Epidemics

Article	Citations
Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies	184
A prospective real-time transfer learning approach to estimate influenza hospitalizations with limited data	100
Collaborative forecasting of influenza-like illness in Italy: The Influcast experience	69
Data pipelines in a public health emergency: The human in the machine	41
Seasonality as a driver of pH1N12009 influenza vaccination campaign impact	40
Modeling the population-level impact of treatment on COVID-19 disease and SARS-CoV-2 transmission	40
Accounting for historical injustices in mathematical models of infectious disease transmission: An analytic overview	39
Asymptomatic but infectious – The silent driver of pathogen transmission. A pragmatic review	38
Modelling the COVID-19 pandemic: Focusing on the case of Greece	30
Realtime case study simulations of transmission of Pancreas Disease (PD) in Norwegian salmonid farming for disease control purposes	29
Age-time-specific transmission of hand-foot-and-mouth disease enterovirus serotypes in Vietnam: A catalytic model with maternal immunity	27
Contribution and quality of mathematical modeling evidence in World Health Organization guidelines: A systematic review	27
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	24
Mumps epidemic dynamics in the United States before vaccination (1923–1932)	24
Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter	23
Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19	22
A phenomenological approach to predicting tuberculosis cases with an assessment of measurement errors	22
Education data needs and challenges for building back from COVID-19	22
Modelling: Understanding pandemics and how to control them	21
Inference for a spatio-temporal model with partial spatial data: African horse sickness virus in Morocco	21
Ensemble	21
Mathematical modeling of COVID-19 in British Columbia: An age-structured model with time-dependent contact rates	21
Estimating the impact of test–trace–isolate–quarantine systems on SARS-CoV-2 transmission in Australia	21
The triple epidemics of arboviruses in Feira de Santana, Brazilian Northeast: Epidemiological characteristics and diffusion patterns	20

Epidemiological characteristics and transmissibility of HPV infection: A long-term retrospective study in Hokkien Golden Triangle, China, 2013–2021	20
The impact of household size on measles transmission: A long-term perspective	20
Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data	20
Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling	19
Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study	19
A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities	18
A model for reconstructing trends and distribution in age at first sex from multiple household surveys with reporting biases	18
Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak	18
Ceasing sampling at wastewater treatment plants where viral dynamics are most predictable	18
Understanding MRSA clonal competition within a UK hospital; the possible importance of density dependence	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
A Cluster-Aggregate-Pool (CAP) ensemble algorithm for improved forecast performance of influenza-like illness	17
Optimizing spatial distribution of wastewater-based epidemiology to advance health equity	17
Modelling the dynamics of SARS-CoV-2 during the first 14 days of infection	17
Coordinated support for local action: Modeling strategies to facilitate behavior adoption in urban-poor communities of Liberia for sustained COVID-19 suppression	16
First wave of SARS-CoV-2 in Santiago Chile: Seroprevalence, asymptomatic infection and infection fatality rate	16
Estimating COVID-19 cases and deaths prevented by non-pharmaceutical interventions, and the impact of individual actions: A retrospective model-based analysis	16
Public health impact of the U.S. Scenario Modeling Hub	15
Sequential Monte Carlo Squared for online inference in stochastic epidemic models	15
Learning associations of COVID-19 hospitalizations with wastewater viral signals by Markov modulated models	15
Projecting the population-level impact of norovirus vaccines	15
Dynamic network strategies for SARS-CoV-2 control on a cruise ship	14
Complex model calibration through emulation, a worked example for a stochastic epidemic model	14
Variation in pneumococcal invasiveness metrics is driven by serotype carriage duration and initial risk of disease	14
Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer	14
Retrospective modelling of the disease and mortality burden of the 1918–1920 influenza pandemic in Zurich, Switzerland	13
RAMPVIS: Answering the challenges of building visualisation capabilities for large-scale emergency responses	13
Investigating the impact of edge weight selection on the pig trade network topology	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
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
Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening	12
Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number	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
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey	12
Agent-based modeling of the COVID-19 pandemic in Florida	12
Verifying infectious disease scenario planning for geographically diverse populations	12
Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example	12
Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland	12
Effective strategies to promote HIV self-testing for men who have sex with men: Evidence from a mathematical model	12
SARS-CoV-2 transmission patterns in educational settings during the Alpha wave in Reggio-Emilia, Italy	12
Bayesian monitoring of COVID-19 in Sweden	11
Does spatial information improve forecasting of influenza-like illness?	11
The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs)	11
Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva	11
A quantitative assessment of epidemiological parameters required to investigate COVID-19 burden	11
Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network	11
A country-specific model of COVID-19 vaccination coverage needed for herd immunity in adult only or population wide vaccination programme	11

Explaining the stable coexistence of drug-resistant and -susceptible pathogens: the resistance acquisition purifying selection model	11
In the shadow of privacy: Overlooked ethical concerns in COVID-19 digital epidemiology	10
Assessing the risk of cascading COVID-19 outbreaks from prison-to-prison transfers	10
Reconstructing the first COVID-19 pandemic wave with minimal data in England	10
Challenges in evaluating risks and policy options around endemic establishment or elimination of novel pathogens	10
Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design	10
Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data	10
Coughs, colds and “freshers’ flu” survey in the University of Cambridge, 2007–2008	10
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	9
Malaria temporal dynamic clustering for surveillance and intervention planning	9
Nationally representative social contact patterns among U.S. adults, August 2020-April 2021	9
COVID-19 in Scottish care homes: A metapopulation model of spread among residents and staff	9
A case for ongoing structural support to maximise infectious disease modelling efficiency for future public health emergencies: A modelling perspective	9
The impact of reactive case detection on malaria transmission in Zanzibar in the presence of human mobility	9
Challenges on the interaction of models and policy for pandemic control	9
A new logistic growth model applied to COVID-19 fatality data	9
The impact of inaccurate assumptions about antibody test accuracy on the parametrisation and results of infectious disease models of epidemics	8
Dose response for Salmonella Typhimurium and Enteritidis and other nontyphoid enteric salmonellae	8
Estimation of the probability of epidemic fade-out from multiple outbreak data	8
Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States	8
Inferring transmission routes for foot-and-mouth disease virus within a cattle herd using approximate Bayesian computation	8
Forecasting SARS-CoV-2 epidemic dynamic in Poland with the pDyn agent-based model	8
Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach	8
Challenges for modelling interventions for future pandemics	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
Infectious disease dynamics and restrictions on social gathering size	8
Rapid transmission of coronavirus disease 2019 within a religious sect in South Korea: A mathematical modeling study	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
Globally local: Hyper-local modeling for accurate forecast of COVID-19	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
A combination of probabilistic and mechanistic approaches for predicting the spread of African swine fever on Merry Island	8
Determinants of RSV epidemiology following suppression through pandemic contact restrictions	8
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland	7
Robust phylodynamic inference and model specification for HIV transmission dynamics	7
Small area population denominators for improved disease surveillance and response	7
Challenges in modeling the emergence of novel pathogens	7
Density forecasting of conjunctivitis burden using high-dimensional environmental time series data	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
Modelling how face masks and symptoms-based quarantine synergistically and cost-effectively reduce SARS-CoV-2 transmission in Bangladesh	7
Recalibrating the notion of modelling for policymaking during pandemics	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
Testing a simple and frugal model of health protective behaviour in epidemic times	7
An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study	7
Timeliness of reporting of SARS-CoV-2 seroprevalence results and their utility for infectious disease surveillance	6
Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study	6
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
Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages	6
Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology	6
Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021	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
Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections	6
Gaps in mobility data and implications for modelling epidemic spread: A scoping review and simulation study	6
Impact of vaccine effectiveness and coverage on preventing large mumps outbreaks on college campuses: Implications for vaccination strategy	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
SIR… or MADAM? The impact of privilege on careers in epidemic modelling	6
Acquisition and clearance dynamics of Campylobacter spp. in children in low- and middle-income countries	6
Contents	6
Optimal capacity sharing for global genomic surveillance	5
Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys	5
Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility	5
Data needs for better surveillance and response to infectious disease threats	5
Data needs for integrated economic-epidemiological models of pandemic mitigation policies	5
The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave	5
The challenges of data in future pandemics	5
Transmission dynamics of Norovirus GII and Enterovirus in Switzerland during the COVID-19 pandemic (2021–2022) as evidenced in wastewater	5
Symptom-based vs asymptomatic testing for controlling SARS-CoV-2 transmission in low- and middle-income countries: A modelling analysis	5
Association between meteorological factors and the epidemics of influenza (sub)types in a subtropical basin of Southwest China	5
Modelling the dynamics of infection, waning of immunity and re-infection with the Omicron variant of SARS-CoV-2 in Aotearoa New Zealand	5
On the contact tracing for COVID-19: A simulation study	5
The African swine fever modelling challenge: Objectives, model description and synthetic data generation	5
Spatially targeted digital chest radiography to reduce tuberculosis in high-burden settings: A study of adaptive decision making	5
When do we need multiple infectious disease models? Agreement between projection rank and magnitude in a multi-model setting	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
Nowcasting and forecasting the 2022 U.S. mpox outbreak: Support for public health decision making and lessons learned	5
Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis	5
Assessing the efficacy of interventions to control indoor SARS-Cov-2 transmission: An agent-based modeling approach	5