Epidemics最新文献

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Impact of COVID-19 control measures on respiratory syncytial virus and hand-foot-and-mouth disease transmission in Hong Kong and South Korea COVID-19 控制措施对香港和韩国呼吸道合胞病毒和手足口病传播的影响。
IF 3 3区 医学
Epidemics Pub Date : 2024-10-10 DOI: 10.1016/j.epidem.2024.100797
Yiu Chung Lau , Sukhyun Ryu , Zhanwei Du , Lin Wang , Peng Wu , Eric H.Y. Lau , Benjamin J. Cowling , Sheikh Taslim Ali
{"title":"Impact of COVID-19 control measures on respiratory syncytial virus and hand-foot-and-mouth disease transmission in Hong Kong and South Korea","authors":"Yiu Chung Lau ,&nbsp;Sukhyun Ryu ,&nbsp;Zhanwei Du ,&nbsp;Lin Wang ,&nbsp;Peng Wu ,&nbsp;Eric H.Y. Lau ,&nbsp;Benjamin J. Cowling ,&nbsp;Sheikh Taslim Ali","doi":"10.1016/j.epidem.2024.100797","DOIUrl":"10.1016/j.epidem.2024.100797","url":null,"abstract":"<div><div>The public health and social measures (PHSMs) for mitigation/control of COVID-19 pandemic influenced the transmission dynamics of many other infectious diseases, including respiratory syncytial virus (RSV) infection, and hand, foot and mouth disease (HFMD) and their disease-burden. This study aimed to infer the transmission dynamics of these respiratory viruses and assess the impact of COVID-19 PHSMs on their community activity. We developed a compartmental framework to infer the transmission dynamics of RSV and HFMD in Hong Kong and South Korea from January 2014 to May 2024. We assessed the impact of PHSMs by comparing the change in virus transmissibility, reproduction number and population susceptibility before, during, and after the COVID-19 pandemic period. A significant reduction in RSV and HFMD activity was observed starting in January 2020, with a resurgence since late 2021. Transmissibility of both diseases decreased by 46 % - 95 % during the lull, while population susceptibility was estimated to increase by maximum of 19 %. On relaxation of the PHSMs, the transmissibility were recovered up to 70 % in Hong Kong and nearly 100 % in South Korea in 2023 with significant epidemics for these viruses. Strict implementation of COVID-19 PHSMs led to low RSV and HFMD activity, but the absence of community infection resulted in reductions in population immunity, and slightly larger epidemics when these diseases re-emerged following the COVID-19 pandemic.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100797"},"PeriodicalIF":3.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478826","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}
引用次数: 0
The effects of HIV self-testing on HIV incidence and awareness of status among men who have sex with men in the United States: Insights from a novel compartmental model 艾滋病病毒自我检测对美国男男性行为者中艾滋病病毒感染率和对感染状况认识的影响:新颖分区模型的启示。
IF 3 3区 医学
Epidemics Pub Date : 2024-10-05 DOI: 10.1016/j.epidem.2024.100796
Alex Viguerie , Chaitra Gopalappa , Cynthia M. Lyles , Paul G. Farnham
{"title":"The effects of HIV self-testing on HIV incidence and awareness of status among men who have sex with men in the United States: Insights from a novel compartmental model","authors":"Alex Viguerie ,&nbsp;Chaitra Gopalappa ,&nbsp;Cynthia M. Lyles ,&nbsp;Paul G. Farnham","doi":"10.1016/j.epidem.2024.100796","DOIUrl":"10.1016/j.epidem.2024.100796","url":null,"abstract":"<div><h3>Background</h3><div>The OraQuick In-Home HIV self-test represents a fast, inexpensive, and convenient method for users to assess their HIV status. If integrated thoughtfully into existing testing practices, accompanied by efficient pathways to formal diagnosis, self-testing could enhance both HIV awareness and reduce HIV incidence. However, currently available self-tests are less sensitive, particularly for recent infection, when compared to gold-standard laboratory tests. It is important to understand the impact if some portion of standard testing is replaced by self-tests. We used a compartmental model to evaluate the effects of self-testing in diverse scenarios among gay, bisexual and other men who have sex with men (MSM) in the United States for the period 2020–2030, and to understand which scenarios maximize the advantages of self-testing.</div></div><div><h3>Methods</h3><div>We introduced a novel 4-compartment model for HIV self-testing. We employed the model under different screening rates, self-test proportions, and delays to diagnosis for those identified through self-tests to determine the potential effects of self-testing on HIV incidence and awareness of status when applied to the US MSM population. We studied scenarios in which self-tests supplement laboratory-based tests, with no replacement, and scenarios in which some replacement occurs. We also examined how future improvements in self-test sensitivity may affect our results.</div></div><div><h3>Results</h3><div>When HIV self-tests are supplemental rather than substitutes for laboratory-based testing, self-testing can decrease HIV incidence among MSM in the US by up to 10 % and increase awareness of status among MSM from 85 % to 91 % over a 10-year period, provided linkage to care and formal diagnosis occur promptly following a positive self-test (90 days or less). As self-tests replace a higher percentage laboratory-based testing algorithms, increases in overall testing rates were necessary to ensure reductions in HIV incidence. However, such needed increases were relatively small (under 10 % for prompt engagement in care and moderate levels of replacement). Improvements in self-test sensitivity and/or decreases in the detection period may further reduce any necessary increases in overall testing by up to 40 %.</div></div><div><h3>Conclusions</h3><div>If properly utilized, self-testing can provide significant long-term reductions to HIV incidence and improve awareness of HIV status. Ensuring that self-testing increases overall testing and that formal diagnosis and engagement in care occur promptly following a positive self-test are necessary to maximize the benefits of self-testing. Future improvements in self-test sensitivity and reductions in the detection period would further reduce HIV incidence and the potential risks associated with replacing laboratory tests with self-tests.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100796"},"PeriodicalIF":3.0,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382152","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}
引用次数: 0
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey 基于废水的流行病学,用于 COVID-19 监测及其他:调查。
IF 3 3区 医学
Epidemics Pub Date : 2024-09-26 DOI: 10.1016/j.epidem.2024.100793
Chen Chen , Yunfan Wang , Gursharn Kaur , Aniruddha Adiga , Baltazar Espinoza , Srinivasan Venkatramanan , Andrew Warren , Bryan Lewis , Justin Crow , Rekha Singh , Alexandra Lorentz , Denise Toney , Madhav Marathe
{"title":"Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey","authors":"Chen Chen ,&nbsp;Yunfan Wang ,&nbsp;Gursharn Kaur ,&nbsp;Aniruddha Adiga ,&nbsp;Baltazar Espinoza ,&nbsp;Srinivasan Venkatramanan ,&nbsp;Andrew Warren ,&nbsp;Bryan Lewis ,&nbsp;Justin Crow ,&nbsp;Rekha Singh ,&nbsp;Alexandra Lorentz ,&nbsp;Denise Toney ,&nbsp;Madhav Marathe","doi":"10.1016/j.epidem.2024.100793","DOIUrl":"10.1016/j.epidem.2024.100793","url":null,"abstract":"<div><div>The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding wastewater-based epidemiology for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"49 ","pages":"Article 100793"},"PeriodicalIF":3.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367150","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}
引用次数: 0
Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks 缓慢进化的多宿主病原体的疫情重建:对三种现有牛分枝杆菌疫情爆发方法的比较研究
IF 3 3区 医学
Epidemics Pub Date : 2024-09-21 DOI: 10.1016/j.epidem.2024.100794
Hélène Duault , Benoit Durand , Laetitia Canini
{"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}
引用次数: 0
Directly observed social contact patterns among school children in rural Gambia 直接观察冈比亚农村学童的社会接触模式
IF 3 3区 医学
Epidemics Pub Date : 2024-09-11 DOI: 10.1016/j.epidem.2024.100790
Isaac Osei , Emmanuel Mendy , Kevin van Zandvoort , Olimatou Jobe , Golam Sarwar , Baleng Mahama Wutor , Stefan Flasche , Nuredin I. Mohammed , Jane Bruce , Brian Greenwood , Grant A. Mackenzie
{"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}
引用次数: 0
The impact of household size on measles transmission: A long-term perspective 家庭规模对麻疹传播的影响:长期视角
IF 3 3区 医学
Epidemics Pub Date : 2024-09-06 DOI: 10.1016/j.epidem.2024.100791
Subekshya Bidari , Wan Yang
{"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}
引用次数: 0
Preface: COVID-19 Scenario Modeling Hubs 前言:COVID-19 情景建模中心。
IF 3 3区 医学
Epidemics Pub Date : 2024-09-01 DOI: 10.1016/j.epidem.2024.100788
Sara L. Loo, Matteo Chinazzi, Ajitesh Srivastava, Srinivasan Venkatramanan, Shaun Truelove, Cecile Viboud
{"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}
引用次数: 0
Investigation of P. vivax elimination via mass drug administration: A simulation study 通过大规模给药消除间日疟原虫的研究:模拟研究
IF 3 3区 医学
Epidemics Pub Date : 2024-09-01 DOI: 10.1016/j.epidem.2024.100789
Md Nurul Anwar , James M. McCaw , Alexander E. Zarebski , Roslyn I. Hickson , Jennifer A. Flegg
{"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}
引用次数: 0
The utility of whole-genome sequencing to identify likely transmission pairs for pathogens with slow and variable evolution 全基因组测序在确定进化缓慢且多变的病原体的可能传播配对方面的作用
IF 3 3区 医学
Epidemics Pub Date : 2024-08-23 DOI: 10.1016/j.epidem.2024.100787
A.J. Wood , C.H. Benton , R.J. Delahay , G. Marion , E. Palkopoulou , C.M. Pooley , G.C. Smith , R.R. Kao
{"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}
引用次数: 0
Improving the contribution of mathematical modelling evidence to guidelines and policy: Experiences from tuberculosis 提高数学建模证据对指导方针和政策的贡献:结核病方面的经验。
IF 3 3区 医学
Epidemics Pub Date : 2024-08-06 DOI: 10.1016/j.epidem.2024.100786
C. Finn McQuaid , Nicolas A. Menzies , Rein M.G.J. Houben , Gabriella B. Gomez , Anna Vassall , Nimalan Arinaminpathy , Peter J. Dodd , Richard G. White
{"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}
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