Epidemics

Article	Citations
Modeling the population-level impact of treatment on COVID-19 disease and SARS-CoV-2 transmission	179
Accounting for historical injustices in mathematical models of infectious disease transmission: An analytic overview	90
Data pipelines in a public health emergency: The human in the machine	65
Seasonality as a driver of pH1N12009 influenza vaccination campaign impact	62
Modelling the COVID-19 pandemic: Focusing on the case of Greece	60
Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies	54
A prospective real-time transfer learning approach to estimate influenza hospitalizations with limited data	49
Asymptomatic but infectious – The silent driver of pathogen transmission. A pragmatic review	38
Collaborative forecasting of influenza-like illness in Italy: The Influcast experience	38
Contribution and quality of mathematical modeling evidence in World Health Organization guidelines: A systematic review	36
Age-time-specific transmission of hand-foot-and-mouth disease enterovirus serotypes in Vietnam: A catalytic model with maternal immunity	33
Assessing the nationwide impact of COVID-19 mitigation policies on the transmission rate of SARS-CoV-2 in Brazil	32
A method to estimate the serial interval distribution under partially-sampled data	31
Modelling: Understanding pandemics and how to control them	28
Realtime case study simulations of transmission of Pancreas Disease (PD) in Norwegian salmonid farming for disease control purposes	28
Mathematical modeling of COVID-19 in British Columbia: An age-structured model with time-dependent contact rates	25
Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19	24
The effective reproductive number: Modeling and prediction with application to the multi-wave Covid-19 pandemic	22
A phenomenological approach to predicting tuberculosis cases with an assessment of measurement errors	21
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	20
Education data needs and challenges for building back from COVID-19	20
The triple epidemics of arboviruses in Feira de Santana, Brazilian Northeast: Epidemiological characteristics and diffusion patterns	20
Inference for a spatio-temporal model with partial spatial data: African horse sickness virus in Morocco	20
Estimating the impact of test–trace–isolate–quarantine systems on SARS-CoV-2 transmission in Australia	20

Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter	19
Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak	19
Ensemble2: Scen	19
Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling	19
Mumps epidemic dynamics in the United States before vaccination (1923–1932)	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	18
Understanding MRSA clonal competition within a UK hospital; the possible importance of density dependence	18
Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data	18
Modelling SARS-CoV-2 transmission in a UK university setting	18
Optimizing spatial distribution of wastewater-based epidemiology to advance health equity	17
First wave of SARS-CoV-2 in Santiago Chile: Seroprevalence, asymptomatic infection and infection fatality rate	17
Estimating COVID-19 cases and deaths prevented by non-pharmaceutical interventions, and the impact of individual actions: A retrospective model-based analysis	17
A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities	17
Estimating the global reduction in transmission and rise in detection capacity of the novel coronavirus SARS-CoV-2 in early 2020	16
Coordinated support for local action: Modeling strategies to facilitate behavior adoption in urban-poor communities of Liberia for sustained COVID-19 suppression	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	16
Ceasing sampling at wastewater treatment plants where viral dynamics are most predictable	16
Retrospective modelling of the disease and mortality burden of the 1918–1920 influenza pandemic in Zurich, Switzerland	15
Dynamic network strategies for SARS-CoV-2 control on a cruise ship	15
Variation in pneumococcal invasiveness metrics is driven by serotype carriage duration and initial risk of disease	15
Public health impact of the U.S. Scenario Modeling Hub	15
Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer	14
Complex model calibration through emulation, a worked example for a stochastic epidemic model	14
Social contact patterns among employees in 3 U.S. companies during early phases of the COVID-19 pandemic, April to June 2020	14
A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data	13
RAMPVIS: Answering the challenges of building visualisation capabilities for large-scale emergency responses	13
Preface of the African swine fever modelling challenge special issue	13
Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example	13
Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks	13
Modelling lymphatic filariasis elimination in American Samoa: GEOFIL predicts need for new targets and six rounds of mass drug administration	13
Agent-based modeling of the COVID-19 pandemic in Florida	12
Effective strategies to promote HIV self-testing for men who have sex with men: Evidence from a mathematical model	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
Considering waning immunity to better explain dengue dynamics	12
SARS-CoV-2 transmission patterns in educational settings during the Alpha wave in Reggio-Emilia, Italy	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
Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network	11
Using video-analysis technology to estimate social mixing and simulate influenza transmission at a mass gathering	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
Challenges in evaluating risks and policy options around endemic establishment or elimination of novel pathogens	11
The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs)	11
Bayesian monitoring of COVID-19 in Sweden	11
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey	11
Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland	11
Coughs, colds and “freshers’ flu” survey in the University of Cambridge, 2007–2008	10
Does spatial information improve forecasting of influenza-like illness?	10

Modeling the transmission of antibiotic-resistant Enterobacterales in the community: A systematic review	10
Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data	10
Lives saved by public health restrictions over the Victorian COVID-19 Delta variant epidemic wave, Aug-Nov 2021	10
Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design	10
Assessing the risk of cascading COVID-19 outbreaks from prison-to-prison transfers	10
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
Globally local: Hyper-local modeling for accurate forecast of COVID-19	9
Challenges for modelling interventions for future pandemics	9
The confounding effect of multi-type human papillomavirus infections on type-specific natural history parameter identification	9
A new logistic growth model applied to COVID-19 fatality data	9
Challenges on the interaction of models and policy for pandemic control	9
A case for ongoing structural support to maximise infectious disease modelling efficiency for future public health emergencies: A modelling perspective	9
COVID-19 in Scottish care homes: A metapopulation model of spread among residents and staff	9
Malaria temporal dynamic clustering for surveillance and intervention planning	9
Dose response for Salmonella Typhimurium and Enteritidis and other nontyphoid enteric salmonellae	9
Nationally representative social contact patterns among U.S. adults, August 2020-April 2021	9
The impact of reactive case detection on malaria transmission in Zanzibar in the presence of human mobility	8
Estimation of the probability of epidemic fade-out from multiple outbreak data	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
Determinants of RSV epidemiology following suppression through pandemic contact restrictions	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
Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India	8
Bayesian evidence synthesis to estimate subnational TB incidence: An application in Brazil	8
Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States	8
Enhancing seasonal influenza projections: A mechanistic metapopulation model for long-term scenario planning	8
A comparison of COVID-19 outbreaks across US Combined Statistical Areas using new methods for estimating	8
Using an agent-based sexual-network model to analyze the impact of mitigation efforts for controlling chlamydia	8
A combination of probabilistic and mechanistic approaches for predicting the spread of African swine fever on Merry Island	8
Participatory syndromic surveillance as a tool for tracking COVID-19 in Bangladesh	8
Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries	8
Modeling the impact of different PrEP targeting strategies combined with a clinic-based HIV-1 nucleic acid testing intervention in Kenya	8
Infectious disease dynamics and restrictions on social gathering size	8
COVSIM: A stochastic agent-based COVID-19 SIMulation model for North Carolina	8
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland	7
A novel method to jointly estimate transmission rate and decay rate parameters in environmental transmission models	7
Trypanosoma cruzi infection in dogs along the US-Mexico border: R changes with vector species composition	7
Modelling how face masks and symptoms-based quarantine synergistically and cost-effectively reduce SARS-CoV-2 transmission in Bangladesh	7
Estimation of the incubation period of COVID-19 using viral load data	7
Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach	7
Social contact patterns following the COVID-19 pandemic: a snapshot of post-pandemic behaviour from the CoMix study	7
Density forecasting of conjunctivitis burden using high-dimensional environmental time series data	7
Recalibrating the notion of modelling for policymaking during pandemics	7
Small area population denominators for improved disease surveillance and response	7
The impact of inaccurate assumptions about antibody test accuracy on the parametrisation and results of infectious disease models of epidemics	7
Forecasting SARS-CoV-2 epidemic dynamic in Poland with the pDyn agent-based model	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
An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study	7
Small area population denominators for improved disease surveillance and response	7
Acquisition and clearance dynamics of Campylobacter spp. in children in low- and middle-income countries	6
Contents	6
Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility	6
The performance of phenomenological models in providing near-term Canadian case projections in the midst of the COVID-19 pandemic: March – April, 2020	6
Challenges in modeling the emergence of novel pathogens	6
Simulated effects of increasing salmonid production on sea lice populations in Norway	6
Impact of vaccine effectiveness and coverage on preventing large mumps outbreaks on college campuses: Implications for vaccination strategy	6
Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections	6
Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021	6
Testing a simple and frugal model of health protective behaviour in epidemic times	6
Inference of epidemic dynamics in the COVID-19 era and beyond	6
SIR… or MADAM? The impact of privilege on careers in epidemic modelling	6
Association between meteorological factors and the epidemics of influenza (sub)types in a subtropical basin of Southwest China	6
Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study	6
Gaps in mobility data and implications for modelling epidemic spread: A scoping review and simulation study	5
Data needs for integrated economic-epidemiological models of pandemic mitigation policies	5
Nowcasting and forecasting the 2022 U.S. mpox outbreak: Support for public health decision making and lessons learned	5
Accounting for the geometry of the respiratory tract in viral infections	5
Symptom-based vs asymptomatic testing for controlling SARS-CoV-2 transmission in low- and middle-income countries: A modelling analysis	5
Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis	5
When do we need multiple infectious disease models? Agreement between projection rank and magnitude in a multi-model setting	5
Data needs for better surveillance and response to infectious disease threats	5
Timeliness of reporting of SARS-CoV-2 seroprevalence results and their utility for infectious disease surveillance	5
Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages	5
The challenges of data in future pandemics	5
Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys	5
Spatially targeted digital chest radiography to reduce tuberculosis in high-burden settings: A study of adaptive decision making	5
Assessing the efficacy of interventions to control indoor SARS-Cov-2 transmission: An agent-based modeling approach	5
Modelling the early phase of the Belgian COVID-19 epidemic using a stochastic compartmental model and studying its implied future trajectories	5
Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology	5

Modeling the population effects of escape mutations in SARS-CoV-2 to guide vaccination strategies	5
Optimal capacity sharing for global genomic surveillance	5
flepiMoP: The evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic	5
Challenges of integrating economics into epidemiological analysis of and policy responses to emerging infectious diseases	5
Lessons for preparedness and reasons for concern from the early COVID-19 epidemic in Iran	5
On the contact tracing for COVID-19: A simulation study	4
Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates	4
Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern	4
The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave	4
The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy	4
Insight into Delta variant dominated second wave of COVID-19 in Nepal	4
The African swine fever modelling challenge: Objectives, model description and synthetic data generation	4
Optimizing age specific strategies of vaccination for prevention of cytomegalovirus infection in the US using agent-based simulation	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
Modelling the dynamics of infection, waning of immunity and re-infection with the Omicron variant of SARS-CoV-2 in Aotearoa New Zealand	4
Geospatial clustering and modelling provide policy guidance to distribute funding for active TB case finding in Ethiopia	4
Complementary roles of wild boar and red deer to animal tuberculosis maintenance in multi-host communities	4
Estimation of R(t) based on illness onset data: An analysis of 1907–1908 smallpox epidemic in Tokyo	4
Association between pertussis vaccination coverage and other sociodemographic factors and pertussis incidence using surveillance data	4
Chimeric Forecasting: An experiment to leverage human judgment to improve forecasts of infectious disease using simulated surveillance data	4
Impact of intensified control on visceral leishmaniasis in a highly-endemic district of Bihar, India: an interrupted time series analysis	4
Precautionary breaks: Planned, limited duration circuit breaks to control the prevalence of SARS-CoV2 and the burden of COVID-19 disease	4
Publisher's note	4
Hospital population density and risk of respiratory infection: Is close contact density dependent?	4
Optimal allocation of PCR tests to minimise disease transmission through contact tracing and quarantine	4