Journal of Medical Virology 72:352–357 (2004) Different Resistance Mutations Can be Detected Simultaneously in the Blood and the Lung of HIV-1 Infected Individuals on Antiretroviral Therapy Natalie C. White, 1 Dominique Israel-Biet, 2 Richard J. Coker, 1 David M. Mitchell, 3 Jonathan N. Weber, 1 and John R. Clarke 1 * 1 Jefferiss Trust Laboratories, Wright-Fleming Institute, Faculty of Medicine, Imperial College School of Medicine, St. Mary’s Hospital, London, United Kingdom 2 Service de Pneumologie, Hospital Europeen Georges Pompidou, Paris, France 3 Chest and Allergy, St. Mary’s Hospital, London, United Kingdom In this retrospective study, matched peripheral blood and lung samples from patients on anti- retroviral therapy were studied in order to in- vestigate whether differences in mutations associated with resistance to nucleoside analo- gues could be detected between the lung and blood. Discordant mutation patterns in the reverse transcriptase (RT) between plasma and cell free bronchoalveolar lavage fluid (BAL-fluid) HIV-1 genomic RNA was observed in five out of seven patients on nucleoside reverse transcrip- tase inhibitor (NRTI) monotherapy and six out of seven on combination therapy. In the cellular compartments, DNA recovered from peripheral blood mononuclear cells (PBMCs) and cells from BAL-cells discordant HIV-1 resistance genotypes were detected in 15 out of 44 matched samples. Differences in resistant genotypes between PBMCs and BAL-cells were most pronounced in patients receiving combination antiretroviral therapy. The pattern and number of mutations in RT associated with resistance differed in the BAL-cells compared to PBMCs in four out of 12 subjects not receiving antiretroviral therapy at the time of bronchoscopy, three from 14 patients on NRTI monotherapy, five out of nine on dual combination therapy and three out of nine on HAART. The differences in the detec- tion of resistance mutations between blood and the lung suggest that the lung is a site of replication for HIV-1. J. Med. Virol. 72:352– 357, 2004. ß 2004 Wiley-Liss, Inc. KEY WORDS: HIV-1; lung; brochoalveolar lavage; discordant mutations; drug resistance INTRODUCTION Despite prolonged suppression of plasma viremia during HAART, there is evidence of low-level viral replication in some patients [Furtado et al., 1999], suggesting that current regimens do not totally sup- press viral replication. Persistent viral replication during therapy could be due the activation of resting CD4 þ T cells and macro- phages, which harbour latent but replication competent HIV provirus [Furtado et al., 1999]. Alternatively, anatomical sites, may act as reservoirs of HIV replica- tion including the lymph node, brain, genital tract, semen, and the lung [Clarke et al., 1990; Di Stefano et al., 1995; Poss et al., 1995; Chun et al., 1997; Delwart et al., 1998; van’t Wout et al., 1998]. Differential viral evolution in these sites compared to the blood compart- ment may be indicative of the significance of these sites to whole body HIV replication [Poss et al., 1995; Wong et al., 1997a,b; van’t Wout et al., 1998]. Prolonged or sub-optimal anti-retroviral therapy leads to viral rebound associated with the selection of mutations in pol associated with reduced drug suscept- ibility [Young et al., 1998; Havlir et al., 2000]. Specific resistance mutations may vary between virus in different body compartments, particularly the brain and spleen in patients on AZT monotherapy [Di Stefano et al., 1995; Atkins et al., 1998]. *Correspondence to: John R. Clarke, Jefferiss Trust Laboratories, Wright-Fleming Institute, Faculty of Medicine, Imperial College School of Medicine, St. Mary’s Hospital, London, UK. E-mail: j.r.clarke@imperial.ac.uk Accepted 8 October 2003 DOI 10.1002/jmv.20010 Published online in Wiley InterScience (www.interscience.wiley.com) ß 2004 WILEY-LISS, INC.