Copyright © Lippincott Williams & Wilkins. Unauthorized reproduction of this article is prohibited. Transmission networks of HIV-1 among men having sex with men in the Netherlands Daniela Bezemer a , Ard van Sighem a , Vladimir V. Lukashov b , Lia van der Hoek b , Nicole Back b , Rob Schuurman c , Charles A.B. Boucher c,d , Eric C.J. Claas e , Maarten C. Boerlijst f , Roel A. Coutinho g,h , Frank de Wolf a,i , for the ATHENA observational cohort Objective: To obtain insight in the HIV-1 transmission networks among men having sex with men (MSM) in the Netherlands. Design: A phylogenetic tree was constructed from polymerase sequences isolated from 2877 HIV-1 subtype B-infected patients monitored as part of the AIDS Therapy Evaluation in the Netherlands (ATHENA) nationwide observational cohort. Methods: For MSM with a known date of infection, the most similar sequences were selected as potential transmission pairs when they clustered with bootstrap value of at least 99%. Time from infection to onward transmission was estimated as the median time between dates of infection for each transmission pair. The source of infections with a resistant strain was traced using the entire phylogenetic tree. Results: Of sequences from 403 MSM with a known date of infection between 1987 and 2007, 175 (43%) formed 63 clusters. Median time to onward transmission was 1.4 years (interquartile range 0.6–2.7). Twenty-four (6%) MSM carried a virus with resistance-related mutations, 13 of these were in eight clusters together with sequences from 28 other patients in the entire phylogenetic tree. Six clusters contained sequences obtained from 29 men all presenting the same resistance-related mutations. Conclusion: From our selection of likely transmission pairs, we conclude that onward transmission of HIV-1 from infected MSM in the Netherlands happens both during and after primary infection. Transmission of resistant strains from the antiretroviral therapy- treated population is limited, but strains with resistance-related mutations have formed subepidemics. ß 2010 Wolters Kluwer Health | Lippincott Williams & Wilkins AIDS 2010, 24:271–282 Keywords: HIV-1, molecular epidemiology, primary infection, transmission network, transmitted drug resistance a HIV Monitoring Foundation, b Department of Medical Microbiology, Academic Medical Centre, Amsterdam, c Department of Virology, University Hospital Utrecht, Utrecht, d Department of Virology, Erasmus Medical Center, Rotterdam, e Department of Medical Microbiology, Leiden University Medical Center, Leiden, f Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, g Department of Internal Medicine, Academic Medical Center, Amsterdam, h Center for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands, and i Department of Infectious Disease Epidemiology, Imperial College London, London, UK. Correspondence to Daniela Bezemer, HIV Monitoring Foundation, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands. Tel: +31 20 5667180; fax: +31 205669189; e-mail: D.O.Bezemer@amc.uva.nl Received: 16 June 2009; revised: 17 September 2009; accepted: 5 October 2009. DOI:10.1097/QAD.0b013e328333ddee ISSN 0269-9370 Q 2010 Wolters Kluwer Health | Lippincott Williams & Wilkins 271