HIV Sequencing Test Comparable to Standard Phenotypic Test in Predicting CCR5 Antagonist Response

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 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.

"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 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.

Researchers found that the genotypic and phenotypic tests performed comparably at predicting response in patients undergoing therapy with maraviroc.

Quest Diagnostics can provide results from the testing service in approximately a week for samples with a TPS result of X4 and in as little as 10 days for samples reflexed to UDS, compared to reported turnaround times of approximately 14 days for the phenotyping test used in the study.

"It is gratifying that sequencing has advanced to a level of sophistication that now enables it to perform comparably to phenotyping," said study investigator Ron M. Kagan Ph.D., director of Bioinformatics, Infectious Diseases, for the Quest Diagnostics Nichols Institute, an advanced test research and development center. "Quest Diagnostics has a strong record of innovation in HIV testing, and we look forward to exploring further the potential of genetic sequencing, and UDS in particular, as tools for helping to manage HIV disease in other applications."