Ks. Lole et al., Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination, J VIROLOGY, 73(1), 1999, pp. 152-160
The development of an effective human immunodeficiency virus type I (HIV-1)
vaccine is likely to depend on knowledge of circulating variants of genes
other than the commonly sequenced gag and env genes. In addition, full-geno
me data are particularly limited for HIV-1 subtype C, currently the most co
mmonly transmitted subtype in India and worldwide. Like,,ise, little is kno
wn about sequence variation of HIV-1 in India, the country facing the large
st burden of HIV worldwide, Therefore, the objective of this study was to c
lone and characterize the complete genome of HIV-1 from seroconverters infe
cted with subtype C variants in India. Cocultured HIV-1 isolates were obtai
ned from six seroincident individuals from Pune, India, and virtually full-
length EIN-I genomes were amplified, cloned, and sequenced from each. Seque
nce analysis revealed that five of the six genomes were of subtype C, while
one was a mosaic of subtypes A and C, with multiple breakpoints in env, ne
f, and the 3' long terminal repeat as determined by both maximal chi(2) ana
lysis and phylogenetic bootstrapping. Sequences were compared for preservat
ion of known cytotoxic T lymphocyte (CTL) epitopes. Compared with those of
the HIV-I, sequence, 38% of well-defined CTL epitopes were identical. The p
roportion of nonconservative substitutions for Env, at 61%, was higher (P <
0.001) than those for Gag (24%), Pol (18%), and Nef (32%). Therefore, char
acterized CTL epitopes demonstrated substantial differences from subtype B
laboratory strains, which were most pronounced in Env, Because these clones
were obtained from Indian seroconverters, they are likely to facilitate va
ccine-related efforts in India by providing potential antigens for vaccine
candidates as well as for assays of vaccine responsiveness.