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Background  Progression rates from initial HIV-1 infection to advanced AIDS vary significantly among infected individuals. A distinct subgroup of HIV-1-infected individuals—termed viremic non-progressors (VNP) or controllers—do not seem to progress to AIDS, maintaining high CD4 +  T cell counts despite high levels of viremia for many years. Several studies have evaluated multiple host factors, including immune activation, trying to elucidate the atypical HIV-1 disease progression in these patients; however, limited work has been done to characterize viral factors in viremic controllers.    Methods  We analyzed HIV-1 isolates from three VNP individuals and compared the replicative fitness, near full-length HIV-1 genomes and intra-patient HIV-1 genetic diversity with viruses from three typical (TP) and one rapid (RP) progressor individuals.    Results  Viremic non-progressors and typical patients were infected for >10 years (range 10–17 years), with a mean CD4 +  T-cell count of 472 cells/mm 3  (442–529) and 400 cells/mm 3  (126–789), respectively. VNP individuals had a less marked decline in CD4 +  cells (mean −0.56, range −0.4 to −0.7 CD4 + /month) than TP patients (mean −10.3, −8.2 to −13.1 CD4 + /month). Interestingly, VNP individuals carried viruses with impaired replicative fitness, compared to HIV-1 isolates from the TP and RP patients (p < 0.05, 95% CI). Although analyses of the near full-length HIV-1 genomes showed no clear patterns of single-nucleotide polymorphisms (SNP) that could explain the decrease in replicative fitness, both the number of SNPs and HIV-1 population diversity correlated inversely with the replication capacity of the viruses ( r  = −0.956 and  r  = −0.878,  p  < 0.01, respectively).    Conclusion  It is likely that complex multifactorial parameters govern HIV-1 disease progression in each individual, starting with the infecting virus (phenotype, load, and quasispecies diversity) and the intrinsic ability of the host to respond to the infection. Here we analyzed a subset of viremic controller patients and demonstrated that similar to the phenomenon observed in patients with a discordant response to antiretroviral therapy (i.e., high CD4 +  cell counts with detectable plasma HIV-1 RNA load), reduced viral replicative fitness seems to be linked to slow disease progression in these antiretroviral-naïve individuals.    Electronic supplementary material  The online version of this article (doi:10.1186/s12981-017-0144-0) contains supplementary material, which is available to authorized users.

Impaired human immunodeficiency virus type 1 replicative fitness in atypical viremic non-progressor individuals