Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay.

Autor: Silver N; St. George's University Hospitals NHS Foundation Trust, London, UK., Paynter M; St. George's University Hospitals NHS Foundation Trust, London, UK., McAllister G; NHS Lothian, Edinburgh, UK., Atchley M; University Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA., Sayir C; University Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA., Short J; St. George's University Hospitals NHS Foundation Trust, London, UK., Winner D; University Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA., Alouani DJ; University Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA., Sharkey FH; ThermoFisher Scientific, Paisley, UK., Bergefall K; ThermoFisher Scientific, Paisley, UK., Templeton K; NHS Lothian, Edinburgh, UK., Carrington D; St. George's University Hospitals NHS Foundation Trust, London, UK., Quiñones-Mateu ME; University Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA. meq@case.edu.; Departments of Pathology, Case Western Reserve University, 2109 Adelbert Rd., Wood Bldg., Room W210C, Cleveland, OH, 44106-4960, USA. meq@case.edu.; Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA. meq@case.edu.
Jazyk: angličtina
Zdroj: AIDS research and therapy [AIDS Res Ther] 2018 Nov 08; Vol. 15 (1), pp. 18. Date of Electronic Publication: 2018 Nov 08.
DOI: 10.1186/s12981-018-0206-y
Abstrakt: Background: The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals.
Methods: We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals.
Results: Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4 + T cell counts in the NHS Lothian patients.
Conclusions: This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
Databáze: MEDLINE
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