Epidemics最新文献

{"title":"Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks","authors":"Hélène Duault ,&nbsp;Benoit Durand ,&nbsp;Laetitia Canini","doi":"10.1016/j.epidem.2024.100794","DOIUrl":"10.1016/j.epidem.2024.100794","url":null,"abstract":"<div><div>In a multi-host system, understanding host-species contribution to transmission is key to appropriately targeting control and preventive measures. Outbreak reconstruction methods aiming to identify who-infected-whom by combining epidemiological and genetic data could contribute to achieving this goal. However, the majority of these methods remain untested on realistic simulated multi-host data. <em>Mycobacterium bovis</em> is a slowly evolving multi-host pathogen and previous studies on outbreaks involving both cattle and wildlife have identified observation biases. Indeed, contrary to cattle, sampling wildlife is difficult. The aim of our study was to evaluate and compare the performances of three existing outbreak reconstruction methods (<em>seqTrack</em>, <em>outbreaker2</em> and <em>TransPhylo</em>) on <em>M. bovis</em> multi-host data simulated with and without biases. Extending an existing transmission model, we simulated 30 bTB outbreaks involving cattle, badgers and wild boars and defined six sampling schemes mimicking observation biases. We estimated general and specific to multi-host systems epidemiological indicators. We tested four alternative transmission scenarios changing the mutation rate or the composition of the epidemiological system. The reconstruction of who-infected-whom was sensitive to the mutation rate and <em>seqTrack</em> reconstructed prolific super-spreaders. <em>TransPhylo</em> and <em>outbreaker2</em> poorly estimated the contribution of each host-species and could not reconstruct the presence of a dead-end epidemiological host. However, the host-species of cattle (but not badger) index cases was correctly reconstructed by <em>seqTrack</em> and <em>outbreaker2</em>. These two specific indicators improved when considering an observation bias. We found an overall poor performance for the three methods on simulated biased and unbiased bTB data. This seemed partly attributable to the low evolutionary rate characteristic of <em>M. bovis</em> leading to insufficient genetic information, but also to the complexity of the simulated multi-host system. This study highlights the importance of an integrated approach and the need to develop new outbreak reconstruction methods adapted to complex epidemiological systems and tested on realistic multi-host data.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100794"},"PeriodicalIF":3.0,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142319703","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":"Directly observed social contact patterns among school children in rural Gambia","authors":"Isaac Osei ,&nbsp;Emmanuel Mendy ,&nbsp;Kevin van Zandvoort ,&nbsp;Olimatou Jobe ,&nbsp;Golam Sarwar ,&nbsp;Baleng Mahama Wutor ,&nbsp;Stefan Flasche ,&nbsp;Nuredin I. Mohammed ,&nbsp;Jane Bruce ,&nbsp;Brian Greenwood ,&nbsp;Grant A. Mackenzie","doi":"10.1016/j.epidem.2024.100790","DOIUrl":"10.1016/j.epidem.2024.100790","url":null,"abstract":"<div><h3>Introduction</h3><p>School-aged children play a major role in the transmission of many respiratory pathogens due to high rate of close contacts in schools. The validity and accuracy of proxy-reported contact data may be limited, particularly for children when attending school. We observed social contacts within schools and assessed the accuracy of proxy-reported versus observed physical contact data among students in rural Gambia.</p></div><div><h3>Methods</h3><p>We enrolled school children who had also been recruited to a survey of <em>Streptococcus pneumoniae</em> carriage and social contacts. We visited participants at school and observed their contact patterns within and outside the classroom for two hours. We recorded the contact type, gender and approximate age of the contactee, and class size. We calculated age-stratified contact matrices to determine in-school contact patterns. We compared proxy-reported estimated physical contacts for the subset of participants (18 %) randomised to be observed on the same day for which the parent or caregiver reported the school contacts.</p></div><div><h3>Results</h3><p>We recorded 3822 contacts for 219 participants from 114 schools. The median number of contacts was 15 (IQR: 11–20). Contact patterns were strongly age-assortative, and mainly involved physical touch (67.5 %). Those aged 5–9 years had the highest mean number of contacts [19.0 (95 %CI: 16.7–21.3)] while the ≥ 15-year age group had fewer contacts [12.8 (95 %CI: 10.9–14.7)]. Forty (18 %) participants had their school-observed contact data collected on the same day as their caregiver reported their estimated physical contacts at school; only 22.5 % had agreement within ±2 contacts between the observed and reported contacts. Fifty-eight percent of proxy-reported contacts were under-estimates.</p></div><div><h3>Conclusions</h3><p>Social contact rates observed among pupils at schools in rural Gambia were high, strongly age-assortative, and physical. Reporting of school contacts by proxies may underestimate the effect of school-age children in modelling studies of transmission of infections. New approaches are needed to quantify contacts within schools.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100790"},"PeriodicalIF":3.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1755436524000513/pdfft?md5=2ccba6450d1e00d97d1ad0d607a86a19&pid=1-s2.0-S1755436524000513-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142172930","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 impact of household size on measles transmission: A long-term perspective","authors":"Subekshya Bidari ,&nbsp;Wan Yang","doi":"10.1016/j.epidem.2024.100791","DOIUrl":"10.1016/j.epidem.2024.100791","url":null,"abstract":"<div><p>Households play an important role in the transmission of infectious diseases due to the close contact therein. Previous modeling studies on disease transmission with household-level mixing have explored the relationship between household size distribution and epidemic characteristics such as final epidemic sizes and the basic reproduction number but have not considered the epidemic impact of declining household sizes caused by demographic shifts. Here, we use a disease transmission model that incorporates demographic changes in household sizes to study the long-term transmission dynamics of measles in communities with varying household size distributions. We explore the impact of incorporating both household- and age-structured mixing on the dynamic properties of the transmission model and compare these dynamics across different household size distributions. Our analysis, based on the household- and age-structured model, shows that communities with larger household sizes require higher vaccination thresholds and bear a greater burden of infections. However, simulations show the apparent impact of changing household sizes is the combined result of changing birth rates and household mixing, and that changing birth rates likely play a larger role than changes in household mixing in shaping measles transmission dynamics (<em>n.b</em>, life-long immunity makes replenishment of population susceptibility from births a crucial transmission driver for measles). In addition, simulations of endemic transmission of measles within a hypothetical population formulated using aggregated world demographic data suggest the decline in household size (driven by changing fertility rates of the population), in addition to increasing vaccination coverage, could have had a significant impact on the incidence of measles over time.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100791"},"PeriodicalIF":3.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1755436524000525/pdfft?md5=06402016900ab2293e62ef84e9728b1b&pid=1-s2.0-S1755436524000525-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142230112","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":"Preface: COVID-19 Scenario Modeling Hubs","authors":"Sara L. Loo,&nbsp;Matteo Chinazzi,&nbsp;Ajitesh Srivastava,&nbsp;Srinivasan Venkatramanan,&nbsp;Shaun Truelove,&nbsp;Cecile Viboud","doi":"10.1016/j.epidem.2024.100788","DOIUrl":"10.1016/j.epidem.2024.100788","url":null,"abstract":"","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"48 ","pages":"Article 100788"},"PeriodicalIF":3.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1755436524000495/pdfft?md5=2b0e80f9c856224833863dcbd69fa0a4&pid=1-s2.0-S1755436524000495-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113953","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":"Investigation of P. vivax elimination via mass drug administration: A simulation study","authors":"Md Nurul Anwar ,&nbsp;James M. McCaw ,&nbsp;Alexander E. Zarebski ,&nbsp;Roslyn I. Hickson ,&nbsp;Jennifer A. Flegg","doi":"10.1016/j.epidem.2024.100789","DOIUrl":"10.1016/j.epidem.2024.100789","url":null,"abstract":"<div><p><em>Plasmodium vivax</em> is the most geographically widespread malaria parasite. <em>P. vivax</em> has the ability to remain dormant (as a hypnozoite) in the human liver and subsequently reactivate, which makes control efforts more difficult. Given the majority of <em>P. vivax</em> infections are due to hypnozoite reactivation, targeting the hypnozoite reservoir with a radical cure is crucial for achieving <em>P. vivax</em> elimination. Stochastic effects can strongly influence dynamics when disease prevalence is low or when the population size is small. Hence, it is important to account for this when modelling malaria elimination. We use a stochastic multiscale model of <em>P. vivax</em> transmission to study the impacts of multiple rounds of mass drug administration (MDA) with a radical cure, accounting for superinfection and hypnozoite dynamics. Our results indicate multiple rounds of MDA with a high-efficacy drug are needed to achieve a substantial probability of elimination. This work has the potential to help guide <em>P. vivax</em> elimination strategies by quantifying elimination probabilities for an MDA approach.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"48 ","pages":"Article 100789"},"PeriodicalIF":3.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1755436524000501/pdfft?md5=3ad29b116b99a1e7d4311f757c00de28&pid=1-s2.0-S1755436524000501-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142158201","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 utility of whole-genome sequencing to identify likely transmission pairs for pathogens with slow and variable evolution","authors":"A.J. Wood ,&nbsp;C.H. Benton ,&nbsp;R.J. Delahay ,&nbsp;G. Marion ,&nbsp;E. Palkopoulou ,&nbsp;C.M. Pooley ,&nbsp;G.C. Smith ,&nbsp;R.R. Kao","doi":"10.1016/j.epidem.2024.100787","DOIUrl":"10.1016/j.epidem.2024.100787","url":null,"abstract":"<div><p>Pathogen whole-genome sequencing (WGS) has been used to track the transmission of infectious diseases in extraordinary detail, especially for pathogens that undergo fast and steady evolution, as is the case with many RNA viruses. However, for other pathogens evolution is less predictable, making interpretation of these data to inform our understanding of their epidemiology more challenging and the value of densely collected pathogen genome data uncertain. Here, we assess the utility of WGS for one such pathogen, in the “who-infected-whom” identification problem. We study samples from hosts (130 cattle, 111 badgers) with confirmed infection of <em>M. bovis</em> (causing bovine Tuberculosis), which has an estimated clock rate as slow as <span><math><mo>∼</mo></math></span>0.1–1 variations per year. For each potential pathway between hosts, we calculate the relative likelihood that such a transmission event occurred. This is informed by an epidemiological model of transmission, and host life history data. By including WGS data, we shrink the number of plausible pathways significantly, relative to those deemed likely on the basis of life history data alone. Despite our uncertainty relating to the evolution of <em>M. bovis</em>, the WGS data are therefore a valuable adjunct to epidemiological investigations, especially for wildlife species whose life history data are sparse.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"48 ","pages":"Article 100787"},"PeriodicalIF":3.0,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1755436524000483/pdfft?md5=75b01705e167d9bd860122bfc9101c00&pid=1-s2.0-S1755436524000483-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142083635","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":"Improving the contribution of mathematical modelling evidence to guidelines and policy: Experiences from tuberculosis","authors":"C. Finn McQuaid ,&nbsp;Nicolas A. Menzies ,&nbsp;Rein M.G.J. Houben ,&nbsp;Gabriella B. Gomez ,&nbsp;Anna Vassall ,&nbsp;Nimalan Arinaminpathy ,&nbsp;Peter J. Dodd ,&nbsp;Richard G. White","doi":"10.1016/j.epidem.2024.100786","DOIUrl":"10.1016/j.epidem.2024.100786","url":null,"abstract":"<div><p>We read with great interest the recent paper by Lo et al., who argue that there is an urgent need to ensure the quality of modelling evidence used to support international and national guideline development. Here we outline efforts by the Tuberculosis Modelling and Analysis Consortium, together with the World Health Organization Global Task Force on Tuberculosis Impact Measurement, to develop material to improve the quality and transparency of country-level tuberculosis modelling to inform decision-making.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"48 ","pages":"Article 100786"},"PeriodicalIF":3.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1755436524000471/pdfft?md5=fb593a872c62d9d9146c6bf4f0019ee3&pid=1-s2.0-S1755436524000471-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914354","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":"Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study","authors":"Houssein H. Ayoub ,&nbsp;Milan Tomy ,&nbsp;Hiam Chemaitelly ,&nbsp;Ryosuke Omori ,&nbsp;Kent Buse ,&nbsp;Nicola Low ,&nbsp;Sarah Hawkes ,&nbsp;Laith J. Abu-Raddad","doi":"10.1016/j.epidem.2024.100785","DOIUrl":"10.1016/j.epidem.2024.100785","url":null,"abstract":"<div><h3>Background</h3><p>This study aimed to examine the transmission dynamics of <em>Neisseria gonorrhoeae</em> (NG) in heterosexual sex work networks (HSWNs) and the impact of variation in sexual behavior and interventions on NG epidemiology.</p></div><div><h3>Methods</h3><p>The study employed an individual-based mathematical model to simulate NG transmission dynamics in sexual networks involving female sex workers (FSWs) and their clients, primarily focusing on the Middle East and North Africa region. A deterministic model was also used to describe NG transmission from clients to their spouses.</p></div><div><h3>Results</h3><p>NG epidemiology in HSWNs displays two distinct patterns. In the common low-partner-number HSWNs, a significant proportion of NG incidence occurs among FSWs, with NG prevalence 13 times higher among FSWs than clients, and three times higher among clients than their spouses. Interventions substantially reduce incidence. Increasing condom use from 10 % to 50 % lowers NG prevalence among FSWs, clients, and their spouses from 12.2 % to 6.4 %, 1.2 % to 0.5 %, and 0.4 % to 0.2 %, respectively. Increasing symptomatic treatment coverage among FSWs from 0 % to 100 % decreases prevalence from 10.6 % to 4.5 %, 0.8 % to 0.4 %, and 0.3 % to 0.1 %, respectively. Increasing asymptomatic treatment coverage among FSWs from 0 % to 50 % decreases prevalence from 8.2 % to 0.4 %, 0.6 % to 0.1 %, and 0.2 % to 0.0 %, respectively, with very low prevalence when coverage exceeds 50 %. In high-partner-number HSWNs, prevalence among FSWs saturates at a high level, and the vast majority of incidence occurs among clients and their spouses, with a limited impact of incremental increases in interventions.</p></div><div><h3>Conclusion</h3><p>NG epidemiology in HSWNs is typically a \"fragile epidemiology\" that is responsive to a range of interventions even if the interventions are incremental, partially efficacious, and only applied to FSWs.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"48 ","pages":"Article 100785"},"PeriodicalIF":3.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S175543652400046X/pdfft?md5=0cbc2180fa22a9a122ea0088659deed4&pid=1-s2.0-S175543652400046X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898705","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":"Inference of epidemic dynamics in the COVID-19 era and beyond","authors":"Anne Cori ,&nbsp;Adam Kucharski","doi":"10.1016/j.epidem.2024.100784","DOIUrl":"10.1016/j.epidem.2024.100784","url":null,"abstract":"<div><p>The COVID-19 pandemic demonstrated the key role that epidemiology and modelling play in analysing infectious threats and supporting decision making in real-time. Motivated by the unprecedented volume and breadth of data generated during the pandemic, we review modern opportunities for analysis to address questions that emerge during a major modern epidemic. Following the broad chronology of insights required — from understanding initial dynamics to retrospective evaluation of interventions, we describe the theoretical foundations of each approach and the underlying intuition. Through a series of case studies, we illustrate real life applications, and discuss implications for future work.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"48 ","pages":"Article 100784"},"PeriodicalIF":3.0,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1755436524000458/pdfft?md5=12b720ca69c05460bd44c8300c5b79f1&pid=1-s2.0-S1755436524000458-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142012248","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":"COVID-19 in Scottish care homes: A metapopulation model of spread among residents and staff","authors":"Matthew Baister ,&nbsp;Ewan McTaggart ,&nbsp;Paul McMenemy ,&nbsp;Itamar Megiddo ,&nbsp;Adam Kleczkowski","doi":"10.1016/j.epidem.2024.100781","DOIUrl":"https://doi.org/10.1016/j.epidem.2024.100781","url":null,"abstract":"<div><p>The movement of populations between locations and activities can result in complex transmission dynamics, posing significant challenges in controlling infectious diseases like COVID-19. Notably, networks of care homes create an ecosystem where staff and visitor movement acts as a vector for disease transmission, contributing to the heightened risk for their vulnerable communities. Care homes in the UK were disproportionately affected by the first wave of the COVID-19 pandemic, accounting for almost half of COVID-19 deaths during the period of 6th March – 15th June 2020 and so there is a pressing need to explore modelling approaches suitable for such systems. We develop a generic compartmental Susceptible - Exposed - Infectious - Recovered - Dead (<strong>SEIRD</strong>) metapopulation model, with care home residents, care home workers, and the general population modelled as subpopulations, interacting on a network describing their mixing habits. We illustrate the model application by analysing the spread of COVID-19 over the first wave of the COVID-19 pandemic in the NHS Lothian health board, Scotland. We explicitly model the outbreak’s reproduction rate and care home visitation level over time for each subpopulation and execute a data fit and sensitivity analysis, focusing on parameters responsible for inter-subpopulation mixing: staff-sharing, staff shift patterns and visitation. The results from our sensitivity analysis show that restricting staff sharing between homes and staff interaction with the general public would significantly mitigate the disease burden. Our findings indicate that protecting care home staff from disease, coupled with reductions in staff-sharing across care homes and expedient cancellations of visitations, can significantly reduce the size of outbreaks in care home settings.</p></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"48 ","pages":"Article 100781"},"PeriodicalIF":3.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1755436524000422/pdfft?md5=8ce8872d61aa25c3648559eaa80cd993&pid=1-s2.0-S1755436524000422-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141583076","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}