Evaluation of Vela Diagnostics HIV-1 genotyping assay on an automated next generation sequencing platform

Abstract

BackgroundAntiretroviral drug resistance testing is an integral part of the management of patients infected with HIV. The traditional Sanger sequencing method is capable of detecting drug resistant mutations (DRMs) that make up at least 10–15% of the viral quasispecies population. Newer next generation sequencing technologies have a greater sensitivity for the detection of minority variant DRMs down to around 1% of the population. ObjectivesHere NGS sequencing on the Vela Diagnostics automated next generation sequencing platform was evaluated and compared to the currently used Sanger sequencing method. Study designSequences from both methods were obtained from a total of 79 patients, with a range of subtypes (CRF01_AE, A1/G, A1/CRF01_AE, A1/CRF02_AG, A1, A, B, C, CRF01_AG, CRF 06_CPX, D, G, B/G, CRF 57_BC/C, G/CRF 02_AG and CRF 14_BG/G) and viral loads (2.43–7 log10 copies/ml). ResultsA high concordance was seen between the two methods for subtyping (96%) and majority variant detection (97.9%). NGS sequencing detected more variants and DRMs than Sanger sequencing. Of the 76 patient samples 86% (n = 66) had identical drug resistance reports. From the ten discrepant reports, nine had extra DRMs detected by NGS sequencing and all discrepancies were seen for NRTI and NNRTI antiviral resistance. ConclusionsThis study demonstrated a good performance of the NGS method for HIV-1 genotyping compared to the Sanger sequencing method for detection of majority variants, however the reproducibility for the detection of minority variants was sub-optimal. Adoption of an NGS sequencing approach has the potential to improve the clinical management of HIV-infected patients.