Autopsy tissue shows HIV continues to evolve and migrate

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Despite the fact that treated HIV patients had undetectable levels of virus in their blood a study found in autopsy tissue samples that the virus evolved and migrated similar to the way it did in patients who had never received ARV treatment.

The new study, by researchers from the University of California – San Francisco, the University of Oxford, the University of Florida and the University of California – Los Angeles,  supports the likelihood that the virus may at least be contributing to the development of non-Aids-defined diseases, such as cancer and cardiovascular disease.

“Looking in tissues of treated HIV patients, we found that HIV in some tissues did not appear to be affected by ARVs. Notably we saw no evidence of drug resistance, which we would have seen if the virus had been exposed to medications. While this is expected in untreated patients, it was a surprise to see this in virally suppressed patients. Our results suggest that HIV in varied tissue compartments can be untouched by the medications,” said study senior author, Dr Michael S McGrath, UCSF professor of laboratory medicine at the AIDS and Cancer Specimen Resource at UCSF.

The tissues examined by the research team came from the National Cancer Institute-supported AIDS and Cancer Specimen Resource at UCSF, which contains samples collected from patients beginning in 1984.

“Our findings suggest the spectrum of ‘non-Aids defining’ diseases such as cancers and cardiovascular disease that are increasingly the cause of death for virally suppressed patients are likely driven to some degree by the presence of active, untreated virus in tissues,” said McGrath. “In addition, our findings suggest that strategies to ‘cure’ HIV infection, which are centred on treatment of blood, must consider targeting tissue based sites of HIV.”

In these studies, the team examined mutations in HIV genetic sequences from patient’s tissues. HIV that continues to replicate and spread shows genetic changes in viral sequences that can only occur if the virus is replication competent and capable of spreading. In patients without ARV treatment, this analysis can reveal if and how much the virus is evolving, a phenomenon typically observed in HIV infection without treatment. HIV replication and evolution is inhibited by ARV therapy, and genetic sequencing of HIV from virally suppressed patients reflects the inhibitory effects of therapy.

In the current study, researchers looked at HIV from tissues taken from five HIV-infected patients who had been treated with ARV therapy, had no detectable virus in the blood and who had died from cancer, and compared it to HIV sequence changes taken from patients who had never received therapy and also had died from cancer.

“The evolution of HIV derived from both treated and untreated patients’ tissues, which showed no evidence for an ARV effect, stood in sharp contrast to other researchers’ findings from blood studies of patients treated with ARVs showing dramatic drops in both the number of HIV particles and evolution of the virus, confirming a predominant blood effect of ARV therapy unappreciated prior to the current study,” added McGrath.

The research team found evolving “wild type” HIV, that is virus unaffected by ARV therapy, in the cerebellum, lymph nodes, lungs, colons and spleens among others tissues.

The team also pointed to a role for HIV-infected macrophages, a long-lived tissue-based immune cell that engulfs and destroys cellular debris, foreign substances, microbes, and cancer cells, in disease progression. “Tissue macrophages, activated due to HIV infection, can turn on or contribute to disease processes, such as cardiovascular disease and neurological disease,” said McGrath.

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 cART-naive (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.

Authors
Rebecca Rose, Susanna L Lamars, David J Nolan, NR Faria, Oliver G Pybus, James J Dollar, Samuel A Maruniak, Andrew C McAvoy, Marco Salemi, Elyse J Singer, Ekaterina Maidji, Cheryl Stoddart, Michael S McGrath

University of California – San Francisco material
Journal of Virology abstract


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