Detection of Human Immunodeficiency Virus Type 1 (HIV-1) A/AE Circulating Recombinant Form (CRF) in India: Possible...

Rapidly evolving viruses such as human immunodeficiency virus (HIV-1) develop marked sequence differences in their genome over the course of an epidemic and in individuals infected for longer duration. This is because of the error prone reverse transcriptase (RT), which rapidly incorporates mutations resulting in genomic diversity, altered cell tropism, immune escape, and variable resistance to antiretroviral drugs. As a result, radically different genomic combinations may be generated in individuals infected by genetically diverse viruses that have mosaic genomes.

Whole blood sample was collected from 25 HIV-1 infected patients. Chromosomal DNA was isolated from the patient's peripheral blood mononuclear cells (PBMCs). Full-length gag gene (~1.5 kb) was amplified. PCR products were subjected to direct automated sequencing. For identification of recombinants Simplot version 2.5 was used.

Out of 25 gag genes that were sequenced, the gene amplified from a 29 years old HIV-1 seropositive male revealed a putative recombinant sequence. This sequence showed maximum homology with HIV-1 subtype A. Simplot analysis revealed the sequence to be a likely recombinant with the following composition: Initial stretch of 1 to 200 nucleotides representing AE circulating recombinant form (CRF), 201 to 440 nucleotides representing HIV-1 subtype A, 441 to 660 nucleotides representing AE CRF again, 661 to 700 nucleotides representing HIV-1 subtype A and the remaining stretch of the nucleotides from 701 to 1076 representing AE CRF.

We document a putative HIV-1 subtype A/ AE CRF. It is important to monitor various CRFs that are being generated and horizontally spread in the community. This has significant implications for development of candidate vaccine for India.