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Effectiveness of interventions to reduce COVID-19 transmission in schools Epidemics (IF 3.8) Pub Date : 2024-03-12 Remy Pasco, Spencer J. Fox, Michael Lachmann, Lauren Ancel Meyers
School reopenings in 2021 and 2022 coincided with the rapid emergence of new SARS-CoV-2 variants in the United States. In-school mitigation efforts varied, depending on local COVID-19 mandates and resources. Using a stochastic age-stratified agent-based model of SARS-CoV-2 transmission, we estimate the impacts of multiple in-school strategies on both infection rates and absenteeism, relative to a baseline
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Nowcasting and forecasting the 2022 U.S. mpox outbreak: Support for public health decision making and lessons learned Epidemics (IF 3.8) Pub Date : 2024-03-02 Kelly Charniga, Zachary J. Madewell, Nina B. Masters, Jason Asher, Yoshinori Nakazawa, Ian H. Spicknall
In June of 2022, the U.S. Centers for Disease Control and Prevention (CDC) Mpox Response wanted timely answers to important epidemiological questions which can now be answered more effectively through infectious disease modeling. Infectious disease models have shown to be valuable tools for decision making during outbreaks; however, model complexity often makes communicating the results and limitations
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Projecting the future impact of emerging SARS-CoV-2 variants under uncertainty: Modeling the initial Omicron outbreak Epidemics (IF 3.8) Pub Date : 2024-03-02 Sean Moore, Sean Cavany, T. Alex Perkins, Guido Felipe Camargo España
Over the past several years, the emergence of novel SARS-CoV-2 variants has led to multiple waves of increased COVID-19 incidence. When the Omicron variant emerged, there was considerable concern about its potential impact in the winter of 2021–2022 due to its increased fitness. However, there was also considerable uncertainty regarding its likely impact due to questions about its relative transmissibility
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flepiMoP: the evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic Epidemics (IF 3.8) Pub Date : 2024-03-02 Joseph C Lemaitre, Sara L Loo, Joshua Kaminsky, Elizabeth C Lee, Clifton McKee, Claire Smith, Sung-mok Jung, Koji Sato, Erica Carcelen, Alison Hill, Justin Lessler, Shaun Truelove
The COVID-19 pandemic led to an unprecedented demand for projections of disease burden and healthcare utilization under scenarios ranging from unmitigated spread to strict social distancing policies. In response, members of the Johns Hopkins Infectious Disease Dynamics Group developed (formerly called the ), a comprehensive open-source software pipeline designed for creating and simulating compartmental
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Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology Epidemics (IF 3.8) Pub Date : 2024-03-01 Michiel van Boven, Jantien A. Backer, Irene Veldhuijzen, Justin Gomme, Rob van Binnendijk, Patricia Kaaijk
Mumps virus is a highly transmissible pathogen that is effectively controlled in countries with high vaccination coverage. Nevertheless, outbreaks have occurred worldwide over the past decades in vaccinated populations. Here we analyse an outbreak of mumps virus genotype G among college students in the Netherlands over the period 2009–2012 using paired serological data. To identify infections in the
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Chimeric Forecasting: An experiment to leverage human judgment to improve forecasts of infectious disease using simulated surveillance data Epidemics (IF 3.8) Pub Date : 2024-02-28 Thomas McAndrew, Graham C. Gibson, David Braun, Abhishek Srivastava, Kate Brown
Forecasts of infectious agents provide public health officials advanced warning about the intensity and timing of the spread of disease. Past work has found that accuracy and calibration of forecasts is weakest when attempting to predict an epidemic peak. Forecasts from a mechanistic model would be improved if there existed accurate information about the timing and intensity of an epidemic. We presented
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Age-time-specific transmission of hand-foot-and-mouth disease enterovirus serotypes in Vietnam: A catalytic model with maternal immunity Epidemics (IF 3.8) Pub Date : 2024-02-27 Yining Chen, Lam Anh Nguyet, Le Nguyen Thanh Nhan, Phan Tu Qui, Le Nguyen Truc Nhu, Nguyen Thi Thu Hong, Nguyen Thi Han Ny, Nguyen To Anh, Le Kim Thanh, Huynh Thi Phuong, Nguyen Ha Thao Vy, Nguyen Thi Le Thanh, Truong Huu Khanh, Nguyen Thanh Hung, Do Chau Viet, Nguyen Tran Nam, Nguyen Van Vinh Chau, H. Rogier van Doorn, Le Van Tan, Hannah Clapham
Hand, foot and mouth disease (HFMD) is highly prevalent in the Asia Pacific region, particularly in Vietnam. To develop effective interventions and efficient vaccination programs, we inferred the age-time-specific transmission patterns of HFMD serotypes enterovirus A71 (EV-A71), coxsackievirus A6 (CV-A6), coxsackievirus A10 (CV-A10), coxsackievirus A16 (CV-A16) in Ho Chi Minh City, Vietnam from a case
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COVSIM: A stochastic agent-based COVID-19 SIMulation model for North Carolina Epidemics (IF 3.8) Pub Date : 2024-02-23 Erik T. Rosenstrom, Julie S. Ivy, Maria E. Mayorga, Julie L. Swann
We document the evolution and use of the stochastic agent-based COVID-19 simulation model (COVSIM) to study the impact of population behaviors and public health policy on disease spread within age, race/ethnicity, and urbanicity subpopulations in North Carolina. We detail the methodologies used to model the complexities of COVID-19, including multiple agent attributes (i.e., age, race/ethnicity, high-risk
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The COVID-19 vaccination campaign in Switzerland and its impact on disease spread Epidemics (IF 3.8) Pub Date : 2024-02-20 M. Bekker-Nielsen Dunbar, L. Held
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Optimal environmental testing frequency for outbreak surveillance Epidemics (IF 3.8) Pub Date : 2024-02-15 Jason W. Olejarz, Kirstin I. Oliveira Roster, Stephen M. Kissler, Marc Lipsitch, Yonatan H. Grad
Public health surveillance for pathogens presents an optimization problem: we require enough sampling to identify intervention-triggering shifts in pathogen epidemiology, such as new introductions or sudden increases in prevalence, but not so much that costs due to surveillance itself outweigh those from pathogen-associated illness. To determine this optimal sampling frequency, we developed a general
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Acquisition and clearance dynamics of Campylobacter spp. in children in low- and middle-income countries Epidemics (IF 3.8) Pub Date : 2024-02-10 Dehao Chen, Arie H. Havelaar, James A. Platts-Mills, Yang Yang
The prevalence of infection is generally high among children in low- and middle-income countries (LMIC), but the dynamics of its acquisition and clearance are understudied. We aim to quantify this process among children under two years old in eight LMIC using a statistical modeling approach, leveraging enzyme-immunoassay-based genus data and quantitative-PCRbased data from the MAL-ED study. We developed
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Projecting Omicron scenarios in the US while tracking population-level immunity Epidemics (IF 3.8) Pub Date : 2024-02-10 Anass Bouchnita, Kaiming Bi, Spencer J. Fox, Lauren Ancel Meyers
Throughout the COVID-19 pandemic, changes in policy, shifts in behavior, and the emergence of new SARS-CoV-2 variants spurred multiple waves of transmission. Accurate assessments of the changing risks were vital for ensuring adequate healthcare capacity, designing mitigation strategies, and communicating effectively with the public. Here, we introduce a model of COVID-19 transmission and vaccination
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Ensemble[formula omitted]: Scenarios ensembling for communication and performance analysis Epidemics (IF 3.8) Pub Date : 2024-02-08 Clara Bay, Guillaume St-Onge, Jessica T. Davis, Matteo Chinazzi, Emily Howerton, Justin Lessler, Michael C. Runge, Katriona Shea, Shaun Truelove, Cecile Viboud, Alessandro Vespignani
Throughout the COVID-19 pandemic, scenario modeling played a crucial role in shaping the decision-making process of public health policies. Unlike forecasts, scenario projections rely on specific assumptions about the future that consider different plausible that may or may not be realized and that depend on policy interventions, unpredictable changes in the epidemic outlook, etc. As a consequence
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Quantifying the impact of interventions against Plasmodium vivax: A model for country-specific use Epidemics (IF 3.8) Pub Date : 2024-02-05 C. Champagne, M. Gerhards, J.T. Lana, A. Le Menach, E. Pothin
In order to evaluate the impact of various intervention strategies on dynamics in low endemicity settings without significant seasonal pattern, we introduce a simple mathematical model that can be easily adapted to reported case numbers similar to that collected by surveillance systems in various countries. The model includes case management, vector control, mass drug administration and reactive case
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Estimating the population effectiveness of interventions against COVID-19 in France: A modelling study Epidemics (IF 3.8) Pub Date : 2024-02-02 Iris Ganser, David L. Buckeridge, Jane Heffernan, Mélanie Prague, Rodolphe Thiébaut
Non-pharmaceutical interventions (NPIs) and vaccines have been widely used to manage the COVID-19 pandemic. However, uncertainty persists regarding the effectiveness of these interventions due to data quality issues, methodological challenges, and differing contextual factors. Accurate estimation of their effects is crucial for future epidemic preparedness. To address this, we developed a population-based
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Reproducibility of COVID-era infectious disease models Epidemics (IF 3.8) Pub Date : 2024-01-23 Alec S. Henderson, Roslyn I. Hickson, Morgan Furlong, Emma S. McBryde, Michael T. Meehan
Infectious disease modelling has been prominent throughout the COVID-19 pandemic, helping to understand the virus’ transmission dynamics and inform response policies. Given their potential importance and translational impact, we evaluated the computational reproducibility of infectious disease modelling articles from the COVID era. We found that four out of 100 randomly sampled studies released between
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Differences between the true reproduction number and the apparent reproduction number of an epidemic time series Epidemics (IF 3.8) Pub Date : 2024-01-13 Oliver Eales, Steven Riley
The time-varying reproduction number measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and analysis of epidemics usually relies on time series data for other outcomes such as symptom onset. A common implicit assumption, when estimating from an epidemic
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The impact of inaccurate assumptions about antibody test accuracy on the parametrisation and results of infectious disease models of epidemics Epidemics (IF 3.8) Pub Date : 2024-01-09 Madhav Chaturvedi, Denise Köster, Nicole Rübsamen, Veronika K Jaeger, Antonia Zapf, André Karch
The parametrisation of infectious disease models is often done based on epidemiological studies that use diagnostic and serology tests to establish disease prevalence or seroprevalence in the population being modelled. During outbreaks of an emerging infectious disease, tests are often used, both for disease control and epidemiological studies, before studies evaluating their accuracy in the population
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Inferring transmission routes for foot-and-mouth disease virus within a cattle herd using approximate Bayesian computation Epidemics (IF 3.8) Pub Date : 2024-01-08 John Ellis, Emma Brown, Claire Colenutt, David Schley, Simon Gubbins
To control an outbreak of an infectious disease it is essential to understand the different routes of transmission and how they contribute to the overall spread of the pathogen. With this information, policy makers can choose the most efficient methods of detection and control during an outbreak. Here we assess the contributions of direct contact and environmental contamination to the transmission
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Epidemiological impact of a large number of false negative SARS-CoV-2 test results in South West England during September and October 2021 Epidemics (IF 3.8) Pub Date : 2024-01-06 L. Hounsome, D. Herr, R. Bryant, R. Smith, L. Loman, J. Harris, U. Youhan, E. Dzene, P. Hadjipantelis, H. Long, T. Laurence, S. Riley, F. Cumming
During September and October 2021, a substantial number of Polymerase Chain Reaction (PCR) tests in England processed at a single laboratory were incorrectly reported as negative. We estimate the number of false negative test results issued and investigate the epidemiological impact of this incident. We estimate the number of COVID-19 cases that would have been reported had the sensitivity of the laboratory
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The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy Epidemics (IF 3.8) Pub Date : 2023-12-29 Sara L. Loo, Emily Howerton, Lucie Contamin, Claire P. Smith, Rebecca K. Borchering, Luke C. Mullany, Samantha Bents, Erica Carcelen, Sung-mok Jung, Tiffany Bogich, Willem G. van Panhuis, Jessica Kerr, Jessi Espino, Katie Yan, Harry Hochheiser, Michael C. Runge, Katriona Shea, Justin Lessler, Cécile Viboud, Shaun Truelove
Between December 2020 and April 2023, the COVID-19 Scenario Modeling Hub (SMH) generated operational multi-month projections of COVID-19 burden in the US to guide pandemic planning and decision-making in the context of high uncertainty. This effort was born out of an attempt to coordinate, synthesize and effectively use the unprecedented amount of predictive modeling that emerged throughout the COVID-19
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Predicting the impact of COVID-19 non-pharmaceutical intervention on short- and medium-term dynamics of enterovirus D68 in the US Epidemics (IF 3.8) Pub Date : 2023-12-18 Sang Woo Park, Kevin Messacar, Daniel C. Douek, Alicen B. Spaulding, C. Jessica E. Metcalf, Bryan T. Grenfell
Recent outbreaks of enterovirus D68 (EV-D68) infections, and their causal linkage with acute flaccid myelitis (AFM), continue to pose a serious public health concern. During 2020 and 2021, the dynamics of EV-D68 and other pathogens have been significantly perturbed by non-pharmaceutical interventions against COVID-19; this perturbation presents a powerful natural experiment for exploring the dynamics
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A case for ongoing structural support to maximise infectious disease modelling efficiency for future public health emergencies: A modelling perspective Epidemics (IF 3.8) Pub Date : 2023-12-13 Epke A. Le Rutte, Andrew J. Shattock, Cheng Zhao, Soushieta Jagadesh, Miloš Balać, Sebastian A. Müller, Kai Nagel, Alexander L. Erath, Kay W. Axhausen, Thomas P. Van Boeckel, Melissa A. Penny
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Effectiveness of a COVID-19 contact tracing app in a simulation model with indirect and informal contact tracing Epidemics (IF 3.8) Pub Date : 2023-12-12 Ka Yin Leung, Esther Metting, Wolfgang Ebbers, Irene Veldhuijzen, Stijn P. Andeweg, Guus Luijben, Marijn de Bruin, Jacco Wallinga, Don Klinkenberg
During the COVID-19 pandemic, contact tracing was used to identify individuals who had been in contact with a confirmed case so that these contacted individuals could be tested and quarantined to prevent further spread of the SARS-CoV-2 virus. Many countries developed mobile apps to find these contacted individuals faster. We evaluate the epidemiological effectiveness of the Dutch app CoronaMelder
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A method to estimate the serial interval distribution under partially-sampled data Epidemics (IF 3.8) Pub Date : 2023-12-02 Kurnia Susvitasari, Paul Tupper, Jessica E. Stockdale, Caroline Colijn
The serial interval of an infectious disease is an important variable in epidemiology. It is defined as the period of time between the symptom onset times of the infector and infectee in a direct transmission pair. Under partially sampled data, purported infector–infectee pairs may actually be separated by one or more unsampled cases in between. Misunderstanding such pairs as direct transmissions will
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Seasonality as a driver of pH1N12009 influenza vaccination campaign impact Epidemics (IF 3.8) Pub Date : 2023-11-27 Kirsty J. Bolton, James M. McCaw, Mathew P. Dafilis, Jodie McVernon, Jane M. Heffernan
Although the most recent respiratory virus pandemic was triggered by a Coronavirus, sustained and elevated prevalence of highly pathogenic avian influenza viruses able to infect mammalian hosts highlight the continued threat of pandemics of influenza A virus (IAV) to global health. Retrospective analysis of pandemic outcomes, including comparative investigation of intervention efficacy in different
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Variation in pneumococcal invasiveness metrics is driven by serotype carriage duration and initial risk of disease Epidemics (IF 3.8) Pub Date : 2023-11-22 Benjamin J. Metcalf, Kristofer Wollein Waldetoft, Bernard W. Beall, Sam P. Brown
Streptococcus pneumoniae is an opportunistic pathogen that, while usually carried asymptomatically, can cause severe invasive diseases like meningitis and bacteremic pneumonia. A central goal in S. pneumoniae public health management is to identify which serotypes (immunologically distinct strains) pose the most risk of invasive disease. The most common invasiveness metrics use cross-sectional data
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The variations of SIkJalpha model for COVID-19 forecasting and scenario projections Epidemics (IF 3.8) Pub Date : 2023-11-15 Ajitesh Srivastava
We proposed the SIkJalpha model at the beginning of the COVID-19 pandemic (early 2020). Since then, as the pandemic evolved, more complexities were added to capture crucial factors and variables that can assist with projecting desired future scenarios. Throughout the pandemic, multi-model collaborative efforts have been organized to predict short-term outcomes (cases, deaths, and hospitalizations)
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Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021 Epidemics (IF 3.8) Pub Date : 2023-11-07 Moses C. Kiti, Obianuju G. Aguolu, Alana Zelaya, Holin Y. Chen, Noureen Ahmed, Jonathan Batross, Carol Y. Liu, Kristin N. Nelson, Samuel M. Jenness, Alessia Melegaro, Faruque Ahmed, Fauzia Malik, Saad B. Omer, Ben A. Lopman
Non-pharmaceutical interventions minimize social contacts, hence the spread of respiratory pathogens such as influenza and SARS-CoV-2. Globally, there is a paucity of social contact data from the workforce. In this study, we quantified two-day contact patterns among USA employees. Contacts were defined as face-to-face conversations, involving physical touch or proximity to another individual and were
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Estimation of waning vaccine effectiveness from population-level surveillance data in multi-variant epidemics Epidemics (IF 3.8) Pub Date : 2023-11-04 Hiroaki Murayama, Akira Endo, Shouto Yonekura
Monitoring time-varying vaccine effectiveness (e.g., due to waning of immunity and the emergence of novel variants) provides crucial information for outbreak control. Existing studies of time-varying vaccine effectiveness have used individual-level data, most importantly dates of vaccination and variant classification, which are often not available in a timely manner or from a wide range of population
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Assessing the utility of COVID-19 case reports as a leading indicator for hospitalization forecasting in the United States Epidemics (IF 3.8) Pub Date : 2023-11-07 Nicholas G. Reich, Yijin Wang, Meagan Burns, Rosa Ergas, Estee Y. Cramer, Evan L. Ray
Identifying data streams that can consistently improve the accuracy of epidemiological forecasting models is challenging. Using models designed to predict daily state-level hospital admissions due to COVID-19 in California and Massachusetts, we investigated whether incorporating COVID-19 case data systematically improved forecast accuracy. Additionally, we considered whether using case data aggregated
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Modelling flock heterogeneity in the transmission of peste des petits ruminants virus and its impact on the effectiveness of vaccination for eradication Epidemics (IF 3.8) Pub Date : 2023-10-31 Bethan Savagar, Bryony A. Jones, Mark Arnold, Martin Walker, Guillaume Fournié
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Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19 Epidemics (IF 3.8) Pub Date : 2023-10-30 James M. Azam, Xiaoxi Pang, Elisha B. Are, Juliet R.C. Pulliam, Matthew J. Ferrari
Background: Outbreak response modelling often involves collaboration among academics, and experts from governmental and non-governmental organizations. We conducted a systematic review of modelling studies on human vaccine-preventable disease (VPD) outbreaks to identify patterns in modelling practices between two collaboration types. We complemented this with a mini comparison of foot-and-mouth disease
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Mathematical methods for scaling from within-host to population-scale in infectious disease systems Epidemics (IF 3.8) Pub Date : 2023-10-30 James W.G. Doran, Robin N. Thompson, Christian A. Yates, Ruth Bowness
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Trypanosoma cruzi infection in dogs along the US-Mexico border: R0 changes with vector species composition Epidemics (IF 3.8) Pub Date : 2023-10-29 Luis Fernando Chaves, Alyssa C. Meyers, Carolyn L. Hodo, John P. Sanders, Rachel Curtis-Robles, Gabriel L. Hamer, Sarah A. Hamer
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A nationwide lockdown and deaths due to COVID-19 in the Indian subcontinent Epidemics (IF 3.8) Pub Date : 2023-10-20 Amit N. Sawant, Mats J. Stensrud
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Model-based estimates of chikungunya epidemiological parameters and outbreak risk from varied data types Epidemics (IF 3.8) Pub Date : 2023-10-18 Alexander D. Meyer, Sandra Mendoza Guerrero, Natalie E. Dean, Kathryn B. Anderson, Steven T. Stoddard, T. Alex Perkins
Assessing the factors responsible for differences in outbreak severity for the same pathogen is a challenging task, since outbreak data are often incomplete and may vary in type across outbreaks (e.g., daily case counts, serology, cases per household). We propose that outbreaks described with varied data types can be directly compared by using those data to estimate a common set of epidemiological
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Epidemiological characteristics and dynamic transmissions of COVID-19 pandemics in Chinese mainland: A trajectory clustering perspective analysis Epidemics (IF 3.8) Pub Date : 2023-09-26 Jingfeng Chen, Shuaiyin Chen, Guangcai Duan, Teng Zhang, Haitao Zhao, Zhuoqing Wu, Haiyan Yang, Suying Ding
Background The corona virus disease 2019 (COVID-19) pandemic has spread to more than 210 countries and regions around the world, with different characteristics recorded depending on the location. A systematic summarization of COVID-19 outbreaks that occurred during the “dynamic zero-COVID” policy period in Chinese mainland had not been previously conducted. In-depth mining of the big data from the
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Differential contagiousness of respiratory disease across the United States Epidemics (IF 3.8) Pub Date : 2023-09-22 Abhishek Mallela, Yen Ting Lin, William S. Hlavacek
The initial contagiousness of a communicable disease within a given population is quantified by the basic reproduction number, R0. This number depends on both pathogen and population properties. On the basis of compartmental models that reproduce Coronavirus Disease 2019 (COVID-19) surveillance data, we used Bayesian inference and the next-generation matrix approach to estimate region-specific R0 values
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Limited impact of contact tracing in a University setting for COVID-19 due to asymptomatic transmission and social distancing Epidemics (IF 3.8) Pub Date : 2023-09-08 Daniel Stocks, Emily Nixon, Adam Trickey, Martin Homer, Ellen Brooks-Pollock
Contact tracing is an important tool for controlling the spread of infectious diseases, including COVID-19. Here, we investigate the spread of COVID-19 and the effectiveness of contact tracing in a university population, using a data-driven ego-centric network model constructed with social contact data collected during 2020 and similar data collected in 2010. We find that during 2020, university staff
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Bayesian monitoring of COVID-19 in Sweden Epidemics (IF 3.8) Pub Date : 2023-08-24 Robin Marin, Håkan Runvik, Alexander Medvedev, Stefan Engblom
In an effort to provide regional decision support for the public healthcare, we design a data-driven compartment-based model of COVID-19 in Sweden. From national hospital statistics we derive parameter priors, and we develop linear filtering techniques to drive the simulations given data in the form of daily healthcare demands. We additionally propose a posterior marginal estimator which provides for
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Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data Epidemics (IF 3.8) Pub Date : 2023-08-15 Zachary Stanke, John L. Spouge
In a pending pandemic, early knowledge of age-specific disease parameters, e.g., susceptibility, infectivity, and the clinical fraction (the fraction of infections coming to clinical attention), supports targeted public health responses like school closures or sequestration of the elderly. The earlier the knowledge, the more useful it is, so the present article examines an early phase of many epidemics
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Bayesian reconstruction of SARS-CoV-2 transmissions highlights substantial proportion of negative serial intervals Epidemics (IF 3.8) Pub Date : 2023-08-07 Cyril Geismar, Vincent Nguyen, Ellen Fragaszy, Madhumita Shrotri, Annalan M.D. Navaratnam, Sarah Beale, Thomas E. Byrne, Wing Lam Erica Fong, Alexei Yavlinsky, Jana Kovar, Susan Hoskins, Isobel Braithwaite, Robert W. Aldridge, Andrew C. Hayward, Peter J. White, Thibaut Jombart, Anne Cori
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SARS-CoV-2 transmission patterns in educational settings during the Alpha wave in Reggio-Emilia, Italy Epidemics (IF 3.8) Pub Date : 2023-08-03 Carla Molina Grané, Pamela Mancuso, Massimo Vicentini, Francesco Venturelli, Olivera Djuric, Mattia Manica, Giorgio Guzzetta, Valentina Marziano, Agnese Zardini, Valeria d’Andrea, Filippo Trentini, Eufemia Bisaccia, Elisabetta Larosa, Silvia Cilloni, Maria Teresa Cassinadri, Patrizio Pezzotti, Marco Ajelli, Paolo Giorgi Rossi, Stefano Merler, Piero Poletti
Different monitoring and control policies have been implemented in schools to minimize the spread of SARS-CoV-2. Transmission in schools has been hard to quantify due to the large proportion of asymptomatic carriers in young individuals. We applied a Bayesian approach to reconstruct the transmission chains between 284 SARS-CoV-2 infections ascertained during 87 school outbreak investigations conducted
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The interplay between susceptibility and vaccine effectiveness control the timing and size of an emerging seasonal influenza wave in England Epidemics (IF 3.8) Pub Date : 2023-07-31 E. van Leeuwen, J. Panovska-Griffiths, S. Elgohari, A. Charlett, C. Watson
Relaxing social distancing measures and reduced level of influenza over the last two seasons may lead to a winter 2022 influenza wave in England. We used an established model for influenza transmission and vaccination to evaluate the rolled out influenza immunisation programme over October to December 2022. Specifically, we explored how the interplay between pre-season population susceptibility and
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The aquaculture disease network model (AquaNet-Mod): A simulation model to evaluate disease spread and controls for the salmonid industry in England and Wales Epidemics (IF 3.8) Pub Date : 2023-07-31 James Guilder, David Ryder, Nick G.H. Taylor, Sarah R. Alewijnse, Rebecca S. Millard, Mark A. Thrush, Edmund J. Peeler, Hannah J. Tidbury
Infectious disease causes significant mortality in wild and farmed systems, threatening biodiversity, conservation and animal welfare, as well as food security. To mitigate impacts and inform policy, tools such as mathematical models and computer simulations are valuable for predicting the potential spread and impact of disease. This paper describes the development of the Aquaculture Disease Network
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Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies Epidemics (IF 3.8) Pub Date : 2023-07-22 Thayer L. Anderson, Anjalika Nande, Carter Merenstein, Brinkley Raynor, Anisha Oommen, Brendan J. Kelly, Michael Z. Levy, Alison L. Hill
The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. “Superspreading,” or “over-dispersion,” is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological
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Epidemiological characteristics and transmissibility of HPV infection: A long-term retrospective study in Hokkien Golden Triangle, China, 2013–2021 Epidemics (IF 3.8) Pub Date : 2023-07-16
Objective Multiple human papillomavirus (HPV)-associated diseases have put a significant disease burden on the world. Therefore, we conducted a study to explore the epidemiological characteristics of HPV and the transmissibility of its genotypes. Methods HPV testing data was collected from Hospital. A transmission dynamics model of HPV was constructed to simulate and compare the transmissibility of
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The effective reproductive number: Modeling and prediction with application to the multi-wave Covid-19 pandemic Epidemics (IF 3.8) Pub Date : 2023-07-20 Razvan G. Romanescu, Songdi Hu, Douglas Nanton, Mahmoud Torabi, Olivier Tremblay-Savard, Md Ashiqul Haque
Classical compartmental models of infectious disease assume that spread occurs through a homogeneous population. This produces poor fits to real data, because individuals vary in their number of epidemiologically-relevant contacts, and hence in their ability to transmit disease. In particular, network theory suggests that super-spreading events tend to happen more often at the beginning of an epidemic
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Public health impact of the U.S. Scenario Modeling Hub Epidemics (IF 3.8) Pub Date : 2023-07-18 Rebecca K. Borchering, Jessica M. Healy, Betsy L. Cadwell, Michael A. Johansson, Rachel B. Slayton, Megan Wallace, Matthew Biggerstaff
Beginning in December 2020, the COVID-19 Scenario Modeling Hub has provided quantitative scenario-based projections for cases, hospitalizations, and deaths, aggregated across up to nine modeling groups. Projections spanned multiple months into the future and provided timely information on potential impacts of epidemiological uncertainties and interventions. Projections results were shared with the
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The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave Epidemics (IF 3.8) Pub Date : 2023-07-18 Miguel E.P. Silva, Martyn Fyles, Li Pi, Jasmina Panovska-Griffiths, Thomas House, Caroline Jay, Elizabeth Fearon
Testing for infection with SARS-CoV-2 is an important intervention in reducing onwards transmission of COVID-19, particularly when combined with the isolation and contact-tracing of positive cases. Many countries with the capacity to do so have made use of lab-processed Polymerase Chain Reaction (PCR) testing targeted at individuals with symptoms and the contacts of confirmed cases. Alternatively,
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Modelling the COVID-19 pandemic: Focusing on the case of Greece Epidemics (IF 3.8) Pub Date : 2023-07-05 Ioannis G. Violaris, Theodoros Lampros, Konstantinos Kalafatakis, Georgios Ntritsos, Konstantinos Kostikas, Nikolaos Giannakeas, Markos Tsipouras, Evripidis Glavas, Dimitrios Tsalikakis, Alexandros Tzallas
The SARS-CoV-2 infection (COVID-19) pandemic created an unprecedented chain of events at a global scale, with European counties initially following individual pathways on the confrontation of the global healthcare crisis, before organizing coordinated public vaccination campaigns, when proper vaccines became available. In the meantime, the viral infection outbreaks were determined by the inability
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Modeling the impact of different PrEP targeting strategies combined with a clinic-based HIV-1 nucleic acid testing intervention in Kenya Epidemics (IF 3.8) Pub Date : 2023-06-27 Deven T. Hamilton, Clara Agutu, Martin Sirengo, Wairimu Chege, Steven M. Goodreau, Adam Elder, Eduard J. Sanders, Susan M. Graham
Background Up to 69% of adults who acquire HIV in Kenya seek care for acute retroviral symptoms, providing an important opportunity for early diagnosis and HIV care engagement. The Tambua Mapema Plus (TMP) trial tested a combined HIV-1 nucleic acid testing, linkage, treatment, and partner notification intervention for adults with symptoms of acute HIV infection presenting to health facilities in coastal
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Contrasting seasonality of African swine fever outbreaks and its drivers Epidemics (IF 3.8) Pub Date : 2023-06-22 Younjung Kim, Pierre Nouvellet, Lisa Rogoll, Christoph Staubach, Katja Schulz, Carola Sauter-Louis, Dirk Udo Pfeiffer, Guillaume Fournié
The seasonality of African swine fever (ASF) outbreaks in domestic pigs differs between temperate and subtropical/tropical regions. We hypothesise that variations in the importance of wild boar-to-farm and farm-to-farm transmission routes shape these contrasting patterns, and we emphasise the implications for effective ASF control.
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Predicted reduction in transmission from deployment of ivermectin-treated birdfeeders for local control of West Nile virus Epidemics (IF 3.8) Pub Date : 2023-06-16 Karen M. Holcomb, Chilinh Nguyen, Nicholas Komar, Brian D. Foy, Nicholas A. Panella, Marissa L. Baskett, Christopher M. Barker
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Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study Epidemics (IF 3.8) Pub Date : 2023-06-21 Sangeeta Bhatia, Jack Wardle, Rebecca K. Nash, Pierre Nouvellet, Anne Cori
The evolution of SARS-CoV-2 has demonstrated that emerging variants can set back the global COVID-19 response. The ability to rapidly assess the threat of new variants is critical for timely optimisation of control strategies. We present a novel method to estimate the effective transmission advantage of a new variant compared to a reference variant combining information across multiple locations and
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Lives saved by public health restrictions over the Victorian COVID-19 Delta variant epidemic wave, Aug-Nov 2021 Epidemics (IF 3.8) Pub Date : 2023-06-14 D. Delport, R. Sacks-Davis, R.G. Abeysuriya, M. Hellard, N. Scott
Background Prior to mid-2021, Australia’s approach to COVID-19 was to eliminate community transmission. However, between August-November 2021, the state of Victoria, Australia, experienced an outbreak of the Delta variant that continued to grow despite extensive lockdowns and public health measures in place. While these public health restrictions were ultimately unable to stop community transmission
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Mumps epidemic dynamics in the United States before vaccination (1923–1932) Epidemics (IF 3.8) Pub Date : 2023-06-16 Laura W. Pomeroy, Senya Magsi, Shannon McGill, Caroline E. Wheeler
Mumps is a vaccine-preventable, reemerging, and highly transmissible infectious disease. Widespread vaccination dramatically reduced cases; however, case counts have been increasing over the past 20 years. To provide a quantitative overview of historical mumps dynamics that can act as baseline information to help identify causes of mumps reemergence, we analyzed timeseries of cases reported from 1923
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Optimizing age specific strategies of vaccination for prevention of cytomegalovirus infection in the US using agent-based simulation Epidemics (IF 3.8) Pub Date : 2023-06-16 Dawei Wang, Yao-Hsuan Chen, Mario Ventresca
Background: There is an urgent need to develop a cytomegalovirus (CMV) vaccine as it remains the leading cause of birth defects in the United States. While several CMV vaccine candidates are currently in late-stage clinical trials, the most effective vaccination program remains an open research question. Methods: To take into account the critical uncertainties when evaluating the vaccine impact on