Epidemics

Article	Citations
Modeling the population-level impact of treatment on COVID-19 disease and SARS-CoV-2 transmission	180
Accounting for historical injustices in mathematical models of infectious disease transmission: An analytic overview	92
Asymptomatic but infectious – The silent driver of pathogen transmission. A pragmatic review	67
Data pipelines in a public health emergency: The human in the machine	64
Seasonality as a driver of pH1N12009 influenza vaccination campaign impact	40
Modelling the COVID-19 pandemic: Focusing on the case of Greece	38
Collaborative forecasting of influenza-like illness in Italy: The Influcast experience	35
Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies	34
A prospective real-time transfer learning approach to estimate influenza hospitalizations with limited data	34
Contribution and quality of mathematical modeling evidence in World Health Organization guidelines: A systematic review	28
Age-time-specific transmission of hand-foot-and-mouth disease enterovirus serotypes in Vietnam: A catalytic model with maternal immunity	28
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
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	21
The impact of household size on measles transmission: A long-term perspective	21
A phenomenological approach to predicting tuberculosis cases with an assessment of measurement errors	21
The triple epidemics of arboviruses in Feira de Santana, Brazilian Northeast: Epidemiological characteristics and diffusion patterns	21
Mumps epidemic dynamics in the United States before vaccination (1923–1932)	20
Education data needs and challenges for building back from COVID-19	20
Mathematical modeling of COVID-19 in British Columbia: An age-structured model with time-dependent contact rates	20
Ensemble2: Scen	20
Epidemiological characteristics and transmissibility of HPV infection: A long-term retrospective study in Hokkien Golden Triangle, China, 2013–2021	20
Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19	20
Modelling: Understanding pandemics and how to control them	20

Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter	20
Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling	19
Estimating the impact of test–trace–isolate–quarantine systems on SARS-CoV-2 transmission in Australia	19
Modelling SARS-CoV-2 transmission in a UK university setting	19
A model for reconstructing trends and distribution in age at first sex from multiple household surveys with reporting biases	19
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
First wave of SARS-CoV-2 in Santiago Chile: Seroprevalence, asymptomatic infection and infection fatality rate	18
Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study	18
A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities	18
Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak	18
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
Ceasing sampling at wastewater treatment plants where viral dynamics are most predictable	17
Coordinated support for local action: Modeling strategies to facilitate behavior adoption in urban-poor communities of Liberia for sustained COVID-19 suppression	17
Optimizing spatial distribution of wastewater-based epidemiology to advance health equity	16
Estimating COVID-19 cases and deaths prevented by non-pharmaceutical interventions, and the impact of individual actions: A retrospective model-based analysis	16
Modelling the dynamics of SARS-CoV-2 during the first 14 days of infection	16
Variation in pneumococcal invasiveness metrics is driven by serotype carriage duration and initial risk of disease	16
Complex model calibration through emulation, a worked example for a stochastic epidemic model	15
Dynamic network strategies for SARS-CoV-2 control on a cruise ship	15
Retrospective modelling of the disease and mortality burden of the 1918–1920 influenza pandemic in Zurich, Switzerland	14
Public health impact of the U.S. Scenario Modeling Hub	14
A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data	13
Preface of the African swine fever modelling challenge special issue	13
Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer	13
Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks	13
Social contact patterns among employees in 3 U.S. companies during early phases of the COVID-19 pandemic, April to June 2020	13
Machine learning approaches for real-time ZIP code and county-level estimation of state-wide infectious disease hospitalizations using local health system data	12
Agent-based modeling of the COVID-19 pandemic in Florida	12
Considering waning immunity to better explain dengue dynamics	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
Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example	12
SARS-CoV-2 transmission patterns in educational settings during the Alpha wave in Reggio-Emilia, Italy	12
The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs)	11
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
Effective strategies to promote HIV self-testing for men who have sex with men: Evidence from a mathematical model	11
Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva	11
Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland	11
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey	11
A country-specific model of COVID-19 vaccination coverage needed for herd immunity in adult only or population wide vaccination programme	11
Bayesian monitoring of COVID-19 in Sweden	11
Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening	11
Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network	11
Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design	10
Lives saved by public health restrictions over the Victorian COVID-19 Delta variant epidemic wave, Aug-Nov 2021	10
In the shadow of privacy: Overlooked ethical concerns in COVID-19 digital epidemiology	10
Using video-analysis technology to estimate social mixing and simulate influenza transmission at a mass gathering	10
Reconstructing the first COVID-19 pandemic wave with minimal data in England	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
Challenges in evaluating risks and policy options around endemic establishment or elimination of novel pathogens	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
Coughs, colds and “freshers’ flu” survey in the University of Cambridge, 2007–2008	10
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
A new logistic growth model applied to COVID-19 fatality data	9
Malaria temporal dynamic clustering for surveillance and intervention planning	9
The confounding effect of multi-type human papillomavirus infections on type-specific natural history parameter identification	9
Globally local: Hyper-local modeling for accurate forecast of COVID-19	8
Challenges for modelling interventions for future pandemics	8
Inferring transmission routes for foot-and-mouth disease virus within a cattle herd using approximate Bayesian computation	8
Modeling the impact of different PrEP targeting strategies combined with a clinic-based HIV-1 nucleic acid testing intervention in Kenya	8
Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries	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
Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India	8
Rapid transmission of coronavirus disease 2019 within a religious sect in South Korea: A mathematical modeling study	8
A combination of probabilistic and mechanistic approaches for predicting the spread of African swine fever on Merry Island	8
Nationally representative social contact patterns among U.S. adults, August 2020-April 2021	8
Estimation of the probability of epidemic fade-out from multiple outbreak data	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
An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study	7
Determinants of RSV epidemiology following suppression through pandemic contact restrictions	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
Modelling how face masks and symptoms-based quarantine synergistically and cost-effectively reduce SARS-CoV-2 transmission in Bangladesh	7
A novel method to jointly estimate transmission rate and decay rate parameters in environmental transmission models	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
Enhancing seasonal influenza projections: A mechanistic metapopulation model for long-term scenario planning	7
Testing a simple and frugal model of health protective behaviour in epidemic times	7
Trypanosoma cruzi infection in dogs along the US-Mexico border: R changes with vector species composition	7
Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States	7
COVSIM: A stochastic agent-based COVID-19 SIMulation model for North Carolina	7
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland	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
Small area population denominators for improved disease surveillance and response	7
Inference of epidemic dynamics in the COVID-19 era and beyond	6
Contents	6
Recalibrating the notion of modelling for policymaking during pandemics	6
Timeliness of reporting of SARS-CoV-2 seroprevalence results and their utility for infectious disease surveillance	6
Gaps in mobility data and implications for modelling epidemic spread: A scoping review and simulation study	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
Impact of vaccine effectiveness and coverage on preventing large mumps outbreaks on college campuses: Implications for vaccination strategy	6
Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages	6
Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections	6
Acquisition and clearance dynamics of Campylobacter spp. in children in low- and middle-income countries	6
Small area population denominators for improved disease surveillance and response	6
Simulated effects of increasing salmonid production on sea lice populations in Norway	6
Association between meteorological factors and the epidemics of influenza (sub)types in a subtropical basin of Southwest China	6
Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility	6
Modeling the population effects of escape mutations in SARS-CoV-2 to guide vaccination strategies	5
Lessons for preparedness and reasons for concern from the early COVID-19 epidemic in Iran	5
Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys	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
Spatially targeted digital chest radiography to reduce tuberculosis in high-burden settings: A study of adaptive decision making	5
Chimeric Forecasting: An experiment to leverage human judgment to improve forecasts of infectious disease using simulated surveillance data	5
Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021	5
Assessing the efficacy of interventions to control indoor SARS-Cov-2 transmission: An agent-based modeling approach	5
Symptom-based vs asymptomatic testing for controlling SARS-CoV-2 transmission in low- and middle-income countries: A modelling analysis	5
Accounting for the geometry of the respiratory tract in viral infections	5
Data needs for better surveillance and response to infectious disease threats	5
Challenges of integrating economics into epidemiological analysis of and policy responses to emerging infectious diseases	5
Nowcasting and forecasting the 2022 U.S. mpox outbreak: Support for public health decision making and lessons learned	5
Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study	5
When do we need multiple infectious disease models? Agreement between projection rank and magnitude in a multi-model setting	5
The challenges of data in future pandemics	5
On the contact tracing for COVID-19: A simulation study	5
Data needs for integrated economic-epidemiological models of pandemic mitigation policies	5
Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis	5

Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern	4
Flusion: Integrating multiple data sources for accurate influenza predictions	4
Preface: Challenges for future pandemics	4
Hospital population density and risk of respiratory infection: Is close contact density dependent?	4
Optimizing age specific strategies of vaccination for prevention of cytomegalovirus infection in the US using agent-based simulation	4
Complementary roles of wild boar and red deer to animal tuberculosis maintenance in multi-host communities	4
Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates	4
Impact of intensified control on visceral leishmaniasis in a highly-endemic district of Bihar, India: an interrupted time series analysis	4
Optimal allocation of PCR tests to minimise disease transmission through contact tracing and quarantine	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
Association between pertussis vaccination coverage and other sociodemographic factors and pertussis incidence using surveillance data	4
Publisher's note	4
The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave	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 US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy	4
How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics	4
Insight into Delta variant dominated second wave of COVID-19 in Nepal	4
Estimation of R(t) based on illness onset data: An analysis of 1907–1908 smallpox epidemic in Tokyo	4
Precautionary breaks: Planned, limited duration circuit breaks to control the prevalence of SARS-CoV2 and the burden of COVID-19 disease	4
The African swine fever modelling challenge: Objectives, model description and synthetic data generation	4
Geospatial clustering and modelling provide policy guidance to distribute funding for active TB case finding in Ethiopia	4