title: Evaluation of two human immunodeficiency virus-1 genotyping systems: ViroSeq 2.0 and an in-house method.
abstract: Commercial HIV-1 genotypic resistance assays are very expensive, particularly for use in resource-constrained settings like India. Hence a cost effective in-house assay for drug resistance was validated against the standard ViroSeq HIV-1 Genotyping System 2.0 (Celera Diagnostics, CA, USA). A total of 50 samples were used for this evaluation (21 proficiency panels and 29 clinical isolates). Known resistance positions within HIV-1 protease (PR) region (1-99 codons) and HIV-1 reverse-transcriptase (RT) region (1-240 codons) were included. The results were analysed for each codon as follows: (i) concordant; (ii) partially concordant; (iii) indeterminate and (iv) discordant. A total of 2750 codons (55 codons per patient samplex50 samples) associated with drug resistance (1050 PR and 1700 RT) were analysed. For PR, 99% of the codon results were concordant and 1% were partially concordant. For RT, 99% of the codon results were concordant, 0.9% were partially concordant and 0.1% were discordant. No indeterminate results were observed and the results were reproducible. Overall, the in-house assay provided comparable results to those of US FDA approved ViroSeq, which costs about a half of the commercial assay ($ 100 vs. $ 230), making it suitable for resource-limited settings.
authors.affiliation: YRG Centre for AIDS Research and Education, Chennai 600 113, India.
authors.forename: S
authors.initials: S
authors.lastname: Saravanan
authors.forename: M
authors.initials: M
authors.lastname: Vidya
authors.forename: P
authors.initials: P
authors.lastname: Balakrishnan
authors.forename: P
authors.initials: P
authors.lastname: Balakrishanan
authors.forename: N
authors.initials: N
authors.lastname: Kumarasamy
authors.forename: Sunil S
authors.initials: SS
authors.lastname: Solomon
authors.forename: S
authors.initials: S
authors.lastname: Solomon
authors.forename: Rami
authors.initials: R
authors.lastname: Kantor
authors.forename: David
authors.initials: D
authors.lastname: Katzenstein
authors.forename: Bharat
authors.initials: B
authors.lastname: Ramratnam
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Mayer
mesh_terms: D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D007194:India; D008826:Microbial Sensitivity Tests / Q000191:economics / Q000379:methods*; D012367:RNA, Viral / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D012367:RNA, Viral