Background: The increase in incidence of HIV infection with limited treatment options has enhanced the morbidity and mortality in South Asian countries. The mutations, geographical and genetic diversity in Pro gene in HIV positive patients from other South Asian countries can be helpful for treatment options.

Aim: To identify mutations and genetic diversity in Pro gene in HIV positive patients in Pakistan and compare the sequences to neighbouring countries China and India.

Methods: The HIV protease gene or pro-gene sequence were retrieved from NCBI. The sequence were studied from Pakistan, China and India were analysed for their linkage and genetic mutations through bioinformatics tools, MEGAX and CLUSTALW

Results: The phylogenetic analysis of samples for maximum likelihood and mutation from South Asian countries Pakistan, China and India individually displayed variation in sequences of HIV pro gene in all these isolates. Whereas Pakistani isolates have more genetic similarities with the isolates from China than India.

Conclusion: The phylogeny analysis depicts there is gradual evolution in viral types and possible entry is through the neighbouring transmission might have been through social connections. The mutations studies provides bases for the novel targets for the drug design and development against HIV.

Keywords: HIV, Protease gene, MEGA, Phylogenetic analysis, Pakistan