The HIV genotyping lab has one of the advanced DNA sequencing platforms currently in the market. The Genotyping Lab was set-up for the purpose of various clinical trials funded by NIH (ACTG and HPTN) and establishing the HIV drug resistance database in India.
ABI Avant 3100 Sequencer is one of the advanced DNA sequencing platforms available today, supported by robotic automation with advanced bioinformatics software to ensure high quality, unparalleled accuracy, and fast sample turnaround.
Currently, the lab offers large-scale HIV genotyping services using Homebrew HIV Genotyping technique since 2002. The test is intended for use in detecting HIV-1 genomic mutations that confer resistance to specific types of antiretroviral drugs. This lab services are extended to the referral cases from other centers / hospitals from different parts of the country.The Homebrew Assay detects mutations in the entire protease gene and two thirds of RT gene (nested product of 700bp RT and 400 bp of PI). The nested product is generated and sequenced bidirectional.
ABI Avant 3100 DNA Sequencer
The softwares used are ABI Data Collection v1.0, ABI Sequence Analysis v 3.7 and multiple sequence alignment Seqscape v2.5, to assembles, edit and identify the mutations within the pol region of HIV-1. The consensus sequence finally compared with Stanford HIV Drug Resistance Online Database, to determine mutations present in the virus.
The Viroseq™ HIV-1 Genotyping System version 2.0 from Celera Diagnostics is commercially available kit and licensed from US-FDA. Currently, this kit is standardized in our lab for certifications from Johns Hopkins University and VQA (US) for the participation in international clinical trials. The Viroseq HIV-1 Genotyping system detects mutations in the RT and Protease region of the pol gene and provides the information on the genetic evidence of viral resistance. The entrie protease gene and two third of RT gene are amplified to generate 1.8 kb amplicon. The amplicon is used as a sequencing template for 7 primers that generate an approximately 1.3 kb consensus sequence. The Viroseq HIV-1 genotyping system software assembles edits and identifies mutations within this 1.3 kb sequence. The software compares the consensus sequence with a known reference, HXB-2, to determine mutations present in the sample. Finally, the Viroseq software uses proprietary algorithm to analyze the mutations and generate the drug resistance report.
The facility maintains a team of expert professionals who specialize in the area of molecular virology, cutting-edge research and development, education, and training especially in the area of HIV genotyping.