Performance evaluation of an in-house human immunodeficiency virus type-1 protease-reverse transcriptase genotyping assay in Cameroon

Most commercial HIV-1 genotyping assays are hampered by high cost in resource-limited settings. Moreover, their performance might be influenced over time by HIV genetic heterogeneity and evolution. An in-house genotyping protocol was developed, and its sequencing performance and reproducibility were...

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Bibliographic Details
Published in:Archives of virology 2011-07, Vol.156 (7), p.1235-1243
Main Authors: Fokam, J., Salpini, R., Santoro, M. M., Cento, V., D’Arrigo, R., Gori, C., Perno, C. F., Colizzi, V., Nanfack, A., Gwom, L. C., Cappelli, G., Takou, D.
Format: Article
Language:English
Subjects:
Adult
Aged
Biological and medical sciences
Biomedical and Life Sciences
Biomedicine
Cameroon - epidemiology
Female
Fundamental and applied biological sciences. Psychology
Genetic Techniques
Genotype
HIV Infections - virology
HIV Reverse Transcriptase - genetics
HIV-1 - classification
HIV-1 - enzymology
HIV-1 - genetics
HIV-1 - isolation & purification
Human immunodeficiency virus 1
Humans
Infectious Diseases
Male
Medical Microbiology
Microbiology
Middle Aged
Miscellaneous
Molecular Sequence Data
Original Article
Performance evaluation
Phylogeny
Virology
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Summary:Most commercial HIV-1 genotyping assays are hampered by high cost in resource-limited settings. Moreover, their performance might be influenced over time by HIV genetic heterogeneity and evolution. An in-house genotyping protocol was developed, and its sequencing performance and reproducibility were compared to that of ViroSeq™. One hundred ninety plasma samples from HIV-1-infected subjects in Cameroon, a resource-limited setting with a high HIV genetic variability, were processed for pol gene sequencing with an in-house protocol, ViroSeq™, or both. Only non-B subtypes were found. The in-house sequencing performance was 98.7% against 92.1% with ViroSeq™. Among 36 sequence pairs obtained using both assays, the overall rate of discordant amino acid positions was negligible (0.24%). With its high sensitivity and reproducibility, as well as its affordable cost (about half of ViroSeq™: 92 € vs. 217 €), this in-house assay is a suitable alternative for HIV-1 genotyping in resource-limited and/or in high-genetic-diversity settings.
ISSN:0304-8608
1432-8798
DOI:10.1007/s00705-011-0982-3