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Understanding disclosed and cryptic HIV transmission risk via genetic analysis

what are we missing and when does it matter?

Ragonnet-Cronin, Manona; Hodcroft, Emma B.b; Wertheim, Joel O.c

Current Opinion in HIV and AIDS: May 2019 - Volume 14 - Issue 3 - p 205–212
doi: 10.1097/COH.0000000000000537
PHYLOGENETICS IN HIV TRANSMISSION: Edited by Morgane Rolland and Josh Herbeck

Purpose of review To discuss the recent HIV phylogenetic analyses examining HIV transmission patterns among and within risk groups.

Recent findings Phylodynamic analysis has recently been applied to multiple HIV outbreaks among people who inject drugs to determine whether HIV transmission is ongoing. Large-scale analyses of datasets of HIV sequences collected for drug-resistance testing provide population-level insights into transmission patterns. One focus across world regions has been to investigate whether age-disparity is a driver of HIV transmission. In sub-Saharan Africa, researchers have examined transmission between heterosexuals and MSM and between high prevalence fishing communities and inland communities. In the US and the UK, cryptic risk groups such as nondisclosed MSM and the partners of transgender women are increasingly being uncovered based on their position in densely sampled molecular transmission networks.

Summary Analysis of HIV genetic sequence can resolve viral transmission patterns between risk groups at unprecedented scales and levels of detail. Future research should focus on understanding the effect of missing data on inferences and the biases of different methods. Uncovering groups and patterns obscured from traditional epidemiolocal analyses is exciting but should not compromise the privacy of the groups in question.

aDepartment of Infectious Disease Epidemiology, Imperial College London, London, UK

bBiozentrum, University of Basel, Basel, Switzerland

cDepartment of Medicine, University of California, San Diego, California, USA

Correspondence to Manon Ragonnet-Cronin, Department of Infectious Disease Epidemiology, Imperial College London, Praed St, London W2 1NY, UK. E-mail:

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