Molecular tools for studying HIV transmission in sexual networksGrabowski, Mary K.a; Redd, Andrew D.bCurrent Opinion in HIV and AIDS: March 2014 - Volume 9 - Issue 2 - p 126–133 doi: 10.1097/COH.0000000000000040 EPIDEMIOLOGY: CONCENTRATED EPIDEMICS: Edited by Chris Beyrer, Stefan D. Baral, and Patrick S. Sullivan Abstract Author Information Purpose of review Phylogenetics is frequently used for studies of population-based HIV transmission. The purpose of this review is to highlight the current utilities and limitations of phylogenetics in HIV epidemiological research from sample collection through to data analysis. Recent findings Studies of HIV phylogenies can provide critical information about HIV epidemics that are otherwise difficult to obtain through traditional study design such as transmission of drug-resistant virus, mixing between demographic groups, and rapidity of viral spread within populations. However, recent results from empirical and theoretical studies of HIV phylogenies challenge some of the key assumptions and interpretations from phylogenetic studies. Recent findings include lack of transmission bottlenecks in MSM and injection drug use epidemics, evidence for preferential transmission of HIV virus in heterosexual epidemics, and limited evidence that tree topologies correlate directly with underlying network structures. Other challenges include a lack of a standardized definition for a phylogenetic transmission cluster and biased or sparse sampling of HIV transmission networks. Summary Phylogenetics is an important tool for HIV research, and offers opportunities to understand critical aspects of the HIV epidemic. Like all epidemiological research, the methods used and interpretation of results from phylogenetic studies should be made cautiously with careful consideration. aBloomberg School of Public Health, Johns Hopkins University bLaboratory of Immunoregulation, NIAID, NIH, Baltimore, Maryland, USA Correspondence to Dr Andrew D. Redd, 851 N. Wolfe St, Rangos Building Room 527, Baltimore, MD 21205, USA. Tel: +1 410 614 0813; fax: +1 410 614 9775; e-mail: Aredd2@jhmi.edu Copyright © 2014 Wolters Kluwer Health, Inc. All rights reserved.