Epidemics

Article	Citations
Accounting for historical injustices in mathematical models of infectious disease transmission: An analytic overview	182
Data pipelines in a public health emergency: The human in the machine	94
Seasonality as a driver of pH1N12009 influenza vaccination campaign impact	67
Modelling the COVID-19 pandemic: Focusing on the case of Greece	66
Collaborative forecasting of influenza-like illness in Italy: The Influcast experience	41
A prospective real-time transfer learning approach to estimate influenza hospitalizations with limited data	39
Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies	37
Modeling the population-level impact of treatment on COVID-19 disease and SARS-CoV-2 transmission	35
Asymptomatic but infectious – The silent driver of pathogen transmission. A pragmatic review	34
Age-time-specific transmission of hand-foot-and-mouth disease enterovirus serotypes in Vietnam: A catalytic model with maternal immunity	29
Contribution and quality of mathematical modeling evidence in World Health Organization guidelines: A systematic review	29
Realtime case study simulations of transmission of Pancreas Disease (PD) in Norwegian salmonid farming for disease control purposes	25
A method to estimate the serial interval distribution under partially-sampled data	25
A phenomenological approach to predicting tuberculosis cases with an assessment of measurement errors	23
The effective reproductive number: Modeling and prediction with application to the multi-wave Covid-19 pandemic	23
Inference for a spatio-temporal model with partial spatial data: African horse sickness virus in Morocco	22
The triple epidemics of arboviruses in Feira de Santana, Brazilian Northeast: Epidemiological characteristics and diffusion patterns	21
Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter	21
The impact of household size on measles transmission: A long-term perspective	21
Modelling: Understanding pandemics and how to control them	21
Education data needs and challenges for building back from COVID-19	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
Mathematical modeling of COVID-19 in British Columbia: An age-structured model with time-dependent contact rates	20
Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19	20

Ensemble2: Scen	20
Epidemiological characteristics and transmissibility of HPV infection: A long-term retrospective study in Hokkien Golden Triangle, China, 2013–2021	20
Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling	19
A model for reconstructing trends and distribution in age at first sex from multiple household surveys with reporting biases	19
Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study	19
Modelling SARS-CoV-2 transmission in a UK university setting	19
Understanding MRSA clonal competition within a UK hospital; the possible importance of density dependence	19
Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data	18
Ceasing sampling at wastewater treatment plants where viral dynamics are most predictable	18
Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak	18
Coordinated support for local action: Modeling strategies to facilitate behavior adoption in urban-poor communities of Liberia for sustained COVID-19 suppression	18
A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities	18
First wave of SARS-CoV-2 in Santiago Chile: Seroprevalence, asymptomatic infection and infection fatality rate	18
Modelling the dynamics of SARS-CoV-2 during the first 14 days of infection	17
Estimating COVID-19 cases and deaths prevented by non-pharmaceutical interventions, and the impact of individual actions: A retrospective model-based analysis	17
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	17
A Cluster-Aggregate-Pool (CAP) ensemble algorithm for improved forecast performance of influenza-like illness	16
Optimizing spatial distribution of wastewater-based epidemiology to advance health equity	16
Complex model calibration through emulation, a worked example for a stochastic epidemic model	15
Variation in pneumococcal invasiveness metrics is driven by serotype carriage duration and initial risk of disease	15
Social contact patterns among employees in 3 U.S. companies during early phases of the COVID-19 pandemic, April to June 2020	15
Dynamic network strategies for SARS-CoV-2 control on a cruise ship	14
Learning associations of COVID-19 hospitalizations with wastewater viral signals by Markov modulated models	14
Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer	14
Public health impact of the U.S. Scenario Modeling Hub	13
Retrospective modelling of the disease and mortality burden of the 1918–1920 influenza pandemic in Zurich, Switzerland	13
Investigating the impact of edge weight selection on the pig trade network topology	13
Sequential Monte Carlo Squared for online inference in stochastic epidemic models	13
A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data	13
Projecting the population-level impact of norovirus vaccines	13
Modelling lymphatic filariasis elimination in American Samoa: GEOFIL predicts need for new targets and six rounds of mass drug administration	12
RAMPVIS: Answering the challenges of building visualisation capabilities for large-scale emergency responses	12
Considering waning immunity to better explain dengue dynamics	12
Machine learning approaches for real-time ZIP code and county-level estimation of state-wide infectious disease hospitalizations using local health system data	12
Preface of the African swine fever modelling challenge special issue	12
Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example	12
Agent-based modeling of the COVID-19 pandemic in Florida	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
Effective strategies to promote HIV self-testing for men who have sex with men: Evidence from a mathematical model	12
A quantitative assessment of epidemiological parameters required to investigate COVID-19 burden	11
Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number	11
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey	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)	11
Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland	11
Bayesian monitoring of COVID-19 in Sweden	11
A country-specific model of COVID-19 vaccination coverage needed for herd immunity in adult only or population wide vaccination programme	11
Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva	11
Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening	11

Lives saved by public health restrictions over the Victorian COVID-19 Delta variant epidemic wave, Aug-Nov 2021	10
Modeling the transmission of antibiotic-resistant Enterobacterales in the community: A systematic review	10
Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network	10
Does spatial information improve forecasting of influenza-like illness?	10
Coughs, colds and “freshers’ flu” survey in the University of Cambridge, 2007–2008	10
Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data	10
Assessing the risk of cascading COVID-19 outbreaks from prison-to-prison transfers	10
Using video-analysis technology to estimate social mixing and simulate influenza transmission at a mass gathering	10
Challenges in evaluating risks and policy options around endemic establishment or elimination of novel pathogens	9
Dose response for Salmonella Typhimurium and Enteritidis and other nontyphoid enteric salmonellae	9
Explaining the stable coexistence of drug-resistant and -susceptible pathogens: the resistance acquisition purifying selection model	9
In the shadow of privacy: Overlooked ethical concerns in COVID-19 digital epidemiology	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
Globally local: Hyper-local modeling for accurate forecast of COVID-19	8
Nationally representative social contact patterns among U.S. adults, August 2020-April 2021	8
Inferring transmission routes for foot-and-mouth disease virus within a cattle herd using approximate Bayesian computation	8
Rapid transmission of coronavirus disease 2019 within a religious sect in South Korea: A mathematical modeling study	8
The confounding effect of multi-type human papillomavirus infections on type-specific natural history parameter identification	8
Challenges for modelling interventions for future pandemics	8
The impact of reactive case detection on malaria transmission in Zanzibar in the presence of human mobility	8
Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries	8
Impact of COVID-19 control measures on respiratory syncytial virus and hand-foot-and-mouth disease transmission in Hong Kong and South Korea	8
A comparison of COVID-19 outbreaks across US Combined Statistical Areas using new methods for estimating	8
Malaria temporal dynamic clustering for surveillance and intervention planning	8
COVID-19 in Scottish care homes: A metapopulation model of spread among residents and staff	8
A new logistic growth model applied to COVID-19 fatality data	8
Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India	8
Modeling the impact of different PrEP targeting strategies combined with a clinic-based HIV-1 nucleic acid testing intervention in Kenya	8
Challenges on the interaction of models and policy for pandemic control	8
A combination of probabilistic and mechanistic approaches for predicting the spread of African swine fever on Merry Island	8
A case for ongoing structural support to maximise infectious disease modelling efficiency for future public health emergencies: A modelling perspective	8
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
COVSIM: A stochastic agent-based COVID-19 SIMulation model for North Carolina	7
Density forecasting of conjunctivitis burden using high-dimensional environmental time series data	7
Determinants of RSV epidemiology following suppression through pandemic contact restrictions	7
Enhancing seasonal influenza projections: A mechanistic metapopulation model for long-term scenario planning	7
Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States	7
Social contact patterns following the COVID-19 pandemic: a snapshot of post-pandemic behaviour from the CoMix study	7
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland	7
Estimation of the probability of epidemic fade-out from multiple outbreak data	7
Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach	7
A novel method to jointly estimate transmission rate and decay rate parameters in environmental transmission models	7
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	7
Trypanosoma cruzi infection in dogs along the US-Mexico border: R changes with vector species composition	6
Inference of epidemic dynamics in the COVID-19 era and beyond	6
Gaps in mobility data and implications for modelling epidemic spread: A scoping review and simulation study	6
Timeliness of reporting of SARS-CoV-2 seroprevalence results and their utility for infectious disease surveillance	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
Acquisition and clearance dynamics of Campylobacter spp. in children in low- and middle-income countries	6
Simulated effects of increasing salmonid production on sea lice populations in Norway	6
Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021	6
Impact of vaccine effectiveness and coverage on preventing large mumps outbreaks on college campuses: Implications for vaccination strategy	6
Robust phylodynamic inference and model specification for HIV transmission dynamics	6
An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study	6
Recalibrating the notion of modelling for policymaking during pandemics	6
Testing a simple and frugal model of health protective behaviour in epidemic times	6
Contents	6
Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology	6
SIR… or MADAM? The impact of privilege on careers in epidemic modelling	6
Challenges in modeling the emergence of novel pathogens	6
Small area population denominators for improved disease surveillance and response	6
Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study	5
Association between meteorological factors and the epidemics of influenza (sub)types in a subtropical basin of Southwest China	5
Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys	5
Modeling the population effects of escape mutations in SARS-CoV-2 to guide vaccination strategies	5
Data needs for better surveillance and response to infectious disease threats	5
Nowcasting and forecasting the 2022 U.S. mpox outbreak: Support for public health decision making and lessons learned	5
When do we need multiple infectious disease models? Agreement between projection rank and magnitude in a multi-model setting	5
Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility	5
Lessons for preparedness and reasons for concern from the early COVID-19 epidemic in Iran	5
Symptom-based vs asymptomatic testing for controlling SARS-CoV-2 transmission in low- and middle-income countries: A modelling analysis	5
Optimal capacity sharing for global genomic surveillance	5
Data needs for integrated economic-epidemiological models of pandemic mitigation policies	5
Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages	5
Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections	5
Assessing the efficacy of interventions to control indoor SARS-Cov-2 transmission: An agent-based modeling approach	5

The challenges of data in future pandemics	5
Accounting for the geometry of the respiratory tract in viral infections	5
flepiMoP: The evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic	5
The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy	4
Complementary roles of wild boar and red deer to animal tuberculosis maintenance in multi-host communities	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
On the contact tracing for COVID-19: A simulation study	4
The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave	4
Spatially targeted digital chest radiography to reduce tuberculosis in high-burden settings: A study of adaptive decision making	4
Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates	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
Precautionary breaks: Planned, limited duration circuit breaks to control the prevalence of SARS-CoV2 and the burden of COVID-19 disease	4
Transmission dynamics of Norovirus GII and Enterovirus in Switzerland during the COVID-19 pandemic (2021–2022) as evidenced in wastewater	4
Geospatial clustering and modelling provide policy guidance to distribute funding for active TB case finding in Ethiopia	4
Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis	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
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
Challenges of integrating economics into epidemiological analysis of and policy responses to emerging infectious diseases	4
Chimeric Forecasting: An experiment to leverage human judgment to improve forecasts of infectious disease using simulated surveillance data	4
Publisher's note	4