title: Natural polymorphisms of HIV-1 CRF01_AE integrase coding region in ARV-naïve individuals in Cambodia, Thailand and Vietnam: an ANRS AC12 working group study.
abstract: The HIV integrase enzyme is essential for the HIV life cycle as it mediates integration of HIV-1 proviral DNA into the infected cell's genome. Recently, the development of drugs capable of inhibiting integrase has provided major new options for HIV-infected, treatment-experienced patients with multidrug resistant virus, as well treatment-naïve patients. More than 40 amino acid substitutions within integrase have been described as associated mostly with resistance of HIV B-subtypes to currently available integrase inhibitors (INIs). We have analyzed the natural polymorphisms of the integrase coding region in 87 antiretroviral-naïve subjects (32 from Cambodia, 37 from Thailand and 18 from Vietnam) infected with CRF01_AE virus, the predominant HIV-1 strain circulating in Southeast Asia. The 864bp integrase coding region was sequenced using the ANRS consensus sequencing technique from plasma samples, and amino acid results were interpreted for drug resistance according to the ANRS (Updated July 2009, version 18) and Stanford algorithms (Version November 6, 2009). Alignment of the 87 amino acid sequences against the 2004 Los Alamos HIV-1 clade B consensus sequence showed that overall, 119 of 288 (41.3%) amino acid positions presented at least one polymorphism each. Substitutions found in >60% of study subjects occurred at: K14, A21, V31, S39, I72, T112, T124, T125, G134, I135, K136, D167, V201, L234 and S283. Also, new amino acid substitutions of as yet unknown significance were identified: E152K/H, S153F/L, N155I and E157G. None of the known integrase resistance mutations were observed, except E157Q found in one Cambodian subject (1.1%, CI 95% 0.02-6.3%). The clinical impact of this substitution on resistance of B and nonB-viruses to the licensed INI raltegravir is unclear. If this substitution is confirmed to compromise the virologic response to raltegravir, further studies will be needed to better assess the prevalence of this substitution among CRF01_AE virus.
authors.affiliation: Institut Pasteur du Cambodge, Laboratoire VIH/Hepatites, Phnom Penh, Cambodia. njanin@pasteur-kh.org
authors.forename: Janin
authors.initials: J
authors.lastname: Nouhin
authors.forename: Tawee
authors.initials: T
authors.lastname: Donchai
authors.forename: Khanh Thu Huynh
authors.initials: KT
authors.lastname: Hoang
authors.forename: Sreymom
authors.initials: S
authors.lastname: Ken
authors.forename: Jiraporn
authors.initials: J
authors.lastname: Kamkorn
authors.forename: Ton
authors.initials: T
authors.lastname: Tran
authors.forename: Ahidjo
authors.initials: A
authors.lastname: Ayouba
authors.forename: Martine
authors.initials: M
authors.lastname: Peeters
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Chaix
authors.forename: Truong Xuan
authors.initials: TX
authors.lastname: Lien
authors.forename: Eric
authors.initials: E
authors.lastname: Nerrienet
authors.forename: Nicole
authors.initials: N
authors.lastname: Ngo-Giang-Huong
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution; D019380:Anti-HIV Agents / Q000627:therapeutic use*; D001483:Base Sequence; D018791:CD4 Lymphocyte Count; D002160:Cambodia; D017931:DNA Primers; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D019427:HIV Integrase / Q000235:genetics*; D015497:HIV-1 / Q000201:enzymology / Q000235:genetics*; D006801:Humans; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D013785:Thailand; D014744:Vietnam
chemical_list: D019380:Anti-HIV Agents; D017931:DNA Primers; D019427:HIV Integrase; C514801:p31 integrase protein, Human immunodeficiency virus 1