Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?
Ann M Dennis,Joshua T. Herbeck,Andrew J. Leigh Brown,Paul Kellam,Paul Kellam,Tulio de Oliveira,Deenan Pillay,Christophe Fraser,Myron S. Cohen +8 more
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TLDR
This work describes the current uses for phylogenetics in generalized epidemics and discusses their promise for elucidating transmission patterns and informing prevention trials, and reviews logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized Epidemics and suggest potential solutions.Abstract:
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.read more
Citations
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Using Contact Patterns to Inform HIV Interventions in Persons Who Inject Drugs in Northern Vietnam.
TL;DR: Collection and analysis of contact patterns in PWID is feasible and can greatly inform infectious disease dynamics and targeting of appropriate interventions, and provide much needed empirical data on mixing to improve mathematical models of disease transmission in this population.
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The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review.
TL;DR: In this article, the authors assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV1 incidence and prevalence) and areas or populations with lower HIV1 burden in sSA.
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Factors Associated With Human Immunodeficiency Virus Infections Linked in Genetic Clusters But Disconnected in Partner Tracing.
Dana K. Pasquale,Dana K. Pasquale,Irene A. Doherty,Irene A. Doherty,William C. Miller,Peter A. Leone,Lynne A Sampson,Sue L. Ledford,Joseph Sebastian,Ann M Dennis +9 more
TL;DR: Based on genetic networks, partnerships which may be stigmatized, may have occurred farther back in time, or may have an intervening partner were more likely to be unobserved in the partner contact network.
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Determining the Direction of Human Immunodeficiency Virus Transmission: Benefits and Potential Harms of Taking Phylogenetic Analysis One Step Further.
Barbara S. Taylor,Hugo Sapién +1 more
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Identification of hidden population structure in time-scaled phylogenies
TL;DR: A fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees is developed and it is found that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance.
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