RT Journal Article SR Electronic(1) A1 Weber, Jan A1 Rangel, Hector R. A1 Chakraborty, Bikram A1 Tadele, Mahlet A1 Martinez, Miguel A. A1 Martinez-Picado, Javier A1 Marotta, Michael L. A1 Mirza, Muneer A1 Ruiz, Lidia A1 Clotet, Bonaventura A1 Wrin, Terri A1 Petropoulos, Christos J. A1 Quiñones-Mateu, Miguel E.YR 2003 T1 A novel TaqMan real-time PCR assay to estimate ex vivo human immunodeficiency virus type 1 fitness in the era of multi-target (pol and env) antiretroviral therapy JF Journal of General Virology, VO 84 IS 8 SP 2217 OP 2228 DO https://doi.org/10.1099/vir.0.19123-0 PB Microbiology Society, SN 1465-2099, AB Despite numerous studies on human immunodeficiency virus type 1 (HIV-1) fitness, many key conceptual and technical questions are still unsolved. For example, the proper system to determine virus fitness of HIV-1 is still unknown. In this study, an assay was developed to estimate HIV-1 fitness based on growth competition experiments and TaqMan real-time PCR. This novel technique was compared with several methods (i.e. virus growth kinetics, growth competition/heteroduplex-tracking analysis and single-cycle replication capacity assay) in order to analyse the impact of various genomic regions and overall genetic background on virus fitness. HIV-1 primary isolates and three different sets of recombinant viruses [i.e. recombinant clones carrying protease (PR), reverse transcriptase (RT) or the 3′ end of Gag, PR and RT (3′Gag/PR/RT), sequences amplified by PCR from the same primary isolates)] were evaluated. Here, it is demonstrated that, in spite of intrinsic differences, both growth competition/TaqMan and single-cycle replication assays detected a significant reduction in HIV-1 fitness as a consequence of drug-resistant mutations in pol. However, this new assay, based on HIV-1 isolates, may be useful to quantify replicative fitness in viruses from patients treated simultaneously with antiretroviral drugs targeting different genomic regions of HIV-1 (e.g. pol and env)., UL https://www.microbiologyresearch.org/content/journal/jgv/10.1099/vir.0.19123-0