HIV-1, which causes Acquired Immune Deficiency Syndrome, exhibits very high genetic diversity with different variants or subtypes prevalent in different parts of the world.
According to CCMB senior scientist Dr Somdatta Sinha and senior research fellow Aridaman Pandit, the existing methods to classify HIV-1 sequence subtypes was based on the focus on specific genes/regions and they lack the capability to analyse whole genome variations.
To overcome the problem, the CCMB team adopted a new approach to identify the distinctive genomic signature in different HIV-1 subtypes. The team applied the approach to cluster the five unclassified HIV-1 sequences from Africa and
Europe, and predicted their possible subtypes.
"HIV hijacks the human cellular machinery to make its own proteins and is completely dependent upon human cells for its survival and growth. There exist two types of HIV, of which type-1 (HIV-1) virus is more infectious, and has higher mortality rate," Aridaman Pandit told this correspondent.
High genetic diversity for HIV-1 exists that is a result of high rates of mutation and multiple cross-species transfers from chimpanzees to human. Because of high mutation rate, variants continuously emerge that have subtle genetic differences.
As a response to HIV-1, the immune system of human engages its cells to eliminate the pathogen. Human immune system is highly variable and has evolved to flight against a large number of pathogens. However, the variability of immune system leads to differences in response of every infected individual.
"Thus, HIV continuously evolves due to both its high mutation rate and the necessity to evade human immune system leading to emergence of new variants. Inability of human immune system to control HIV-1 spread and lack of cure both add to the success story of HIV-1 as a pathogen," they said.
Some of the variants adapt towards the human sub-population in a geographical region and are called subtypes of HIV. These subtypes represent antigenically distinct types of strains. Subtle genetic differences that exist in HIV subtypes lead to difference in their infectivity, disease progression, mode of transmission, and development of resistance towards drugs.
Thus, proper recognition of HIV subtype is important for monitoring the ongoing epidemics. As different subtypes also have different rates to develop the drug resistance, it can also play a role in monitoring the drug therapy.
"Our methodology of detecting the genomic signatures can be used to detect emergence of new subtypes, and can also curate HIV-1 sequences that the earlier methods could not classify properly," the CCMB scientists added.