HIV Maintains an Evolving and Dispersed Population in Multiple Tissues during Suppressive Combined Antiretroviral Therapy in Individuals with Cancer

Abstract

While combined antiretroviral therapy (cART) can result in undetectable plasma viral loads, it does not eradicate HIV infection. Furthermore, HIV-infected individuals while on cART remain at an increased risk of developing serious comorbidities, such as cancer, neurological disease, and atherosclerosis, suggesting that during cART, tissue-based HIV may contribute to such pathologies. We obtained DNA and RNA env, nef, and pol sequences using single-genome sequencing from postmortem tissues of three HIV ؉ cART-treated (cART ؉ ) individuals with undetectable viral load and metastatic cancer at death and performed time-scaled Bayesian evolutionary analyses. We used a sensitive in situ hybridization technique to visualize HIV gag-pol mRNA transcripts in cerebellum and lymph node tissues from one patient. Tissue-associated virus evolved at similar rates in cART ؉ and cARTnaive (cART ؊ ) patients. Phylogenetic trees were characterized by two distinct features: (i) branching patterns consistent with constant viral evolution and dispersal among tissues and (ii) very recently derived clades containing both DNA and RNA sequences from multiple tissues. Rapid expansion of virus near death corresponded to wide-spread metastasis. HIV RNA ؉ cells clustered in cerebellum tissue but were dispersed in lymph node tissue, mirroring the evolutionary patterns observed for that patient. Activated, infiltrating macrophages were associated with HIV RNA. Our data provide evidence that tissues serve as a sanctuary for wild-type HIV during cART and suggest the importance of macrophages as an alternative reservoir and mechanism of virus spread. IMPORTANCECombined antiretroviral therapy (cART) reduces plasma HIV to undetectable levels; however, removal of cART results in plasma HIV rebound, thus highlighting its inability to entirely rid the body of infection. Additionally, HIV-infected individuals on cART remain at high risk of serious diseases, which suggests a contribution from residual HIV. In this study, we isolated and sequenced HIV from postmortem tissues from three HIV ؉ cART ؉ individuals who died with metastatic cancer and had no detectable plasma viral load. Using high-resolution evolutionary analyses, we found that tissue-based HIV continues to replicate, evolve, and migrate among tissues during cART. Furthermore, cancer onset and metastasis coincided with increased HIV expansion, suggesting a linked mechanism. HIV-expressing cells were associated with tissue macrophages, a target of HIV infection. Our results suggest the importance of tissues, and macrophages in particular, as a target for novel anti-HIV therapies.A lthough current combined antiretroviral therapy (cART) regimens can extend the lives of individuals infected with human immunodeficiency virus (HIV) by years or decades, two major problems remain. First, HIV is never eradicated in treated patients and plasma viral loads (VL) will rebound if treatment is stopped. Subsets of T cells (1-7) and lymph (8, 9) are considered likely reservoirs of virus during cART. Vi...

No evidence of ongoing HIV replication or compartmentalization in tissues during combination antiretroviral therapy: Implications for HIV eradication

“…Lorenzo-Redondo et al (24) recently reported finding genetic changes in HIV proviruses [proviruses are the integrated form of retrovirus DNA (27)] in the 6 months following the initiation of cART, leading to the generation of populations of HIV proviruses in tissues that were distinct from the population of HIV proviruses in PBMCs. That report and others (23,25,28,29) suggested that HIV replication that was restricted to tissue sanctuary sites resulted in the generation of markedly different populations of HIV proviruses in blood and tissues after prolonged cART. In contrast, if the reservoir consists of cells (or their descendants) that were infected before cART was initiated, there will be no additional genetic changes in the populations of proviruses during cART.…”

HIV persists throughout deep tissues with repopulation from multiple anatomical sources

“…In general, most studies aiming to characterize HIV DNA reservoirs in persons with HIV (PWH) have necessarily focused on blood, with a few other compartments that are relatively easy to sample such as the gut, through endoscopy (5,10,11,24), the genital tract, through genital secretions (12,(25)(26)(27)(28)(29)(30), or the CNS, through cerebrospinal fluid (CSF) (31)(32)(33)(34)(35)(36)(37). Of note, one study in PWH diagnosed with cancer allowed the analysis of HIV reservoirs in selected anatomic tissues collected during autopsy (38,39). More recently, De Scheerder et al investigated the origins of HIV rebound, and although this study was limited by the number of anatomical sites, they showed that viral rebound originated from diverse cellular and tissue reservoirs (40).…”

On the effective depth of viral sequence data

“…1 ). Many common viruses, including influenza ( Hamada et al 2012 ; Lakdawala et al 2015 ; Sobel Leonard et al 2017 ), HIV and related viruses ( Ait-Khaled et al 1995 ; Rose et al 2016 ; Feder et al 2017 ), and cytomegalovirus (CMV) ( Renzette et al 2013 ), have been identified as existing as separate subpopulations within a host, which may exhibit distinct viral diversity. In so far as mathematical models of viral evolution fit a model population to data from genome sequencing, failure to consider this structure may lead to overconfidence in the extent to which a model reproduces the true within-host viral population.…”