The HIV virus: Back to the beginning

“Under funding from the Department of Biotechnology,Government of India,we have carried out sequencing of genetic material (RNA/DNA) of over 75 near-full-length primary HIV-1 strains and also sequenced HIV-2 Envelope Genes. This will help set up a database of Indian strains and define the molecular characteristics of Indian HIV viruses,” says Dr Jayanta Bhattacharya,Assistant Director of NARI and a scientist with the Department of Molecular Virology.

In addition,NARI has developed more than 50 functional HIV-1 envelope clones from uncultured patients’ blood and these are being studied. “What is done is genes from the patients’ blood are amplified without culturing it in the laboratory,” says Bhattacharya. He explains that virus culture involves mixing of HIV+ white blood cells (also called peripheral blood mononuclear cells) with white blood cells obtained from a healthy uninfected donor. This helps in growing the virus particles to a detectable amount that can be used for further analyses.

The virus cultured in the laboratory may not represent the parental virus replicating in the patient. Hence scientists use the polymerase chain reaction (PCR) test to amplify the genes directly from the patients’ blood (precisely from plasma as plasma viruses represent viruses circulating in the body) and then clone them into vectors (vectors are plasmid,small circular DNA) capable of expression in a mammalian cell. The engineered viruses are not infectious but still retain the primary virus surface protein. These viruses are then used for genetic and biological experiments including testing their sensitivity to drugs,inhibitors and antibodies,explains Paranjape.

Research has shown that HIV-1 clade C strains circulating in India almost exclusively use CCR5 as the co-receptor for entry early during infection. Receptors are cell surface proteins that HIV uses for entering host cells. However,in one recent study,NARI scientists found that the clade C virus from patients could use several co-receptors. They were able to show,in an AIDS patient,that HIV-1 was able to use seven different co-receptors. This perhaps means that in that particular patient the viral surface protein had gone through complex evolutionary mechanisms and adapted to use multiple co-receptors for faster disease progression.

Scientists are now exploring at a micro level how the clade C viruses use CD4 and CCR5 receptors at different disease stages and are examining the relationship between the degree of interaction between the virus and receptors and sensitivity to inhibitors that interferes with viral entry. The latest class of anti-viral drugs licensed by the Food and Drug Administration belong to the category of fusion inhibitors that block the co-receptor,preventing the entry of the virus,says Bhattacharya.

Such studies will provide a better understanding of the transmission mechanism. They may also throw new light on the mechanism of action of fusion inhibitors,which often fail as a mode of treatment.