Molecular evolution of HIV-1 CRF01_AE Env in Thai patients.

BACKGROUND: The envelope glycoproteins (Env), gp120 and gp41, are the most variable proteins of human immunodeficiency virus type 1 (HIV-1), and are the major targets of humoral immune responses against HIV-1. A circulating recombinant form of HIV-1, CRF01_AE, is prevalent throughout Southeast Asia; however, only limited information regarding the immunological characteristics of CRF01_AE Env is currently available. In this study, we attempted to examine the evolutionary pattern of CRF01_AE Env under the selection pressure of host immune responses. METHODOLOGY/PRINCIPAL FINDINGS: Peripheral blood samples were collected periodically over 3 years from 15 HIV-1-infected individuals residing in northern Thailand, and amplified env genes from the samples were subjected to computational analysis. The V5 region of gp120 showed highest variability in several samples over 3 years, whereas the V1/V2 and/or V4 regions of gp120 also showed high variability in many samples. In addition, the N-terminal part of the C3 region of gp120 showed highest amino acid diversity among the conserved regions of gp120. Chronological changes in the numbers of amino acid residues in gp120 variable regions and potential N-linked glycosylation (PNLG) sites are involved in increasing the variability of Env gp120. Furthermore, the C3 region contained several amino acid residues potentially under positive selection, and APOBEC3 family protein-mediated G to A mutations were frequently detected in such residues. CONCLUSIONS/SIGNIFICANCE: Several factors, including amino acid substitutions particularly in gp120 C3 and V5 regions as well as changes in the number of PNLG sites and in the length of gp120 variable regions, were revealed to be involved in the molecular evolution of CRF01_AE Env. In addition, a similar tendency was observed between CRF01_AE and subtype C Env with regard to the amino acid variation of gp120 V3 and C3 regions. These results may provide important information for understanding the immunological characteristics of CRF01_AE Env.

Sustained appearance of drug resistance-associated mutations in HIV-1 CRF01_AE protease and reverse transcriptase derived from protease inhibitor-naive Thai patients.

Previous studies revealed that HIV-1 CRF01_AE viruses derived from antiretroviral drug-naïve Thai patients contained several protease (PR) inhibitor (PI) resistance-associated mutations. In this report, we examined the sustained appearance of drug resistance-associated mutations in CRF01_AE PR and reverse transcriptase (RT). Peripheral blood samples were collected every 3 months from April 2008 to April 2009 from 39 HIV-1-infected Thai patients, including 17 drug-naive and 22 RT inhibitors (RTIs)-treated individuals, and polymerase chain reaction-mediated-amplification and sequencing analysis of the viral genome encoding PR and RT were performed. We successfully analyzed the deduced amino acid sequence of CRF01_AE PR and RT derived from samples continuously collected from 15 drug-naïve and 20 RTIs-treated patients. Drug resistance-associated mutations were continuously detected in CRF01_AE PR derived from most patients. The continuous appearance of such PR mutations was observed not only in the proviral DNA genome derived from peripheral blood mononuclear cells, but also in the viral RNA genome of plasma virus. In contrast, RTI resistance-associated mutations were only sporadically detected in samples derived from drug-naive and RTIs-treated patients, except for the continuous appearance of two mutations in samples derived from two drug-naive patients. Our results demonstrate that many PI resistance-associated mutations and only a few RTI resistance-associated mutations continuously appear in CRF01_AE viruses derived from PI-naïve patients residing in northern Thailand.