title: 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 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.
  
  
  
  Combined 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.
authors.affiliation: Bioinfoexperts, LLC, Thibodaux, Louisiana, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Rose
authors.affiliation: Bioinfoexperts, LLC, Thibodaux, Louisiana, USA.
authors.forename: Susanna L
authors.initials: SL
authors.lastname: Lamers
authors.affiliation: Bioinfoexperts, LLC, Thibodaux, Louisiana, USA Department of Pathology, Immunology and Laboratory Medicine and the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Nolan
authors.affiliation: Department of Medicine, University of California at San Francisco, San Francisco, California, USA.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Maidji
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: N R
authors.initials: NR
authors.lastname: Faria
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: Department of Pathology, Immunology and Laboratory Medicine and the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
authors.forename: James J
authors.initials: JJ
authors.lastname: Dollar
authors.affiliation: Department of Pathology, Immunology and Laboratory Medicine and the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
authors.forename: Samuel A
authors.initials: SA
authors.lastname: Maruniak
authors.affiliation: Department of Pathology, Immunology and Laboratory Medicine and the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: McAvoy
authors.affiliation: Department of Pathology, Immunology and Laboratory Medicine and the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
authors.forename: Marco
authors.initials: M
authors.lastname: Salemi
authors.affiliation: Department of Medicine, University of California at San Francisco, San Francisco, California, USA.
authors.forename: Cheryl A
authors.initials: CA
authors.lastname: Stoddart
authors.affiliation: National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA.
authors.forename: Elyse J
authors.initials: EJ
authors.lastname: Singer
authors.affiliation: The AIDS and Cancer Specimen Resource, University of California at San Francisco, San Francisco, California, USA Departments of Laboratory Medicine, Pathology, and Medicine, University of California at San Francisco, San Francisco, California, USA MMcGrath@php.ucsf.edu.
authors.forename: Michael S
authors.initials: MS
authors.lastname: McGrath
mesh_terms: D044966:Anti-Retroviral Agents / Q000627:therapeutic use*; D023241:Antiretroviral Therapy, Highly Active; D001344:Autopsy; D002531:Cerebellum / Q000821:virology; D004279:DNA, Viral / Q000235:genetics; D014644:Genetic Variation; D006678:HIV / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D015658:HIV Infections / Q000150:complications* / Q000188:drug therapy / Q000821:virology*; D017403:In Situ Hybridization; D008198:Lymph Nodes / Q000821:virology; D009369:Neoplasms / Q000150:complications*; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D000072230:Sustained Virologic Response; D019562:Viral Load; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054311:nef Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D044966:Anti-Retroviral Agents; D004279:DNA, Viral; D012367:RNA, Viral; D054299:env Gene Products, Human Immunodeficiency Virus; D054311:nef Gene Products, Human Immunodeficiency Virus; D054302:pol Gene Products, Human Immunodeficiency Virus