PLoS Articles
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UNC-authored articles published by the Public Library of Science (PLoS)
Works (2111)
21. Weight trimming and propensity score weighting
- Title Tesim:
- Weight trimming and propensity score weighting
- Creator:
- Stuart, E.A, Lee, B.K, and Lessler, J
- Date of publication:
- 2011
- Abstract Tesim:
- Propensity score weighting is sensitive to model misspecification and outlying weights that can unduly influence results. The authors investigated whether trimming large weights downward can improve the performance of propensity score weighting and whether the benefits of trimming differ by propensity score estimation method. In a simulation study, the authors examined the performance of weight trimming following logistic regression, classification and regression trees (CART), boosted CART, and random forests to estimate propensity score weights. Results indicate that although misspecified logistic regression propensity score models yield increased bias and standard errors, weight trimming following logistic regression can improve the accuracy and precision of final parameter estimates. In contrast, weight trimming did not improve the performance of boosted CART and random forests. The performance of boosted CART and random forests without weight trimming was similar to the best performance obtainable by weight trimmed logistic regression estimated propensity scores. While trimming may be used to optimize propensity score weights estimated using logistic regression, the optimal level of trimming is difficult to determine. These results indicate that although trimming can improve inferences in some settings, in order to consistently improve the performance of propensity score weighting, analysts should focus on the procedures leading to the generation of weights (i.e., proper specification of the propensity score model) rather than relying on ad-hoc methods such as weight trimming.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/2cz5-p780
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pone.0018174
- Journal Issue:
- 3
- Journal Title:
- PLoS ONE
- Journal Volume:
- 6
- Keyword:
- random forest, computer simulation, propensity score, controlled study, statistical model, article, data mining, machine learning, weight reduction, artificial intelligence, logistic regression analysis, Logistic Models, Propensity Score, accuracy, and Models, Statistical
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States, Department of Epidemiology and Biostatistics, Drexel University School of Public Health, Philadelphia, PA, United States, and Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Person:
- Stuart, E.A, Lee, B.K, and Lessler, J
- Publisher:
- Public Library of Science
- Source:
- 5d3b5757-61a0-42af-8326-586ccfdb5e73
22. Visualizing clinical evidence: Citation networks for the incubation periods of respiratory viral infections
- Title Tesim:
- Visualizing clinical evidence: Citation networks for the incubation periods of respiratory viral infections
- Creator:
- Cummings, D.A.T, Reich, N.G, Lessler, J, and Perl, T.M
- Date of publication:
- 2011
- Abstract Tesim:
- Simply by repetition, medical facts can become enshrined as truth even when there is little empirical evidence supporting them. We present an intuitive and clear visual design for tracking the citation history of a particular scientific fact over time. We apply this method to data from a previously published literature review on the incubation period of nine respiratory viral infections. The resulting citation networks reveal that the conventional wisdom about the incubation period for these diseases was based on a small fraction of available data and in one case, on no retrievable empirical evidence. Overall, 50% of all incubation period statements did not provide a source for their estimate and 65% of original sources for incubation period data were not incorporated into subsequent publications. More standardized and widely available methods for visualizing these histories of medical evidence are needed to ensure that conventional wisdom cannot stray too far from empirically supported knowledge.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/w4gx-ha33
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pone.0019496
- Journal Issue:
- 4
- Journal Title:
- PLoS ONE
- Journal Volume:
- 6
- Keyword:
- Review Literature as Topic, adenovirus infection, measles, literature, epidemic, Respiratory Tract Infections, Viruses, Databases, Bibliographic, Coronavirus infection, methodology, statistical analysis, publication, bibliographic database, human, Data Interpretation, Statistical, viral respiratory tract infection, influenza B, metabolism, Parainfluenza virus infection, virology, severe acute respiratory syndrome, Infectious Disease Incubation Period, article, respiratory syncytial virus infection, Evidence-Based Medicine, incubation time, Publications, Rhinovirus infection, Human metapneumovirus infection, influenza A, Research Design, systematic review, respiratory tract infection, Humans, standard, evidence based medicine, virus, and disease transmission
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States and Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Person:
- Cummings, D.A.T, Reich, N.G, Lessler, J, and Perl, T.M
- Publisher:
- Public Library of Science
- Source:
- f9e7a287-d84a-4016-8860-a0f30f77ceee
23. Urban Cholera Transmission Hotspots and Their Implications for Reactive Vaccination: Evidence from Bissau City, Guinea Bissau
- Title Tesim:
- Urban Cholera Transmission Hotspots and Their Implications for Reactive Vaccination: Evidence from Bissau City, Guinea Bissau
- Creator:
- Azman, A.S, Luquero, F.J, Grenfell, B.T, Banga, C.N, Palma, P.P, Grais, R.F, Rodrigues, A, and Lessler, J
- Date of publication:
- 2012
- Abstract Tesim:
- Background: Use of cholera vaccines in response to epidemics (reactive vaccination) may provide an effective supplement to traditional control measures. In Haiti, reactive vaccination was considered but, until recently, rejected in part due to limited global supply of vaccine. Using Bissau City, Guinea-Bissau as a case study, we explore neighborhood-level transmission dynamics to understand if, with limited vaccine and likely delays, reactive vaccination can significantly change the course of a cholera epidemic. Methods and Findings: We fit a spatially explicit meta-population model of cholera transmission within Bissau City to data from 7,551 suspected cholera cases from a 2008 epidemic. We estimated the effect reactive vaccination campaigns would have had on the epidemic under different levels of vaccine coverage and campaign start dates. We compared highly focused and diffuse strategies for distributing vaccine throughout the city. We found wide variation in the efficiency of cholera transmission both within and between areas of the city. "Hotspots", where transmission was most efficient, appear to drive the epidemic. In particular one area, Bandim, was a necessary driver of the 2008 epidemic in Bissau City. If vaccine supply were limited but could have been distributed within the first 80 days of the epidemic, targeting vaccination at Bandim would have averted the most cases both within this area and throughout the city. Regardless of the distribution strategy used, timely distribution of vaccine in response to an ongoing cholera epidemic can prevent cases and save lives. Conclusions: Reactive vaccination can be a useful tool for controlling cholera epidemics, especially in urban areas like Bissau City. Particular neighborhoods may be responsible for driving a city's cholera epidemic; timely and targeted reactive vaccination at such neighborhoods may be the most effective way to prevent cholera cases both within that neighborhood and throughout the city.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/hw47-qr87
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pntd.0001901
- Journal Issue:
- 11
- Journal Title:
- PLoS Neglected Tropical Diseases
- Journal Volume:
- 6
- Keyword:
- article, Urban Population, cholera, sensitivity analysis, nonbiological model, simulation, human, urban area, drug efficacy, immunity, Disease Transmission, Infectious, Humans, Vaccination, Guinea-Bissau, disease transmission, vaccination, Models, Statistical, epidemic, cholera vaccine, Cholera Vaccines, and Cholera
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States, Epicentre, Paris, France, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States, National Public Health, Ministry of Health, Bissau City, Guinea-Bissau, and Médicos Sin Fronteras, Barcelona, Spain
- Person:
- Azman, A.S, Luquero, F.J, Grenfell, B.T, Banga, C.N, Palma, P.P, Grais, R.F, Rodrigues, A, and Lessler, J
- Publisher:
- Public Library of Science
- Source:
- cc6bbbcf-a9ea-4940-abbd-aba2a7c7c152
24. Synchrony of Sylvatic Dengue Isolations: A Multi-Host, Multi-Vector SIR Model of Dengue Virus Transmission in Senegal
- Title Tesim:
- Synchrony of Sylvatic Dengue Isolations: A Multi-Host, Multi-Vector SIR Model of Dengue Virus Transmission in Senegal
- Creator:
- Althouse, B.M, Weaver, S.C, Lessler, J, Sall, A.A, Watts, D.M, Cummings, D.A.T, Diallo, M, and Hanley, K.A
- Date of publication:
- 2012
- Abstract Tesim:
- Isolations of sylvatic dengue-2 virus from mosquitoes, humans and non-human primates in Senegal show synchronized multi-annual dynamics over the past 50 years. Host demography has been shown to directly affect the period between epidemics in other pathogen systems, therefore, one might expect unsynchronized multi-annual cycles occurring in hosts with dramatically different birth rates and life spans. However, in Senegal, we observe a single synchronized eight-year cycle across all vector species, suggesting synchronized dynamics in all vertebrate hosts. In the current study, we aim to explore two specific hypotheses: 1) primates with different demographics will experience outbreaks of dengue at different periodicities when observed as isolated systems, and that coupling of these subsystems through mosquito biting will act to synchronize incidence; and 2) the eight-year periodicity of isolations observed across multiple primate species is the result of long-term cycling in population immunity in the host populations. To test these hypotheses, we develop a multi-host, multi-vector Susceptible, Infected, Removed (SIR) model to explore the effects of coupling multiple host-vector systems of dengue virus transmission through cross-species biting rates. We find that under small amounts of coupling, incidence in the host species synchronize. Long-period multi-annual dynamics are observed only when prevalence in troughs reaches vanishingly small levels (<10-10), suggesting that these dynamics are inconsistent with sustained transmission in this setting, but are consistent with local dengue virus extinctions followed by reintroductions. Inclusion of a constant introduction of infectious individuals into the system causes the multi-annual periods to shrink, while the effects of coupling remain the same. Inclusion of a stochastic rate of introduction allows for multi-annual periods at a cost of reduced synchrony. Thus, we conclude that the eight-year period separating amplifications of dengue may be explained by cycling in immunity with stochastic introductions.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/4qd0-7m66
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pntd.0001928
- Journal Issue:
- 11
- Journal Title:
- PLoS Neglected Tropical Diseases
- Journal Volume:
- 6
- Keyword:
- virus transmission, Incidence, Culicidae, dengue, Models, Statistical, stochastic model, mosquito, geographic distribution, Prevalence, Senegal, Dengue Virus, incidence, host pathogen interaction, article, yellow fever, periodicity, disease surveillance, epidemic, Dengue, nonhuman, bite, Disease Vectors, Primates, seasonal variation, chikungunya, Primate Diseases, Humans, Animals, and prevalence
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States, Institut Pasteur de Dakar, Dakar, Senegal, Office of Research and Sponsored Projects, University of Texas at El Paso, El Paso, TX, United States, and Department of Biology, New Mexico State University, Las Cruces, NM, United States
- Person:
- Althouse, B.M, Weaver, S.C, Lessler, J, Sall, A.A, Watts, D.M, Cummings, D.A.T, Diallo, M, and Hanley, K.A
- Publisher:
- Public Library of Science
- Source:
- 35ff9ab6-0596-4afe-80c4-ceffef8e9c84
25. Evidence for antigenic seniority in influenza A (H3N2) antibody responses in southern China
- Title Tesim:
- Evidence for antigenic seniority in influenza A (H3N2) antibody responses in southern China
- Creator:
- Guan, Y, Zhu, H, Riley, S, Wang, S, Cummings, D.A.T, Read, J.M, Lessler, J, Smith, G.J.D, and Jiang, C.Q
- Date of publication:
- 2012
- Abstract Tesim:
- A key observation about the human immune response to repeated exposure to influenza A is that the first strain infecting an individual apparently produces the strongest adaptive immune response. Although antibody titers measure that response, the interpretation of titers to multiple strains - from the same sera - in terms of infection history is clouded by age effects, cross reactivity and immune waning. From July to September 2009, we collected serum samples from 151 residents of Guangdong Province, China, 7 to 81 years of age. Neutralization tests were performed against strains representing six antigenic clusters of H3N2 influenza circulating between 1968 and 2008, and three recent locally circulating strains. Patterns of neutralization titers were compared based on age at time of testing and age at time of the first isolation of each virus. Neutralization titers were highest for H3N2 strains that circulated in an individual's first decade of life (peaking at 7 years). Further, across strains and ages at testing, statistical models strongly supported a pattern of titers declining smoothly with age at the time a strain was first isolated. Those born 10 or more years after a strain emerged generally had undetectable neutralization titers to that strain (<1:10). Among those over 60 at time of testing, titers tended to increase with age. The observed pattern in H3N2 neutralization titers can be characterized as one of antigenic seniority: repeated exposure and the immune response combine to produce antibody titers that are higher to more 'senior' strains encountered earlier in life.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/hhjd-7y35
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.ppat.1002802
- Journal Issue:
- 7
- Journal Title:
- PLoS Pathogens
- Journal Volume:
- 8
- Keyword:
- virus neutralization, China, female, Child, human, article, Antibodies, Neutralizing, Influenza A Virus, H3N2 Subtype, virus strain, serology, Influenza, Human, Adolescent, blood sampling, Aged, 80 and over, adult, Influenza virus A H3N2, influenza, serodiagnosis, virus isolation, antigenicity, child, age, middle aged, immunology, Middle Aged, adaptive immunity, neutralizing antibody, major clinical study, virology, antibody response, immune response, Female, nonhuman, blood, Adult, male, aged, Neutralization Tests, Aged, Male, Antibodies, Viral, Humans, classification, Young Adult, virus antibody, adolescent, school child, and Adaptive Immunity
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China, School of Public Health, Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analysis and Modelling, Imperial College, London, United Kingdom, Guangzhou No. 12 Hospital, Guangzhou, Guangdong, China, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States, Department of Epidemiology and Population Health, Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom, and Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
- Page Start:
- 26
- Person:
- Guan, Y, Zhu, H, Riley, S, Wang, S, Cummings, D.A.T, Read, J.M, Lessler, J, Smith, G.J.D, and Jiang, C.Q
- Publisher:
- Public Library of Science
- Source:
- 9bb66bbc-62f7-4bc4-9358-1f256db5c95e
26. Balancing Evidence and Uncertainty when Considering Rubella Vaccine Introduction
- Title Tesim:
- Balancing Evidence and Uncertainty when Considering Rubella Vaccine Introduction
- Creator:
- Metcalf, C.J.E and Lessler, J
- Date of publication:
- 2013
- Abstract Tesim:
- Background:Despite a safe and effective vaccine, rubella vaccination programs with inadequate coverage can raise the average age of rubella infection; thereby increasing rubella cases among pregnant women and the resulting congenital rubella syndrome (CRS) in their newborns. The vaccination coverage necessary to reduce CRS depends on the birthrate in a country and the reproductive number, R0, a measure of how efficiently a disease transmits. While the birthrate within a country can be known with some accuracy, R0 varies between settings and can be difficult to measure. Here we aim to provide guidance on the safe introduction of rubella vaccine into countries in the face of substantial uncertainty in R0.Methods:We estimated the distribution of R0 in African countries based on the age distribution of rubella infection using Bayesian hierarchical models. We developed an age specific model of rubella transmission to predict the level of R0 that would result in an increase in CRS burden for specific birth rates and coverage levels. Combining these results, we summarize the safety of introducing rubella vaccine across demographic and coverage contexts.Findings:The median R0 of rubella in the African region is 5.2, with 90% of countries expected to have an R0 between 4.0 and 6.7. Overall, we predict that countries maintaining routine vaccination coverage of 80% or higher are can be confident in seeing a reduction in CRS over a 30 year time horizon.Conclusions:Under realistic assumptions about human contact, our results suggest that even in low birth rate settings high vaccine coverage must be maintained to avoid an increase in CRS. These results lend further support to the WHO recommendation that countries reach 80% coverage for measles vaccine before introducing rubella vaccination, and highlight the importance of maintaining high levels of vaccination coverage once the vaccine is introduced.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/er48-5906
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pone.0067639
- Journal Issue:
- 7
- Journal Title:
- PLoS ONE
- Journal Volume:
- 8
- Keyword:
- Africa, article, Bayes theorem, Male, world health organization, Bayes Theorem, Child, Preschool, Birth Rate, Adult, Child, human, Humans, Rubella, Cluster Analysis, birth rate, Infant, rubella, Adolescent, Rubella Vaccine, rubella vaccine, measles, Rubella Syndrome, Congenital, Vaccination, Infant, Newborn, demography, measles vaccine, Pregnancy Complications, Infectious, Young Adult, nonhuman, Pregnancy, disease transmission, and Female
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- Department of Zoology, Oxford University, Oxford, United Kingdom and Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Person:
- Metcalf, C.J.E and Lessler, J
- Publisher:
- Public Library of Science
- Source:
- 7bf112e7-9275-4ce0-b085-d163bbe147e4
27. A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
- Title Tesim:
- A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
- Creator:
- Hu, K, Edlund, S, Filter, M, Harry, A, Käsbohrer, A, Appel, B, Lessler, J, Thoens, C, Kaufman, J, and Douglas, J
- Date of publication:
- 2014
- Abstract Tesim:
- Foodborne disease outbreaks of recent years demonstrate that due to increasingly interconnected supply chains these type of crisis situations have the potential to affect thousands of people, leading to significant healthcare costs, loss of revenue for food companies, and-in the worst cases-death. When a disease outbreak is detected, identifying the contaminated food quickly is vital to minimize suffering and limit economic losses. Here we present a likelihood-based approach that has the potential to accelerate the time needed to identify possibly contaminated food products, which is based on exploitation of food products sales data and the distribution of foodborne illness case reports. Using a real world food sales data set and artificially generated outbreak scenarios, we show that this method performs very well for contamination scenarios originating from a single "guilty" food product. As it is neither always possible nor necessary to identify the single offending product, the method has been extended such that it can be used as a binary classifier. With this extension it is possible to generate a set of potentially "guilty" products that contains the real outbreak source with very high accuracy. Furthermore we explore the patterns of food distributions that lead to "hard-to-identify" foods, the possibility of identifying these food groups a priori, and the extent to which the likelihood-based method can be used to quantify uncertainty. We find that high spatial correlation of sales data between products may be a useful indicator for "hard-to-identify" products.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/4rn7-ym48
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pcbi.1003692
- Journal Issue:
- 7
- Journal Title:
- PLoS Computational Biology
- Journal Volume:
- 10
- Keyword:
- data analysis, Models, Biological, Foodborne disease, epidemic, Contamination, biological model, receiver operating characteristic, Disease Outbreaks, statistical distribution, Supply chains, Economic loss, Food microbiology, food quality, food contamination, biology, Data performance, Chemical contamination, Losses, food analysis, article, public health, statistical model, Computational Biology, Crises situations, food poisoning, likelihood based method, Humans, Product sales, statistics and numerical data, human, Likelihood Functions, Sales, Food-borne illness, controlled study, Public Health, food intake, feasibility study, cluster analysis, Food companies, Health care costs, classification algorithm, analytic method, food industry, Food Industry, sensitivity analysis, Disease outbreaks, Cluster Analysis, Data challenges, marketing, and Foodborne Diseases
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- IBM Almaden Research Center, San Jose, CA, United States, Federal Institute for Risk Assessment, Berlin, Germany, and Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Person:
- Hu, K, Edlund, S, Filter, M, Harry, A, Käsbohrer, A, Appel, B, Lessler, J, Thoens, C, Kaufman, J, and Douglas, J
- Publisher:
- Public Library of Science
- Source:
- 80c28d28-1133-44d3-894f-0cdb6bdf6af5
28. The Role of Viral Introductions in Sustaining Community-Based HIV Epidemics in Rural Uganda: Evidence from Spatial Clustering, Phylogenetics, and Egocentric Transmission Models
- Title Tesim:
- The Role of Viral Introductions in Sustaining Community-Based HIV Epidemics in Rural Uganda: Evidence from Spatial Clustering, Phylogenetics, and Egocentric Transmission Models
- Creator:
- Redd, A.D, Wawer, M.J, Tobian, A.A.R, Grabowski, M.K, Cummings, D.A.T, Serwadda, D, Ndyanabo, A, Beyrer, C, Lessler, J, Nalugoda, F, Lutalo, T, Quinn, T.C, Munshaw, S, Chang, L.W, Ray, S.C, Nelson, M.I, Laeyendecker, O, Reynolds, S.J, Kagaayi, J, Jennings, J.M, Gray, R.H, Mueller, A.C, Manucci, J, and Bwanika, J.B
- Date of publication:
- 2014
- Abstract Tesim:
- Background:It is often assumed that local sexual networks play a dominant role in HIV spread in sub-Saharan Africa. The aim of this study was to determine the extent to which continued HIV transmission in rural communities-home to two-thirds of the African population-is driven by intra-community sexual networks versus viral introductions from outside of communities.Methods and Findings:We analyzed the spatial dynamics of HIV transmission in rural Rakai District, Uganda, using data from a cohort of 14,594 individuals within 46 communities. We applied spatial clustering statistics, viral phylogenetics, and probabilistic transmission models to quantify the relative contribution of viral introductions into communities versus community- and household-based transmission to HIV incidence. Individuals living in households with HIV-incident (n = 189) or HIV-prevalent (n = 1,597) persons were 3.2 (95% CI: 2.7-3.7) times more likely to be HIV infected themselves compared to the population in general, but spatial clustering outside of households was relatively weak and was confined to distances <500 m. Phylogenetic analyses of gag and env genes suggest that chains of transmission frequently cross community boundaries. A total of 95 phylogenetic clusters were identified, of which 44% (42/95) were two individuals sharing a household. Among the remaining clusters, 72% (38/53) crossed community boundaries. Using the locations of self-reported sexual partners, we estimate that 39% (95% CI: 34%-42%) of new viral transmissions occur within stable household partnerships, and that among those infected by extra-household sexual partners, 62% (95% CI: 55%-70%) are infected by sexual partners from outside their community. These results rely on the representativeness of the sample and the quality of self-reported partnership data and may not reflect HIV transmission patterns outside of Rakai.Conclusions:Our findings suggest that HIV introductions into communities are common and account for a significant proportion of new HIV infections acquired outside of households in rural Uganda, though the extent to which this is true elsewhere in Africa remains unknown. Our results also suggest that HIV prevention efforts should be implemented at spatial scales broader than the community and should target key populations likely responsible for introductions into communities.Please see later in the article for the Editors' Summary.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/bczn-f369
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pmed.1001610
- Journal Issue:
- 3
- Journal Title:
- PLoS Medicine
- Journal Volume:
- 11
- Keyword:
- genetic association, major clinical study, disease surveillance, reverse transcription polymerase chain reaction, incidence, concurrent sexual partnership, Incidence, Rural Population, follow up, Epidemics, article, male, female, human, Prevalence, HIV Seropositivity, HIV Infections, Female, enzyme linked immunosorbent assay, Western blotting, virus transmission, HIV-1, Phylogeny, young adult, simulation, population research, community acquired infection, Models, Theoretical, prostitution, Adolescent, Sexual Behavior, risk factor, Middle Aged, adult, Young Adult, adolescent, Male, viral contamination, Uganda, Humans, and Adult
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States, Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States, Rakai Health Sciences Program, Kalisizo, Uganda, School of Public Health, College of Medicine, Makerere University, Kampala, Uganda, Rakai Health Sciences Program, Kalisizo, Uganda, School of Medicine, Johns Hopkins University, Baltimore, MD, United States, and Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, United States
- Person:
- Redd, A.D, Wawer, M.J, Tobian, A.A.R, Grabowski, M.K, Cummings, D.A.T, Serwadda, D, Ndyanabo, A, Beyrer, C, Lessler, J, Nalugoda, F, Lutalo, T, Quinn, T.C, Munshaw, S, Chang, L.W, Ray, S.C, Nelson, M.I, Laeyendecker, O, Reynolds, S.J, Kagaayi, J, Jennings, J.M, Gray, R.H, Mueller, A.C, Manucci, J, and Bwanika, J.B
- Publisher:
- Public Library of Science
- Source:
- da86cf6a-cfa4-4037-a02b-020bef0004ff
29. The Contribution of Social Behaviour to the Transmission of Influenza A in a Human Population
- Title Tesim:
- The Contribution of Social Behaviour to the Transmission of Influenza A in a Human Population
- Creator:
- Wei, V.W.I, Cummings, D.A, Riley, S, Kwok, K.O, Cowling, B.J, Read, J.M, Kucharski, A.J, and Lessler, J
- Date of publication:
- 2014
- Abstract Tesim:
- Variability in the risk of transmission for respiratory pathogens can result from several factors, including the intrinsic properties of the pathogen, the immune state of the host and the host's behaviour. It has been proposed that self-reported social mixing patterns can explain the behavioural component of this variability, with simulated intervention studies based on these data used routinely to inform public health policy. However, in the absence of robust studies with biological endpoints for individuals, it is unclear how age and social behaviour contribute to infection risk. To examine how the structure and nature of social contacts influenced infection risk over the course of a single epidemic, we designed a flexible disease modelling framework: the population was divided into a series of increasingly detailed age and social contact classes, with the transmissibility of each age-contact class determined by the average contacts of that class. Fitting the models to serologically confirmed infection data from the 2009 Hong Kong influenza A/H1N1p pandemic, we found that an individual's risk of infection was influenced strongly by the average reported social mixing behaviour of their age group, rather than by their personal reported contacts. We also identified the resolution of social mixing that shaped transmission: epidemic dynamics were driven by intense contacts between children, a post-childhood drop in risky contacts and a subsequent rise in contacts for individuals aged 35-50. Our results demonstrate that self-reported social contact surveys can account for age-associated heterogeneity in the transmission of a respiratory pathogen in humans, and show robustly how these individual-level behaviours manifest themselves through assortative age groups. Our results suggest it is possible to profile the social structure of different populations and to use these aggregated data to predict their inherent transmission potential.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/bg3m-nk60
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.ppat.1004206
- Journal Issue:
- 6
- Journal Title:
- PLoS Pathogens
- Journal Volume:
- 10
- Keyword:
- age, Middle Aged, article, adolescent, Follow-Up Studies, Risk, human, influenza A, Aged, Self Report, Adolescent, risk, Adult, comparative study, child, immunology, Child, Health Surveys, social behavior, Child Behavior, Influenza A virus (H1N1), adult, Social Behavior, self report, health survey, aging, Disease Susceptibility, Influenza, Human, Hong Kong, disease predisposition, virus transmission, virology, Epidemics, Influenza A virus, Adolescent Behavior, growth, development and aging, infection risk, Models, Biological, transmission, middle aged, Influenza A Virus, H1N1 Subtype, biological model, nonbiological model, follow up, adolescent behavior, young adult, Humans, Aging, questionnaire, child behavior, aged, Young Adult, and epidemic
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- School of Public Health, The University of Hong Kong, Hong Kong, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States, MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom, Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom, and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Person:
- Wei, V.W.I, Cummings, D.A, Riley, S, Kwok, K.O, Cowling, B.J, Read, J.M, Kucharski, A.J, and Lessler, J
- Publisher:
- Public Library of Science
- Source:
- e571a831-4d67-485b-b07e-4a8797eb967c
30. Estimating the Life Course of Influenza A(H3N2) Antibody Responses from Cross-Sectional Data
- Title Tesim:
- Estimating the Life Course of Influenza A(H3N2) Antibody Responses from Cross-Sectional Data
- Creator:
- Kucharski, A.J, Cummings, D.A.T, Read, J.M, Lessler, J, Zhu, H, Riley, S, Jiang, C.Q, and Guan, Y
- Date of publication:
- 2015
- Abstract Tesim:
- The immunity of a host population against specific influenza A strains can influence a number of important biological processes, from the emergence of new virus strains to the effectiveness of vaccination programmes. However, the development of an individual’s long-lived antibody response to influenza A over the course of a lifetime remains poorly understood. Accurately describing this immunological process requires a fundamental understanding of how the mechanisms of boosting and cross-reactivity respond to repeated infections. Establishing the contribution of such mechanisms to antibody titres remains challenging because the aggregate effect of immune responses over a lifetime are rarely observed directly. To uncover the aggregate effect of multiple influenza infections, we developed a mechanistic model capturing both past infections and subsequent antibody responses. We estimated parameters of the model using cross-sectional antibody titres to nine different strains spanning 40 years of circulation of influenza A(H3N2) in southern China. We found that “antigenic seniority” and quickly decaying cross-reactivity were important components of the immune response, suggesting that the order in which individuals were infected with influenza strains shaped observed neutralisation titres to a particular virus. We also obtained estimates of the frequency and age distribution of influenza infection, which indicate that although infections became less frequent as individuals progressed through childhood and young adulthood, they occurred at similar rates for individuals above age 30 y. By establishing what are likely to be important mechanisms driving epochal trends in population immunity, we also identified key directions for future studies. In particular, our results highlight the need for longitudinal samples that are tested against multiple historical strains. This could lead to a better understanding of how, over the course of a lifetime, fast, transient antibody dynamics combine with the longer-term immune responses considered here.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/gep3-0353
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pbio.1002082
- Journal Issue:
- 3
- Journal Title:
- PLoS Biology
- Journal Volume:
- 13
- Keyword:
- virus neutralization, blood, Influenza A virus (H3N2), blood analysis, aged, antibody response, Cross-Sectional Studies, adult, immunology, Article, human, Child, Preschool, cross protection, Influenza A Virus, H3N2 Subtype, Longitudinal Studies, Immunologic Memory, longitudinal study, Cross Protection, virology, geographic distribution, Aged, cross reaction, biological model, young adult, virus antibody, Models, Immunological, time factor, nonhuman, antigenicity, Humans, Influenza, Human, Influenza virus A H3N2, immunological memory, Child, preschool child, Adult, Antibodies, Viral, middle aged, Middle Aged, virus strain, child, Time Factors, cross-sectional study, adaptive immunity, China, Adolescent, influenza A (H3N2), adolescent, age distribution, Age Distribution, Adaptive Immunity, and antibody titer
- Language Label:
- English
- License Label:
- Attribution 4.0 International
- ORCID:
- Other Affiliation:
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States, Department of Epidemiology and Population Health, Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China, MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom, and Guangzhou No. 12 Hospital, Guangzhou, Guangdong, China
- Person:
- Kucharski, A.J, Cummings, D.A.T, Read, J.M, Lessler, J, Zhu, H, Riley, S, Jiang, C.Q, and Guan, Y
- Publisher:
- Public Library of Science
- Source:
- 24eeb499-4caa-4943-ae0d-366224ba8cb2
Collection Details
- Total items
-
2111
- Size
-
unknown
- Date created
-
February 2, 2022