Epidemics

Article	Citations
Filtering and improved Uncertainty Quantification in the dynamic estimation of effective reproduction numbers	178
Modeling the population-level impact of treatment on COVID-19 disease and SARS-CoV-2 transmission	83
Seasonality as a driver of pH1N12009 influenza vaccination campaign impact	65
Publisher's note	59
Preface of the African swine fever modelling challenge special issue	56
Contact patterns and HPV-genotype interactions yield heterogeneous HPV-vaccine impacts depending on sexual behaviors: An individual-based model	51
Synchronized spread of COVID-19 in the cities of Bahia, Brazil	47
Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern	37
Modelling lymphatic filariasis elimination in American Samoa: GEOFIL predicts need for new targets and six rounds of mass drug administration	33
RAMPVIS: Answering the challenges of building visualisation capabilities for large-scale emergency responses	31
Response to COVID-19 during the Tokyo Olympic Games: Did we properly assess the risk?	29
Data pipelines in a public health emergency: The human in the machine	28
Modelling the COVID-19 pandemic: Focusing on the case of Greece	26
Precautionary breaks: Planned, limited duration circuit breaks to control the prevalence of SARS-CoV2 and the burden of COVID-19 disease	24
Social mixing patterns relevant to infectious diseases spread by close contact in urban Blantyre, Malawi	23
Bayesian sequential data assimilation for COVID-19 forecasting	23
Association between pertussis vaccination coverage and other sociodemographic factors and pertussis incidence using surveillance data	21
Mathematical modelling Treponema infection in free-ranging Olive baboons (Papio anubis) in Tanzania	21
Complementary roles of wild boar and red deer to animal tuberculosis maintenance in multi-host communities	20
A novel method to jointly estimate transmission rate and decay rate parameters in environmental transmission models	20
COVSIM: A stochastic agent-based COVID-19 SIMulation model for North Carolina	19
Limited impact of contact tracing in a University setting for COVID-19 due to asymptomatic transmission and social distancing	19
Accounting for historical injustices in mathematical models of infectious disease transmission: An analytic overview	19
The impact of inaccurate assumptions about antibody test accuracy on the parametrisation and results of infectious disease models of epidemics	19
Mathematical methods for scaling from within-host to population-scale in infectious disease systems	18

The aquaculture disease network model (AquaNet-Mod): A simulation model to evaluate disease spread and controls for the salmonid industry in England and Wales	18
Modelling plausible scenarios for the Omicron SARS-CoV-2 variant from early-stage surveillance	18
Enhancing seasonal influenza projections: A mechanistic metapopulation model for long-term scenario planning	18
Predicting the impact of COVID-19 non-pharmaceutical intervention on short- and medium-term dynamics of enterovirus D68 in the US	18
Optimizing age specific strategies of vaccination for prevention of cytomegalovirus infection in the US using agent-based simulation	18
Effectiveness of interventions to reduce COVID-19 transmission in schools	18
Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks	17
Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach	16
Forecasting SARS-CoV-2 epidemic dynamic in Poland with the pDyn agent-based model	16
A prospective real-time transfer learning approach to estimate influenza hospitalizations with limited data	15
The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy	15
Collaborative forecasting of influenza-like illness in Italy: The Influcast experience	15
Social contact patterns following the COVID-19 pandemic: a snapshot of post-pandemic behaviour from the CoMix study	15
Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies	15
Asymptomatic but infectious – The silent driver of pathogen transmission. A pragmatic review	15
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland	15
Using an agent-based sexual-network model to analyze the impact of mitigation efforts for controlling chlamydia	14
Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar	14
The early phase of the COVID-19 epidemic in Lombardy, Italy	14
Optimal allocation of PCR tests to minimise disease transmission through contact tracing and quarantine	14
Estimating pathogen spread using structured coalescent and birth–death models: A quantitative comparison	13
How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics	13
Hospital population density and risk of respiratory infection: Is close contact density dependent?	12
Projecting Omicron scenarios in the US while tracking population-level immunity	12
A mixed methods analysis of participation in a social contact survey	12
Preface: COVID-19 Scenario Modeling Hubs	12
Considering waning immunity to better explain dengue dynamics	12
Influence of setting-dependent contacts and protective behaviours on asymptomatic SARS-CoV-2 infection amongst members of a UK university	12
Testing a simple and frugal model of health protective behaviour in epidemic times	11
Flusion: Integrating multiple data sources for accurate influenza predictions	11
An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study	11
Assessing population-level target product profiles of universal human influenza A vaccines	11
Epidemiological characteristics and dynamic transmissions of COVID-19 pandemics in Chinese mainland: A trajectory clustering perspective analysis	11
Small area population denominators for improved disease surveillance and response	11
Estimation of the incubation period of COVID-19 using viral load data	11
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	11
Modelling how face masks and symptoms-based quarantine synergistically and cost-effectively reduce SARS-CoV-2 transmission in Bangladesh	11
A method to estimate the serial interval distribution under partially-sampled data	11
Recalibrating the notion of modelling for policymaking during pandemics	10
How much leeway is there to relax COVID-19 control measures?	10
Preface: Challenges for future pandemics	10
Estimation of R(t) based on illness onset data: An analysis of 1907–1908 smallpox epidemic in Tokyo	10
Bayesian validation framework for dynamic epidemic models	10
Risk heterogeneity in compartmental HIV transmission models of ART as prevention in Sub-Saharan Africa: A scoping review	10
Ecology and public health burden of Keystone virus in Florida	10
Assessing the nationwide impact of COVID-19 mitigation policies on the transmission rate of SARS-CoV-2 in Brazil	10
Optimal environmental testing frequency for outbreak surveillance	9
Density forecasting of conjunctivitis burden using high-dimensional environmental time series data	9
Realtime case study simulations of transmission of Pancreas Disease (PD) in Norwegian salmonid farming for disease control purposes	9
Modeling nation-wide U.S. swine movement networks at the resolution of the individual premises	9

Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example	9
Trypanosoma cruzi infection in dogs along the US-Mexico border: R changes with vector species composition	9
Insight into Delta variant dominated second wave of COVID-19 in Nepal	9
Effective strategies to promote HIV self-testing for men who have sex with men: Evidence from a mathematical model	8
Seroprevalence and incidence of Puumala orthohantavirus in its bank vole (Myodes glareolus) host population in northeastern France: Between-site and seasonal variability	8
Age-time-specific transmission of hand-foot-and-mouth disease enterovirus serotypes in Vietnam: A catalytic model with maternal immunity	8
The triple epidemics of arboviruses in Feira de Santana, Brazilian Northeast: Epidemiological characteristics and diffusion patterns	8
Policy-driven mathematical modeling for COVID-19 pandemic response in the Philippines	8
Small area population denominators for improved disease surveillance and response	8
SARS-CoV-2 transmission patterns in educational settings during the Alpha wave in Reggio-Emilia, Italy	8
Simulated effects of increasing salmonid production on sea lice populations in Norway	8
Contribution and quality of mathematical modeling evidence in World Health Organization guidelines: A systematic review	8
Challenges in modeling the emergence of novel pathogens	8
Agent-based modeling of the COVID-19 pandemic in Florida	8
Network models and the interpretation of prolonged infection plateaus in the COVID19 pandemic	8
Mathematical modelling of respiratory syncytial virus (RSV) in low- and middle-income countries: A systematic review	8
A quantitative assessment of epidemiological parameters required to investigate COVID-19 burden	8
Inference for a spatio-temporal model with partial spatial data: African horse sickness virus in Morocco	7
Inferring ASF transmission in domestic pigs and wild boars using a paired model iterative approach	7
A country-specific model of COVID-19 vaccination coverage needed for herd immunity in adult only or population wide vaccination programme	7
Quantifying the impact of prevalence-dependent adaptive behavior on COVID-19 transmission: A modeling case study in Maryland	7
SIR… or MADAM? The impact of privilege on careers in epidemic modelling	7
Lockdowns exert selection pressure on overdispersion of SARS-CoV-2 variants	7
Acquisition and clearance dynamics of Campylobacter spp. in children in low- and middle-income countries	7
Ensemble2: Scen	7
Estimating the impact of test–trace–isolate–quarantine systems on SARS-CoV-2 transmission in Australia	7
Infectious disease modelling for SARS-CoV-2 in Africa to guide policy: A systematic review	7
Quantifying the impact of interventions against Plasmodium vivax: A model for country-specific use	7
The COVID-19 vaccination campaign in Switzerland and its impact on disease spread	7
Estimating vaccine efficacy during open-label follow-up of COVID-19 vaccine trials based on population-level surveillance data	7
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey	6
Assessing K-12 school reopenings under different COVID-19 Spread scenarios – United States, school year 2020/21: A retrospective modeling study	6
Epidemiological characteristics and transmissibility of HPV infection: A long-term retrospective study in Hokkien Golden Triangle, China, 2013–2021	6
Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva	6
Mumps epidemic dynamics in the United States before vaccination (1923–1932)	6
The impact of household size on measles transmission: A long-term perspective	6
Combining seroprevalence and capture-mark-recapture data to estimate the force of infection of brucellosis in a managed population of Alpine ibex	6
A multilayer network model of Covid-19: Implications in public health policy in Costa Rica	6
Assessing the impact of autologous virus neutralizing antibodies on viral rebound time in postnatally SHIV-infected ART-treated infant rhesus macaques	6
Improving the contribution of mathematical modelling evidence to guidelines and policy: Experiences from tuberculosis	6
Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data	6
Epidemic SI COVID-19 modeling in LMICs: Accompanying commentary	6
A phenomenological approach to predicting tuberculosis cases with an assessment of measurement errors	6
Bayesian monitoring of COVID-19 in Sweden	5
Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number	5
Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland	5
Education data needs and challenges for building back from COVID-19	5
Estimating the generation time for influenza transmission using household data in the United States	5
The effective reproductive number: Modeling and prediction with application to the multi-wave Covid-19 pandemic	5
Mathematical modeling of COVID-19 in British Columbia: An age-structured model with time-dependent contact rates	5
The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs)	5
Modelling: Understanding pandemics and how to control them	5
Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network	5
Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19	5
Estimation of waning vaccine effectiveness from population-level surveillance data in multi-variant epidemics	5
Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter	5
Climate change and communicable diseases in the Gulf Cooperation Council (GCC) countries	5
Competition between RSV and influenza: Limits of modelling inference from surveillance data	5
Inference of epidemic dynamics in the COVID-19 era and beyond	5
Stochastic modelling of African swine fever in wild boar and domestic pigs: Epidemic forecasting and comparison of disease management strategies	5
Using next generation matrices to estimate the proportion of infections that are not detected in an outbreak	5
Challenges in estimation, uncertainty quantification and elicitation for pandemic modelling	5
Sustaining effective COVID-19 control in Malaysia through large-scale vaccination	5
Rational evaluation of various epidemic models based on the COVID-19 data of China	5
Zika virus outbreak in Brazil under current and future climate	5
Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening	5
Quantifying transmission fitness costs of multi-drug resistant tuberculosis	4
Gecko: A time-series model for COVID-19 hospital admission forecasting	4
The impact of mobility network properties on predicted epidemic dynamics in Dhaka and Bangkok	4
The performance of phenomenological models in providing near-term Canadian case projections in the midst of the COVID-19 pandemic: March – April, 2020	4
Contents	4
Modeling waning and boosting of COVID-19 in Canada with vaccination	4
Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design	4
Large-scale measurement of aggregate human colocation patterns for epidemiological modeling	4
Corrigendum to “The impact of inaccurate assumptions about antibody test accuracy on the parametrisation and results of infectious disease models of epidemics” [Epidemics 46 (2024) 100741]	4
Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility	4
Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling	4
Modelling SARS-CoV-2 transmission in a UK university setting	4
Challenges in modelling the dynamics of infectious diseases at the wildlife–human interface	4
Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data	4

Coughs, colds and “freshers’ flu” survey in the University of Cambridge, 2007–2008	4
Challenges in evaluating risks and policy options around endemic establishment or elimination of novel pathogens	4
Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology	4
Impact of vaccine effectiveness and coverage on preventing large mumps outbreaks on college campuses: Implications for vaccination strategy	4
A model for reconstructing trends and distribution in age at first sex from multiple household surveys with reporting biases	4