Epidemics最新文献

{"title":"Differential contagiousness of respiratory disease across the United States","authors":"Abhishek Mallela ,&nbsp;Yen Ting Lin ,&nbsp;William S. Hlavacek","doi":"10.1016/j.epidem.2023.100718","DOIUrl":"10.1016/j.epidem.2023.100718","url":null,"abstract":"<div><p>The initial contagiousness of a communicable disease within a given population is quantified by the basic reproduction number, <span><math><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span>. 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 <span><math><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span> values for 280 of 384 metropolitan statistical areas (MSAs) in the United States (US), which account for 95% of the US population living in urban areas and 82% of the total population. We focused on MSA populations after finding that these populations were more uniformly impacted by COVID-19 than state populations. Our maximum a posteriori (MAP) estimates for <span><math><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span> range from 1.9 to 7.7 and quantify the relative susceptibilities of regional populations to spread of respiratory diseases.</p></div><div><h3>One-Sentence Summary</h3><p>Initial contagiousness of Coronavirus Disease 2019 varied over a 4-fold range across urban areas of the United States.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"45 ","pages":"Article 100718"},"PeriodicalIF":3.8,"publicationDate":"2023-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41140424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Limited impact of contact tracing in a University setting for COVID-19 due to asymptomatic transmission and social distancing","authors":"Daniel Stocks ,&nbsp;Emily Nixon ,&nbsp;Adam Trickey ,&nbsp;Martin Homer ,&nbsp;Ellen Brooks-Pollock","doi":"10.1016/j.epidem.2023.100716","DOIUrl":"10.1016/j.epidem.2023.100716","url":null,"abstract":"<div><p>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 and students consistently reported fewer social contacts than in 2010, however those contacts occurred more frequently and were of longer duration. We find that contact tracing in the presence of social distancing is less impactful than without social distancing. By combining multiple data sources, we show that University-aged populations are likely to develop asymptomatic COVID-19 infections. We find that asymptomatic index cases cannot be reliably discovered through contact tracing and consequently transmission in their social network is not significantly reduced through contact tracing. In summary, social distancing restrictions had a large impact on limiting COVID-19 outbreaks in universities; to reduce transmission further contact tracing should be used in conjunction with alternative interventions.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"45 ","pages":"Article 100716"},"PeriodicalIF":3.8,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10553284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicted reduction in transmission from deployment of ivermectin-treated birdfeeders for local control of West Nile virus","authors":"Karen M. Holcomb ,&nbsp;Chilinh Nguyen ,&nbsp;Nicholas Komar ,&nbsp;Brian D. Foy ,&nbsp;Nicholas A. Panella ,&nbsp;Marissa L. Baskett ,&nbsp;Christopher M. Barker","doi":"10.1016/j.epidem.2023.100697","DOIUrl":"10.1016/j.epidem.2023.100697","url":null,"abstract":"<div><p>Ivermectin (IVM)-treated birds provide the potential for targeted control of <em>Culex</em> mosquitoes to reduce West Nile virus (WNV) transmission. Ingestion of IVM increases mosquito mortality, which could reduce WNV transmission from birds to humans and in enzootic maintenance cycles affecting predominantly bird-feeding mosquitoes and from birds to humans. This strategy might also provide an alternative method for WNV control that is less hampered by insecticide resistance and the logistics of large-scale pesticide applications. Through a combination of field studies and modeling, we assessed the feasibility and impact of deploying IVM-treated birdfeed in residential neighborhoods to reduce WNV transmission. We first tracked 105 birds using radio telemetry and radio frequency identification to monitor their feeder usage and locations of nocturnal roosts in relation to five feeder sites in a neighborhood in Fort Collins, Colorado. Using these results, we then modified a compartmental model of WNV transmission to account for the impact of IVM on mosquito mortality and spatial movement of birds and mosquitoes on the neighborhood level. We found that, while the number of treated lots in a neighborhood strongly influenced the total transmission potential, the arrangement of treated lots in a neighborhood had little effect. Increasing the proportion of treated birds, regardless of the WNV competency status, resulted in a larger reduction in infection dynamics than only treating competent birds. Taken together, model results indicate that deployment of IVM-treated feeders could reduce local transmission throughout the WNV season, including reducing the enzootic transmission prior to the onset of human infections, with high spatial coverage and rates of IVM-induced mortality in mosquitoes. To improve predictions, more work is needed to refine estimates of daily mosquito movement in urban areas and rates of IVM-induced mortality. Our results can guide future field trials of this control strategy.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"44 ","pages":"Article 100697"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10529638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10530219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study","authors":"Sangeeta Bhatia ,&nbsp;Jack Wardle ,&nbsp;Rebecca K. Nash ,&nbsp;Pierre Nouvellet ,&nbsp;Anne Cori","doi":"10.1016/j.epidem.2023.100692","DOIUrl":"10.1016/j.epidem.2023.100692","url":null,"abstract":"<div><p>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.</p><p>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 over time. Through an extensive simulation study designed to mimic real-time epidemic contexts, we show that our method performs well across a range of scenarios and provide guidance on its optimal use and interpretation of results. We also provide an open-source software implementation of our method. The computational speed of our tool enables users to rapidly explore spatial and temporal variations in the estimated transmission advantage.</p><p>We estimate that the SARS-CoV-2 Alpha variant is 1.46 (95% Credible Interval 1.44–1.47) and 1.29 (95% CrI 1.29–1.30) times more transmissible than the wild type, using data from England and France respectively. We further estimate that Delta is 1.77 (95% CrI 1.69–1.85) times more transmissible than Alpha (England data).</p><p>Our approach can be used as an important first step towards quantifying the threat of emerging or co-circulating variants of infectious pathogens in real-time.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"44 ","pages":"Article 100692"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10284428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10175115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimating age-stratified transmission and reproduction numbers during the early exponential phase of an epidemic: A case study with COVID-19 data","authors":"Zachary Stanke,&nbsp;John L. Spouge","doi":"10.1016/j.epidem.2023.100714","DOIUrl":"10.1016/j.epidem.2023.100714","url":null,"abstract":"<div><p>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, exponential growth. Using age-stratified COVID-19 case counts collected in Canada, China, Israel, Italy, the Netherlands, and the United Kingdom before April 23, 2020, we present a linear analysis of the exponential phase that attempts to estimate the age-specific disease parameters given above. Some combinations of the parameters can be estimated by requiring that they change smoothly with age. The estimation yielded: (1) the case susceptibility, defined for each age-group as the product of susceptibility to infection and the clinical fraction; (2) the mean number of transmissions of infection per contact within each age-group; and (3) the reproduction number of infection within each age-group, i.e., the diagonal of the age-stratified next-generation matrix. Our restriction to data from the exponential phase indicates the combinations of epidemic parameters that are intrinsically easiest to estimate with early age-stratified case counts. For example, conclusions concerning the age-dependence of case susceptibility appeared more robust than corresponding conclusions about infectivity. Generally, the analysis produced some results consistent with conclusions confirmed much later in the COVID-19 pandemic. Notably, our analysis showed that in some countries, the reproduction number of infection within the half-decade 70–75 was unusually large compared to other half-decades. Our analysis therefore could have anticipated that without countermeasures, COVID-19 would spread rapidly once seeded in homes for the elderly.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"44 ","pages":"Article 100714"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10528737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10176205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effective reproductive number: Modeling and prediction with application to the multi-wave Covid-19 pandemic","authors":"Razvan G. Romanescu ,&nbsp;Songdi Hu ,&nbsp;Douglas Nanton ,&nbsp;Mahmoud Torabi ,&nbsp;Olivier Tremblay-Savard ,&nbsp;Md Ashiqul Haque","doi":"10.1016/j.epidem.2023.100708","DOIUrl":"10.1016/j.epidem.2023.100708","url":null,"abstract":"<div><p>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, which is inconsistent with the homogeneity assumption. In this paper we argue that a flexible decay shape for the effective reproductive number (<span><math><msub><mrow><mi>R</mi></mrow><mrow><mi>t</mi></mrow></msub></math></span>) indexed by the susceptible fraction (<span><math><msub><mrow><mi>S</mi></mrow><mrow><mi>t</mi></mrow></msub></math></span>) is a theory-informed modeling choice, which better captures the progression of disease incidence over human populations. This, in turn, produces better retrospective fits, as well as more accurate prospective predictions of observed epidemic curves. We extend this framework to fit multi-wave epidemics, and to accommodate public health restrictions on mobility. We demonstrate the performance of this model by doing a prediction study over two years of the SARS-CoV2 pandemic.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"44 ","pages":"Article 100708"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10177124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mumps epidemic dynamics in the United States before vaccination (1923–1932)","authors":"Laura W. Pomeroy ,&nbsp;Senya Magsi ,&nbsp;Shannon McGill ,&nbsp;Caroline E. Wheeler","doi":"10.1016/j.epidem.2023.100700","DOIUrl":"10.1016/j.epidem.2023.100700","url":null,"abstract":"<div><p>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 to 1932 in the United States. During that time, 239,230 mumps cases were reported in 70 cities. Larger cities reported annual epidemics and smaller cities reported intermittent, sporadic outbreaks. The critical community size above which transmission continuously occurred was likely between 365,583 and 781,188 individuals but could range as high as 3,376,438 individuals. Mumps cases increased as city size increased, suggesting density-dependent transmission. Using a density-dependent SEIR model, we calculated a mean effective reproductive number (<span><math><msub><mrow><mi>R</mi></mrow><mrow><mi>e</mi></mrow></msub></math></span>) of 1.2. <span><math><msub><mrow><mi>R</mi></mrow><mrow><mi>e</mi></mrow></msub></math></span> varied by city and over time, with periodic high values that could characterize short periods of very high transmission known as superspreading events. Case counts most often peaked in March, with higher-than-average transmission from December through April and showed a correlation with weekly births. While certain city pairs in Midwestern states had synchronous outbreaks, most outbreaks were less synchronous and not driven by distance between cities. This work demonstrates the importance of long-term infectious disease surveillance data and will inform future studies on mumps reemergence and control.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"44 ","pages":"Article 100700"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10179593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modelling the COVID-19 pandemic: Focusing on the case of Greece","authors":"Ioannis G. Violaris ,&nbsp;Theodoros Lampros ,&nbsp;Konstantinos Kalafatakis ,&nbsp;Georgios Ntritsos ,&nbsp;Konstantinos Kostikas ,&nbsp;Nikolaos Giannakeas ,&nbsp;Markos Tsipouras ,&nbsp;Evripidis Glavas ,&nbsp;Dimitrios Tsalikakis ,&nbsp;Alexandros Tzallas","doi":"10.1016/j.epidem.2023.100706","DOIUrl":"10.1016/j.epidem.2023.100706","url":null,"abstract":"<div><p>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 of the immune system to retain a long-lasting protection as well as the appearance of SARS-CoV-2 variants with differential transmissibility and virulence. How do these different parameters regulate the domestic impact of the viral epidemic outbreak? We developed two versions of a mathematical model, an original and a revised one, able to capture multiple factors affecting the epidemic dynamics. We tested the original one on five European countries with different characteristics, and the revised one in one of them, Greece. For the development of the model, we used a modified version of the classical SEIR model, introducing various parameters related to the estimated epidemiology of the pathogen, governmental and societal responses, and the concept of quarantine. We estimated the temporal trajectories of the identified and overall active cases for Cyprus, Germany, Greece, Italy and Sweden, for the first 250 days. Finally, using the revised model, we estimated the temporal trajectories of the identified and overall active cases for Greece, for the duration of the 1230 days (until June 2023). As shown by the model, small initial numbers of exposed individuals are enough to threaten a large percentage of the population. This created an important political dilemma in most countries. Force the virus to extinction with extremely long and restrictive measures or merely delay its spread and aim for herd immunity. Most countries chose the former, which enabled the healthcare systems to absorb the societal pressure, caused by the increased numbers of patients, requiring hospitalization and intensive care.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"44 ","pages":"Article 100706"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10548188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing age specific strategies of vaccination for prevention of cytomegalovirus infection in the US using agent-based simulation","authors":"Dawei Wang ,&nbsp;Yao-Hsuan Chen ,&nbsp;Mario Ventresca","doi":"10.1016/j.epidem.2023.100698","DOIUrl":"10.1016/j.epidem.2023.100698","url":null,"abstract":"<div><h3>Background:</h3><p>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.</p></div><div><h3>Methods:</h3><p>To take into account the critical uncertainties when evaluating the vaccine impact on both vertical (congenital) and horizontal CMV transmissions, we developed a CMV agent-based model representative of the US population and contact network structures.</p></div><div><h3>Results:</h3><p>We evaluated 648 vaccination scenarios under various assumptions of vaccination age, vaccine efficacy, protection duration, and vaccination coverage. The optimal age of vaccination under all scenarios is shown to be during early childhood. However, a relatively modest benefit was also seen with vaccination of females of reproduction age (around age of 25) assuming near universal coverage and long vaccine-mediated protection.</p></div><div><h3>Conclusions:</h3><p>This study highlights the important need for a pediatric vaccination program in mitigating CMV in the United States. Our model is poised to investigate further location-based vaccine effectiveness questions in future planning of both clinical trials as well as eventual program implementation.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"44 ","pages":"Article 100698"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10167906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contrasting seasonality of African swine fever outbreaks and its drivers","authors":"Younjung Kim,&nbsp;Pierre Nouvellet,&nbsp;Lisa Rogoll,&nbsp;Christoph Staubach,&nbsp;Katja Schulz,&nbsp;Carola Sauter-Louis,&nbsp;Dirk Udo Pfeiffer,&nbsp;Guillaume Fournié","doi":"10.1016/j.epidem.2023.100703","DOIUrl":"10.1016/j.epidem.2023.100703","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"44 ","pages":"Article 100703"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10167915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}