AEGiS-12IAC: Cloning of full-length HIV-1 genomes from recent infections in India: recombination and CTL epitope variation.

12th International AIDS Conference

Geneva, Switzerland - June 28-July 3, 1998

Cloning of full-length HIV-1 genomes from recent infections in India: recombination and CTL epitope variation.

Int Conf AIDS 1998 Jun 28-Jul 3; 12:21 (abstract no. 11194)

Ray S, Lole KS, Paranjape RS, Kulkarni S, Gadkari D, Sheppard H, Bollinger RC
Johns Hopkins University, Baltimore, MD, USA.

BACKGROUND: The development of an effective HIV-1 vaccine is likely to depend on knowledge of circulating variants of genes other than the commonly-sequenced gag and env. In addition, full-genome data are particularly limited for HIV-1 subtype C, currently the most commonly transmitted subtype in India and worldwide. In addition, little is known about sequence variation of HIV-1 in India. The objective of this study was to clone and characterize the complete genome of HIV-1 from individuals infected with subtype C variants in India.

METHODS: Full-length HIV-1 genomes were amplified, cloned, and sequenced from cocultured isolates obtained from three seroincident and three seroprevalent individuals from Pune, India. Recombination breakpoints were assessed by maximal chi 2 analysis and phylogenetic bootstrapping. CTL epitopes were compared for preservation of amino acid charge, size, and hydrophobicity.

RESULTS: Bi-directional sequencing showed only one predicted lethal mutation (a stop codon in pol) in one clone, while all 9 open reading frames in the others were intact. Sequence analysis revealed that one of the seroincident genomes was a mosaic of subtypes A and C, with breakpoints in env, nef, and the 3O LTR. Of the 93 best defined CTL epitopes in gag, pol, env, and nef described by Brander and Walker, 69% were identical or differed by conservative substitutions, while 31% differed by non-conservative substitutions when compared with the defined epitope. The proportion of nonconservative substitutions was highest for env at 55%, as compared (p < 0.001) with gag (20%), pol (23%), and nef (32%).

CONCLUSIONS: We cloned full-length genomes from seroconversion and seroprevalent HIV-1 infections in India, one of which revealed a mosaic of subtypes A and C. Analysis of characterized CTL epitopes demonstrated substantial differences from laboratory strains, most pronounced in env. These isolates are likely to represent currently transmitted strains, and are expected to facilitate vaccine-related efforts in India by providing potential antigens for vaccine candidates as well as for assays of vaccine responsiveness.

Keywords: AEGIS, HIV-1, HIV Infections, Epitopes, Recombination, Genetic, Variation (Genetics), Genome, Genome, Viral, India, immunology, genetics, ICA12
980628
11194