THE PREVALENCE OF TRANSMITTED DRUG RESISTANCE MUTATIONS BY NEXT GENERATION AND POPULATION SEQUENCING METHODS IN SEROCONVERTING HIV-1 CARRIERS

Background: In seroconverting, recently infected therapy naïve HIV patients, transmitted drug resistance mutations (TDRMs) are associated with treatment failure. Treatment guidelines therefore recommend performing baseline resistance testing before treatment. In this study we determined the prevalence of low and high frequency TDRMs, in patients diagnosed between 2000 and 2005 (early cohort) compared to those diagnosed between 2010 and 2015 (late cohort) using Sanger based (SBS) and next generation sequencing (NGS).

Methods: Viral RNA was extracted from plasma samples and PCR amplicons covering the reverse transcriptase (RT) and protease (PR) coding regions were sequenced by SBS and by the Illumina Miseq (NGS). ABL DeepChek-HIV software was used to analyze sequencing data (using 1% threshold for mutation detection) and TDRMs were defined based on Bennet et al., 2009.

Results: 60 samples were sequenced by NGS and SBS. Phred quality scores obtained by the Miseq were excellent (Q>30). The most prevalent TDRM was the NNRTI mutation K103N (2 patients, late cohort) and the most frequently identified lower prevalence TDRMs were K65R/E and F77L (both NRTI mutations). Overall a significant difference was found in the total number of mutations (in the RT only) between the two cohorts (P=0.032).

Discussion: From our preliminary data there seems to be a trend of increscent in overall prevalence of mutations between the early and late cohorts. Samples from the later cohort have a higher numbers of TDRMs. Monitoring TDRMs in newly identified HIV naïve patients should be continued.