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The objective of the research work described in this book was to develop molecular tools that can assist clinicians in taking more informed therapeutic decisions towards their HIV-1 infected patients. We demonstrated use of partial HIV-1 p24 gene sequence can function as a tool for viral subtyping. We report a HIV-1 viral load assay which is robust, reliable, economical and effective in resource limited settings like India. Through an extensive study spanning across 206 HIV-1 RT gene sequences, an effective and economical HIV-1 drug resistance genotyping method was developed and clinically validated. A primer extension-based process was explored for its ability to interrogate clinically important single nucleotide polymorphisms within the HIV-1 genome thus indicating its potential to be a cost effective, sensitive and specific HIV-1 mutation detection system. Finally we described a HCV genotyping assay, which has potential to influence therapeutic decisions in HIV-1/HCV co-infected patients. Our work will add value to the existing set of tools available for an inclusive management of HIV-1 that include HCV as a co-infection.