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A composite likelihood approach for estimating HIV prevalence in the presence of spatial variation.

ABSTRACT: Since 1990, the World Health Organization has recommended HIV surveillance among pregnant women as an essential surveillance activity for countries with generalized HIV epidemics. Despite the widespread availability and potential usefulness of antenatal HIV surveillance, analyses of such data present important challenges. Within an individual clinic, the HIV status of its attendees may be correlated because of similarities in HIV risk among women close in age. Between-clinic correlation may also arise as women often seek antenatal care at clinics located close to their home, and individuals living in nearby communities may share important characteristics or behaviours related to susceptibility. A general estimating equation-based approach for spatially-correlated, binary data such as that antenatal HIV surveillance based on a pairwise composite likelihood has been described. We present an extended version of this model that can accommodate penalized spline estimators and apply it to antenatal HIV surveillance data collected in 2011 in Botswana to estimate the effects of proximity to the 'hotspot' of the country's HIV epidemic and age on HIV prevalence. Finally, we compare the results with a logistic regression analysis, which ignores potential correlation of responses.

SUBMITTER: Wirth KE

PROVIDER: S-EPMC5029272 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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A composite likelihood approach for estimating HIV prevalence in the presence of spatial variation.

Wirth Kathleen E KE Agniel Denis D Barr Christopher D CD Austin Matthew D MD DeGruttola Victor V

Statistics in medicine 20150726 28

Since 1990, the World Health Organization has recommended HIV surveillance among pregnant women as an essential surveillance activity for countries with generalized HIV epidemics. Despite the widespread availability and potential usefulness of antenatal HIV surveillance, analyses of such data present important challenges. Within an individual clinic, the HIV status of its attendees may be correlated because of similarities in HIV risk among women close in age. Between-clinic correlation may also ...[more]

PMID: 26215657

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Project description:BackgroundHIV prevalence data among pregnant women have been critical to estimating HIV trends and geographical patterns of HIV in many African countries. Although antenatal HIV prevalence data are known to be biased representations of HIV prevalence in the general population, mathematical models have made various adjustments to control for known sources of bias, including the effect of HIV on fertility, the age profile of pregnant women and sexual experience.Methods and findingsWe assessed whether assumptions about antenatal bias affect conclusions about trends and geographical variation in HIV prevalence, using simulated datasets generated by an agent-based model of HIV and fertility in South Africa. Results suggest that even when controlling for age and other previously-considered sources of bias, antenatal bias in South Africa has not been constant over time, and trends in bias differ substantially by age. Differences in the average duration of infection explain much of this variation. We propose an HIV duration-adjusted measure of antenatal bias that is more stable, which yields higher estimates of HIV incidence in recent years and at older ages. Simpler measures of antenatal bias, which are not age-adjusted, yield estimates of HIV prevalence and incidence that are too high in the early stages of the HIV epidemic, and that are less precise. Antenatal bias in South Africa is substantially greater in urban areas than in rural areas.ConclusionsAge-standardized approaches to defining antenatal bias are likely to improve precision in model-based estimates, and further recency adjustments increase estimates of HIV incidence in recent years and at older ages. Incompletely adjusting for changing antenatal bias may explain why previous model estimates overstated the early HIV burden in South Africa. New assays to estimate the fraction of HIV-positive pregnant women who are recently infected could play an important role in better estimating antenatal bias.

Project description:BackgroundSeveral phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE) of the species tree (topology, branch lengths, and population sizes) from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units.ResultsWe show that the MPE of the species tree is statistically consistent as the number M of genes goes to infinity. In addition, the probability that the MPE of the species tree matches the true species tree converges to 1 at rate O(M -1). The simulation results confirm that the maximum pseudo-likelihood approach is statistically consistent even when the species tree is in the anomaly zone. We applied our method, Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST) to a mammal dataset. The four major clades found in the MP-EST tree are consistent with those in the Bayesian concatenation tree. The bootstrap supports for the species tree estimated by the MP-EST method are more reasonable than the posterior probability supports given by the Bayesian concatenation method in reflecting the level of uncertainty in gene trees and controversies over the relationship of four major groups of placental mammals.ConclusionsMP-EST can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.

Dataset Information

A composite likelihood approach for estimating HIV prevalence in the presence of spatial variation.

Publications

A composite likelihood approach for estimating HIV prevalence in the presence of spatial variation.

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