Epidemics最新文献

{"title":"Estimating effective reproduction numbers using wastewater data from multiple sewersheds for SARS-CoV-2 in California counties","authors":"Sindhu Ravuri ,&nbsp;Elisabeth Burnor ,&nbsp;Isobel Routledge ,&nbsp;Natalie M. Linton ,&nbsp;Mugdha Thakur ,&nbsp;Alexandria Boehm ,&nbsp;Marlene Wolfe ,&nbsp;Heather N. Bischel ,&nbsp;Colleen C. Naughton ,&nbsp;Alexander T. Yu ,&nbsp;Lauren A. White ,&nbsp;Tomás M. León","doi":"10.1016/j.epidem.2024.100803","DOIUrl":"10.1016/j.epidem.2024.100803","url":null,"abstract":"<div><div>The effective reproduction number serves as a metric of population-wide, time-varying disease spread. During the early years of the COVID-19 pandemic, this metric was primarily derived from case data, which has varied in quality and representativeness due to changes in testing volume, test-seeking behavior, and resource constraints. Deriving nowcasting estimates from alternative data sources such as wastewater provides complementary information that could inform future public health responses. We estimated county-aggregated, sewershed-restricted wastewater-based SARS-CoV-2 effective reproduction numbers from May 1, 2022 to April 30, 2023 for five counties in California with heterogeneous population sizes, clinical testing rates, demographics, wastewater coverage, and sampling frequencies. We used two methods to produce sewershed-restricted effective reproduction numbers, both based on smoothed and deconvolved wastewater concentrations. We then population-weighted and aggregated these sewershed-level estimates to arrive at county-level effective reproduction numbers. Using mean absolute error (MAE), Spearman’s rank correlation (ρ), confusion matrix classification, and cross-correlation analyses, we compared the timing and trajectory of our two wastewater-based models to: (1) a publicly available, county-level ensemble of case-based estimates, and (2) county-aggregated, sewershed-restricted case-based estimates. Both wastewater models demonstrated high concordance with the traditional case-based estimates, as indicated by low mean absolute errors (MAE ≤ 0.09), significant positive Spearman correlation (ρ ≥ 0.66), and high confusion matrix classification accuracy (≥ 0.81). The relative timings of wastewater- and case-based estimates were less clear, with cross-correlation analyses suggesting strong associations for a wide range of temporal lags that varied by county and wastewater model type. This methodology provides a generalizable, robust, and operationalizable framework for estimating county-level wastewater-based effective reproduction numbers. Our retrospective evaluation supports the potential usage of real-time wastewater-based nowcasting as a complementary epidemiological tool for surveillance by public health agencies at the state and local levels. Based on this research, we produced publicly available wastewater-based nowcasts for the California Communicable diseases Assessment Tool (<span><span>calcat.cdph.ca.gov</span><svg><path></path></svg></span>).</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"50 ","pages":"Article 100803"},"PeriodicalIF":3.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142899655","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":"Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States","authors":"Sang Woo Park ,&nbsp;Brooklyn Noble ,&nbsp;Emily Howerton ,&nbsp;Bjarke F. Nielsen ,&nbsp;Sarah Lentz ,&nbsp;Lilliam Ambroggio ,&nbsp;Samuel Dominguez ,&nbsp;Kevin Messacar ,&nbsp;Bryan T. Grenfell","doi":"10.1016/j.epidem.2024.100808","DOIUrl":"10.1016/j.epidem.2024.100808","url":null,"abstract":"<div><div>The introduction of non-pharmaceutical interventions (NPIs) against COVID-19 disrupted circulation of many respiratory pathogens and eventually caused large, delayed outbreaks, owing to the build up of the susceptible pool during the intervention period. In contrast to other common respiratory pathogens that re-emerged soon after the NPIs were lifted, longer delays (<span><math><mo>&gt;</mo></math></span> 3 years) in the outbreaks of <em>Mycoplasma pneumoniae</em> (Mp), a bacterium commonly responsible for respiratory infections and pneumonia, have been reported in Europe and Asia. As Mp cases are continuing to increase in the US, predicting the size of an imminent outbreak is timely for public health agencies and decision makers. Here, we use simple mathematical models to provide robust predictions about a large Mp outbreak ongoing in the US. Our model further illustrates that NPIs and waning immunity are important factors in driving long delays in epidemic resurgence.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100808"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792672","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":"Serodynamics: A primer and synthetic review of methods for epidemiological inference using serological data","authors":"James A. Hay ,&nbsp;Isobel Routledge ,&nbsp;Saki Takahashi","doi":"10.1016/j.epidem.2024.100806","DOIUrl":"10.1016/j.epidem.2024.100806","url":null,"abstract":"<div><div>We present a review and primer of methods to understand epidemiological dynamics and identify past exposures from serological data, referred to as serodynamics. We discuss processing and interpreting serological data prior to fitting serodynamical models, and review approaches for estimating epidemiological trends and past exposures, ranging from serocatalytic models applied to binary serostatus data, to more complex models incorporating quantitative antibody measurements and immunological understanding. Although these methods are seemingly disparate, we demonstrate how they are derived within a common mathematical framework. Finally, we discuss key areas for methodological development to improve scientific discovery and public health insights in seroepidemiology.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100806"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796246","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":"Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach","authors":"Nicolò Gozzi ,&nbsp;Matteo Chinazzi ,&nbsp;Jessica T. Davis ,&nbsp;Kunpeng Mu ,&nbsp;Ana Pastore y Piontti ,&nbsp;Marco Ajelli ,&nbsp;Alessandro Vespignani ,&nbsp;Nicola Perra","doi":"10.1016/j.epidem.2024.100805","DOIUrl":"10.1016/j.epidem.2024.100805","url":null,"abstract":"<div><div>The emergence of SARS-CoV-2 variants of concern (VOCs) punctuated the dynamics of the COVID-19 pandemic in multiple occasions. The stages subsequent to their identification have been particularly challenging due to the hurdles associated with a prompt assessment of transmissibility and immune evasion characteristics of the newly emerged VOC. Here, we retrospectively analyze the performance of a modeling strategy developed to evaluate, in real-time, the risks posed by the Alpha and Omicron VOC soon after their emergence. Our approach utilized multi-strain, stochastic, compartmental models enriched with demographic information, age-specific contact patterns, the influence of non-pharmaceutical interventions, and the trajectory of vaccine distribution. The models’ preliminary assessment about Omicron’s transmissibility and immune evasion closely match later findings. Additionally, analyses based on data collected since our initial assessments demonstrate the retrospective accuracy of our real-time projections in capturing the emergence and subsequent dominance of the Alpha VOC in seven European countries and the Omicron VOC in South Africa. This study shows the value of relatively simple epidemic models in assessing the impact of emerging VOCs in real time, the importance of timely and accurate data, and the need for regular evaluation of these methodologies as we prepare for future global health crises.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100805"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792598","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":"Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling","authors":"Rachael Pung,&nbsp;Adam J. Kucharski","doi":"10.1016/j.epidem.2024.100802","DOIUrl":"10.1016/j.epidem.2024.100802","url":null,"abstract":"<div><div>Infectious disease models provide a systematic way to estimate crucial features of epidemic dynamics and explore different transmission and control scenarios. Given the importance of model-based analysis in managing public health crises, there has been an increase in post-pandemic creation of both academia-driven modelling centres, hubs and consortiums and government-driven public health agencies with in-house modelling units or teams. However, in the past, the delineation of roles and responsibilities between government- and academia-led modelling groups has often been unclear. Who should perform which tasks and when? This ambiguity can increase the risk of duplicated work or unaddressed gaps in analysis. It also raises questions about the sustainability of modelling capacity for addressing routine operational analytical needs while also developing new approaches that can be tailored for emergencies. In the sections below, we discuss factors that could inform decisions about where to locate infectious disease modelling activity. Rather than giving a fixed set of rules, we outlined key considerations and trade-offs that could be taken into account to enable academic and government modelling activities to complement each other effectively, which can in turn be refined as new public health crises emerge in future.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100802"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142683156","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":"Hospital population density and risk of respiratory infection: Is close contact density dependent?","authors":"George Shirreff ,&nbsp;Anne C.M. Thiébaut ,&nbsp;Bich-Tram Huynh ,&nbsp;NODS-Cov2 Investigation Group ,&nbsp;Guillaume Chelius ,&nbsp;Antoine Fraboulet ,&nbsp;Didier Guillemot ,&nbsp;Lulla Opatowski ,&nbsp;Laura Temime","doi":"10.1016/j.epidem.2024.100807","DOIUrl":"10.1016/j.epidem.2024.100807","url":null,"abstract":"<div><div>Respiratory infections acquired in hospital depend on close contact, which may be affected by hospital population density. Models of infectious disease transmission typically assume that contact rates are independent of density (frequency dependence) or proportional to it (linear density dependence), without justification. We evaluate these assumptions by measuring contact rates in hospitals under different population densities. We analysed data from a study in 15 wards in which staff, patients and visitors carried wearable sensors which detected close contacts. We proposed a general model, non-linear density dependence, and fit this to data on several types of interactions. Finally, we projected the fitted models to predict the effect of increasing population density on epidemic risk. We identified considerable heterogeneity in density dependence between wards, even those with the same medical specialty. Interactions between all persons present usually depended little on the population density. However, increasing patient density was associated with higher rates of patient contact for staff and for other patients. Simulations suggested that a 10 % increase in patient population density would carry a markedly increased risk in many wards. This study highlights the variance in density dependent dynamics and the complexity of predicting contact rates.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100807"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796175","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":"Forecasting SARS-CoV-2 epidemic dynamic in Poland with the pDyn agent-based model","authors":"Karol Niedzielewski ,&nbsp;Rafał P. Bartczuk ,&nbsp;Natalia Bielczyk ,&nbsp;Dominik Bogucki ,&nbsp;Filip Dreger ,&nbsp;Grzegorz Dudziuk ,&nbsp;Łukasz Górski ,&nbsp;Magdalena Gruziel-Słomka ,&nbsp;Jędrzej Haman ,&nbsp;Artur Kaczorek ,&nbsp;Jan Kisielewski ,&nbsp;Bartosz Krupa ,&nbsp;Antoni Moszyński ,&nbsp;Jędrzej M. Nowosielski ,&nbsp;Maciej Radwan ,&nbsp;Marcin Semeniuk ,&nbsp;Urszula Tymoszuk ,&nbsp;Jakub Zieliński ,&nbsp;Franciszek Rakowski","doi":"10.1016/j.epidem.2024.100801","DOIUrl":"10.1016/j.epidem.2024.100801","url":null,"abstract":"<div><div>We employ pDyn (derived from “pandemics dynamics”), an agent-based epidemiological model, to forecast the fourth wave of the SARS-CoV-2 epidemic, primarily driven by the Delta variant, in Polish society. The model captures spatiotemporal dynamics of the epidemic spread, predicting disease-related states based on pathogen properties and behavioral factors. We assess pDyn’s validity, encompassing pathogen variant succession, immunization level, and the proportion of vaccinated among confirmed cases. We evaluate its predictive capacity for pandemic dynamics, including wave peak timing, magnitude, and duration for confirmed cases, hospitalizations, ICU admissions, and deaths, nationally and regionally in Poland. Validation involves comparing pDyn’s estimates with real-world data (excluding data used for calibration) to evaluate whether pDyn accurately reproduced the epidemic dynamics up to the simulation time. To assess the accuracy of pDyn’s predictions, we compared simulation results with real-world data acquired after the simulation date. The findings affirm pDyn’s accuracy in forecasting and enhancing our understanding of epidemic mechanisms.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100801"},"PeriodicalIF":3.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649434","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":"Optimizing spatial distribution of wastewater-based epidemiology to advance health equity","authors":"Maria L. Daza-Torres ,&nbsp;J. Cricelio Montesinos-López ,&nbsp;César Herrera ,&nbsp;Yury E. García ,&nbsp;Colleen C. Naughton ,&nbsp;Heather N. Bischel ,&nbsp;Miriam Nuño","doi":"10.1016/j.epidem.2024.100804","DOIUrl":"10.1016/j.epidem.2024.100804","url":null,"abstract":"<div><div>In 2022, the US Centers for Disease Control and Prevention commissioned the National Academies of Sciences, Engineering, and Medicine to assess the role of community-level wastewater-based epidemiology (WBE) beyond COVID-19. WBE is recognized as a promising mechanism for promptly identifying infectious diseases, including COVID-19 and other novel pathogens. An important conclusion from this initiative is the critical importance of maintaining equity and expanding access to fully realize the benefits of wastewater surveillance for marginalized communities. To address this need, we propose an optimization framework that strategically allocates wastewater monitoring resources at the wastewater treatment plant (WWTP) level, ensuring more effective and equitable distribution of surveillance efforts to serve underserved populations.</div><div>The purpose of the framework is to obtain a balanced spatial distribution, inclusive population coverage, and efficient representation of disadvantaged groups in the allocation of resources for WBE. Furthermore, the framework concentrates on areas with high population density and gives priority to vulnerable regions, as well as identifying signals that display significant variations from other monitored sources. The optimization objective is to maximize a weighted combination of these critical factors. This problem is formulated as an integer optimization problem and solved using simulated annealing. We evaluate various scenarios, considering different weighting factors, to optimize the allocation of WWTPs with monitoring systems. This optimization framework provides an opportunity to enhance WBE by providing customized monitoring strategies created to address specific priorities and situations, thus enhancing the decision-making processes in public health responses.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100804"},"PeriodicalIF":3.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644710","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":"Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries","authors":"Margaret J. de Villiers ,&nbsp;Edward de Villiers ,&nbsp;Shevanthi Nayagam ,&nbsp;Timothy B. Hallett","doi":"10.1016/j.epidem.2024.100798","DOIUrl":"10.1016/j.epidem.2024.100798","url":null,"abstract":"<div><div>Population-level vaccination effects of the hepatitis B vaccine were investigated in four low- and middle-income countries with different levels of vertical and horizontal transmission. Indirect vaccination effects constitute a large proportion of overall vaccination effects of the vaccination programmes in all four countries (over 70% by 2030 in all four countries). However, countries with higher levels of vertical transmission benefit less from indirect vaccination effects from the infant hepatitis B vaccine series during the first decades of the vaccination programme, making the birth dose vaccine more important in these countries. Vaccination, even at levels that do not fully control transmission, has a great effect on the development of disease as it also increases the average age of infection, thereby causing a decrease in the number of chronic infections relative to the number of acute infections.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100798"},"PeriodicalIF":3.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142631155","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":"Modelling plausible scenarios for the Omicron SARS-CoV-2 variant from early-stage surveillance","authors":"Christopher J. Banks ,&nbsp;Ewan Colman ,&nbsp;Anthony J. Wood ,&nbsp;Thomas Doherty ,&nbsp;Rowland R. Kao","doi":"10.1016/j.epidem.2024.100800","DOIUrl":"10.1016/j.epidem.2024.100800","url":null,"abstract":"<div><div>We used a spatially explicit agent-based model of SARS-CoV-2 transmission combined with spatially fine-grained COVID-19 observation data from Public Health Scotland to investigate the initial rise of the Omicron (BA.1) variant of concern. We evaluated plausible scenarios for transmission rate advantage and vaccine immune escape relative to the Delta variant based on the data that would have been available at that time. We also explored possible outcomes of different levels of imposed non-pharmaceutical intervention. The initial results of these scenarios were used to inform the Scottish Government in the early outbreak stages of the Omicron variant.</div><div>Using the model with parameters fit over the Delta variant epidemic, some initial assumptions about Omicron transmission rate advantage and vaccine escape, and a simple growth rate fitting procedure, we were able to capture the initial outbreak dynamics for Omicron. We found that the modelled dynamics hold up to retrospective scrutiny. The modelled imposition of extra non-pharmaceutical interventions planned by the Scottish Government at the time would likely have little effect in light of the transmission rate advantage held by the Omicron variant and the fact that the planned interventions would have occurred too late in the outbreak’s trajectory. Finally, we found that any assumptions made about the projected distribution of vaccines in the model population had little bearing on the outcome, in terms of outbreak size and timing. Instead, it was the landscape of prior immunity that was most important.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100800"},"PeriodicalIF":3.0,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689487","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}