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Kang H, Auzenbergs M, Clapham H, Maure C, Kim JH, Salje H, Taylor CG, Lim A, Clark A, Edmunds WJ, Sahastrabuddhe S, Brady OJ, Abbas K. Chikungunya seroprevalence, force of infection, and prevalence of chronic disability after infection in endemic and epidemic settings: a systematic review, meta-analysis, and modelling study. THE LANCET. INFECTIOUS DISEASES 2024; 24:488-503. [PMID: 38342105 DOI: 10.1016/s1473-3099(23)00810-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 02/13/2024]
Abstract
BACKGROUND Chikungunya is an arboviral disease transmitted by Aedes aegypti and Aedes albopictus mosquitoes with a growing global burden linked to climate change and globalisation. We aimed to estimate chikungunya seroprevalence, force of infection (FOI), and prevalence of related chronic disability and hospital admissions in endemic and epidemic settings. METHODS In this systematic review, meta-analysis, and modelling study, we searched PubMed, Ovid, and Web of Science for articles published from database inception until Sept 26, 2022, for prospective and retrospective cross-sectional studies that addressed serological chikungunya virus infection in any geographical region, age group, and population subgroup and for longitudinal prospective and retrospective cohort studies with data on chronic chikungunya or hospital admissions in people with chikungunya. We did a systematic review of studies on chikungunya seroprevalence and fitted catalytic models to each survey to estimate location-specific FOI (ie, the rate at which susceptible individuals acquire chikungunya infection). We performed a meta-analysis to estimate the proportion of symptomatic patients with laboratory-confirmed chikungunya who had chronic chikungunya or were admitted to hospital following infection. We used a random-effects model to assess the relationship between chronic sequelae and follow-up length using linear regression. The systematic review protocol is registered online on PROSPERO, CRD42022363102. FINDINGS We identified 60 studies with data on seroprevalence and chronic chikungunya symptoms done across 76 locations in 38 countries, and classified 17 (22%) of 76 locations as endemic settings and 59 (78%) as epidemic settings. The global long-term median annual FOI was 0·007 (95% uncertainty interval [UI] 0·003-0·010) and varied from 0·0001 (0·00004-0·0002) to 0·113 (0·07-0·20). The highest estimated median seroprevalence at age 10 years was in south Asia (8·0% [95% UI 6·5-9·6]), followed by Latin America and the Caribbean (7·8% [4·9-14·6]), whereas median seroprevalence was lowest in the Middle East (1·0% [0·5-1·9]). We estimated that 51% (95% CI 45-58) of people with laboratory-confirmed symptomatic chikungunya had chronic disability after infection and 4% (3-5) were admitted to hospital following infection. INTERPRETATION We inferred subnational heterogeneity in long-term average annual FOI and transmission dynamics and identified both endemic and epidemic settings across different countries. Brazil, Ethiopia, Malaysia, and India included both endemic and epidemic settings. Long-term average annual FOI was higher in epidemic settings than endemic settings. However, long-term cumulative incidence of chikungunya can be similar between large outbreaks in epidemic settings with a high FOI and endemic settings with a relatively low FOI. FUNDING International Vaccine Institute.
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Affiliation(s)
- Hyolim Kang
- London School of Hygiene and Tropical Medicine, London, UK; Seoul National University College of Medicine School, Seoul, South Korea.
| | | | - Hannah Clapham
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Clara Maure
- International Vaccine Institute, Seoul, South Korea
| | | | - Henrik Salje
- Department of Genetics, Cambridge University, Cambridge, UK
| | | | - Ahyoung Lim
- London School of Hygiene and Tropical Medicine, London, UK
| | - Andrew Clark
- London School of Hygiene and Tropical Medicine, London, UK
| | - W John Edmunds
- London School of Hygiene and Tropical Medicine, London, UK; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Sushant Sahastrabuddhe
- International Vaccine Institute, Seoul, South Korea; Centre International de Recherche en Infectiologie, Université Jean Monnet, Université Claude Bernard Lyon, INSERM, Saint-Etienne, France
| | - Oliver J Brady
- London School of Hygiene and Tropical Medicine, London, UK
| | - Kaja Abbas
- London School of Hygiene and Tropical Medicine, London, UK; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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Kada S, Paz-Bailey G, Adams LE, Johansson MA. Age-specific case data reveal varying dengue transmission intensity in US states and territories. PLoS Negl Trop Dis 2024; 18:e0011143. [PMID: 38427702 PMCID: PMC10936865 DOI: 10.1371/journal.pntd.0011143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/13/2024] [Accepted: 02/08/2024] [Indexed: 03/03/2024] Open
Abstract
Dengue viruses (DENV) are endemic in the US territories of Puerto Rico, American Samoa, and the US Virgin Islands, with focal outbreaks also reported in the states of Florida and Hawaii. However, little is known about the intensity of dengue virus transmission over time and how dengue viruses have shaped the level of immunity in these populations, despite the importance of understanding how and why levels of immunity against dengue may change over time. These changes need to be considered when responding to future outbreaks and enacting dengue management strategies, such as guiding vaccine deployment. We used catalytic models fitted to case surveillance data stratified by age from the ArboNET national arboviral surveillance system to reconstruct the history of recent dengue virus transmission in Puerto Rico, American Samoa, US Virgin Islands, Florida, Hawaii, and Guam. We estimated average annual transmission intensity (i.e., force of infection) of DENV between 2010 and 2019 and the level of seroprevalence by age group in each population. We compared models and found that assuming all reported cases are secondary infections generally fit the surveillance data better than assuming all cases are primary infections. Using the secondary case model, we found that force of infection was highly heterogeneous between jurisdictions and over time within jurisdictions, ranging from 0.00008 (95% CrI: 0.00002-0.0004) in Florida to 0.08 (95% CrI: 0.044-0.14) in American Samoa during the 2010-2019 period. For early 2020, we estimated that seropositivity in 10 year-olds ranged from 0.09% (0.02%-0.54%) in Florida to 56.3% (43.7%-69.3%) in American Samoa. In the absence of serological data, age-specific case notification data collected through routine surveillance combined with mathematical modeling are powerful tools to monitor arbovirus circulation, estimate the level of population immunity, and design dengue management strategies.
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Affiliation(s)
- Sarah Kada
- US Center for Disease Control and Prevention (CDC), Dengue Branch, San Juan, Puerto Rico
| | - Gabriela Paz-Bailey
- US Center for Disease Control and Prevention (CDC), Dengue Branch, San Juan, Puerto Rico
| | - Laura E. Adams
- US Center for Disease Control and Prevention (CDC), Dengue Branch, San Juan, Puerto Rico
| | - Michael A. Johansson
- US Center for Disease Control and Prevention (CDC), Dengue Branch, San Juan, Puerto Rico
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Colby E, Olsen J, Angulo FJ, Kelly P, Halsby K, Pilz A, Sot U, Chmielewski T, Pancer K, Moïsi JC, Jodar L, Stark JH. Estimated Incidence of Symptomatic Lyme Borreliosis Cases in Lublin, Poland in 2021. Microorganisms 2023; 11:2481. [PMID: 37894139 PMCID: PMC10608808 DOI: 10.3390/microorganisms11102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Lyme borreliosis (LB), the most common tick-borne disease in Europe, is endemic to Poland. Despite public health surveillance with mandatory reporting of LB cases by physicians and laboratories, many symptomatic LB cases are not included in surveillance in Poland. We estimated the extent of the under-ascertainment of symptomatic LB cases via surveillance in the Polish province of Lublin to better understand Poland's LB burden. The number of incident symptomatic LB cases in Lublin in 2010 was estimated from two seroprevalence studies conducted among adults in Lublin, as well as estimates of the proportion of asymptomatic LB cases and the duration of LB antibody persistence. The estimated number of incident symptomatic LB cases was compared to the number of surveillance-reported cases in Lublin to derive an under-ascertainment multiplier. This multiplier was applied to the number of surveillance-reported cases in 2021 to estimate the number and population-based incidence of symptomatic LB cases in Lublin in 2021. We estimate that there are 5.9 symptomatic LB cases for every surveillance-reported LB case in Lublin. Adjusting for under-ascertainment, the estimated number of symptomatic LB cases in Lublin in 2021 was 6204 (population-based incidence: 467.6/100,000). After adjustment for under-ascertainment, the incidence of symptomatic LB in Lublin, Poland, is high.
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Affiliation(s)
- Emily Colby
- Vaccines, Antivirals, and Evidence Generation, Pfizer Biopharma Group, Collegeville, PA 19426, USA
| | - Julia Olsen
- Vaccines, Antivirals, and Evidence Generation, Pfizer Biopharma Group, Collegeville, PA 19426, USA
| | - Frederick J. Angulo
- Vaccines, Antivirals, and Evidence Generation, Pfizer Biopharma Group, Collegeville, PA 19426, USA
| | - Patrick Kelly
- Vaccines, Antivirals, and Evidence Generation, Pfizer Biopharma Group, Collegeville, PA 19426, USA
| | - Kate Halsby
- Pfizer Vaccines, Tadworth, Surrey KT20 7NS, UK
| | - Andreas Pilz
- Vaccines, Pfizer Corporation Austria, 1210 Vienna, Austria
| | - Urszula Sot
- Vaccine Medical Affairs, Pfizer Poland Inc., 02-092 Warsaw, Poland
| | | | | | | | - Luis Jodar
- Vaccines, Antivirals, and Evidence Generation, Pfizer Biopharma Group, Collegeville, PA 19426, USA
| | - James H. Stark
- Vaccines, Antivirals, and Evidence Generation, Pfizer Biopharma Group, Cambridge, MA 02139, USA
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Ruhs EC, Chia WN, Foo R, Peel AJ, Li Y, Larman HB, Irving AT, Wang L, Brook CE. Applications of VirScan to broad serological profiling of bat reservoirs for emerging zoonoses. Front Public Health 2023; 11:1212018. [PMID: 37808979 PMCID: PMC10559906 DOI: 10.3389/fpubh.2023.1212018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Bats are important providers of ecosystem services such as pollination, seed dispersal, and insect control but also act as natural reservoirs for virulent zoonotic viruses. Bats host multiple viruses that cause life-threatening pathology in other animals and humans but, themselves, experience limited pathological disease from infection. Despite bats' importance as reservoirs for several zoonotic viruses, we know little about the broader viral diversity that they host. Bat virus surveillance efforts are challenged by difficulties of field capture and the limited scope of targeted PCR- or ELISA-based molecular and serological detection. Additionally, virus shedding is often transient, thus also limiting insights gained from nucleic acid testing of field specimens. Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a broad serological tool used previously to comprehensively profile viral exposure history in humans, offers an exciting prospect for viral surveillance efforts in wildlife, including bats. Methods Here, for the first time, we apply PhIP-Seq technology to bat serum, using a viral peptide library originally designed to simultaneously assay exposures to the entire human virome. Results Using VirScan, we identified past exposures to 57 viral genera-including betacoronaviruses, henipaviruses, lyssaviruses, and filoviruses-in semi-captive Pteropus alecto and to nine viral genera in captive Eonycteris spelaea. Consistent with results from humans, we find that both total peptide hits (the number of enriched viral peptides in our library) and the corresponding number of inferred past virus exposures in bat hosts were correlated with poor bat body condition scores and increased with age. High and low body condition scores were associated with either seropositive or seronegative status for different viruses, though in general, virus-specific age-seroprevalence curves defied assumptions of lifelong immunizing infection, suggesting that many bat viruses may circulate via complex transmission dynamics. Discussion Overall, our work emphasizes the utility of applying biomedical tools, like PhIP-Seq, first developed for humans to viral surveillance efforts in wildlife, while highlighting opportunities for taxon-specific improvements.
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Affiliation(s)
- Emily Cornelius Ruhs
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- Grainger Bioinformatics Center, Field Museum of Natural History, Chicago, IL, United States
| | - Wan Ni Chia
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- CoV Biotechnology Pte Ltd., Singapore, Singapore
| | - Randy Foo
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Alison J. Peel
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisband, QLD, Australia
| | - Yimei Li
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- Quantitative and Computational Biology, Princeton University, Princeton, NJ, United States
| | - H. Benjamin Larman
- HBL – Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, United States
| | - Aaron T. Irving
- Second Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang University-University of Edinburgh Institute, Haining, Zhejiang, China
- BIMET - Biomedical and Translational Research Centre of Zhejiang Province, Zhejiang Province, China
| | - Linfa Wang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
| | - Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
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Menezes A, Takahashi S, Routledge I, Metcalf CJE, Graham AL, Hay JA. serosim: An R package for simulating serological data arising from vaccination, epidemiological and antibody kinetics processes. PLoS Comput Biol 2023; 19:e1011384. [PMID: 37578985 PMCID: PMC10449138 DOI: 10.1371/journal.pcbi.1011384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/24/2023] [Accepted: 07/24/2023] [Indexed: 08/16/2023] Open
Abstract
serosim is an open-source R package designed to aid inference from serological studies, by simulating data arising from user-specified vaccine and antibody kinetics processes using a random effects model. Serological data are used to assess population immunity by directly measuring individuals' antibody titers. They uncover locations and/or populations which are susceptible and provide evidence of past infection or vaccination to help inform public health measures and surveillance. Both serological data and new analytical techniques used to interpret them are increasingly widespread. This creates a need for tools to simulate serological studies and the processes underlying observed titer values, as this will enable researchers to identify best practices for serological study design, and provide a standardized framework to evaluate the performance of different inference methods. serosim allows users to specify and adjust model inputs representing underlying processes responsible for generating the observed titer values like time-varying patterns of infection and vaccination, population demography, immunity and antibody kinetics, and serological sampling design in order to best represent the population and disease system(s) of interest. This package will be useful for planning sampling design of future serological studies, understanding determinants of observed serological data, and validating the accuracy and power of new statistical methods.
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Affiliation(s)
- Arthur Menezes
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Saki Takahashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Isobel Routledge
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Princeton School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America
| | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - James A. Hay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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Analysis of serological surveys of antibodies to SARS-CoV-2 in the United States to estimate parameters needed for transmission modeling and to evaluate and improve the accuracy of predictions. J Theor Biol 2023; 556:111296. [PMID: 36208669 PMCID: PMC9532270 DOI: 10.1016/j.jtbi.2022.111296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022]
Abstract
Seroprevalence studies can estimate proportions of the population that have been infected or vaccinated, including infections that were not reported because of the lack of symptoms or testing. Based on information from studies in the United States from mid-summer 2020 through the end of 2021, we describe proportions of the population with antibodies to SARS-CoV-2 as functions of age and time. Slices through these surfaces at arbitrary times provide initial and target conditions for simulation modeling. They also provide the information needed to calculate age-specific forces of infection, attack rates, and - together with contact rates - age-specific probabilities of infection on contact between susceptible and infectious people. We modified the familiar Susceptible-Exposed-Infectious-Removed (SEIR) model to include features of the biology of COVID-19 that might affect transmission of SARS-CoV-2 and stratified by age and location. We consulted the primary literature or subject matter experts for contact rates and other parameter values. Using time-varying Oxford COVID-19 Government Response Tracker assessments of US state and DC efforts to mitigate the pandemic and compliance with non-pharmaceutical interventions (NPIs) from a YouGov survey fielded in the US during 2020, we estimate that the efficacy of social-distancing when possible and mask-wearing otherwise at reducing susceptibility or infectiousness was 31% during the fall of 2020. Initialized from seroprevalence among people having commercial laboratory tests for purposes other than SARS-CoV-2 infection assessments on 7 September 2020, our age- and location-stratified SEIR population model reproduces seroprevalence among members of the same population on 25 December 2020 quite well. Introducing vaccination mid-December 2020, first of healthcare and other essential workers, followed by older adults, people who were otherwise immunocompromised, and then progressively younger people, our metapopulation model reproduces seroprevalence among blood donors on 4 April 2021 less well, but we believe that the discrepancy is due to vaccinations being under-reported or blood donors being disproportionately vaccinated, if not both. As experimenting with reliable transmission models is the best way to assess the indirect effects of mitigation measures, we determined the impact of vaccination, conditional on NPIs. Results indicate that, during this period, vaccination substantially reduced infections, hospitalizations and deaths. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics."
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Bailly S, Hozé N, Bisser S, Zhu-Soubise A, Fritzell C, Fernandes-Pellerin S, Mbouangoro A, Rousset D, Djossou F, Cauchemez S, Flamand C. Transmission dynamics of Q fever in French Guiana: A population-based cross-sectional study. LANCET REGIONAL HEALTH. AMERICAS 2022; 16:100385. [PMID: 36777152 PMCID: PMC9903881 DOI: 10.1016/j.lana.2022.100385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/20/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
Background Q fever is a zoonosis caused by Coxiella burnetii which is among the major agents of community-acquired pneumonia in French Guiana. Despite its relatively high incidence, its epidemiology in French Guiana remains unclear, and all previous studies have considered transmission from livestock unlikely, suggesting that a wild reservoir is responsible for transmission. Methods A country-wide seroprevalence survey of 2697 participants from French Guiana was conducted. Serum samples were tested for phase II IgG antibodies by ELISA and indirect immunofluorescence assays (IFAs). Factors associated with Q fever were investigated, and a serocatalytic model was used to reconstruct the annual force of infection. Findings The overall weighted seroprevalence was estimated at 9.6% (95% confidence interval (CI): 8.2%-11.0%). The model revealed constant, low-level circulation across French Guiana, particularly affecting middle-aged males (odds ratio (OR): 3.0, 95% credible interval (CrI): 1.7-5.8) and individuals living close to sheep farms (OR: 4, 95% CrI: 1.5-12). The overall annual number of cases was estimated at 579 (95% CrI: 492-670). In the region around Cayenne, the main urban municipality, the high seroprevalence was explained by an outbreak that may have occurred between 1996 and 2003 and that infected 10% (95% CrI: 6.9%-14%) of the population and males and females alike. Interpretation This study reveals for the first time Q fever dynamics of transmission and the role of domestic livestock in transmission in French Guiana and highlights the urgent need to reinforce Q fever surveillance in livestocks of the entire Guianese territory. Funding This study was supported by the "European Regional Development Fund" under EPI-ARBO grant agreement (GY0008695), the "Regional Health Agency of French Guiana" and the "National Center of Spatial Studies". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Sarah Bailly
- Epidemiology Unit, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | - Nathanaël Hozé
- Mathematical Modeling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, Paris, France
| | - Sylvie Bisser
- Medical Laboratory, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | | | - Camille Fritzell
- Epidemiology Unit, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | | | - Adija Mbouangoro
- Medical Laboratory, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | - Dominique Rousset
- Virology Laboratory, Institut Pasteur in French Guiana, Cayenne, French Guiana
| | - Félix Djossou
- Infectious and Tropical Disease Unit, Centre Hospitalier de Cayenne, Cayenne, French Guiana
| | - Simon Cauchemez
- Mathematical Modeling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, Paris, France
| | - Claude Flamand
- Epidemiology Unit, Institut Pasteur in French Guiana, Cayenne, French Guiana,Mathematical Modeling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, Paris, France,Corresponding author.
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de Glanville WA, Nyarobi JM, Kibona T, Halliday JEB, Thomas KM, Allan KJ, Johnson PCD, Davis A, Lankester F, Claxton JR, Rostal MK, Carter RW, de Jong RMF, Rubach MP, Crump JA, Mmbaga BT, Nyasebwa OM, Swai ES, Willett B, Cleaveland S. Inter-epidemic Rift Valley fever virus infection incidence and risks for zoonotic spillover in northern Tanzania. PLoS Negl Trop Dis 2022; 16:e0010871. [PMID: 36306281 PMCID: PMC9665400 DOI: 10.1371/journal.pntd.0010871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 11/15/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a mosquito-borne pathogen that has caused epidemics involving people and animals across Africa and the Arabian Peninsula. A number of studies have found evidence for the circulation of RVFV among livestock between these epidemics but the population-level incidence of infection during this inter-epidemic period (IEP) is rarely reported. General force of infection (FOI) models were applied to age-adjusted cross-sectional serological data to reconstruct the annual FOI and population-level incidence of RVFV infection among cattle, goats, and sheep in northern Tanzania from 2009 through 2015, a period without reported Rift Valley fever (RVF) cases in people or animals. To evaluate the potential for zoonotic RVFV spillover during this period, the relationship between village-level livestock RVFV FOI and human RVFV seropositivity was quantified using multi-level logistic regression. The predicted average annual incidence was 72 (95% Credible Interval [CrI] 63, 81) RVFV infections per 10,000 animals and 96 (95% CrI 81, 113), 79 (95% CrI 62, 98), and 39 (95% CrI 28, 52) per 10,000 cattle, sheep, and goats, respectively. There was variation in transmission intensity between study villages, with the highest estimated village-level FOI 2.49% (95% CrI 1.89, 3.23) and the lowest 0.12% (95% CrI 0.02, 0.43). The human RVFV seroprevalence was 8.2% (95% Confidence Interval 6.2, 10.9). Human seropositivity was strongly associated with the village-level FOI in livestock, with the odds of seropositivity in an individual person increasing by around 1.2 times (95% CrI 1.1, 1.3) for each additional annual RVFV seroconversion per 1,000 animals. A history of raw milk consumption was also positively associated with human seropositivity. RVFV has circulated at apparently low levels among livestock in northern Tanzania in the period since the last reported epidemic. Although our data do not allow us to confirm human RVFV infections during the IEP, a strong association between human seropositivity and the FOI in cattle, goats, and sheep supports the hypothesis that RVFV circulation among livestock during the IEP poses a risk for undetected zoonotic spillover in northern Tanzania. We provide further evidence for the likely role of raw milk consumption in RVFV transmission from animals to people.
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Affiliation(s)
- William A. de Glanville
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- University of Global Health Equity, Kigali, Rwanda
- * E-mail: (WAdG); (SC)
| | - James M. Nyarobi
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Tito Kibona
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Jo E. B. Halliday
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kate M. Thomas
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Kilimanjaro Clinical Research Institute, Moshi, United Republic of Tanzania
| | - Kathryn J. Allan
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Paul C. D. Johnson
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alicia Davis
- School of Social and Political Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Felix Lankester
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, United States of America
- Global Animal Health Tanzania, Arusha, Tanzania
| | - John R. Claxton
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Melinda K. Rostal
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- EcoHealth Alliance, New York, New York, United States of America
| | - Ryan W. Carter
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rosanne M. F. de Jong
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Matthew P. Rubach
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore, Singapore
| | - John A. Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, United Republic of Tanzania
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
| | - Obed M. Nyasebwa
- Ministry of Livestock and Fisheries, Dodoma, United Republic of Tanzania
| | - Emanuel S. Swai
- Ministry of Livestock and Fisheries, Dodoma, United Republic of Tanzania
| | - Brian Willett
- MRC University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sarah Cleaveland
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (WAdG); (SC)
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Cox V, O’Driscoll M, Imai N, Prayitno A, Hadinegoro SR, Taurel AF, Coudeville L, Dorigatti I. Estimating dengue transmission intensity from serological data: A comparative analysis using mixture and catalytic models. PLoS Negl Trop Dis 2022; 16:e0010592. [PMID: 35816508 PMCID: PMC9302823 DOI: 10.1371/journal.pntd.0010592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 07/21/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
Background Dengue virus (DENV) infection is a global health concern of increasing magnitude. To target intervention strategies, accurate estimates of the force of infection (FOI) are necessary. Catalytic models have been widely used to estimate DENV FOI and rely on a binary classification of serostatus as seropositive or seronegative, according to pre-defined antibody thresholds. Previous work has demonstrated the use of thresholds can cause serostatus misclassification and biased estimates. In contrast, mixture models do not rely on thresholds and use the full distribution of antibody titres. To date, there has been limited application of mixture models to estimate DENV FOI. Methods We compare the application of mixture models and time-constant and time-varying catalytic models to simulated data and to serological data collected in Vietnam from 2004 to 2009 (N ≥ 2178) and Indonesia in 2014 (N = 3194). Results The simulation study showed larger mean FOI estimate bias from the time-constant and time-varying catalytic models (-0.007 (95% Confidence Interval (CI): -0.069, 0.029) and -0.006 (95% CI -0.095, 0.043)) than from the mixture model (0.001 (95% CI -0.036, 0.065)). Coverage of the true FOI was > 95% for estimates from both the time-varying catalytic and mixture model, however the latter had reduced uncertainty. When applied to real data from Vietnam, the mixture model frequently produced higher FOI and seroprevalence estimates than the catalytic models. Conclusions Our results suggest mixture models represent valid, potentially less biased, alternatives to catalytic models, which could be particularly useful when estimating FOI from data with largely overlapping antibody titre distributions. Characterising the transmission intensity of dengue virus is essential to inform the implementation of interventions, such as vector control and vaccination, and to better understand the environmental drivers of transmission locally and globally. It is therefore important to understand how methodological differences and model choice may influence the accuracy of estimates of transmission intensity. Using a simulation study, we assessed the performance of catalytic and mixture models to reconstruct the force of infection (FOI) from simulated antibody titre data. Furthermore, we estimated the FOI of dengue virus from antibody titre data collected in Vietnam and Indonesia. The models produced consistent estimates of FOI when they were applied to data with clear separation between the distributions of seronegative and seropositive antibody titres. We observed greater bias in FOI estimates obtained from catalytic models than from mixture models when they were applied to data with high overlap in the bimodal distribution of antibody titres. Our results indicate that mixture models could be preferential to estimate dengue virus FOI when the antibody titre distributions of the seronegative and seropositive components largely overlap.
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Affiliation(s)
- Victoria Cox
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail:
| | - Megan O’Driscoll
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, United Kingdom
| | - Ari Prayitno
- Department of Child Health, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Sri Rezeki Hadinegoro
- Department of Child Health, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | | | | | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, United Kingdom
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Rees EM, Lau CL, Kama M, Reid S, Lowe R, Kucharski AJ. Estimating the duration of antibody positivity and likely time of Leptospira infection using data from a cross-sectional serological study in Fiji. PLoS Negl Trop Dis 2022; 16:e0010506. [PMID: 35696427 PMCID: PMC9232128 DOI: 10.1371/journal.pntd.0010506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/24/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Background Leptospirosis is a zoonotic disease prevalent throughout the world, but with particularly high burden in Oceania (including the Pacific Island Countries and Territories). Leptospirosis is endemic in Fiji, with outbreaks often occurring following heavy rainfall and flooding. As a result of non-specific clinical manifestation and diagnostic challenges, cases are often misdiagnosed or under-ascertained. Furthermore, little is known about the duration of persistence of antibodies to leptospirosis, which has important clinical and epidemiological implications. Methodology and principal findings Using the results from a serosurvey conducted in Fiji in 2013, we fitted serocatalytic models to estimate the duration of antibody positivity and the force of infection (FOI, the rate at which susceptible individuals acquire infection or seroconversion), whilst accounting for seroreversion. Additionally, we estimated the most likely timing of infection. Using the reverse catalytic model, we estimated the duration of antibody persistence to be 8.33 years (4.76–12.50; assuming constant FOI) and 7.25 years (3.36–11.36; assuming time-varying FOI), which is longer than previous estimates. Using population age-structured seroprevalence data alone, we were not able to distinguish between these two models. However, by bringing in additional longitudinal data on antibody kinetics we were able to estimate the most likely time of infection, lending support to the time-varying FOI model. We found that most individuals who were antibody-positive in the 2013 serosurvey were likely to have been infected within the previous two years, and this finding is consistent with surveillance data showing high numbers of cases reported in 2012 and 2013. Conclusions This is the first study to use serocatalytic models to estimate the FOI and seroreversion rate for Leptospira infection. As well as providing an estimate for the duration of antibody positivity, we also present a novel method to estimate the most likely time of infection from seroprevalence data. These approaches can allow for richer, longitudinal information to be inferred from cross-sectional studies, and could be applied to other endemic diseases where antibody waning occurs. Leptospirosis is a bacterial zoonotic disease that occurs in almost all regions of the world, with a particularly high burden of disease in Oceania. It is widely considered to be a Neglected Zoonotic Disease, and it is often mis-diagnosed and under-ascertained. Very little information exists about the persistence of antibodies to leptospirosis, which is important for understanding how long individuals may have partial protection against reinfection. In this study, we show how data collected from a large population survey of leptospirosis antibodies can be used to estimate the duration of antibody persistence. Knowledge of the duration of antibody persistence enables an estimation of the duration of immunity to re-infection, which is most likely antibody-mediated. We also estimate the rate at which susceptible individuals acquire infection (force of infection), whilst accounting for antibody waning. This provides more accurate estimates of population-wide disease burden. Finally, we show how the results from a cross-sectional population survey can be used to estimate when infections may have occurred. This is particularly useful in areas with limited surveillance. This approach could be applied to other neglected diseases for which data are limited and where antibody waning occurs.
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Affiliation(s)
- Eleanor M. Rees
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Colleen L. Lau
- School of Public Health, Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Mike Kama
- Fiji Centre for Communicable Disease Control, Suva, Fiji
- The University of the South Pacific, Suva, Fiji
| | - Simon Reid
- School of Public Health, Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Barcelona Supercomputing Center, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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11
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Post pandemic fatigue: what are effective strategies? Sci Rep 2022; 12:9706. [PMID: 35690631 PMCID: PMC9188281 DOI: 10.1038/s41598-022-13597-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 05/12/2022] [Indexed: 01/08/2023] Open
Abstract
Recurrent updates in non-pharmaceutical interventions (NPIs) aim to control successive waves of the coronavirus disease 2019 (COVID-19) but are often met with low adherence by the public. This study evaluated the effectiveness of gathering restrictions and quarantine policies based on a modified Susceptible-Exposed-Infectious-Hospitalized-Recovered (SEIHR) model by incorporating cross-boundary travellers with or without quarantine to study the transmission dynamics of COVID-19 with data spanning a nine-month period during 2020 in Hong Kong. The asymptotic stability of equilibria reveals that the model exhibits the phenomenon of backward bifurcation, which in this study is a co-existence between a stable disease-free equilibrium (DFE) and an endemic equilibrium (EE). Even if the basic reproduction number ([Formula: see text]) is less than unity, this disease cannot be eliminated. The effect of each parameter on the overall dynamics was assessed using Partial Rank Correlation Coefficients (PRCCs). Transmission rates (i.e., [Formula: see text] and [Formula: see text]), effective contact ratio [Formula: see text] between symptomatic individuals and quarantined people, and transfer rate [Formula: see text] related to infection during quarantine were identified to be the most sensitive parameters. The effective contact ratios between the infectors and susceptible individuals in late July were found to be over twice as high as that in March of 2020, reflecting pandemic fatigue and the potential existence of infection during quarantine.
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12
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Combining seroprevalence and capture-mark-recapture data to estimate the force of infection of brucellosis in a managed population of Alpine ibex. Epidemics 2022; 38:100542. [DOI: 10.1016/j.epidem.2022.100542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 01/04/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
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Rees EM, Waterlow NR, Lowe R, Kucharski AJ. Estimating the duration of seropositivity of human seasonal coronaviruses using seroprevalence studies. Wellcome Open Res 2021; 6:138. [PMID: 34708157 PMCID: PMC8517721 DOI: 10.12688/wellcomeopenres.16701.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2021] [Indexed: 01/08/2023] Open
Abstract
Background: The duration of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain, but it is of key clinical and epidemiological importance. Seasonal human coronaviruses (HCoV) have been circulating for longer and, therefore, may offer insights into the long-term dynamics of reinfection for such viruses. Methods: Combining historical seroprevalence data from five studies covering the four circulating HCoVs with an age-structured reverse catalytic model, we estimated the likely duration of seropositivity following seroconversion. Results: We estimated that antibody persistence lasted between 0.9 (95% Credible interval: 0.6 - 1.6) and 3.8 (95% CrI: 2.0 - 7.4) years. Furthermore, we found the force of infection in older children and adults (those over 8.5 [95% CrI: 7.5 - 9.9] years) to be higher compared with young children in the majority of studies. Conclusions: These estimates of endemic HCoV dynamics could provide an indication of the future long-term infection and reinfection patterns of SARS-CoV-2.
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Affiliation(s)
- Eleanor M. Rees
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Naomi R. Waterlow
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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Rees EM, Waterlow NR, Lowe R, Kucharski AJ. Estimating the duration of seropositivity of human seasonal coronaviruses using seroprevalence studies. Wellcome Open Res 2021; 6:138. [PMID: 34708157 PMCID: PMC8517721 DOI: 10.12688/wellcomeopenres.16701.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background: The duration of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain, but it is of key clinical and epidemiological importance. Seasonal human coronaviruses (HCoV) have been circulating for longer and, therefore, may offer insights into the long-term dynamics of reinfection for such viruses. Methods: Combining historical seroprevalence data from five studies covering the four circulating HCoVs with an age-structured reverse catalytic model, we estimated the likely duration of seropositivity following seroconversion. Results: We estimated that antibody persistence lasted between 0.9 (95% Credible interval: 0.6 - 1.6) and 3.8 (95% CrI: 2.0 - 7.4) years. Furthermore, we found the force of infection in older children and adults (those over 8.5 [95% CrI: 7.5 - 9.9] years) to be higher compared with young children in the majority of studies. Conclusions: These estimates of endemic HCoV dynamics could provide an indication of the future long-term infection and reinfection patterns of SARS-CoV-2.
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Affiliation(s)
- Eleanor M. Rees
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Naomi R. Waterlow
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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15
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Moore SM. The current burden of Japanese encephalitis and the estimated impacts of vaccination: Combining estimates of the spatial distribution and transmission intensity of a zoonotic pathogen. PLoS Negl Trop Dis 2021; 15:e0009385. [PMID: 34644296 PMCID: PMC8544850 DOI: 10.1371/journal.pntd.0009385] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/25/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022] Open
Abstract
Japanese encephalitis virus (JEV) is a major cause of neurological disability in Asia and causes thousands of severe encephalitis cases and deaths each year. Although Japanese encephalitis (JE) is a WHO reportable disease, cases and deaths are significantly underreported and the true burden of the disease is not well understood in most endemic countries. Here, we first conducted a spatial analysis of the risk factors associated with JE to identify the areas suitable for sustained JEV transmission and the size of the population living in at-risk areas. We then estimated the force of infection (FOI) for JE-endemic countries from age-specific incidence data. Estimates of the susceptible population size and the current FOI were then used to estimate the JE burden from 2010 to 2019, as well as the impact of vaccination. Overall, 1,543.1 million (range: 1,292.6-2,019.9 million) people were estimated to live in areas suitable for endemic JEV transmission, which represents only 37.7% (range: 31.6-53.5%) of the over four billion people living in countries with endemic JEV transmission. Based on the baseline number of people at risk of infection, there were an estimated 56,847 (95% CI: 18,003-184,525) JE cases and 20,642 (95% CI: 2,252-77,204) deaths in 2019. Estimated incidence declined from 81,258 (95% CI: 25,437-273,640) cases and 29,520 (95% CI: 3,334-112,498) deaths in 2010, largely due to increases in vaccination coverage which have prevented an estimated 314,793 (95% CI: 94,566-1,049,645) cases and 114,946 (95% CI: 11,421-431,224) deaths over the past decade. India had the largest estimated JE burden in 2019, followed by Bangladesh and China. From 2010-2019, we estimate that vaccination had the largest absolute impact in China, with 204,734 (95% CI: 74,419-664,871) cases and 74,893 (95% CI: 8,989-286,239) deaths prevented, while Taiwan (91.2%) and Malaysia (80.1%) had the largest percent reductions in JE burden due to vaccination. Our estimates of the size of at-risk populations and current JE incidence highlight countries where increasing vaccination coverage could have the largest impact on reducing their JE burden. Japanese encephalitis is a vector-transmitted, zoonotic disease that is endemic throughout a large portion of Asia. Vaccination has significantly reduced the JE burden in several formerly high-burden countries, but vaccination coverage remains limited in several other countries with high JE burdens. A better understanding of both the spatial distribution and the magnitude of the burden in endemic countries is critical for future disease prevention efforts. To estimate the number of people living in areas within Asia suitable for JEV transmission we conducted a spatial analysis of the risk factors associated with JE. We estimate that over one billion people live in areas suitable for local JEV transmission. We then combined these population-at-risk estimates with estimates of the force of infection (FOI) to model the national-level burden of JE (annual cases and deaths) over the past decade. Increases in vaccination coverage have reduced JE incidence from over 80,000 cases in 2010 to fewer than 57,000 cases in 2019. We estimate that vaccination has prevented almost 315,000 cases and 115,000 deaths in the past decade. Our results also call attention to the countries, and high-risk areas within countries, where increases in vaccination coverage are most needed.
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Affiliation(s)
- Sean M. Moore
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
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16
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Arık SÖ, Shor J, Sinha R, Yoon J, Ledsam JR, Le LT, Dusenberry MW, Yoder NC, Popendorf K, Epshteyn A, Euphrosine J, Kanal E, Jones I, Li CL, Luan B, Mckenna J, Menon V, Singh S, Sun M, Ravi AS, Zhang L, Sava D, Cunningham K, Kayama H, Tsai T, Yoneoka D, Nomura S, Miyata H, Pfister T. A prospective evaluation of AI-augmented epidemiology to forecast COVID-19 in the USA and Japan. NPJ Digit Med 2021; 4:146. [PMID: 34625656 PMCID: PMC8501040 DOI: 10.1038/s41746-021-00511-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/25/2021] [Indexed: 12/18/2022] Open
Abstract
The COVID-19 pandemic has highlighted the global need for reliable models of disease spread. We propose an AI-augmented forecast modeling framework that provides daily predictions of the expected number of confirmed COVID-19 deaths, cases, and hospitalizations during the following 4 weeks. We present an international, prospective evaluation of our models' performance across all states and counties in the USA and prefectures in Japan. Nationally, incident mean absolute percentage error (MAPE) for predicting COVID-19 associated deaths during prospective deployment remained consistently <8% (US) and <29% (Japan), while cumulative MAPE remained <2% (US) and <10% (Japan). We show that our models perform well even during periods of considerable change in population behavior, and are robust to demographic differences across different geographic locations. We further demonstrate that our framework provides meaningful explanatory insights with the models accurately adapting to local and national policy interventions. Our framework enables counterfactual simulations, which indicate continuing Non-Pharmaceutical Interventions alongside vaccinations is essential for faster recovery from the pandemic, delaying the application of interventions has a detrimental effect, and allow exploration of the consequences of different vaccination strategies. The COVID-19 pandemic remains a global emergency. In the face of substantial challenges ahead, the approach presented here has the potential to inform critical decisions.
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Affiliation(s)
- Sercan Ö Arık
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA.
| | - Joel Shor
- Google, Japan, Shibuya, 3-Chrome-21-3, Tokyo, Japan
| | | | - Jinsung Yoon
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | | | - Long T Le
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | | | | | | | | | | | - Elli Kanal
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | - Isaac Jones
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | - Chun-Liang Li
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | - Beth Luan
- Google, Japan, Shibuya, 3-Chrome-21-3, Tokyo, Japan
| | - Joe Mckenna
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | - Vikas Menon
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | | | - Mimi Sun
- Google Health, 1600 Amphitheatre Parkway, Mountain View, CA, USA
| | | | - Leyou Zhang
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | - Dario Sava
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
| | | | | | - Thomas Tsai
- Harvard School of Public Health, 677 Huntington Ave, Boston, MA, USA
| | - Daisuke Yoneoka
- Department of Health Policy and Management, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, Japan
- Division of Biostatistics and Bioinformatics, Graduate School of Public Health, St Luke's International University, 3-6-2 Tsukiji, Chuo-ku, Tokyo, Japan
| | - Shuhei Nomura
- Department of Health Policy and Management, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, Japan
- Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Miyata
- Department of Health Policy and Management, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, Japan
- Department of Healthcare Quality Assessment, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Tomas Pfister
- Google Cloud AI, 1170 Bordeaux Dr, Sunnyvale, CA, USA
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Saha D, Ota MOC, Pereira P, Buchy P, Badur S. Rotavirus vaccines performance: dynamic interdependence of host, pathogen and environment. Expert Rev Vaccines 2021; 20:945-957. [PMID: 34224290 DOI: 10.1080/14760584.2021.1951247] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION As of January 2021, rotavirus vaccination programs have been implemented in 109 countries and their use has resulted in a positive impact on rotavirus-related diarrheal hospitalizations and mortality in children below 5 years of age. Despite these successes, several countries in Africa and Asia where disease burden is high have not yet implemented rotavirus vaccination at all or at a scale sufficient enough to demonstrate impact. This could be, among other reasons, due to poor vaccine coverage and the modest levels of efficacy and effectiveness of the vaccines in these resource-limited settings. AREAS COVERED We review various factors related to the human host (malnutrition, maternally derived antibodies and breastfeeding, genetic factors, blood group, and co-administration with oral polio vaccine), rotavirus pathogen (force of infection, strain diversity and coinfections), and the environment (related to the human microbiome) which reflect complex and interconnected processes leading to diminished vaccine performance in resource-limited settings. EXPERT OPINION Addressing the limiting factors for vaccine efficacy is needed but likely to take a long time to be resolved. An immediate solution is to increase the immunization coverage to higher values generating an overall effect of adequate proportion of protected population to reduce the prevalence of rotavirus disease.
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Shanmugasundaram D, Awasthi S, Dwibedi B, Geetha S, Jain M, Malik S, Patel B, Singh H, Tripathi S, Viswanathan R, Agarwal A, Bonu R, Jain S, Jena SK, Priyasree J, Pushpalatha K, Ali S, Biswas D, Jain A, Narang R, Madhuri S, George S, Kaduskar O, Kiruthika G, Sabarinathan R, Sapakal G, Gupta N, Murhekar MV. Burden of congenital rubella syndrome (CRS) in India based on data from cross-sectional serosurveys, 2017 and 2019-20. PLoS Negl Trop Dis 2021; 15:e0009608. [PMID: 34297716 PMCID: PMC8376255 DOI: 10.1371/journal.pntd.0009608] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 08/19/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
Background India has set a goal to eliminate measles and rubella/Congenital Rubella Syndrome (CRS) by 2023. Towards this goal, India conducted nationwide supplementary immunization activity (SIA) with measles-rubella containing vaccine (MRCV) targeting children aged between 9 months to <15 years and established a hospital-based sentinel surveillance for CRS. Reliable data about incidence of CRS is necessary to monitor progress towards the elimination goal. Methods We conducted serosurveys in 2019–20 among pregnant women attending antenatal clinics of 6 hospitals, which were also sentinel sites for CRS surveillance, to estimate the prevalence of IgG antibodies against rubella. We systematically sampled 1800 women attending antenatal clinics and tested their sera for IgG antibodies against rubella. We used rubella seroprevalence data from the current survey and the survey conducted in 2017 among antenatal women from another 6 CRS surveillance sites to construct a catalytic models to estimate the incidence and burden of CRS. Result The seroprevalence of rubella antibodies was 82.3% (95% CI: 80.4–84.0). Rubella seropositivity did not differ by age group and educational status. Based on the constant and age-dependent force of infection models, we estimated that the annual incidence of CRS in India was 225.58 per 100,000 live births (95% CI: 217.49–232.41) and 65.47 per 100,000 live births (95% CI: 41.60–104.16) respectively. This translated to an estimated 14,520 (95% CI: 9,225–23,100) and 50,028 (95% CI: 48,234–51,543) infants with CRS every year based on age-dependent and constant force of infection models respectively. Conclusions Our findings indicated that about one fifth of women in the reproductive age group in India were susceptible for rubella. The estimates of CRS incidence will serve as a baseline to monitor the impact of MRCV SIAs, as well progress towards the elimination goal of rubella/CRS. Rubella infection during the first trimester of pregnancy can affect fetus, resulting in spontaneous abortion, stillbirth or birth of a baby with a combination of birth defects known as congenital rubella syndrome (CRS). Vaccination with rubella containing vaccine (RCV) is recommended as one of the strategies for eliminating rubella/CRS. The Southeast Asia region has set a target to eliminate rubella/CRS by 2023. Towards this goal, India completed nationwide immunization campaigns using measles-rubella vaccine during 2017–19, targeting children aged 9 months to <15 years. A case-based surveillance for CRS was initiated in five sentinel hospitals (Phase-1) in 2016 and later expanded to additional 6 sites (Phase-2) in 2019, to estimate burden of CRS and monitor its trend. As an adjunct to CRS surveillance, periodic serologic surveys were also planned to monitor the rubella seroprevalence among the pregnant women. A serosurvey conducted in 2017 indicated that 83.4% pregnant women attending antenatal clinics of Phase-1 sentinel hospitals had IgG antibodies against rubella. The second serosurvey conducted during 2019–20 in 6 Phase-2 sites indicated a comparable seroprevalence of 82.3%. Using seroprevalence data from these two serosurveys, we estimated that the annual incidence of CRS in India was 225.58 per 100,000 live births with constant force of infection and 65.47 per 100,000 live births with age-dependent force of infection models. This incidence rates translated to an estimated 14,520 to 50,028 infants with CRS every year. The estimates of CRS incidence will serve as a baseline to monitor the progress towards the elimination goal of rubella/CRS in India.
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Affiliation(s)
| | - Shally Awasthi
- King George Medical University, Lucknow, Uttar Pradesh, India
| | | | - S Geetha
- Govt Medical College, Thiruvananthapuram, Kerala, India
| | - Manish Jain
- Mahatma Gandhi Institute of Medical Sciences, Sewagram, Maharashtra, India
| | - Shikha Malik
- All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Bhupeshwari Patel
- All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | | | | | | | - Anjoo Agarwal
- King George Medical University, Lucknow, Uttar Pradesh, India
| | | | - Shuchi Jain
- Mahatma Gandhi Institute of Medical Sciences, Sewagram, Maharashtra, India
| | | | - J Priyasree
- Govt Medical College, Thiruvananthapuram, Kerala, India
| | - K Pushpalatha
- All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Syed Ali
- Govt Medical College, Thiruvananthapuram, Kerala, India
| | - Debasis Biswas
- All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Amita Jain
- King George Medical University, Lucknow, Uttar Pradesh, India
| | - Rahul Narang
- Mahatma Gandhi Institute of Medical Sciences, Sewagram, Maharashtra, India.,All India Institute of Medical Sciences, Bibinagar, Telangana
| | | | - Suji George
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ojas Kaduskar
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - G Kiruthika
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - R Sabarinathan
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Gajanan Sapakal
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | - Manoj V Murhekar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
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19
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Rees EM, Waterlow NR, Lowe R, Kucharski AJ. Estimating the duration of seropositivity of human seasonal coronaviruses using seroprevalence studies. Wellcome Open Res 2021; 6:138. [PMID: 34708157 PMCID: PMC8517721 DOI: 10.12688/wellcomeopenres.16701.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 11/20/2022] Open
Abstract
Background: The duration of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain, but it is of key clinical and epidemiological importance. Seasonal human coronaviruses (HCoV) have been circulating for longer and, therefore, may offer insights into the long-term dynamics of reinfection for such viruses. Methods: Combining historical seroprevalence data from five studies covering the four circulating HCoVs with an age-structured reverse catalytic model, we estimated the likely duration of seropositivity following seroconversion. Results: We estimated that antibody persistence lasted between 0.9 (95% Credible interval: 0.6 - 1.6) and 3.8 (95% CrI: 2.0 - 7.4) years. Furthermore, we found the force of infection in older children and adults (those over 8.5 [95% CrI: 7.5 - 9.9] years) to be higher compared with young children in the majority of studies. Conclusions: These estimates of endemic HCoV dynamics could provide an indication of the future long-term infection and reinfection patterns of SARS-CoV-2.
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Affiliation(s)
- Eleanor M. Rees
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Naomi R. Waterlow
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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20
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de Thoisy B, Duron O, Epelboin L, Musset L, Quénel P, Roche B, Binetruy F, Briolant S, Carvalho L, Chavy A, Couppié P, Demar M, Douine M, Dusfour I, Epelboin Y, Flamand C, Franc A, Ginouvès M, Gourbière S, Houël E, Kocher A, Lavergne A, Le Turnier P, Mathieu L, Murienne J, Nacher M, Pelleau S, Prévot G, Rousset D, Roux E, Schaub R, Talaga S, Thill P, Tirera S, Guégan JF. Ecology, evolution, and epidemiology of zoonotic and vector-borne infectious diseases in French Guiana: Transdisciplinarity does matter to tackle new emerging threats. INFECTION GENETICS AND EVOLUTION 2021; 93:104916. [PMID: 34004361 DOI: 10.1016/j.meegid.2021.104916] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 02/06/2023]
Abstract
French Guiana is a European ultraperipheric region located on the northern Atlantic coast of South America. It constitutes an important forested region for biological conservation in the Neotropics. Although very sparsely populated, with its inhabitants mainly concentrated on the Atlantic coastal strip and along the two main rivers, it is marked by the presence and development of old and new epidemic disease outbreaks, both research and health priorities. In this review paper, we synthetize 15 years of multidisciplinary and integrative research at the interface between wildlife, ecosystem modification, human activities and sociodemographic development, and human health. This study reveals a complex epidemiological landscape marked by important transitional changes, facilitated by increased interconnections between wildlife, land-use change and human occupation and activity, human and trade transportation, demography with substantial immigration, and identified vector and parasite pharmacological resistance. Among other French Guianese characteristics, we demonstrate herein the existence of more complex multi-host disease life cycles than previously described for several disease systems in Central and South America, which clearly indicates that today the greater promiscuity between wildlife and humans due to demographic and economic pressures may offer novel settings for microbes and their hosts to circulate and spread. French Guiana is a microcosm that crystallizes all the current global environmental, demographic and socioeconomic change conditions, which may favor the development of ancient and future infectious diseases.
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Affiliation(s)
- Benoît de Thoisy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, French Guiana.
| | - Olivier Duron
- UMR MIVEGEC, IRD, CNRS, Université de Montpellier, Centre IRD de Montpellier, Montpellier, France; Centre de Recherche en Écologie et Évolution de la Santé, Montpellier, France
| | - Loïc Epelboin
- Infectious Diseases Department, Centre Hospitalier de Cayenne, Cayenne, French Guiana
| | - Lise Musset
- Laboratoire de Parasitologie, Centre Collaborateur OMS Pour La Surveillance Des Résistances Aux Antipaludiques, Centre National de Référence du Paludisme, Pôle zones Endémiques, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Philippe Quénel
- Université de Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR-S 1085 Rennes, France
| | - Benjamin Roche
- UMR MIVEGEC, IRD, CNRS, Université de Montpellier, Centre IRD de Montpellier, Montpellier, France; Centre de Recherche en Écologie et Évolution de la Santé, Montpellier, France
| | - Florian Binetruy
- UMR MIVEGEC, IRD, CNRS, Université de Montpellier, Centre IRD de Montpellier, Montpellier, France
| | - Sébastien Briolant
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France; Aix Marseille Université, IRD, SSA, AP-HM, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), France; IHU Méditerranée Infection, Marseille, France
| | | | - Agathe Chavy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, French Guiana
| | - Pierre Couppié
- Dermatology Department, Centre Hospitalier de Cayenne, Cayenne, French Guiana
| | - Magalie Demar
- TBIP, Université de Guyane, Cayenne, French Guiana; Université de Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019-UMR 9017-CIIL Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Maylis Douine
- Centre d'Investigation Clinique Antilles-Guyane, Inserm 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana
| | - Isabelle Dusfour
- Département de Santé Globale, Institut Pasteur, Paris, France; Institut Pasteur de la Guyane, Vectopôle Amazonien Emile Abonnenc, Cayenne, French Guiana
| | - Yanouk Epelboin
- Institut Pasteur de la Guyane, Vectopôle Amazonien Emile Abonnenc, Cayenne, French Guiana
| | - Claude Flamand
- Epidemiology Unit, Institut Pasteur de la Guyane, Cayenne, French Guiana; Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France
| | - Alain Franc
- UMR BIOGECO, INRAE, Université de Bordeaux, Cestas, France; Pleiade, EPC INRIA-INRAE-CNRS, Université de Bordeaux Talence, France
| | - Marine Ginouvès
- TBIP, Université de Guyane, Cayenne, French Guiana; Université de Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019-UMR 9017-CIIL Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Sébastien Gourbière
- UMR 5096 Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, Perpignan, France
| | - Emeline Houël
- CNRS, UMR EcoFoG, AgroParisTech, Cirad, INRAE, Université des Antilles, Université de Guyane, Cayenne, France
| | - Arthur Kocher
- Transmission, Infection, Diversification & Evolution Group, Max-Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Laboratoire Evolution et Diversité Biologique (UMR 5174), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, French Guiana
| | - Paul Le Turnier
- Service de Maladies Infectieuses et Tropicales, Hôtel Dieu - INSERM CIC 1413, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Luana Mathieu
- Université de Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR-S 1085 Rennes, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (UMR 5174), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Mathieu Nacher
- Centre d'Investigation Clinique Antilles-Guyane, Inserm 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana
| | - Stéphane Pelleau
- Université de Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR-S 1085 Rennes, France; Malaria: Parasites and Hosts, Institut Pasteur, Paris, France
| | - Ghislaine Prévot
- TBIP, Université de Guyane, Cayenne, French Guiana; Université de Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019-UMR 9017-CIIL Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Dominique Rousset
- Laboratoire de Virologie, Institut Pasteur de la Guyane, Cayenne Cedex, French Guiana
| | - Emmanuel Roux
- ESPACE-DEV (Institut de Recherche pour le Développement, Université de la Réunion, Université des Antilles, Université de Guyane, Université de Montpellier, Montpellier, France; International Joint Laboratory "Sentinela" Fundação Oswaldo Cruz, Universidade de Brasília, Institut de Recherche pour le Développement, Rio de Janeiro RJ-21040-900, Brazil
| | - Roxane Schaub
- TBIP, Université de Guyane, Cayenne, French Guiana; Université de Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019-UMR 9017-CIIL Centre d'Infection et d'Immunité de Lille, Lille, France; Centre d'Investigation Clinique Antilles-Guyane, Inserm 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana
| | - Stanislas Talaga
- UMR MIVEGEC, IRD, CNRS, Université de Montpellier, Centre IRD de Montpellier, Montpellier, France; Institut Pasteur de la Guyane, Vectopôle Amazonien Emile Abonnenc, Cayenne, French Guiana
| | - Pauline Thill
- Service Universitaire des Maladies Infectieuses et du Voyageur, Centre Hospitalier Dron, Tourcoing, France
| | - Sourakhata Tirera
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, French Guiana
| | - Jean-François Guégan
- UMR MIVEGEC, IRD, CNRS, Université de Montpellier, Centre IRD de Montpellier, Montpellier, France; UMR ASTRE, INRAE, CIRAD, Université de Montpellier, Montpellier, France.
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21
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Milne G, Webster JP, Walker M. Toward Improving Interventions Against Toxoplasmosis by Identifying Routes of Transmission Using Sporozoite-specific Serological Tools. Clin Infect Dis 2021; 71:e686-e693. [PMID: 32280956 PMCID: PMC7744992 DOI: 10.1093/cid/ciaa428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 04/10/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Horizontal transmission of Toxoplasma gondii occurs primarily via ingestion of environmental oocysts or consumption of undercooked/raw meat containing cyst-stage bradyzoites. The relative importance of these 2 transmission routes remains unclear. Oocyst infection can be distinguished from bradyzoite infection by identification of immunoglobulin G (IgG) antibodies against T. gondii embryogenesis-related protein (TgERP). These antibodies are, however, thought to persist for only 6-8 months in human sera, limiting the use of TgERP serology to only those patients recently exposed to T. gondii. Yet recent serological survey data indicate a more sustained persistence of anti-TgERP antibodies. Elucidating the duration of anti-TgERP IgG will help to determine whether TgERP serology has epidemiological utility for quantifying the relative importance of different routes of T. gondii transmission. METHODS We developed a serocatalytic mathematical model to capture the change in seroprevalence of non-stage-specific IgG and anti-TgERP IgG antibodies with human age. The model was fitted to published datasets collected in an endemic region of Brazil to estimate the duration of anti-TgERP IgG antibodies, accounting for variable age-force of infection profiles and uncertainty in the diagnostic performance of TgERP serology. RESULTS We found that anti-TgERP IgG persists for substantially longer than previously recognized, with estimates ranging from 8.3 to 41.1 years. The Brazilian datasets were consistent with oocysts being the predominant transmission route in these settings. CONCLUSIONS The longer than previously recognized duration of anti-TgERP antibodies indicates that anti-TgERP serology could be a useful tool for delineating T. gondii transmission routes in human populations. TgERP serology may therefore be an important epidemiological tool for informing the design of tailored, setting-specific public health information campaigns and interventions.
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Affiliation(s)
- Gregory Milne
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire, United Kingdom.,London Centre for Neglected Tropical Disease Research, Imperial College London Faculty of Medicine, St Mary's Hospital Campus, London, United Kingdom
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire, United Kingdom.,London Centre for Neglected Tropical Disease Research, Imperial College London Faculty of Medicine, St Mary's Hospital Campus, London, United Kingdom
| | - Martin Walker
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire, United Kingdom.,London Centre for Neglected Tropical Disease Research, Imperial College London Faculty of Medicine, St Mary's Hospital Campus, London, United Kingdom
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22
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Alexander N, Carabali M, Lim JK. Estimating force of infection from serologic surveys with imperfect tests. PLoS One 2021; 16:e0247255. [PMID: 33661951 PMCID: PMC7932155 DOI: 10.1371/journal.pone.0247255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 02/04/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The force of infection, or the rate at which susceptible individuals become infected, is an important public health measure for assessing the extent of outbreaks and the impact of control programs. METHODS AND FINDINGS We present Bayesian methods for estimating force of infection using serological surveys of infections which produce a lasting immune response, accounting for imperfections of the test, and uncertainty in such imperfections. In this estimation, the sensitivity and specificity can either be fixed, or belief distributions of their values can be elicited to allow for uncertainty. We analyse data from two published serological studies of dengue, one in Colombo, Sri Lanka, with a single survey and one in Medellin, Colombia, with repeated surveys in the same individuals. For the Colombo study, we illustrate how the inferred force of infection increases as the sensitivity decreases, and the reverse for specificity. When 100% sensitivity and specificity are assumed, the results are very similar to those from a standard analysis with binomial regression. For the Medellin study, the elicited distribution for sensitivity had a lower mean and higher variance than the one for specificity. Consequently, taking uncertainty in sensitivity into account resulted in a wide credible interval for the force of infection. CONCLUSIONS These methods can make more realistic estimates of force of infection, and help inform the choice of serological tests for future serosurveys.
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Affiliation(s)
- Neal Alexander
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Mabel Carabali
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Jacqueline K. Lim
- Global Dengue and Aedes-transmitted Diseases Consortium (GDAC), International Vaccine Institute, Seoul, Korea
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23
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Estimating disease prevalence and temporal dynamics using biased capture serological data in a wildlife reservoir: The example of brucellosis in Alpine ibex (Capra ibex). Prev Vet Med 2020; 187:105239. [PMID: 33373957 DOI: 10.1016/j.prevetmed.2020.105239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/17/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
The monitoring of the disease prevalence in a population is an essential component of its adaptive management. However, field data often lead to biased estimates. This is the case for brucellosis infection of ibex in the Bargy massif (France). A test-and-cull program is being carried out in this area to manage the infection: captured animals are euthanized when seropositive, and marked and released when seronegative. Because this mountainous species is difficult to capture, field workers tend to focus the capture effort on unmarked animals. Indeed, marked animals are less likely to be infected, as they were controlled and negative during previous years. As the proportion of marked animals in the population becomes large, captured animals can no longer be considered as an unbiased sample of the population. We designed an integrated Bayesian model to correct this bias, by estimating the seroprevalence in the population as the combination of the separate estimates of the seroprevalence among unmarked animals (estimated from the data) and marked animals (estimated with a catalytic infection model, to circumvent the scarcity of the data). As seroprevalence may not be the most responsive parameter to management actions, we also estimated the proportion of animals in the population with an active bacterial infection. The actual infection status of captured animals was thus inferred as a function of their age and their level of antibodies, using a model based on bacterial cultures carried out for a sample of animals. Focusing on the population of adult females in the core area of the massif, i.e. with the highest seroprevalence, this observational study shows that seroprevalence has been divided by two between 2013 (51%) and 2018 (21%). Moreover, the likely estimated proportion of actively infected females in the same population, though very imprecise, has decreased from a likely estimate of 34% to less than 15%, suggesting that the management actions have been effective in reducing infection prevalence.
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24
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Capai L, Hozé N, Chiaroni J, Gross S, Djoudi R, Charrel R, Izopet J, Bosseur F, Priet S, Cauchemez S, de Lamballerie X, Falchi A, Gallian P. Seroprevalence of hepatitis E virus among blood donors on Corsica, France, 2017. ACTA ACUST UNITED AC 2020; 25. [PMID: 32046820 PMCID: PMC7014670 DOI: 10.2807/1560-7917.es.2020.25.5.1900336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Hepatitis E virus (HEV) is an emerging zoonotic pathogen and an important cause of acute viral hepatitis in European countries. Corsica Island has been previously identified as a hyperendemic area for HEV. Aim Our aim was to characterise the prevalence and titres of IgG antibodies to HEV among blood donors on Corsica and establish a model of the annual force of infection. Methods Between September 2017 and January 2018, 2,705 blood donations were tested for anti-HEV IgG using the Wantai HEV IgG enzyme immunoassay. Results The overall seroprevalence was 56.1%. In multivariate analysis, seroprevalence was higher in men than in women (60.0% vs 52.2%; p < 0.01), increased with age and was significantly higher among donors born on Corsica (60.6% vs 53.2%; p < 0.01). No significant difference was observed between the five districts of the island. IgG anti-HEV titres were mostly low (70% of positive donors had titres < 3 IU/mL). In Corsican natives, increasing seroprevalence by age could be explained by models capturing a loss of immunity (annual probability of infection: 4.5%; duration of immunity: 55 years) or by age-specific probabilities of infection (3.8% for children, 1.3% for adults). Conclusion We confirmed the high HEV seroprevalence on Corsica and identified three aspects that should be further explored: (i) the epidemiology in those younger than 18 years, (ii) common sources of contamination, in particular drinking water, that may explain the wide exposure of the population, and (iii) the actual protection afforded by the low IgG titres observed and the potential susceptibility to secondary HEV infection.
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Affiliation(s)
- Lisandru Capai
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Nathanaël Hozé
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Jacques Chiaroni
- Etablissement Français du Sang Provence alpes Côte d'Azur et Corse, Marseille, France
| | - Sylvie Gross
- Etablissement Français du Sang, 93210, La Plaine-Saint-Denis, France
| | - Rachid Djoudi
- Etablissement Français du Sang, 93210, La Plaine-Saint-Denis, France
| | - Rémi Charrel
- Unité des Virus Émergents (UVE): Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection, Marseille, France
| | - Jacques Izopet
- Institut National de la Santé et de la Recherche Médicale Unité 1043, Université Toulouse III, Toulouse, France.,Laboratoire de Virologie, Institut Fédératif de Biologie, Centre Hospitalier et Universitaire, Toulouse, France
| | - Frédéric Bosseur
- Sciences Pour l'Environnement - UMR CNRS 6134 Université de Corse, Corte, France
| | - Stéphane Priet
- Unité des Virus Émergents (UVE): Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection, Marseille, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE): Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection, Marseille, France
| | - Alessandra Falchi
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Pierre Gallian
- Unité des Virus Émergents (UVE): Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection, Marseille, France.,Etablissement Français du Sang, 93210, La Plaine-Saint-Denis, France.,Etablissement Français du Sang Provence alpes Côte d'Azur et Corse, Marseille, France
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25
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Saha S, Mishra A, Dana SK, Hens C, Bairagi N. Infection spreading and recovery in a square lattice. Phys Rev E 2020; 102:052307. [PMID: 33327064 DOI: 10.1103/physreve.102.052307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
We investigate spreading and recovery of disease in a square lattice, and, in particular, emphasize the role of the initial distribution of infected patches in the network on the progression of an endemic and initiation of a recovery process, if any, due to migration of both the susceptible and infected hosts. The disease starts in the lattice with three possible initial distribution patterns of infected and infection-free sites, viz., infected core patches (ICP), infected peripheral patches (IPP), and randomly distributed infected patches (RDIP). Our results show that infection spreads monotonically in the lattice with increasing migration without showing any sign of recovery in the ICP case. In the IPP case, it follows a similar monotonic progression with increasing migration; however, a self-organized healing process starts for higher migration, leading the lattice to full recovery at a critical rate of migration. Encouragingly, for the initial RDIP arrangement, chances of recovery are much higher with a lower rate of critical migration. An eigenvalue-based semianalytical study is made to determine the critical migration rate for realizing a stable infection-free lattice. The initial fraction of infected patches and the force of infection play significant roles in the self-organized recovery. They follow an exponential law, for the RDIP case, that governs the recovery process. For the frustrating case of ICP arrangement, we propose a random rewiring of links in the lattice allowing long-distance migratory paths that effectively initiate a recovery process. Global prevalence of infection thereby declines and progressively improves with the rewiring probability that follows a power law with the critical migration and leads to the birth of emergent infection-free networks.
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Affiliation(s)
- Suman Saha
- Centre for Mathematical Biology and Ecology, Department of Mathematics, Jadavpur University, Kolkata 700032, India
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone, Faridabad 121001, India
| | - Arindam Mishra
- Centre for Mathematical Biology and Ecology, Department of Mathematics, Jadavpur University, Kolkata 700032, India
| | - Syamal K Dana
- Centre for Mathematical Biology and Ecology, Department of Mathematics, Jadavpur University, Kolkata 700032, India
| | - Chittaranjan Hens
- Physics and Applied Mathematics Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Nandadulal Bairagi
- Centre for Mathematical Biology and Ecology, Department of Mathematics, Jadavpur University, Kolkata 700032, India
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26
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Dixon MA, Winskill P, Harrison WE, Whittaker C, Schmidt V, Sarti E, Bawm S, Dione MM, Thomas LF, Walker M, Basáñez MG. Force-of-infection of Taenia solium porcine cysticercosis: a modelling analysis to assess global incidence and prevalence trends. Sci Rep 2020; 10:17637. [PMID: 33077748 PMCID: PMC7572398 DOI: 10.1038/s41598-020-74007-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 09/14/2020] [Indexed: 11/26/2022] Open
Abstract
The World Health Organization (WHO) called, in 2012, for a validated strategy towards Taenia solium taeniasis/cysticercosis control and elimination. Estimating pig force-of-infection (FoI, the average rate at which susceptible pigs become infected) across geographical settings will help understand local epidemiology and inform effective intervention design. Porcine cysticercosis (PCC) age-prevalence data (from 15 studies in Latin America, Africa and Asia) were identified through systematic review. Catalytic models were fitted to the data using Bayesian methods, incorporating uncertainty in diagnostic performance, to estimate rates of antibody seroconversion, viable metacestode acquisition, and seroreversion/infection loss. There was evidence of antibody seroreversion across 5 studies, and of infection loss in 6 studies measured by antigen or necropsy, indicating transient serological responses and natural resolution of infection. Concerted efforts should be made to collect robust data using improved diagnostics to better understand geographical heterogeneities in T. solium transmission to support post-2020 WHO targets.
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Affiliation(s)
- Matthew A Dixon
- Department of Infectious Disease Epidemiology and London Centre for Neglected Tropical Disease Research (LCNTDR), Faculty of Medicine, School of Public Health, Imperial College London, London, W2 1PG, UK.
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, W2 1PG, UK.
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Wendy E Harrison
- SCI Foundation, Edinburgh House, 170 Kennington Lane, London, SE11 5DP, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Veronika Schmidt
- Department of Neurology, Center for Global Health, Technical University Munich (TUM), Munich, Germany
- Centre for Global Health, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Elsa Sarti
- Sanofi Pasteur Latin America, Av. Universidad N° 1738, Colonia Coyoacán, 04000, Mexico, D.F., Mexico
| | - Saw Bawm
- University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - Michel M Dione
- International Livestock Research Institute, 01 BP 1496, Ouagadougou, Burkina Faso
| | - Lian F Thomas
- International Livestock Research Institute (ILRI), Old Naivasha Road, PO Box 30709-00100, Nairobi, Kenya
- Institute for Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool, L69 7BE, UK
| | - Martin Walker
- Department of Pathobiology and Population Sciences and London Centre for Neglected Tropical Disease Research (LCNTDR), Royal Veterinary College, Hatfield, AL9 7TA, UK
| | - Maria-Gloria Basáñez
- Department of Infectious Disease Epidemiology and London Centre for Neglected Tropical Disease Research (LCNTDR), Faculty of Medicine, School of Public Health, Imperial College London, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, W2 1PG, UK
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Huang AT, Garcia-Carreras B, Hitchings MDT, Yang B, Katzelnick LC, Rattigan SM, Borgert BA, Moreno CA, Solomon BD, Trimmer-Smith L, Etienne V, Rodriguez-Barraquer I, Lessler J, Salje H, Burke DS, Wesolowski A, Cummings DAT. A systematic review of antibody mediated immunity to coronaviruses: kinetics, correlates of protection, and association with severity. Nat Commun 2020; 11:4704. [PMID: 32943637 PMCID: PMC7499300 DOI: 10.1038/s41467-020-18450-4] [Citation(s) in RCA: 605] [Impact Index Per Article: 151.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 01/05/2023] Open
Abstract
Many public health responses and modeled scenarios for COVID-19 outbreaks caused by SARS-CoV-2 assume that infection results in an immune response that protects individuals from future infections or illness for some amount of time. The presence or absence of protective immunity due to infection or vaccination (when available) will affect future transmission and illness severity. Here, we review the scientific literature on antibody immunity to coronaviruses, including SARS-CoV-2 as well as the related SARS-CoV, MERS-CoV and endemic human coronaviruses (HCoVs). We reviewed 2,452 abstracts and identified 491 manuscripts relevant to 5 areas of focus: 1) antibody kinetics, 2) correlates of protection, 3) immunopathogenesis, 4) antigenic diversity and cross-reactivity, and 5) population seroprevalence. While further studies of SARS-CoV-2 are necessary to determine immune responses, evidence from other coronaviruses can provide clues and guide future research.
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Affiliation(s)
- Angkana T Huang
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Bernardo Garcia-Carreras
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Matt D T Hitchings
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Bingyi Yang
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Leah C Katzelnick
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Susan M Rattigan
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Brooke A Borgert
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Carlos A Moreno
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Benjamin D Solomon
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Luke Trimmer-Smith
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Veronique Etienne
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Comparative, Diagnostic & Population Medicine, University of Florida, Gainesville, FL, USA
| | | | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Henrik Salje
- Department of Biology, University of Florida, Gainesville, FL, USA
- Department of Genetics, University of Cambridge, Cambridge, UK
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
| | - Donald S Burke
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Derek A T Cummings
- Department of Biology, University of Florida, Gainesville, FL, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
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28
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Smith OM, Edworthy A, Taylor JM, Jones MS, Tormanen A, Kennedy CM, Fu Z, Latimer CE, Cornell KA, Michelotti LA, Sato C, Northfield T, Snyder WE, Owen JP. Agricultural intensification heightens food safety risks posed by wild birds. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13723] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Olivia M. Smith
- School of Biological Sciences Washington State University Pullman WA USA
- Department of Entomology University of Georgia Athens GA USA
| | - Amanda Edworthy
- Department of Entomology Washington State University Pullman WA USA
- Department of Forest and Conservation Sciences University of British Columbia Vancouver BC USA
| | - Joseph M. Taylor
- Department of Entomology University of Georgia Athens GA USA
- Department of Entomology Washington State University Pullman WA USA
| | - Matthew S. Jones
- Department of Entomology Washington State University Pullman WA USA
- WSU‐Tree Fruit Research and Extension Center Wenatchee WA USA
| | - Aaron Tormanen
- School of Biological Sciences Washington State University Pullman WA USA
- Department of Entomology Washington State University Pullman WA USA
- Department of Biological Sciences Arkansas Tech University Russellville AR USA
| | | | - Zhen Fu
- Department of Entomology Washington State University Pullman WA USA
- Department of Entomology Texas A&M University College Station TX USA
| | | | - Kevin A. Cornell
- School of Biological Sciences Washington State University Pullman WA USA
| | - Lucas A. Michelotti
- Department of Entomology University of Georgia Athens GA USA
- Department of Entomology Washington State University Pullman WA USA
| | - Chika Sato
- School of Biological Sciences Washington State University Pullman WA USA
| | - Tobin Northfield
- Department of Entomology Washington State University Pullman WA USA
- WSU‐Tree Fruit Research and Extension Center Wenatchee WA USA
- Centre for Tropical Environmental Sustainability Science James Cook University Brisbane Qld Australia
| | - William E. Snyder
- Department of Entomology University of Georgia Athens GA USA
- Department of Entomology Washington State University Pullman WA USA
| | - Jeb P. Owen
- Department of Entomology Washington State University Pullman WA USA
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29
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Herzog CM, de Glanville WA, Willett BJ, Cattadori IM, Kapur V, Hudson PJ, Buza J, Swai ES, Cleaveland S, Bjørnstad ON. Peste des petits ruminants Virus Transmission Scaling and Husbandry Practices That Contribute to Increased Transmission Risk: An Investigation among Sheep, Goats, and Cattle in Northern Tanzania. Viruses 2020; 12:E930. [PMID: 32847058 PMCID: PMC7552010 DOI: 10.3390/v12090930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 11/22/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) causes an infectious disease of high morbidity and mortality among sheep and goats which impacts millions of livestock keepers globally. PPRV transmission risk varies by production system, but a deeper understanding of how transmission scales in these systems and which husbandry practices impact risk is needed. To investigate transmission scaling and husbandry practice-associated risk, this study combined 395 household questionnaires with over 7115 cross-sectional serosurvey samples collected in Tanzania among agropastoral and pastoral households managing sheep, goats, or cattle (most managed all three, n = 284, 71.9%). Although self-reported compound-level herd size was significantly larger in pastoral than agropastoral households, the data show no evidence that household herd force of infection (FOI, per capita infection rate of susceptible hosts) increased with herd size. Seroprevalence and FOI patterns observed at the sub-village level showed significant spatial variation in FOI. Univariate analyses showed that household herd FOI was significantly higher when households reported seasonal grazing camp attendance, cattle or goat introduction to the compound, death, sale, or giving away of animals in the past 12 months, when cattle were grazed separately from sheep and goats, and when the household also managed dogs or donkeys. Multivariable analyses revealed that species, production system type, and goat or sheep introduction or seasonal grazing camp attendance, cattle or goat death or sales, or goats given away in the past 12 months significantly increased odds of seroconversion, whereas managing pigs or cattle attending seasonal grazing camps had significantly lower odds of seroconversion. Further research should investigate specific husbandry practices across production systems in other countries and in systems that include additional atypical host species to broaden understanding of PPRV transmission.
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Affiliation(s)
- Catherine M. Herzog
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
| | - William A. de Glanville
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; (W.A.d.G.); (S.C.)
| | - Brian J. Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK;
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
| | - Joram Buza
- Nelson Mandela African Institute of Science and Technology, Arusha Box 447, Tanzania;
| | - Emmanuel S. Swai
- Department of Veterinary Services, Ministry of Livestock and Fisheries, Dodoma Box 2870, Tanzania;
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; (W.A.d.G.); (S.C.)
| | - Ottar N. Bjørnstad
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
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30
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Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Glendinning P, Gog JR, Hart WS, Heesterbeek H, House T, Keeling M, Kiss IZ, Kretzschmar ME, Lloyd AL, McBryde ES, McCaw JM, McKinley TJ, Miller JC, Morris M, O'Neill PD, Parag KV, Pearson CAB, Pellis L, Pulliam JRC, Ross JV, Tomba GS, Silverman BW, Struchiner CJ, Tildesley MJ, Trapman P, Webb CR, Mollison D, Restif O. Key questions for modelling COVID-19 exit strategies. Proc Biol Sci 2020; 287:20201405. [PMID: 32781946 PMCID: PMC7575516 DOI: 10.1098/rspb.2020.1405] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.
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Affiliation(s)
- Robin N. Thompson
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
- Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | | | - Valerie Isham
- Department of Statistical Science, University College London, Gower Street, London WC1E 6BT, UK
| | - Daniel Arribas-Bel
- School of Environmental Sciences, University of Liverpool, Brownlow Street, Liverpool L3 5DA, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, North Road, Bath BA2 7AY, UK
| | - Tom Britton
- Department of Mathematics, Stockholm University, Kräftriket, 106 91 Stockholm, Sweden
| | - Peter Challenor
- College of Engineering, Mathematical and Physical Sciences, University of Exeter, Exeter EX4 4QE, UK
| | - Lauren H. K. Chappell
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Hannah Clapham
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore117549, Singapore
| | - Nik J. Cunniffe
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - A. Philip Dawid
- Statistical Laboratory, University of Cambridge, Wilberforce Road, Cambridge CB3 0WB, UK
| | - Christl A. Donnelly
- Department of Statistics, University of Oxford, St Giles', Oxford OX1 3LB, UK
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial CollegeLondon, Norfolk Place, London W2 1PG, UK
| | - Rosalind M. Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Sebastian Funk
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Nigel Gilbert
- Department of Sociology, University of Surrey, Stag Hill, Guildford GU2 7XH, UK
| | - Paul Glendinning
- Department of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Julia R. Gog
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - William S. Hart
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
| | - Hans Heesterbeek
- Department of Population Health Sciences, Utrecht University, Yalelaan, 3584 CL Utrecht, The Netherlands
| | - Thomas House
- IBM Research, The Hartree Centre, Daresbury, Warrington WA4 4AD, UK
- Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Matt Keeling
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - István Z. Kiss
- School of Mathematical and Physical Sciences, University of Sussex, Falmer, Brighton BN1 9QH, UK
| | - Mirjam E. Kretzschmar
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
| | - Alun L. Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
| | - Emma S. McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia
| | - James M. McCaw
- School of Mathematics and Statistics, University of Melbourne, Carlton, Victoria 3010, Australia
| | - Trevelyan J. McKinley
- College of Medicine and Health, University of Exeter, Barrack Road, Exeter EX2 5DW, UK
| | - Joel C. Miller
- Department of Mathematics and Statistics, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Martina Morris
- Department of Sociology, University of Washington, Savery Hall, Seattle, WA 98195, USA
| | - Philip D. O'Neill
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial CollegeLondon, Norfolk Place, London W2 1PG, UK
| | - Carl A. B. Pearson
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Jonkershoek Road, Stellenbosch 7600, South Africa
| | - Lorenzo Pellis
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Juliet R. C. Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Jonkershoek Road, Stellenbosch 7600, South Africa
| | - Joshua V. Ross
- School of Mathematical Sciences, University of Adelaide, South Australia 5005, Australia
| | | | - Bernard W. Silverman
- Department of Statistics, University of Oxford, St Giles', Oxford OX1 3LB, UK
- Rights Lab, University of Nottingham, Highfield House, Nottingham NG7 2RD, UK
| | - Claudio J. Struchiner
- Escola de Matemática Aplicada, Fundação Getúlio Vargas, Praia de Botafogo, 190 Rio de Janeiro, Brazil
| | - Michael J. Tildesley
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Pieter Trapman
- Department of Mathematics, Stockholm University, Kräftriket, 106 91 Stockholm, Sweden
| | - Cerian R. Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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31
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Khosravi A, Chaman R, Rohani-Rasaf M, Zare F, Mehravaran S, Emamian MH. The basic reproduction number and prediction of the epidemic size of the novel coronavirus (COVID-19) in Shahroud, Iran. Epidemiol Infect 2020; 148:e115. [PMID: 32517845 PMCID: PMC7322167 DOI: 10.1017/s0950268820001247] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/19/2020] [Accepted: 06/04/2020] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to estimate the basic reproduction number (R0) of COVID-19 in the early stage of the epidemic and predict the expected number of new cases in Shahroud in Northeastern Iran. The R0 of COVID-19 was estimated using the serial interval distribution and the number of incidence cases. The 30-day probable incidence and cumulative incidence were predicted using the assumption that daily incidence follows a Poisson distribution determined by daily infectiousness. Data analysis was done using 'earlyR' and 'projections' packages in R software. The maximum-likelihood value of R0 was 2.7 (95% confidence interval (CI): 2.1-3.4) for the COVID-19 epidemic in the early 14 days and decreased to 1.13 (95% CI 1.03-1.25) by the end of day 42. The expected average number of new cases in Shahroud was 9.0 ± 3.8 cases/day, which means an estimated total of 271 (95% CI: 178-383) new cases for the period between 02 April to 03 May 2020. By day 67 (27 April), the effective reproduction number (Rt), which had a descending trend and was around 1, reduced to 0.70. Based on the Rt for the last 21 days (days 46-67 of the epidemic), the prediction for 27 April to 26 May is a mean daily cases of 2.9 ± 2.0 with 87 (48-136) new cases. In order to maintain R below 1, we strongly recommend enforcing and continuing the current preventive measures, restricting travel and providing screening tests for a larger proportion of the population.
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Affiliation(s)
- A. Khosravi
- Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran
| | - R. Chaman
- Department of Epidemiology, School of Public Health, Shahroud University of Medical Sciences, Shahroud, Iran
| | - M. Rohani-Rasaf
- Department of Epidemiology, School of Public Health, Shahroud University of Medical Sciences, Shahroud, Iran
| | - F. Zare
- Center for Health Related Social and Behavioral Sciences Research, Shahroud University of Medical Sciences, Shahroud, Iran
| | - S. Mehravaran
- ASCEND Center for Biomedical Research, Morgan State University, Baltimore, USA
| | - M. H. Emamian
- Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran
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32
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Endo A, Nishiura H. Age and geographic dependence of Zika virus infection during the outbreak on Yap island, 2007. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2020; 17:4115-4126. [PMID: 32987571 DOI: 10.3934/mbe.2020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Intensive surveillance of Zika virus infection conducted on Yap Island has provided crucial information on the epidemiological characteristics of the virus, but the rate of infection and medical attendance stratified by age and geographical location of the epidemic have yet to be fully clarified. In the present study, we reanalyzed surveillance data reported in a previous study. Likelihood-based Bayesian inference was used to gauge the age and geographically dependent force of infection and age-dependent reporting rate, with unobservable variables imputed by the data augmentation method. The inferred age-dependent component of the force of infection was suggested to be up to 3-4 times higher among older adults than among children. The age-dependent reporting rate ranged from 0.7% (5-9 years old) to 3.3% (50-54 years old). The proportion of serologically confirmed cases among total probable or confirmed cases was estimated to be 44.9%. The cumulative incidence of infection varied by municipality: Median values were over 80% in multiple locations (Gagil, Tomil, and Weloy), but relatively low values (below 50%) were derived in other locations. However, the possibility of a comparably high incidence of infection was not excluded even in municipalities with the lowest estimates. The results suggested a high degree of heterogeneity in the Yap epidemic. The force of infection and reporting rate were higher among older age groups, and this discrepancy implied that the demographic patterns were remarkably different between all infected and medically attended individuals. A higher reporting rate may have reflected more severe clinical presentation among adults. The symptomatic ratio in dengue cases is known to correlate with age, and our findings presumably indicate a similar tendency in Zika virus disease.
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Affiliation(s)
- A Endo
- Graduate School of Medicine, Hokkaido University, Kita 15 Jo Nishi 7 Chome, Kita-ku, Sapporo 060-8638, Japan
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, Bloomsbury, London WC1E 7HT, United Kingdom
| | - H Nishiura
- Graduate School of Medicine, Hokkaido University, Kita 15 Jo Nishi 7 Chome, Kita-ku, Sapporo 060-8638, Japan
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33
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Quan TM, Thao TTN, Duy NM, Nhat TM, Clapham H. Estimates of the global burden of Japanese encephalitis and the impact of vaccination from 2000-2015. eLife 2020; 9:51027. [PMID: 32450946 PMCID: PMC7282807 DOI: 10.7554/elife.51027] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 05/17/2020] [Indexed: 11/13/2022] Open
Abstract
Japanese encephalitis (JE) is a mosquito-borne disease, known for its high mortality and disability rate among symptomatic cases. Many effective vaccines are available for JE, and the use of a recently developed and inexpensive vaccine, SA 14-14-2, has been increasing over the recent years particularly with Gavi support. Estimates of the local burden and the past impact of vaccination are therefore increasingly needed, but difficult due to the limitations of JE surveillance. In this study, we implemented a mathematical modelling method (catalytic model) combined with age-stratifed case data from our systematic review which can overcome some of these limitations. We estimate in 2015 JEV infections caused 100,308 JE cases (95% CI: 61,720-157,522) and 25,125 deaths (95% CI: 14,550-46,031) globally, and that between 2000 and 2015 307,774 JE cases (95% CI: 167,442-509,583) were averted due to vaccination globally. Our results highlight areas that could have the greatest benefit from starting vaccination or from scaling up existing programs and will be of use to support local and international policymakers in making vaccine allocation decisions.
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Affiliation(s)
- Tran Minh Quan
- Oxford University Clinical Research Unit, Wellcome Trust Asia Program, Ho Chi Minh City, Viet Nam.,Biological Science Department, University of Notre Dame, Notre Dame, United States
| | - Tran Thi Nhu Thao
- Oxford University Clinical Research Unit, Wellcome Trust Asia Program, Ho Chi Minh City, Viet Nam.,Virology Department, Institute of Virology and Immunology, University of Bern, Bern, Switzerland
| | - Nguyen Manh Duy
- Oxford University Clinical Research Unit, Wellcome Trust Asia Program, Ho Chi Minh City, Viet Nam
| | - Tran Minh Nhat
- Oxford University Clinical Research Unit, Wellcome Trust Asia Program, Ho Chi Minh City, Viet Nam
| | - Hannah Clapham
- Oxford University Clinical Research Unit, Wellcome Trust Asia Program, Ho Chi Minh City, Viet Nam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
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Pastoral production is associated with increased peste des petits ruminants seroprevalence in northern Tanzania across sheep, goats and cattle. Epidemiol Infect 2020; 147:e242. [PMID: 31364555 DOI: 10.1017/s0950268819001262] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in small ruminant populations globally. Using cross-sectional serosurvey data collected in 2016, our study investigated PPRV seroprevalence and risk factors among sheep, goats and cattle in 20 agropastoral (AP) and pastoral (P) villages in northern Tanzania. Overall observed seroprevalence was 21.1% (95% exact confidence interval (CI) 20.1-22.0) with 5.8% seroprevalence among agropastoral (95% CI 5.0-6.7) and 30.7% among pastoral villages (95% CI 29.3-32.0). Seropositivity varied significantly by management (production) system. Our study applied the catalytic framework to estimate the force of infection. The associated reproductive numbers (R0) were estimated at 1.36 (95% CI 1.32-1.39), 1.40 (95% CI 1.37-1.44) and 1.13 (95% CI 1.11-1.14) for sheep, goats and cattle, respectively. For sheep and goats, these R0 values are likely underestimates due to infection-associated mortality. Spatial heterogeneity in risk among pairs of species across 20 villages was significantly positively correlated (R2: 0.59-0.69), suggesting either cross-species transmission or common, external risk factors affecting all species. The non-negligible seroconversion in cattle may represent spillover or cattle-to-cattle transmission and must be investigated further to understand the role of cattle in PPRV transmission ahead of upcoming eradication efforts.
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The seroprevalence of cytomegalovirus infection in Belgium anno 2002 and 2006: a comparative analysis with hepatitis A virus seroprevalence. Epidemiol Infect 2020; 147:e154. [PMID: 31063104 PMCID: PMC6518518 DOI: 10.1017/s0950268819000487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytomegalovirus (CMV) infection is endemic worldwide but its seroprevalence varies widely. The goal of this study was to estimate the age-specific seroprevalence of CMV infection in Belgium based on two cross-sectional serological datasets from 2002 and 2006. The seroprevalence was estimated relying on diagnostic test results based on cut-off values pre-specified by the manufacturers of the tests as well as relying on mixture models applied to continuous pathogen-specific immunoglobulin G antibody titre concentrations. The age-specific seroprevalence of hepatitis A virus (HAV), based on three Belgian cross-sectional serological datasets from 1993, 2002 and 2006, was used as a comparator since individuals acquire lifelong immunity upon recovery, implying an increasing seroprevalence with age. The age group weighted overall CMV seroprevalence derived from the mixture model was 32% (95% confidence interval (CI) 31-34%) in 2002 and 31% (95% CI 30-32%) in 2006. We demonstrated that CMV epidemiology differs from the immunizing infection HAV. This was the first large-scale study of CMV and HAV serial datasets in Belgium, estimating seroprevalence specified by age and birth cohort.
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Identifying Age Cohorts Responsible for Peste Des Petits Ruminants Virus Transmission among Sheep, Goats, and Cattle in Northern Tanzania. Viruses 2020; 12:v12020186. [PMID: 32046120 PMCID: PMC7077219 DOI: 10.3390/v12020186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/13/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in global sheep and goat populations. To better control this disease and inform eradication strategies, an improved understanding of how PPRV transmission risk varies by age is needed. Our study used a piece-wise catalytic model to estimate the age-specific force of infection (FOI, per capita infection rate of susceptible hosts) among sheep, goats, and cattle from a cross-sectional serosurvey dataset collected in 2016 in Tanzania. Apparent seroprevalence increased with age, reaching 53.6%, 46.8%, and 11.6% (true seroprevalence: 52.7%, 52.8%, 39.2%) for sheep, goats, and cattle, respectively. Seroprevalence was significantly higher among pastoral animals than agropastoral animals across all ages, with pastoral sheep and goat seroprevalence approaching 70% and 80%, respectively, suggesting pastoral endemicity. The best fitting piece-wise catalytic models merged age groups: two for sheep, three for goats, and four for cattle. The signal of these age heterogeneities were weak, except for a significant FOI peak among 2.5-3.5-year-old pastoral cattle. The subtle age-specific heterogeneities identified in this study suggest that targeting control efforts by age may not be as effective as targeting by other risk factors, such as production system type. Further research should investigate how specific husbandry practices affect PPRV transmission.
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Reynolds JJH, Carver S, Cunningham MW, Logan KA, Vickers W, Crooks KR, VandeWoude S, Craft ME. Feline immunodeficiency virus in puma: Estimation of force of infection reveals insights into transmission. Ecol Evol 2019; 9:11010-11024. [PMID: 31641451 PMCID: PMC6802039 DOI: 10.1002/ece3.5584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 12/30/2022] Open
Abstract
Determining parameters that govern pathogen transmission (such as the force of infection, FOI), and pathogen impacts on morbidity and mortality, is exceptionally challenging for wildlife. Vital parameters can vary, for example across host populations, between sexes and within an individual's lifetime.Feline immunodeficiency virus (FIV) is a lentivirus affecting domestic and wild cat species, forming species-specific viral-host associations. FIV infection is common in populations of puma (Puma concolor), yet uncertainty remains over transmission parameters and the significance of FIV infection for puma mortality. In this study, the age-specific FOI of FIV in pumas was estimated from prevalence data, and the evidence for disease-associated mortality was assessed.We fitted candidate models to FIV prevalence data and adopted a maximum likelihood method to estimate parameter values in each model. The models with the best fit were determined to infer the most likely FOI curves. We applied this strategy for female and male pumas from California, Colorado, and Florida.When splitting the data by sex and area, our FOI modeling revealed no evidence of disease-associated mortality in any population. Both sex and location were found to influence the FOI, which was generally higher for male pumas than for females. For female pumas at all sites, and male pumas from California and Colorado, the FOI did not vary with puma age, implying FIV transmission can happen throughout life; this result supports the idea that transmission can occur from mothers to cubs and also throughout adult life. For Florida males, the FOI was a decreasing function of puma age, indicating an increased risk of infection in the early years, and a decreased risk at older ages.This research provides critical insight into pathogen transmission and impact in a secretive and solitary carnivore. Our findings shed light on the debate on whether FIV causes mortality in wild felids like puma, and our approach may be adopted for other diseases and species. The methodology we present can be used for identifying likely transmission routes of a pathogen and also estimating any disease-associated mortality, both of which can be difficult to establish for wildlife diseases in particular.
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Affiliation(s)
| | - Scott Carver
- School of Biological SciencesUniversity of TasmaniaHobartTas.Australia
| | | | | | - Winston Vickers
- Wildlife Health CenterUniversity of California DavisDavisCAUSA
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsCOUSA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Meggan E. Craft
- Department of Veterinary Population MedicineUniversity of MinnesotaSt PaulMNUSA
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Bhavsar A, Tam CC, Garg S, Jammy GR, Taurel AF, Chong SN, Nealon J. Estimated dengue force of infection and burden of primary infections among Indian children. BMC Public Health 2019; 19:1116. [PMID: 31412836 PMCID: PMC6694619 DOI: 10.1186/s12889-019-7432-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/01/2019] [Indexed: 12/17/2022] Open
Abstract
Background Comprehensive, age-stratified dengue surveillance data are unavailable from India and many more dengue cases occur than are reported. Additional information on dengue transmission dynamics can inform understanding of disease endemicity and infection risk. Methods Using age-stratified dengue IgG seroprevalence data from 2556 Indian children aged 5–10 years, we estimated annual force of infection (FOI) at each of 6 sites using a binomial regression model. We estimated the ages by which 50 and 70% of children were first infected; and predicted seroprevalence in children aged 1–10 years assuming constant force-of-infection. Applying these infection rates to national census data, we then calculated the number of primary dengue infections occurring, annually, in Indian children. Results Annual force-of-infection at all sites combined was 11.9% (95% CI 8.8–16.2), varying across sites from 3.5% (95% CI 2.8–4.4) to 21.2% (95% CI 18.4–24.5). Overall, 50 and 70% of children were infected by 5.8 (95% CI 4.3–7.9) and 10.1 (95% CI 7.4–13.7) years respectively. In all sites except Kalyani, > 70% of children had been infected before their 11th birthday, and goodness-of-fit statistics indicated a relatively constant force-of-infection over time except at two sites (Wardha and Hyderabad). Nationwide, we estimated 17,013,527 children (95% CI: 14,518,438- 19,218,733), equivalent to 6.5% of children aged < 11 years, experience their first infection annually. Conclusions Dengue force-of-infection in India is comparable to other highly endemic countries. Significant variation across sites exists, likely reflecting local epidemiological variation. The number of annual primary infections is indicative of a significant, under-reported burden of secondary infections and symptomatic episodes. Trial registration Registered retrospectively with clinicaltrials.gov (NCT01477671; 18/11/2011) and clinical trials registry of India (ctri.nic.in; CTRI/2011/12/002243; 15/12/2011). Date of enrollment of 1st subject: 22/9/2011. Electronic supplementary material The online version of this article (10.1186/s12889-019-7432-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amit Bhavsar
- Sanofi Pasteur- India, Mumbai, India.,Present address: GSK Biologicals, Rixensart, Belgium
| | - Clarence C Tam
- Present address: Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore.,London School of Hygiene & Tropical Medicine, London, UK
| | - Suneela Garg
- Maulana Azad Medical College, Bahadur Shah Zafar Marg, New Delhi, Delhi, 10002, India
| | - Guru Rajesh Jammy
- SHARE INDIA - Mediciti Institute of Medical Sciences, Hyderabad, India
| | - Anne-Frieda Taurel
- Sanofi Pasteur- Singapore, Asia & JPAC, 38 Beach Road # 18-11, South Beach Tower, Singapore, 189767, Singapore
| | - Sher-Ney Chong
- Present address: Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore.,Sanofi Pasteur- Singapore, Asia & JPAC, 38 Beach Road # 18-11, South Beach Tower, Singapore, 189767, Singapore
| | - Joshua Nealon
- Sanofi Pasteur- Singapore, Asia & JPAC, 38 Beach Road # 18-11, South Beach Tower, Singapore, 189767, Singapore.
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Brook CE, Ranaivoson HC, Broder CC, Cunningham AA, Héraud J, Peel AJ, Gibson L, Wood JLN, Metcalf CJ, Dobson AP. Disentangling serology to elucidate henipa- and filovirus transmission in Madagascar fruit bats. J Anim Ecol 2019; 88:1001-1016. [PMID: 30908623 PMCID: PMC7122791 DOI: 10.1111/1365-2656.12985] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/13/2019] [Indexed: 01/23/2023]
Abstract
Bats are reservoirs for emerging human pathogens, including Hendra and Nipah henipaviruses and Ebola and Marburg filoviruses. These viruses demonstrate predictable patterns in seasonality and age structure across multiple systems; previous work suggests that they may circulate in Madagascar's endemic fruit bats, which are widely consumed as human food. We aimed to (a) document the extent of henipa- and filovirus exposure among Malagasy fruit bats, (b) explore seasonality in seroprevalence and serostatus in these bat populations and (c) compare mechanistic hypotheses for possible transmission dynamics underlying these data. To this end, we amassed and analysed a unique dataset documenting longitudinal serological henipa- and filovirus dynamics in three Madagascar fruit bat species. We uncovered serological evidence of exposure to Hendra-/Nipah-related henipaviruses in Eidolon dupreanum, Pteropus rufus and Rousettus madagascariensis, to Cedar-related henipaviruses in E. dupreanum and R. madagascariensis and to Ebola-related filoviruses in P. rufus and R. madagascariensis. We demonstrated significant seasonality in population-level seroprevalence and individual serostatus for multiple viruses across these species, linked to the female reproductive calendar. An age-structured subset of the data highlighted evidence of waning maternal antibodies in neonates, increasing seroprevalence in young and decreasing seroprevalence late in life. Comparison of mechanistic epidemiological models fit to these data offered support for transmission hypotheses permitting waning antibodies but retained immunity in adult-age bats. Our findings suggest that bats may seasonally modulate mechanisms of pathogen control, with consequences for population-level transmission. Additionally, we narrow the field of candidate transmission hypotheses by which bats are presumed to host and transmit potentially zoonotic viruses globally.
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Affiliation(s)
- Cara E. Brook
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
- Present address:
Department of Integrative BiologyUC BerkeleyBerkeleyCalifornia.
| | - Hafaliana C. Ranaivoson
- Virology UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
- Department of Animal BiologyUniversity of AntananarivoAntananarivoMadagascar
| | - Christopher C. Broder
- Department of Microbiology and ImmunologyUniformed Services UniversityBethesdaMaryland
| | | | | | - Alison J. Peel
- Environmental Futures Research InstituteGriffith UniversityNathanQueenslandAustralia
| | - Louise Gibson
- Institute of ZoologyZoological Society of LondonLondonUK
| | - James L. N. Wood
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - C. Jessica Metcalf
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
| | - Andrew P. Dobson
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
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Blaizot S, Herzog SA, Abrams S, Theeten H, Litzroth A, Hens N. Sample size calculation for estimating key epidemiological parameters using serological data and mathematical modelling. BMC Med Res Methodol 2019; 19:51. [PMID: 30845904 PMCID: PMC6407263 DOI: 10.1186/s12874-019-0692-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 02/25/2019] [Indexed: 11/20/2022] Open
Abstract
Background Our work was motivated by the need to, given serum availability and/or financial resources, decide on which samples to test in a serum bank for different pathogens. Simulation-based sample size calculations were performed to determine the age-based sampling structures and optimal allocation of a given number of samples for testing across various age groups best suited to estimate key epidemiological parameters (e.g., seroprevalence or force of infection) with acceptable precision levels in a cross-sectional seroprevalence survey. Methods Statistical and mathematical models and three age-based sampling structures (survey-based structure, population-based structure, uniform structure) were used. Our calculations are based on Belgian serological survey data collected in 2001–2003 where testing was done, amongst others, for the presence of Immunoglobulin G antibodies against measles, mumps, and rubella, for which a national mass immunisation programme was introduced in 1985 in Belgium, and against varicella-zoster virus and parvovirus B19 for which the endemic equilibrium assumption is tenable in Belgium. Results The optimal age-based sampling structure to use in the sampling of a serological survey as well as the optimal allocation distribution varied depending on the epidemiological parameter of interest for a given infection and between infections. Conclusions When estimating epidemiological parameters with acceptable levels of precision within the context of a single cross-sectional serological survey, attention should be given to the age-based sampling structure. Simulation-based sample size calculations in combination with mathematical modelling can be utilised for choosing the optimal allocation of a given number of samples over various age groups. Electronic supplementary material The online version of this article (10.1186/s12874-019-0692-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stéphanie Blaizot
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.
| | - Sereina A Herzog
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Steven Abrams
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, UHASSELT, Hasselt University, Hasselt, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Amber Litzroth
- Service of Epidemiology of infectious diseases, Scientific Directorate Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Niel Hens
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Interuniversity Institute for Biostatistics and statistical Bioinformatics, UHASSELT, Hasselt University, Hasselt, Belgium
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Cauchemez S, Hoze N, Cousien A, Nikolay B, Ten Bosch Q. How Modelling Can Enhance the Analysis of Imperfect Epidemic Data. Trends Parasitol 2019; 35:369-379. [PMID: 30738632 PMCID: PMC7106457 DOI: 10.1016/j.pt.2019.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 01/02/2023]
Abstract
Mathematical models play an increasingly important role in our understanding of the transmission and control of infectious diseases. Here, we present concrete examples illustrating how mathematical models, paired with rigorous statistical methods, are used to parse data of different levels of detail and breadth and estimate key epidemiological parameters (e.g., transmission and its determinants, severity, impact of interventions, drivers of epidemic dynamics) even when these parameters are not directly measurable, when data are limited, and when the epidemic process is only partially observed. Finally, we assess the hurdles to be taken to increase availability and applicability of these approaches in an effort to ultimately enhance their public health impact. Many data can be used to estimate the transmission potential of a pathogen, including descriptions of the transmission chains, human cluster sizes, sources of infection, and epidemic curves. An important agenda in public health is understanding the impact of control methods. However, the dynamic nature of epidemics makes this task challenging. Models can disentangle the natural course of outbreaks from the effect of external factors. In the absence of reliable surveillance data, models can reconstruct epidemic history by combining age-specific seroprevalence data with an understanding of the natural history of infection. Mechanisms of immunity are hard to observe at an individual level, yet they affect population-level dynamics. Models can tease out such signatures. Morbidity and mortality can be difficult to estimate when many infections are unobserved and severe infections are reported more often. Models can be used to correct for under-reporting and selection bias.
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Affiliation(s)
- Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France; All the authors made equal contributions.
| | - Nathanaël Hoze
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France; All the authors made equal contributions
| | - Anthony Cousien
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France; All the authors made equal contributions
| | - Birgit Nikolay
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France; All the authors made equal contributions
| | - Quirine Ten Bosch
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France; All the authors made equal contributions
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Caldwell JM, Donahue MJ, Harvell CD. Host size and proximity to diseased neighbours drive the spread of a coral disease outbreak in Hawai'i. Proc Biol Sci 2019; 285:rspb.2017.2265. [PMID: 29321299 DOI: 10.1098/rspb.2017.2265] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/04/2017] [Indexed: 11/12/2022] Open
Abstract
Understanding how disease risk varies over time and across heterogeneous populations is critical for managing disease outbreaks, but this information is rarely known for wildlife diseases. Here, we demonstrate that variation in host and pathogen factors drive the direction, duration and intensity of a coral disease outbreak. We collected longitudinal health data for 200 coral colonies, and found that disease risk increased with host size and severity of diseased neighbours, and disease spread was highest among individuals between 5 and 20 m apart. Disease risk increased by 2% with every 10 cm increase in host size. Healthy colonies with severely diseased neighbours (greater than 75% affected tissue) were 1.6 times more likely to develop disease signs compared with colonies with moderately diseased neighbours (25-75% affected tissue). Force of infection ranged from 7 to 20 disease cases per 1000 colonies (mean = 15 cases per 1000 colonies). The effective reproductive ratio, or average number of secondary infections per infectious individual, ranged from 0.16 to 1.22. Probability of transmission depended strongly on proximity to diseased neighbours, which demonstrates that marine disease spread can be highly constrained within patch reefs.
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Affiliation(s)
- Jamie M Caldwell
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Megan J Donahue
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - C Drew Harvell
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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Juarez JG, Pennington PM, Bryan JP, Klein RE, Beard CB, Berganza E, Rizzo N, Cordon-Rosales C. A decade of vector control activities: Progress and limitations of Chagas disease prevention in a region of Guatemala with persistent Triatoma dimidiata infestation. PLoS Negl Trop Dis 2018; 12:e0006896. [PMID: 30399143 PMCID: PMC6239342 DOI: 10.1371/journal.pntd.0006896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 11/16/2018] [Accepted: 10/03/2018] [Indexed: 01/15/2023] Open
Abstract
INTRODUCTION Chagas disease, a neglected tropical disease that affects millions of Latin Americans, has been effectively controlled in Guatemala after multiple rounds of indoor residual insecticide spraying (IRS). However, a few foci remain with persistent Triatoma dimidiata infestation. One such area is the municipality of Comapa, Department of Jutiapa, in the southeastern region of Guatemala, where control interventions appear less effective. We carried out three cross sectional entomological and serological surveys in Comapa to evaluate a decade of vector control activities. Baseline serological (1999) and entomological (2001-2) surveys were followed by three rounds of insecticide applications (2003-2005) and intermittent focal spraying of infested houses, until approximately 2012. Household inspections to determine entomological indices and construction materials were conducted in 2001, 2007 and 2011. Seroprevalence surveys were conducted in school-age children in 1999, 2007 and 2015, and in women of child bearing age (15-44 years) only in 2015. After multiple rounds of indoor residual sprayings (IRS), the infestation index decreased significantly from 39% (2001-2) to 27% (2011). Household construction materials alone predicted <10% of infested houses. Chagas seroprevalence in Comapa declined in school-aged children by 10-fold, from 10% (1999) to 1% (2015). However, seroprevalence in women of child bearing age remains >10%. CONCLUSION After a decade of vector control activities in Comapa, there is evidence of significantly reduced transmission. However, the continued risk for vector-borne and congenital transmission pose a threat to the 2022 Chagas disease elimination goal. Systematic integrated vector control and improved Chagas disease screening and treatment programs for congenital and vector-borne disease are needed to reach the elimination goal in regions with persistent vector infestation.
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Affiliation(s)
- Jose G. Juarez
- Center of Health Studies, Universidad del Valle de Guatemala, Ciudad de Guatemala, Guatemala
| | - Pamela M. Pennington
- Center of Biotechnology, Universidad del Valle de Guatemala, Ciudad de Guatemala, Guatemala
| | - Joe P. Bryan
- Centers for Disease Control and Prevention Central America Regional Office, Guatemala City, Guatemala
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Robert E. Klein
- Visiting Investigator, Universidad del Valle de Guatemala, Ciudad de Guatemala, Guatemala
| | - Charles B. Beard
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Elsa Berganza
- Area de Salud de Jutiapa, Ministerio de Salud Pública y Asistencia Social de Guatemala, Guatemala
| | - Nidia Rizzo
- Center of Health Studies, Universidad del Valle de Guatemala, Ciudad de Guatemala, Guatemala
| | - Celia Cordon-Rosales
- Center of Health Studies, Universidad del Valle de Guatemala, Ciudad de Guatemala, Guatemala
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Brinks R. Illness-Death Model in Chronic Disease Epidemiology: Characteristics of a Related, Differential Equation and an Inverse Problem. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2018; 2018:5091096. [PMID: 30275874 PMCID: PMC6157110 DOI: 10.1155/2018/5091096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 08/07/2018] [Accepted: 08/16/2018] [Indexed: 02/01/2023]
Abstract
Chronic diseases impose a huge burden for mankind. Recently, a mathematical relation between the incidence and prevalence of a chronic disease in terms of a differential equation has been described. In this article, we study the characteristics of this differential equation. Furthermore, we prove the ill-posedness of a related inverse problem arising in chronic disease epidemiology. An example application for the inverse problem about type 1 diabetes in German women aged up to 35 years is given.
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Affiliation(s)
- Ralph Brinks
- Hiller Research Unit for Rheumatology, University Hospital Duesseldorf, Duesseldorf, Germany
- Institute for Biometry and Epidemiology, German Diabetes Center, Duesseldorf, Germany
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Targeting vaccinations for the licensed dengue vaccine: Considerations for serosurvey design. PLoS One 2018; 13:e0199450. [PMID: 29944696 PMCID: PMC6019750 DOI: 10.1371/journal.pone.0199450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 06/07/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The CYD-TDV vaccine was unusual in that the recommended target population for vaccination was originally defined not only by age, but also by transmission setting as defined by seroprevalence. WHO originally recommended countries consider vaccination against dengue with CYD-TDV vaccine in geographic settings only where prior infection with any dengue serotype, as measured by seroprevalence, was >170% in the target age group. Vaccine was not recommended in settings where seroprevalence was <50%. Test-and-vaccinate strategies suggested following new analysis by Sanofi will still require age-stratified seroprevalence surveys to optimise age-group targeting. Here we address considerations for serosurvey design in the context of vaccination program planning. METHODS To explore how the design of seroprevalence surveys affects estimates of transmission intensity, 100 age-specific seroprevalence surveys were simulated using a beta-binomial distribution and a simple catalytic model for different combinations of age-range, survey size, transmission setting, and test sensitivity/specificity. We then used a Metropolis-Hastings Markov Chain Monte-Carlo algorithm to estimate the force of infection from each simulated dataset. RESULTS Sampling from a wide age-range led to more accurate estimates than merely increasing sample size in a narrow age-range. This finding was consistent across all transmission settings. The optimum test sensitivity and specificity given an imperfect test differed by setting with high sensitivity being important in high transmission settings and high specificity important in low transmission settings. CONCLUSIONS When assessing vaccination suitability by seroprevalence surveys, countries should ensure an appropriate age-range is sampled, considering epidemiological evidence about the local burden of disease.
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Force of infection of Helicobacter pylori in Mexico: evidence from a national survey using a hierarchical Bayesian model. Epidemiol Infect 2018; 146:961-969. [PMID: 29656725 DOI: 10.1017/s0950268818000857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Helicobacter pylori (H. pylori) is present in the stomach of half of the world's population. The force of infection describes the rate at which susceptibles acquire infection. In this article, we estimated the age-specific force of infection of H. pylori in Mexico. Data came from a national H. pylori seroepidemiology survey collected in Mexico in 1987-88. We modelled the number of individuals with H. pylori at a given age as a binomial random variable. We assumed that the cumulative risk of infection by a given age follows a modified exponential catalytic model, allowing some fraction of the population to remain uninfected. The cumulative risk of infection was modelled for each state in Mexico and were shrunk towards the overall national cumulative risk curve using Bayesian hierarchical models. The proportion of the population that can be infected (i.e. susceptible population) is 85.9% (95% credible interval (CR) 84.3%-87.5%). The constant rate of infection per year of age among the susceptible population is 0.092 (95% CR 0.084-0.100). The estimated force of infection was highest at birth 0.079 (95% CR 0.071-0.087) decreasing to zero as age increases. This Bayesian hierarchical model allows stable estimation of state-specific force of infection by pooling information between the states, resulting in more realistic estimates.
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Abrams S, Wienke A, Hens N. Modelling time varying heterogeneity in recurrent infection processes: an application to serological data. J R Stat Soc Ser C Appl Stat 2018. [PMID: 29540937 PMCID: PMC5836988 DOI: 10.1111/rssc.12236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Frailty models are often used in survival analysis to model multivariate time‐to‐event data. In infectious disease epidemiology, frailty models have been proposed to model heterogeneity in the acquisition of infection and to accommodate association in the occurrence of multiple types of infection. Although traditional frailty models rely on the assumption of lifelong immunity after recovery, refinements have been made to account for reinfections with the same pathogen. Recently, Abrams and Hens quantified the effect of misspecifying the underlying infection process on the basic and effective reproduction number in the context of bivariate current status data on parvovirus B19 and varicella zoster virus. Furthermore, Farrington, Unkel and their co‐workers introduced and applied time varying shared frailty models to paired bivariate serological data. In this paper, we consider an extension of the proposed frailty methodology by Abrams and Hens to account for age‐dependence in individual heterogeneity through the use of age‐dependent shared and correlated gamma frailty models. The methodology is illustrated by using two data applications.
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Affiliation(s)
| | | | - Niel Hens
- Hasselt University Diepenbeek.,University of Antwerp Wilrijk Belgium
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The changing epidemiology of varicella and herpes zoster in Hong Kong before universal varicella vaccination in 2014. Epidemiol Infect 2018. [PMID: 29526171 PMCID: PMC6533643 DOI: 10.1017/s0950268818000444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In Hong Kong, universal varicella vaccination started in July 2014. Before this, children could receive varicella vaccine via the private market. We analysed the epidemiology of varicella and zoster before universal vaccination. We estimated varicella vaccination coverage through surveys in preschool children. We estimated the burden of varicella and zoster with varicella notifications from 1999/00 to 2013/14, Accident and Emergency Department (A&E) attendance and inpatient admissions to public hospitals from 2004/05 to 2013/14. We fitted a catalytic model to serological data on antibodies against varicella-zoster virus to estimate the force of infection. We found that varicella vaccination coverage gradually increased to about 50% before programme inception. In children younger than 5 years, the annual rate of varicella notifications, varicella admission and zoster A&E attendance generally declined. The annual notification, A&E attendance and hospitalisation rate of varicella and zoster generally increased for individuals between 10 and 59 years old. Varicella serology indicated an age shift during the study period towards a higher proportion of infections in slightly older individuals, but the change was most notable before vaccine licensure. In conclusion, we observed a shift in the burden of varicella to slightly older age groups with a corresponding increase in incidence but it cannot necessarily be attributed to private market vaccine coverage alone. Increasing varicella vaccination uptake in the private market might affect varicella transmission and epidemiology, but not to the level of interrupting transmission.
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Cucunubá ZM, Nouvellet P, Conteh L, Vera MJ, Angulo VM, Dib JC, Parra-Henao GJ, Basáñez MG. Modelling historical changes in the force-of-infection of Chagas disease to inform control and elimination programmes: application in Colombia. BMJ Glob Health 2017; 2:e000345. [PMID: 29147578 PMCID: PMC5680445 DOI: 10.1136/bmjgh-2017-000345] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/23/2017] [Accepted: 07/24/2017] [Indexed: 12/26/2022] Open
Abstract
Background WHO's 2020 milestones for Chagas disease include having all endemic Latin American countries certified with no intradomiciliary Trypanosoma cruzi transmission, and infected patients under care. Evaluating the variation in historical exposure to infection is crucial for assessing progress and for understanding the priorities to achieve these milestones. Methods Focusing on Colombia, all the available age-structured serological surveys (undertaken between 1995 and 2014) were searched and compiled. A total of 109 serosurveys were found, comprising 83 742 individuals from rural (indigenous and non-indigenous) and urban settings in 14 (out of 32) administrative units (departments). Estimates of the force-of-infection (FoI) were obtained by fitting and comparing three catalytic models using Bayesian methods to reconstruct temporal and spatial patterns over the course of three decades (between 1984 and 2014). Results Significant downward changes in the FoI were identified over the course of the three decades, and in some specific locations the predicted current seroprevalence in children aged 0-5 years is <1%. However, pronounced heterogeneity exists within departments, especially between indigenous, rural and urban settings, with the former exhibiting the highest FoI (up to 66 new infections/1000 people susceptible/year). The FoI in most of the indigenous settings remain unchanged during the three decades investigated. Current prevalence in adults in these 15 departments varies between 10% and 90% depending on the dynamics of historical exposure. Conclusions Assessing progress towards the control of Chagas disease requires quantifying the impact of historical exposure on current age-specific prevalence at subnational level. In Colombia, despite the evident progress, there is a marked heterogeneity indicating that in some areas the vector control interventions have not been effective, hindering the possibility of achieving interruption by 2020. A substantial burden of chronic cases remains even in locations where serological criteria for transmission interruption may have been achieved, therefore still demanding diagnosis and treatment interventions.
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Affiliation(s)
- Zulma M Cucunubá
- Department of Infectious Disease Epidemiology, Faculty of Medicine (St Mary's campus), Imperial College London, London, UK.,Department of Infectious Disease Epidemiology, London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK.,Grupode Parasitología-RED CHAGAS, Instituto Nacional de Salud, Bogotá, Colombia
| | - Pierre Nouvellet
- Department of Infectious Disease Epidemiology, Faculty of Medicine (St Mary's campus), Imperial College London, London, UK.,Department of Infectious Disease Epidemiology, Faculty of Medicine (St Mary's campus), Medical Research Council Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London, UK
| | - Lesong Conteh
- Department of Infectious Disease Epidemiology, Faculty of Medicine (St Mary's campus), Imperial College London, London, UK.,Department of Infectious Disease Epidemiology, Faculty of Medicine (St Mary's campus), Medical Research Council Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London, UK.,Department of Infectious Disease Epidemiology, Faculty of Medicine (St Mary's campus), Health Economics Group, School of Public Health, Imperial College London, London, UK
| | - Mauricio Javier Vera
- Grupo de Enfermedades Endemo-Epidémicas, Subdirección Enfermedades Transmisibles, Ministerio de Salud y Protección Social, Bogotá, Colombia
| | - Victor Manuel Angulo
- Centro de Investigaciones en Enfermedades Tropicales (CINTROP), Universidad Industrial de Santander, Piedecuesta, Colombia
| | | | | | - María Gloria Basáñez
- Department of Infectious Disease Epidemiology, Faculty of Medicine (St Mary's campus), Imperial College London, London, UK.,Department of Infectious Disease Epidemiology, London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK
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A systematic review of varicella seroprevalence in European countries before universal childhood immunization: deriving incidence from seroprevalence data. Epidemiol Infect 2017; 145:2666-2677. [PMID: 28826422 PMCID: PMC5647669 DOI: 10.1017/s0950268817001546] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Surveillance systems for varicella in Europe are highly heterogeneous or completely absent. We estimated the varicella incidence based on seroprevalence data, as these data are largely available and not biased by under-reporting or underascertainment. We conducted a systematic literature search for varicella serological data in Europe prior to introduction of universal varicella immunization. Age-specific serological data were pooled by country and serological profiles estimated using the catalytic model with piecewise constant force of infection. From the estimated profiles, we derived the annual incidence of varicella infection (/100·000) for six age groups (<5, 5–9, 10–14, 15–19, 20–39 and 40–65 years). In total, 43 studies from 16 countries were identified. By the age of 15 years, over 90% of the population has been infected by varicella in all countries except for Greece (86·6%) and Italy (85·3%). Substantial variability across countries exists in the age-specific annual incidence of varicella primary infection among the <5 years old (from 7052 to 16 122 per 100 000) and 5–9 years old (from 3292 to 11 798 per 100 000). The apparent validity and robustness of our estimates highlight the importance of serological data for the characterization of varicella epidemiology, even in the absence of sampling or assay standardization.
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