454 sequencing identifies HIV drug resistance at early stage

454 Life Sciences, a member of the Roche group, and a Yale School of Medicine researcher today announced that they have used the company’s Genome Sequencer™ system to identify previously undetectable rare drug resistant HIV variants in samples from an earlier performed clinical trial. The work, presented today by Michael Kozal, M.D. of the Yale University School of Medicine and the VA CT Health Care System, was a blinded-retrospective analysis of 258 blood samples taken before drug treatment from HIV infected individuals. The results were presented today at the XVI International HIV Drug Resistance Workshop in Barbados and showed that the fraction of patients that harbored resistance mutations is at least twice as high as previously thought. Most low level mutations are undetectable by current resistance testing methods that are used in the clinic. The additional low abundant resistant variants detected by Ultra Deep sequencing were found to be extremely important as it enabled the prediction of early antiretroviral treatment failure with strong statistical significance.

“Current genotypic resistance technology available to clinicians is limited to detecting resistance mutations that are present at levels of approximately 20% or greater in the circulating viral population in a patient. Thus, the current technology used in the clinic may miss many low-level resistant HIV strains which can grow rapidly under drug selection pressure and lead to therapy failure. This retrospective study clearly shows that even resistance mutations present at the 1% level lead to premature failure of therapy” explained Michael Kozal, M.D. the senior author on the study. “In the future, hopefully clinicians can use this knowledge to choose better antiretroviral drug combinations that have the ability to suppress these resistant HIV strains which will lead to better clinical responses in patients.”

While treatment of HIV has been largely successful, with dramatic increases in survival over the last decade, a significant number of patients develop drug resistance shortly after treatment is initiated. The collaboration between 454 Life Sciences and Yale University aimed to determine if patients that fail therapy early were initially infected with a drug resistant HIV strain or if mutations arose in response to treatment.

This research project examined samples from 258 subjects of the FIRST study, a large multi-center study conducted in the US comparing three different approaches to antiretroviral therapy. The FIRST study, which lasted 5 years, evaluated the long-term clinical and virologic effects of three initial antiretroviral drug regimens for treatment naïve HIV-infected persons. The CPCRA Statistical Center at the University of Minnesota correlated the sequence data with the patient outcomes, to which 454 Life Sciences was blinded.

“454 Sequencing can instantly generate hundreds of thousands of long clonal sequence reads that accurately enable the sensitive detection of rare mutations” explained Egholm Michael, Ph.D. vice president of research and development at 454 Life Sciences. “Ultra Deep Sequencing provides an essential tool for research on viral diseases and their treatments. The ability to use 454 Sequencing to detect rare viral mutations is a crucial research tool to better understand the early stages of HIV drug resistance.”

It is estimated that 22 million people have died from AIDS and over 42 million people are living with HIV/AIDS worldwide. In the U.S. alone, 40,000 new infections occur each year.

Source : Russo Partners, LLC