title: Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy.
abstract: The impact of antiretroviral therapy (ART) on the genetics of simian immunodeficiency virus (SIV) or human immunodeficiency virus (HIV) populations has been incompletely characterized. We analyzed SIV genetic variation before, during, and after ART in a macaque model. Six pigtail macaques were infected with an SIV/HIV chimeric virus, RT-SHIV(mne), in which SIV reverse transcriptase (RT) was replaced by HIV-1 RT. Three animals received a short course of efavirenz (EFV) monotherapy before combination ART was started. All macaques received 20 weeks of tenofovir, emtricitabine, and EFV. Plasma virus populations were analyzed by single-genome sequencing. Population diversity was measured by average pairwise difference, and changes in viral genetics were assessed by phylogenetic and panmixia analyses. After 20 weeks of ART, viral diversity was not different from pretherapy viral diversity despite more than 10,000-fold declines in viremia, indicating that, within this range, there is no relationship between diversity and plasma viremia. In two animals with consistent SIV RNA suppression to <15 copies/ml during ART, there was no evidence of viral evolution. In contrast, in the four macaques with viremias >15 copies/ml during therapy, there was divergence between pre- and during-ART virus populations. Drug resistance mutations emerged in two of these four animals, resulting in virologic failure in the animal with the highest level of pretherapy viremia. Taken together, these findings indicate that viral diversity does not decrease with suppressive ART, that ongoing replication occurs with viremias >15 copies/ml, and that in this macaque model of ART drug resistance likely emerges as a result of incomplete suppression and preexisting drug resistance mutations.
authors.affiliation: HIV Drug Resistance Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD 21702-1201, USA. kearneym@ncifcrf.gov
authors.forename: Mary
authors.initials: M
authors.lastname: Kearney
authors.forename: Jon
authors.initials: J
authors.lastname: Spindler
authors.forename: Wei
authors.initials: W
authors.lastname: Shao
authors.forename: Frank
authors.initials: F
authors.lastname: Maldarelli
authors.forename: Sarah
authors.initials: S
authors.lastname: Palmer
authors.forename: Shiu-Lok
authors.initials: SL
authors.lastname: Hu
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Lifson
authors.forename: Vineet N
authors.initials: VN
authors.lastname: KewalRamani
authors.forename: John W
authors.initials: JW
authors.lastname: Mellors
authors.forename: John M
authors.initials: JM
authors.lastname: Coffin
authors.forename: Zandrea
authors.initials: Z
authors.lastname: Ambrose
mesh_terms: D000818:Animals; D044966:Anti-Retroviral Agents / Q000008:administration & dosage*; D023241:Antiretroviral Therapy, Highly Active; D016000:Cluster Analysis; D004195:Disease Models, Animal; D019143:Evolution, Molecular; D014644:Genetic Variation; D054303:HIV Reverse Transcriptase / Q000235:genetics*; D008251:Macaca; D010802:Phylogeny; D010949:Plasma / Q000821:virology; D012367:RNA, Viral / Q000235:genetics; D011994:Recombinant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D016097:Simian Acquired Immunodeficiency Syndrome / Q000188:drug therapy* / Q000821:virology*; D015302:Simian Immunodeficiency Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D019562:Viral Load
chemical_list: D044966:Anti-Retroviral Agents; D012367:RNA, Viral; D011994:Recombinant Proteins; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase