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PLOS ONE Study Finds HIV Genotypic Sequencing Test Performs Comparably To Standard Phenotypic Test In Predicting Potential Response To CCR5 Antagonist

MADISON, N.J., Oct. 2, 2012 /PRNewswire/ -- A laboratory-developed blood test that uses deep-sequencing technology performed comparably to the industry's standard phenotypic test in helping to predict potential clinical response to HIV-1 antiretroviral CCR5-antagonist therapy, according to a new study from researchers at Quest Diagnostics (NYSE: DGX) and Pfizer. The findings underscore the potential of advanced sequencing technologies to aid in the cost-effective management of patients infected with HIV using CCR5 antagonists.

The study, "A Genotypic Test for HIV-1 Tropism Combining Sanger Sequencing with Ultradeep Sequencing Predicts Virologic Response in Treatment-Experienced Patients," was published online September 27 in the peer-reviewed, open-access journal PLOS ONE: http://dx.plos.org/10.1371/journal.pone.0046334 .

"Phenotyping to identify HIV tropism has played a critical role for the past five years in disease management for thousands of HIV-infected patients in the United States," said study investigator Rick L. Pesano, M.D., Ph.D., medical director, infectious diseases, Quest Diagnostics. "By demonstrating that faster, more cost-effective viral-genomic sequencing performs comparably to phenotypic testing, our study suggests another option for determining HIV tropism, an essential step in determining if a CCR5 antagonist therapy is a potential treatment option."

The study compared the performance of a genotypic laboratory-developed test from Quest Diagnostics to a widely offered phenotypic laboratory test in the United States to determine HIV-1 tropism on patient samples. Tropism refers to the type of cellular co-receptor, CCR5 or CXCR4, through which HIV-1 infects human cells. Viruses that use CCR5 are called R5-tropic ("R5") and those that use CXCR4 are called X4-tropic ("X4").  CCR5 antagonists can reduce HIV-1 viral loads in patients with only R5 virus, but are not recommended in patients with X4 virus or a dual-mixed combination of R5/X4. 

Tropism varies by patient, and X4 virus may emerge over time in patients initially infected with R5 virus. Phenotyping examines the ability of the patient's cloned virus to infect cells, while genotypic tests examine the genetic sequence of the patient's virus. Although phenotyping has been the standard tropism detection method in the United States, genotypic tropism tests are widely used and supported by medical guidelines in Europe.

The Quest Diagnostics laboratory-developed test used in the study employed triplicate population sequencing (TPS), which involves genotyping the third variable (V3) loop, a region of the virus that binds to the CCR5 or CXCR4 co-receptor, and bioinformatics, to infer tropism in patients harboring R5, X4 or dual-mixed virus. A highly sensitive test is required to ensure the detection of X4 virus and exclude patients with low levels of X4 virus from receiving CCR5 antagonist therapy. For this reason, if TPS only detected R5 virus, highly sensitive ultradeep sequencing (UDS), which is able to detect minority X4 HIV-1 variants, was performed as a "reflex" test.

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