Abstract
Background Current therapy guidelines recommend resistance testing to guide therapy in antiretroviral ARV treatment naive patients as well as patients with suboptimal virologic responses or virologic failure Objective This study evaluated workflow optimization and automation improvements to the ViroSeq HIV Genotyping System through the use of the semi automated extraction platforms Abbott Molecular Inc m sp and bioM eacute rieux Inc NucliSens easyMAG for sample extraction NanoDrop Spectrophotometer Thermo Scientific CA and Agilent Bioanalyzer Agilent Technologies Germany for amplicon quantitation and Applied Biosystems Instruments ABI Life Technologies Ca for increased sequencing throughput Table Methods Clinical plasma samples were processed in parallel with Viroseq HIV Genotyping System per manufacturer instructions along with above described automated options Resistance associated mutations from the different approaches were evaluated and assessed for clinical impact Results All samples tested in this study gave valid results regardless of the procedure used Samples extracted with m sp demonstrated resistance associated mutations in samples while complete drug resistance concordance was observed in samples Ninety one percent of the samples extracted with easyMAG had concordance at the nucleotide level and concordance for drug resistance mutations No apparent difference was observed in sequence quality between manual and semi automated extractions and comparable drug resistance profiles were obtained regardless of the extraction method Conclusion The ViroSeq HIV Genotyping System is compatible with the semi automated extraction systems alternative amplicon quantitation devices as well as with high throughput sequencing platform such as the ABI sequencer This study also indicated that the assay can accurately sequence HIV virus below copies mL Significant workflow and turnaround time advantages were observed in this study with the automation of the Viroseq HIV Genotyping System
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