HIV-1 strains from India are highly divergent from prototypic African and US/European strains, but are linked to a South African isolate.

Objective: To gain molecular insights into different HIV-1 strains present in two different states of India, nucleotide sequences derived from the env region of four HIV-1 strains were analysed.
Design: HIV-1 was isolated from high-risk patients from the states of Maharashtra (city of Bombay) and Goa. The molecular analysis of the env region encompassed all variable domains of the external glycoprotein, gp120.
Methods: Genomic DNA from cultured cells infected with each of the four Indian HIV-1 strains independently was amplified by polymerase chain reaction (PCR). PCR fragments were cloned and sequenced and a phylogenetic tree constructed.
Results: All four Indian HIV-1 sequences were closely related to each other. The closest related sequence to them was from a South African isolate, HIV-1NOF, with a homology of 85-87%. In the phylogenetic tree, the Indian and the South African HIV-1 sequences cluster together and constitute a subtype different from the North American/European, Central African, Uganda/Rwanda and Northern Thailand subtypes. Interestingly, the viruses of this subtype are characterized by an additional potential N-glycosylation site C-terminal to the CD4-binding domain.
Conclusion: The low variation between the HIV-1 sequences from randomly chosen individuals from high-risk cohorts in two Indian states suggests a rapid and recent spread of HIV and, possibly, introduction of the virus by the same route, most probably heterosexual transmission. The rapid spread of HIV-1 variants in India, which form a subgroup of their own together with a South African strain, necessitate consideration of these strains in vaccine development.