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Comparative analysis of HIV sequences in real time for public health

Wertheim, Joel O.a; Chato, Connorb; Poon, Art F.Y.b,c

Current Opinion in HIV and AIDS: May 2019 - Volume 14 - Issue 3 - p 213–220
doi: 10.1097/COH.0000000000000539
PHYLOGENETICS IN HIV TRANSMISSION: Edited by Morgane Rolland and Josh Herbeck

Purpose of review The purpose of this study is to summarize recent advances in public health applications of comparative methods for HIV-1 sequence analysis in real time, including genetic clustering methods.

Recent findings Over the past 2 years, several groups have reported the deployment of established genetic clustering methods to guide public health decisions for HIV prevention in ‘near real time’. However, it remains unresolved how well the readouts of comparative methods like clusters translate to events that are actionable for public health. A small number of recent studies have begun to elucidate the linkage between clusters and HIV-1 incidence, whereas others continue to refine and develop new comparative methods for such applications.

Summary Although the use of established methods to cluster HIV-1 sequence databases has become a widespread activity, there remains a critical gap between clusters and public health value.

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

bDepartment of Pathology and Laboratory Medicine

cDepartment of Microbiology and Immunology, Western University, London, Ontario, Canada

Correspondence to Art F.Y. Poon, PhD, Health Sciences Addition 422, Western University, London, ON, Canada. Tel: +1 519 661 2111; e-mail:

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