal agent-based modelling of malaria	25
A method to estimate the serial interval distribution under partially-sampled data	25
Supporting LGBTQ+ epidemiologists in the UK during research-related travel and international collaboration	25
Age-time-specific transmission of hand-foot-and-mouth disease enterovirus serotypes in Vietnam: A catalytic model with maternal immunity	24
Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter	23
A phenomenological approach to predicting tuberculosis cases with an assessment of measurement errors	23
Education data needs and challenges for building back from COVID-19	22
Inference for a spatio-temporal model with partial spatial data: African horse sickness virus in Morocco	22
Epidemiological characteristics and transmissibility of HPV infection: A long-term retrospective study in Hokkien Golden Triangle, China, 2013–2021	21
The impact of household size on measles transmission: A long-term perspective	21
Mumps epidemic dynamics in the United States before vaccination (1923–1932)	20
The effective reproductive number: Modeling and prediction with application to the multi-wave Covid-19 pandemic	19
Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19	19
Estimating the impact of test–trace–isolate–quarantine systems on SARS-CoV-2 transmission in Australia	19

Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak	18
Mathematical modeling of COVID-19 in British Columbia: An age-structured model with time-dependent contact rates	18
Modelling: Understanding pandemics and how to control them	18
Ensemble	18
A binary prototype for time-series surveillance and intervention	17
A model for reconstructing trends and distribution in age at first sex from multiple household surveys with reporting biases	16
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	15
A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities	15
Wastewater-based surveillance for influenza and respiratory syncytial virus: Insights from a 21-month study in Oklahoma	15
Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data	15
Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling	15
Granular insights: A wastewater-based machine learning approach for localized COVID-19 hospitalization forecasting	15
Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study	15
Estimating COVID-19 cases and deaths prevented by non-pharmaceutical interventions, and the impact of individual actions: A retrospective model-based analysis	14
Modelling the dynamics of SARS-CoV-2 during the first 14 days of infection	14
Modelling the transmission and impact of Omicron variants of Covid-19 in different ethnicity groups in Aotearoa New Zealand	14
Variation in pneumococcal invasiveness metrics is driven by serotype carriage duration and initial risk of disease	13
Optimizing spatial distribution of wastewater-based epidemiology to advance health equity	13
A Cluster-Aggregate-Pool (CAP) ensemble algorithm for improved forecast performance of influenza-like illness	13
Investigating the impact of edge weight selection on the pig trade network topology	13
Complex model calibration through emulation, a worked example for a stochastic epidemic model	13
Ceasing sampling at wastewater treatment plants where viral dynamics are most predictable	13
Learning associations of COVID-19 hospitalizations with wastewater viral signals by Markov modulated models	13
Wastewater surveillance: From COVID-19 emergency response to a pillar of continuous public health	13
Public health impact of the U.S. Scenario Modeling Hub	13
First wave of SARS-CoV-2 in Santiago Chile: Seroprevalence, asymptomatic infection and infection fatality rate	13
Projecting the population-level impact of norovirus vaccines	13
A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data	12
Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks	12
SARS-CoV-2 transmission patterns in educational settings during the Alpha wave in Reggio-Emilia, Italy	12
Sequential Monte Carlo Squared for online inference in stochastic epidemic models	12
Preface of the African swine fever modelling challenge special issue	12
Foundation models for time series forecasting and policy evaluation in infectious disease epidemics	12
Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer	12
Retrospective modelling of the disease and mortality burden of the 1918–1920 influenza pandemic in Zurich, Switzerland	12
RAMPVIS: Answering the challenges of building visualisation capabilities for large-scale emergency responses	12
Modelling lymphatic filariasis elimination in American Samoa: GEOFIL predicts need for new targets and six rounds of mass drug administration	12
Considering waning immunity to better explain dengue dynamics	11
Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example	11
Agent-based modeling of the COVID-19 pandemic in Florida	11
Verifying infectious disease scenario planning for geographically diverse populations	11
The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs)	10
A country-specific model of COVID-19 vaccination coverage needed for herd immunity in adult only or population wide vaccination programme	10
Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva	10
Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number	10
Using wastewater surveillance to improve infectious disease control in correctional facilities and congregate living settings: A modeling perspective	10
Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening	10
Bayesian monitoring of COVID-19 in Sweden	10
Short term forecast of new daily pandemic hospitalizations: A time series model for a single hospital	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

Characterizing co-circulating respiratory virus genomic diversity in Switzerland with hybrid-capture sequencing and phylogenetic reconstructions: Insights into the 2023/24 season	10
In the shadow of privacy: Overlooked ethical concerns in COVID-19 digital epidemiology	9
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey	9
Reconstructing the first COVID-19 pandemic wave with minimal data in England	9
Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design	9
Maternal immunity drives age-related patterns of RSV disease	9
Coughs, colds and “freshers’ flu” survey in the University of Cambridge, 2007–2008	9
Explaining the stable coexistence of drug-resistant and -susceptible pathogens: the resistance acquisition purifying selection model	9
Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data	9
Does spatial information improve forecasting of influenza-like illness?	8
Dose response for Salmonella Typhimurium and Enteritidis and other nontyphoid enteric salmonellae	8
COVID-19 in Scottish care homes: A metapopulation model of spread among residents and staff	8
The bridge between two worlds: Global South researchers' journeys through Global North academic training and beyond	8
Lives saved by public health restrictions over the Victorian COVID-19 Delta variant epidemic wave, Aug-Nov 2021	8
Malaria temporal dynamic clustering for surveillance and intervention planning	8
Modeling the transmission of antibiotic-resistant Enterobacterales in the community: A systematic review	8
From survey to solutions: Tackling diversity and inclusion gaps through an inclusion task force	8
A case for ongoing structural support to maximise infectious disease modelling efficiency for future public health emergencies: A modelling perspective	8
Nationally representative social contact patterns among U.S. adults, August 2020-April 2021	8
Modeling the impact of different PrEP targeting strategies combined with a clinic-based HIV-1 nucleic acid testing intervention in Kenya	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 combination of probabilistic and mechanistic approaches for predicting the spread of African swine fever on Merry Island	7
Infectious disease dynamics and restrictions on social gathering size	7
Forecasting SARS-CoV-2 epidemic dynamic in Poland with the pDyn agent-based model	7
The impact of inaccurate assumptions about antibody test accuracy on the parametrisation and results of infectious disease models of epidemics	7
A novel method to jointly estimate transmission rate and decay rate parameters in environmental transmission models	7
Inferring transmission routes for foot-and-mouth disease virus within a cattle herd using approximate Bayesian computation	7
Pseudo-time reconstruction for analyzing transmission direction in COVID-19 contact-tracing data	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
Some mathematical reasons why meta-analyses of nonpharmaceutical interventions like facemasks could be inaccurate	7
Enhancing seasonal influenza projections: A mechanistic metapopulation model for long-term scenario planning	7
An optimized geo-hierarchical ensemble model to forecast hospitalizations from respiratory viruses in the United States	7
Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach	7
A comparison of COVID-19 outbreaks across US Combined Statistical Areas using new methods for estimating	7
The impact of reactive case detection on malaria transmission in Zanzibar in the presence of human mobility	7
Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries	7
Estimating influenza transmission parameters: Comparing two study designs, 2023–2024	7
Social contact patterns following the COVID-19 pandemic: a snapshot of post-pandemic behaviour from the CoMix study	7
COVSIM: A stochastic agent-based COVID-19 SIMulation model for North Carolina	7
An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study	6
Inference of epidemic dynamics in the COVID-19 era and beyond	6
Contents	6
Impact of vaccine effectiveness and coverage on preventing large mumps outbreaks on college campuses: Implications for vaccination strategy	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
Robust phylodynamic inference and model specification for HIV transmission dynamics	6
Modelling how face masks and symptoms-based quarantine synergistically and cost-effectively reduce SARS-CoV-2 transmission in Bangladesh	6
Testing a simple and frugal model of health protective behaviour in epidemic times	6
Acquisition and clearance dynamics of Campylobacter spp. in children in low- and middle-income countries	6
Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology	6
Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages	6
Small area population denominators for improved disease surveillance and response	6
Density forecasting of conjunctivitis burden using high-dimensional environmental time series data	6
Small area population denominators for improved disease surveillance and response	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
Association between meteorological factors and the epidemics of influenza (sub)types in a subtropical basin of Southwest China	6
Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections	6
SIR… or MADAM? The impact of privilege on careers in epidemic modelling	6
Breaking down barriers: A funder's perspective on achieving equity and inclusivity in infectious disease modelling and epidemiology	6
Environmental drivers of Ixodes ricinus tick population dynamics: Mechanistic modelling using longitudinal field surveys and climate data	6
Trypanosoma cruzi infection in dogs along the US-Mexico border: R changes with vector species composition	6
Timeliness of reporting of SARS-CoV-2 seroprevalence results and their utility for infectious disease surveillance	5
UnMuted: Defining SARS-CoV-2 lineages according to temporally consistent mutation clusters in wastewater samples	5
Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys	5
Data needs for integrated economic-epidemiological models of pandemic mitigation policies	5
When do we need multiple infectious disease models? Agreement between projection rank and magnitude in a multi-model setting	5
Predicting local COVID-19 emergences: A time-series classification approach and value of data from social media, search engines, and neighbouring regions	5
Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study	5
Gaps in mobility data and implications for modelling epidemic spread: A scoping review and simulation study	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
Integrating macroeconomic and public health impacts in social planning policies for pandemic response	5
Accounting for the geometry of the respiratory tract in viral infections	5
Optimal capacity sharing for global genomic surveillance	5
Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility	5
Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021	5
COVID-19 hospital admissions and wastewater data in Canada: A statistical analysis	5
Transmission dynamics of Norovirus GII and Enterovirus in Switzerland during the COVID-19 pandemic (2021–2022) as evidenced in wastewater	5
flepiMoP: The evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic	5
The challenges of data in future pandemics	5

Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern	4
Optimizing age specific strategies of vaccination for prevention of cytomegalovirus infection in the US using agent-based simulation	4
The African swine fever modelling challenge: Objectives, model description and synthetic data generation	4
On the contact tracing for COVID-19: A simulation study	4
Impact of intensified control on visceral leishmaniasis in a highly-endemic district of Bihar, India: an interrupted time series analysis	4
Improving policy-oriented agent-based modeling with history matching: A case study	4
Publisher's note	4
Complementary roles of wild boar and red deer to animal tuberculosis maintenance in multi-host communities	4
Nowcasting and forecasting the 2022 U.S. mpox outbreak: Support for public health decision making and lessons learned	4
The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave	4
Chimeric Forecasting: An experiment to leverage human judgment to improve forecasts of infectious disease using simulated surveillance data	4
Value of risk-contact data from digital contact monitoring apps in infectious disease modeling	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
Association between pertussis vaccination coverage and other sociodemographic factors and pertussis incidence using surveillance data	4
Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis	4
Challenges of integrating economics into epidemiological analysis of and policy responses to emerging infectious diseases	4
Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates	4
Evaluating age-dependent transmission and vaccination policy in Singapore’s SARS-CoV-2 epidemic: A computational modelling approach	4