Abstract: Genotypic drug resistance testing is standard of care in HIV management. The ViroSeq HIV-1 Genotyping System is commonly used in detecting HIV genomic mutations that confer resistance to specific types of antiretroviral drugs as an aid in treating HIV infection. Of note, the assay is FDA approved to detect only HIV-1 Group M Subtype B viral resistance. Subtype B was the most prevalent strain in developed counties when the assay was introduced into clinical care approximately 10 years ago. However, previously thought less common strains in the United States have gained in prevalence. The response to medications by non-B subtypes compared to B subtypes as well as whether the targeted mutations in non-B subtypes contribute to drug resistance the same as B subtypes need to be further studied. The purpose of this study was to identify whether HIV-1 viruses routinely tested using the ViroSeq assay in UTMB Molecular Diagnostics Laboratory are Group M Subtype B. HIV sequences generated between January and September of 2008 were aligned with HIV-1 subtype reference strains and analyzed by phylogenetic methods. About 16 of 588 HIV sequences (2.7%) examined were identified as non-B subtypes including 3 of 416 (0.7%) prisoner and 13 of 172 (7.6%) regular patient samples.
Fangling Xu, Chet Schwab, Xiaodong Liang, Scott Weaver, Albert Li, Mark R. Sanborn, Gavin A. Cloherty and Jianli Dong, 2010. Low Prevalence of Non-Subtype B HIV-1 Strains in the Texas Prisoner Population. Journal of Molecular Genetics, 2: 41-44.