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HIV-I drug resistance assay from geneOmbio Technologies

Due to the availability of a large number of antiviral drugs, the mortality and morbidity associated with Human Immunodeficiency Virus (HIV) has decreased significantly even in developing countries like India. However resistance to these drugs is also increasing, as the virus keeps evolving into its subtypes and recombinants. Thus it is crucial for a doctor to have the right genotypic tests to detect the HIV subtypes and recombinants prevalent in this country. Based on this data, clinicians can then adapt therapy to obtain the best therapeutic response. Genotypic guidance of start and/or switch of therapy although used commonly in the Western countries, are comparatively less implemented by health professionals in India.

The current genotypic PCR-based assays amplify and sequence the protease gene and/or the reverse transcriptase (RT) gene and often have limitations. They are not always able to detect all HIV-1 group M subtypes since historically most attention has been focused on HIV-1 subtype B, minority species are sometimes missed and most of the assays do not cover the whole region of interest. One of the popular HIV-I drug resistance genotyping test used by several laboratories across the country is called Viroseq (Abbot Diagnostics, USA). However, due to high cost, this assay reaches lesser section of the society than what it should.

geneOmbio Technologies, a Pune based genomics company were one of the few in the country to initiate research work to develop an economical and indigenous HIV-I drug resistance assay. For this assay, the company uses its indigenously developed spin column based HIV-I RNA extraction kit rather than imported ones available in the market. geneOmbio's one step reverse transcription kit is routinely used to transcribe the protease and RT gene of the HIV-I viral genome to DNA to make it amenable to polymerase chain reaction. This reverse transcription and subsequent PCR is done by a single tube reaction using a highly convenient one step RT-PCR process using the in house developed kit. One of the important features of this assay is availability of 'back up' RT PCR primers. These primers are used when 'drop out' specimens are encountered that fail to respond to the first pairs.

Institute of Infectious Diseases (Pune) has supported this development through its encouragement and support by way of providing clinical samples at initial stages of research, correlation study between genotype and phenotype and facilitating its enrolment in an external quality assurance scheme.

"Like other assays our drug resistance test scans 1-99 codons of the protease gene. However, it scans more than 360 codons of the RT gene unlike few others that scan only up to approximately 240 codons of this gene," said, Sachin Purohit, Managing Director, geneOmbio.

Dr Pratap Mukhopadhyaya, CEO and R&D Head, geneOmbio, said, "A typical HIV-I Drug Resistance Interpretation report provides important information resistance profile of different drugs such as Nucleoside Reverse Transcriptase Inhibitors (NRTIs), Non Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) and Protease inhibitors (PIs). Given the fact that multiple mutations within the HIV-I genome increase the resistance and/or susceptibility towards a drug, we provide a scoring value indicating level of resistance against each drug by a particular virus isolated from a clinical sample."

geneOmbio Technologies regularly participates in external quality assurance scheme (EQAS) coordinated by TreatAsia (Bangkok). TreatAsia assists in international validation of HIV-I drug resistance assay only across several Asian countries. geneOmbio Technologies has obtained license from the Government of India for importing HIV-I infected plasma from National Reference laboratory (NRL) Australia. This is required for analysis of HIV-I drug resistance from infected samples followed by comparison under the TreatAsia programme.