Abstract
Laboratories offering HIV-1 genotyping testing require reliable and up-to-date software and database solutions to optimally analyse Sanger sequences and generate clinical report drug resistance interpretations. In this study, we evaluated 2 downstream analysis software applications; the newly FDA-registered Data Processing Module (DPM v1.0) from ABL which connects to several external and validated contents, and the ViroScore-HIV [VS] software (for Research Use Only), which offers an end to end solution, from FASTA files to clinical reporting, including alignments and base-calling. Results (NRTI, NNRTI and PI drug resistance determinations) were compared with the respective determinations obtained from TG-HIV (GuideLines v.17.0). On a total of 51 samples, the agreement between the 2 methodologies (DPM and VS) was very good (>99.9%) but only 12% shown equivalent interpretation profiles between TruGene TG, with Geno2Pheno (G2P) and Stanford HIVdb (SD). Drug resistance interpretations comparisons (excluding AZT, DDI, D4T and RPV) performed between TG and SD; TG and G2P; SD and G2P gave a median agreement of 92.2, 82.9, 81% respectively with 93.4; 79.6; 85.3% for the PIs, 87.5; 81.9; 80.7% for the NRTIs and 90.1; 82.9 and 79.5% for the NNRTIs. Compared to TruGene, 56.9%; 56.9% of the samples showed at least 1 moderate positive drug resistance switch (Sensitive [S] to Intermediate [I] or I to Resistant [R]), 5.9%; 7.8% a high positive switch (S to R), 33.3%; 43.1% a moderate negative switch (I to S; R to I) and 9.8%; 29.4% a high negative switch (R to S) for SD and G2P respectively suing both platforms. This study demonstrated usability and robustness of 2 HIV genotyping software applications for clinical and R/D labs involved in HIV-1 genotyping. Differences of drug resistance interpretations were due to lack up-to-date guidelines in TruGene software, a common issue present in FDA approved assay. DPM software could be easily applied as a valuable interpretation tool helping physician to select the best therapy for their patients.
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