Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries

摘要: Objectives: Increased trends of primarydrug resistance mutations (DRMs) among treatment-naive HIV-1-infected patients in low- and middle-income countries (LMICs) the non-availability pre-antiretroviral therapy (ART) genotypic testing (GRT) may severely affect future therapeutic outcomes. The main objective this study was therefore to develop a simplified, cost- labour-efficient but high-throughput GRT protocol be applied large-scale surveillance DRMs LMICs. Patientsand methods: Ninety-six therapy-naive belonging tothree cohorts were included: Indian followed at St John’s Medical College Hospital, Bangalore, India (n¼49); East Africans (n¼21), who had migrated Sweden; Caucasians (n¼26) living Sweden. by population sequencing (GRT-PS) on individual plasma samples next-generation (GRT-NGS) equimolar multiplexed (n¼24) using Illumina MiSeq performed. Results: multiplexing procedurewasshown tobetechnically feasible gave high-quality reads independent ofwhetherHIV-1subtypeCorBwasanalysed.GRT-NGSdetectedalltheDRMsfoundbyGRT-PS.Additionalclinically importantlow-abundance(,20%oftheviralpopulation)majorDRMs(e.g.K101E,K103N,Y181Cand M184V)were detected GRT-NGS not GRT-PS. frequency low-abundance higher African compared with Caucasian individuals. Conclusions: Our amplicon is cost-efficient promising approach for primary LMICs where routine pre-ART standard care. This strategy useful optimizing regimens those settings.