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

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Abstract

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.

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Acknowledgments

This work was supported financially by grants from the Italian National Institute of Health, Rome, through funding from the Italian Cooperation to the government of Cameroon, and by the European Commission Framework 7 Programme (CHAIN, the Collaborative HIV and Anti-HIV Drug Resistance Network, Integrated Project no. 223131). We would like to thank Prof Lutz Gürtler for his precious contributions in the revision of the manuscript.

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Correspondence to R. Salpini.

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J. Fokam and R. Salpini contributed equally to this work.

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Fokam, J., Salpini, R., Santoro, M.M. et al. Performance evaluation of an in-house human immunodeficiency virus type-1 protease-reverse transcriptase genotyping assay in Cameroon. Arch Virol 156, 1235–1243 (2011). https://doi.org/10.1007/s00705-011-0982-3

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