Understanding the HIV genome is pivotal to gain further insight in its evolution, both within and outside the host cell, and also into drug resistant mutations. The HIV virus can generate huge variations within each infected person because of a lack of proofreading mechanism and by generating recombinants.The proofreading mechanism is the key to faithful replication of genetic material in every organism to keep the errors in the replication to a minimum.However, HIV genome deliberately makes a huge number of mistakes which gives them the ability to survive and infect new cells within the host. Recombination/Template switching during reverse transcription can also generate extreme variations when reverse transcriptase slips the HIV template that it is copying and shifts to an alternate template. Understanding the vastly varying HIV sequence is key. However,Understanding the dynamics of the virus within the host cell and how it impacts the host's immune system is a challenging task.Identifying a consensus HIV sequence among ever replicating viral genome is the single most important factor to study HIV transmission and prevention and to educate and design drugs. Polymerase chain reaction (PCR) can detect the small amount of viral genome from the blood or plasma of the HIV_ infected individuals.Primers as short sequences complementary to the target sequence are vital factors for the success of a PCR reaction. Developing a universal primer that can amplify all the known HIV viral genomes is the ultimate challenge, which will help us to unravel the mystery surrounding HIV replication, transmission, etc.It may eventually lead to designing drugs and vaccines and propose policies to prevent HIV transmission. To better understand the HIV sequence further, and in an effort to find a primer that can amplify all the possible HIV viral strains, we designed an algorithm to develop a universal primer based on several factors that play a role in the primer functionality. We hope this new algorithm will help us get a deeper understanding of the HIV sequence and will play an important role in HIV diagnostics, prevention, drug development and ultimately, in the effort towards the cure of HIV.