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Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic.

ABSTRACT: The human displacement and sexual behavior are the main factors driving the HIV-1 pandemic to the current profile. The intrinsic structure of the HIV transmission among different individuals has valuable importance for the understanding of the epidemic and for the public health response. The aim of this study was to characterize the HIV-1 subtype B (HIV-1B) epidemic in South America through the identification of transmission links and infer trends about geographical patterns and median time of transmission between individuals. Sequences of the protease and reverse transcriptase coding regions from 4,810 individuals were selected from GenBank. Maximum likelihood phylogenies were inferred and submitted to ClusterPicker to identify transmission links. Bayesian analyses were applied only for clusters including ?5 dated samples in order to estimate the median maximum inter-transmission interval. This study analyzed sequences sampled from 12 South American countries, from individuals of different exposure categories, under different antiretroviral profiles, and from a wide period of time (1989-2013). Continentally, Brazil, Argentina and Venezuela were revealed important sites for the spread of HIV-1B among countries inside South America. Of note, from all the clusters identified about 70% of the HIV-1B infections are primarily occurring among individuals living in the same geographic region. In addition, these transmissions seem to occur early after the infection of an individual, taking in average 2.39 years (95% CI 1.48-3.30) to succeed. Homosexual/Bisexual individuals transmit the virus as quickly as almost half time of that estimated for the general population sampled here. Public health services can be broadly benefitted from this kind of information whether to focus on specific programs of response to the epidemic whether as guiding of prevention campaigns to specific risk groups.

SUBMITTER: Junqueira DM

PROVIDER: S-EPMC4892525 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic.

Junqueira Dennis Maletich DM de Medeiros Rubia Marília RM Gräf Tiago T Almeida Sabrina Esteves de Matos SE

PloS one 20160603 6

The human displacement and sexual behavior are the main factors driving the HIV-1 pandemic to the current profile. The intrinsic structure of the HIV transmission among different individuals has valuable importance for the understanding of the epidemic and for the public health response. The aim of this study was to characterize the HIV-1 subtype B (HIV-1B) epidemic in South America through the identification of transmission links and infer trends about geographical patterns and median time of t ...[more]

PMID: 27258369

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Project description:BackgroundSimple phenomenological growth models can be useful for estimating transmission parameters and forecasting epidemic trajectories. However, most existing phenomenological growth models only support single-peak outbreak dynamics whereas real epidemics often display more complex transmission trajectories.MethodsWe develop and apply a novel sub-epidemic modeling framework that supports a diversity of epidemic trajectories including stable incidence patterns with sustained or damped oscillations to better understand and forecast epidemic outbreaks. We describe how to forecast an epidemic based on the premise that the observed coarse-scale incidence can be decomposed into overlapping sub-epidemics at finer scales. We evaluate our modeling framework using three outbreak datasets: Severe Acute Respiratory Syndrome (SARS) in Singapore, plague in Madagascar, and the ongoing Ebola outbreak in the Democratic Republic of Congo (DRC) and four performance metrics.ResultsThe sub-epidemic wave model outperforms simpler growth models in short-term forecasts based on performance metrics that account for the uncertainty of the predictions namely the mean interval score (MIS) and the coverage of the 95% prediction interval. For example, we demonstrate how the sub-epidemic wave model successfully captures the 2-peak pattern of the SARS outbreak in Singapore. Moreover, in short-term sequential forecasts, the sub-epidemic model was able to forecast the second surge in case incidence for this outbreak, which was not possible using the simple growth models. Furthermore, our findings support the view that the national incidence curve of the Ebola epidemic in DRC follows a stable incidence pattern with periodic behavior that can be decomposed into overlapping sub-epidemics.ConclusionsOur findings highlight how overlapping sub-epidemics can capture complex epidemic dynamics, including oscillatory behavior in the trajectory of the epidemic wave. This observation has significant implications for interpreting apparent noise in incidence data where the oscillations could be dismissed as a result of overdispersion, rather than an intrinsic part of the epidemic dynamics. Unless the oscillations are appropriately modeled, they could also give a false positive, or negative, impression of the impact from public health interventions. These preliminary results using sub-epidemic models can help guide future efforts to better understand the heterogenous spatial and social factors shaping sub-epidemic patterns for other infectious diseases.

Project description:Objective: Hypothyroid patients frequently request specific therapies from their physicians. Combination therapy is vigorously discussed at professional meetings. We wished to determine if physician prescribing patterns for hypothyroidism changed during 2017 after specific educational events. Methods: A survey addressing treatment of hypothyroidism was emailed to American Thyroid Association (ATA) members on three occasions in 2017. The Spring emails were sent prior to a satellite symposium addressing hypothyroidism, and prior to the annual Endocrine Society and ATA meetings; the December emails were sent after these events. Physicians were presented with thirteen theoretical patients and chose from 6 therapeutic options, including levothyroxine, synthetic combination therapy, thyroid extract, and liothyronine monotherapy. The patient scenarios successively incorporated factors potentially providing reasons for considering combination therapy. Multivariate repeated measures logistic regression analyses first examined effects of physician characteristics on prescribing the various therapies. Then, analyses also incorporated timing, by comparing prescribing patterns in February, March, and December. Results: In analyses of prescribing levothyroxine monotherapy vs. any T3 therapy, there was a trend of borderline significance (p = 0.053) for T3 therapy to be prescribed more in December compared with February-March combined. When multivariate analyses were performed controlling for time and physician characteristics, choice of therapy was only significantly affected by country of practice (OR 1.7, CI 1.3-2.2). Physician choice of therapies was also examined for the options of continuing (1) levothyroxine, vs. (2) increasing levothyroxine, (3) adding liothyronine either with or without levothyroxine reduction, or (4) replacing levothyroxine with desiccated thyroid extract or liothyronine. When multivariate analyses incorporating time and physician characteristics were performed, respondents in December (OR 1.5, CI 1.0-2.3) and those practicing in North America (OR 1.8, CI 1.2-2.6) were more likely to prescribe liothyronine. Conclusions: This survey shows that although current North American guidelines do not recommend combination therapy, such therapy is being prescribed more over time and is also more commonly prescribed in North America. It is possible our guidelines are failing to incorporate evidence that physicians are considering when prescribing combination therapy. Such evidence could include data about patient preferences, and this needs to be a focus of future studies.

Project description:BackgroundBetween 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. We aim to describe the spatiotemporal and molecular features of the three distinct epidemic waves and explore the role of vaccination campaigns, precipitation, and population movement in shaping cholera spread in this complex setting.MethodsIn this descriptive epidemiological study, we analysed cholera linelist data to describe the spatiotemporal progression of the epidemics. We placed whole-genome sequence data from pandemic Vibrio cholerae collected throughout these epidemics into the global phylogenetic context. Using whole-genome sequence data in combination with other molecular attributes, we characterise the relatedness of strains circulating in each wave and the region. We investigated the association of rainfall and the instantaneous basic reproduction number using distributed lag non-linear models, compared county-level attack rates between those with early and late reactive vaccination campaigns, and explored the consistency of the spatial patterns of displacement and suspected cholera case reports.FindingsThe 2014 (6389 cases) and 2015 (1818 cases) cholera epidemics in South Sudan remained spatially limited whereas the 2016-17 epidemic (20?438 cases) spread among settlements along the Nile river. Initial cases of each epidemic were reported in or around Juba soon after the start of the rainy season, but we found no evidence that rainfall modulated transmission during each epidemic. All isolates analysed had similar genotypic and phenotypic characteristics, closely related to sequences from Uganda and Democratic Republic of the Congo. Large-scale population movements between counties of South Sudan with cholera outbreaks were consistent with the spatial distribution of cases. 21 of 26 vaccination campaigns occurred during or after the county-level epidemic peak. Counties vaccinated on or after the peak incidence week had 2·2 times (95% CI 2·1-2·3) higher attack rates than those where vaccination occurred before the peak.InterpretationPandemic V cholerae of the same clonal origin was isolated throughout the study period despite interepidemic periods of no reported cases. Although the complex emergency in South Sudan probably shaped some of the observed spatial and temporal patterns of cases, the full scope of transmission determinants remains unclear. Timely and well targeted use of vaccines can reduce the burden of cholera; however, rapid vaccine deployment in complex emergencies remains challenging.FundingThe Bill & Melinda Gates Foundation.

Dataset Information

Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic.

Publications

Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic.

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