• Article

Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencingdrug resistance assay in a routine diagnostic laboratory

Garcia-Diaz, A., Guerrero-Ramos, A., McCormick, A.L., Macartney, M.J., Conibear, T., Johnson, M., Haque, T. and Webster, D.P. 2013. Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencingdrug resistance assay in a routine diagnostic laboratory. Journal of Clinical Virology. 58 (2), pp. 468-473. https://doi.org/10.1016/j.jcv.2013.07.009

TitleEvaluation of the Roche prototype 454 HIV-1 ultradeep sequencingdrug resistance assay in a routine diagnostic laboratory
AuthorsGarcia-Diaz, A., Guerrero-Ramos, A., McCormick, A.L., Macartney, M.J., Conibear, T., Johnson, M., Haque, T. and Webster, D.P.
Abstract

Background - Studies have shown that low-frequency resistance mutations can influence treatment outcome. However, the lack of a standardized high-throughput assay has precluded their detection in clinical settings.

Objective - To evaluate the performance of the Roche prototype 454 UDS HIV-1 drug resistance assay (UDS assay) in a routine diagnostic laboratory.

Study design - 50 plasma samples, previously characterized by population sequencing and that had shown ≥1 resistance associated mutation (RAM), were retrospectively tested by the UDS assay, including 18 B and 32 non-B subtypes; viral loads between 114–1,806,407 cp/ml; drug-naive (n = 27) and drug-experienced (n = 23) individuals.

Results - The UDS assay was successful for 37/50 (74%) samples. It detected all RAMs found by population sequencing at frequencies above 20%. In addition, 39 low-frequency RAMs were exclusively detected by the UDS assay at frequencies below 20% in both drug-naïve (19/26, 73%) and drug-experienced (9/18, 50%) individuals. UDS results would lead to changes from susceptible to resistant to efavirenz (EFV) in one drug-naive individual with suboptimal response to an EFV-containing regimen and from susceptible to resistance to lamivudine (3TC) in one drug naïve subject who subsequently failed a 3TC-containing regimen and in a treatment experienced subject who had failed a 3TC-containing regimen.

Conclusions - The UDS assay performed well across a wide range of subtypes and viral loads; it showed perfect agreement with population sequencing for all RAMs analyzed. In addition, the UDS assay detected additional mutations at frequencies below 20% which correlate with patients’ treatment history and had in some cases important prognostic implications.

JournalJournal of Clinical Virology
Journal citation58 (2), pp. 468-473
ISSN1386-6532
Year2013
PublisherElsevier
Digital Object Identifier (DOI)https://doi.org/10.1016/j.jcv.2013.07.009
Publication dates
Published15 Aug 2013

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