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 sample × 50 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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 211-216 |
| Number of pages | 6 |
| Journal | Journal of Virological Methods |
| Volume | 159 |
| Issue number | 2 |
| DOIs | |
| State | Published - Aug 2009 |
| Externally published | Yes |
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Keywords
- Concordance
- HIV-1 genotyping evaluation
- In-house HIV-1 drug resistance assay
- Indeterminate rate
- Mixtures
- ViroSeq™ HIV-1 genotyping
ASJC Scopus subject areas
- Virology
Cite this
Evaluation of two human immunodeficiency virus-1 genotyping systems : ViroSeq™ 2.0 and an in-house method. / Saravanan, S.; Vidya, M.; Balakrishanan, P.; Kumarasamy, N.; Solomon, Sunil; Solomon, S.; Kantor, Rami; Katzenstein, David; Ramratnam, Bharat; Mayer, Kenneth H.
In: Journal of Virological Methods, Vol. 159, No. 2, 08.2009, p. 211-216.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Evaluation of two human immunodeficiency virus-1 genotyping systems
T2 - ViroSeq™ 2.0 and an in-house method
AU - Saravanan, S.
AU - Vidya, M.
AU - Balakrishanan, P.
AU - Kumarasamy, N.
AU - Solomon, Sunil
AU - Solomon, S.
AU - Kantor, Rami
AU - Katzenstein, David
AU - Ramratnam, Bharat
AU - Mayer, Kenneth H.
PY - 2009/8
Y1 - 2009/8
N2 - 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 sample × 50 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.
AB - 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 sample × 50 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.
KW - Concordance
KW - HIV-1 genotyping evaluation
KW - In-house HIV-1 drug resistance assay
KW - Indeterminate rate
KW - Mixtures
KW - ViroSeq™ HIV-1 genotyping
UR - http://www.scopus.com/inward/record.url?scp=67349212106&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=67349212106&partnerID=8YFLogxK
U2 - 10.1016/j.jviromet.2009.03.021
DO - 10.1016/j.jviromet.2009.03.021
M3 - Article
C2 - 19490976
AN - SCOPUS:67349212106
VL - 159
SP - 211
EP - 216
JO - Journal of Virological Methods
JF - Journal of Virological Methods
SN - 0166-0934
IS - 2
ER -