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

• Published in: Archives of virology Vol. 156; no. 7; pp. 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: Journal Article
• Language: English
• Published: Vienna Springer Vienna 01.07.2011; Springer; Springer Nature B.V
• Subjects: Adult; Aged; amino acids; Biological and medical sciences; Biomedical and Life Sciences; Biomedicine; Cameroon; Cameroon - epidemiology; classification; enzymology; epidemiology; evolution; Female; Fundamental and applied biological sciences. Psychology; genetic heterogeneity; Genetic Techniques; genetics; Genotype; genotyping; HIV Infections; HIV Infections - virology; HIV Reverse Transcriptase; HIV Reverse Transcriptase - genetics; HIV-1; HIV-1 - classification; HIV-1 - enzymology; HIV-1 - genetics; HIV-1 - isolation & purification; Human immunodeficiency virus; Human immunodeficiency virus 1; Humans; Infectious Diseases; isolation & purification; Male; Medical Microbiology; Microbiology; Middle Aged; Miscellaneous; Molecular Sequence Data; nucleotide sequences; Original Article; Performance evaluation; Phylogeny; Virology; Cameroon; Africa; Drug Resistance Surveillance; Human Immunodeficiency Virus; Plasma Viral Load; Drug Resistance Mutation; Reverse Transcriptase Region; Performance evaluation; RNA-directed DNA polymerase; Typing; HIV-1 virus; Enzyme; Transferases; Retroviridae; Genotype; Lentivirus; Virus; Peptidases; Nucleotidyltransferases; Hydrolases; Human immunodeficiency virus
• ISSN: 0304-8608; 1432-8798; 1432-8798
• DOI: 10.1007/s00705-011-0982-3

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.