Prospective Evaluation of the Vela Diagnostics Next-Generation Sequencing Platform for HIV-1 Genotypic Resistance Testing

Abstract

Genotypic antiretroviral drug resistance testing is a critical component of the global efforts to control the HIV-1 epidemic. This study investigates the semiautomated, next-generation sequencing (NGS)based Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay in a prospective cohort of HIV-1einfected patients. Two-hundred sixty-nine samples were successfully sequenced by both NGS and Sanger sequencing. Among the 261 protease/reverse transcriptase (PR/RT) sequences, a mean of 0.37 drug resistance mutations were identified by both Sanger and NGS, 0.08 by NGS alone, and 0.03 by Sanger alone. Among the 50 integrase sequences, a mean of 0.3 drug resistance mutations were detected by both Sanger and NGS, and 0.08 by NGS alone. NGS estimated higher levels of drug resistance to one or more antiretroviral drugs for 6.5% of PR/RT sequences and 4.0% of integrase sequences, whereas Sanger estimated higher levels of drug resistance for 3.8% of PR/RT sequences. Although the samples successfully sequenced by the Sentosa SQ HIV Genotyping Assay demonstrated similar predicted resistance compared with Sanger, 44% of Sentosa runs failed quality control requiring 17 additional runs. This semi-automated NGS-based assay may aid in HIV-1 genotypic drug resistance testing, though numerous quality control issues were observed when this platform was used in a clinical laboratory setting. With additional refinement, the Sentosa SQ HIV-1 Genotyping Assay may contribute to the global efforts to control HIV-1.

Whole-Genome Approach to Assessing Human Cytomegalovirus Dynamics in Transplant Patients Undergoing Antiviral Therapy

“…These findings highlight the importance of ensuring sound interpretation of data, particularly as HTS becomes more widely applied to genotypic resistance testing. It is notable that far more progress in applying HTS in the clinical setting has been achieved in the HIV field, and yet numerous quality control issues remain (Weber et al, 2019). In this study, we opted for a conservative approach in assessing the data, by only analyzing datasets meeting specific quality criteria, and scoring variants at a frequency of >2%.…”

Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

“…However, NGS involves complex laboratory and analytic methods that are not yet well-standardized between laboratories, although recommendations for bioinformatic analysis pipelines have been proposed [ 7 , 8 , 9 ]. HIVDR genotyping tests based on different NGS platforms are also commercially available [ 10 , 11 , 12 , 13 ]. The clinical significance of LAV is largely unknown, although there is a general agreement that LAV detected by more sensitive methods such as NGS may increase the predictive value of HIVDR genotyping for clinical outcomes as compared to SS [ 14 , 15 , 16 , 17 ].…”

Are We Ready for NGS HIV Drug Resistance Testing? The Second “Winnipeg Consensus” Symposium

“…While primarily applied in research settings, recent attempts have been made to incorporate NGS into HIVDR public health surveillance and clinical settings. The Vela Sentosa ® SQ HIV-1 Genotyping platform from Vela Diagnostics has been recently approved as the first commercial NGS HIVDR assay for clinical HIVDR testing by regulatory agencies in several settings, including the U.S. Food and Drug Administration (US FDA) [41][42][43]. This Ion Torrent technology-based Sentosa ® platform accommodates sequencing of HIVDR relevant genes with sensitivity for MRV detection at 10% when the viral load (VL) is ≥5,000 copies/mL or 20% as VL is lower.…”