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Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of HIV Transmission in MSM

Nadine Bachmann, Katharina Kusejko, Huyen Nguyen, Sandra E Chaudron, Claus Kadelka, Teja Turk, Jürg Böni, Matthieu Perreau, Thomas Klimkait, Sabine Yerly, Manuel Battegay, Andri Rauch, Alban Ramette, Pietro Vernazza, Enos Bernasconi, Matthias Cavassini, Huldrych F Günthard, Roger D Kouyos & Swiss HIV Cohort Study

abstract

BACKGROUND
Identifying local outbreaks and their drivers is a key step towards curbing HIV transmission and potentially achieving HIV elimination. Such outbreaks can be identified as transmission clusters extracted from phylogenetic trees constructed of densely sampled viral sequences. In this study, we combined phylogenetic transmission clusters with extensive data on virological suppression and behavioral risk of cluster members to quantify the drivers of ongoing transmission over ten years.

METHODS
Using the comprehensive Swiss HIV Cohort Study and its drug-resistance database, we reconstructed phylogenetic trees for each year between 2007-2017. We identified HIV transmission clusters dominated by men who have sex with men(MSM) and determined their annual growth. We used Poisson regression to assess if cluster-growth was associated with a per-cluster-infectivity and behavioral-risk score.

RESULTS
Both infectivity and behavioral risk scores were significantly higher in growing MSM transmission clusters compared to non-growing clusters (p≤0.01). The fraction of transmission clusters without infectious members acquiring new infections increased significantly over the study period. The infectivity score was significantly associated with per-capita incidence of MSM transmission clusters in eight years, while the behavioral risk score was significantly associated with per-capita incidence of MSM transmission clusters in three years.

CONCLUSIONS
We present a phylogenetic method to identify hotspots of ongoing transmission among MSM. Our results demonstrate the effectiveness of treatment as prevention at the population level. However, the significantly increasing number of new infections among transmission clusters without infectious members highlight a relative shift from diagnosed to undiagnosed individuals as drivers of HIV transmission in Swiss MSM.
   
citation Bachmann N, Kusejko K, Nguyen H, Chaudron S E, Kadelka C, Turk T, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Ramette A, Vernazza P, Bernasconi E, Cavassini M, Günthard H F, Kouyos R D, Swiss HIV Cohort Study . Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of HIV Transmission in MSM. Clin Infect Dis 2020;.
   
type journal paper/review (English)
date of publishing 17-04-2020
journal title Clin Infect Dis
ISSN electronic 1537-6591
PubMed 32300807
DOI 10.1093/cid/ciaa411