HIV drug resistance testing among patients failing second line antiretroviral therapy-Comparison of in-house and commercial sequencing. J Virol Methods, pii: S0166-0934(16)30289-0: doi: 10.1016/j.jviromet.2016.11.010 (2016).

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Title: HIV drug resistance testing among patients failing second line antiretroviral therapy-Comparison of in-house and commercial sequencing
Authors: Chimukangara B, Varyani B, Shamu T, Mutsvangwa J, Manasa J, White E, Chimbetete C, Luethy R, Katzenstein D.
Journal: J Virol Methods,pii: S0166-0934(16)30289-0: doi: 10.1016/j.jviromet.2016.11.010 (2016)

Journal Impact Factor (I.F.): 1.781
Number of citations (Google Scholar): 5

Abstract

INTRODUCTION: HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing.

METHODS: Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database.

RESULTS: Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (0.56) and 99.11 (0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens.

CONCLUSIONS: The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant.


HIGHLIGHTS:

- In-house sequencing can provide reliable genotyping information.

- Low-cost sequencing achieved by adopting SATURN protocol.

- In-house and commercial sequencing make testing feasible, accessible and affordable.

- High quality resistance testing improves patient care.


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KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), K-RITH Tower Building, Nelson R Mandela School of Medicine, UKZN

Contact: Prof. Tulio de Oliveira, Tel: +27 31 260 4898, Email: tuliodna@gmail.com & deoliveira@ukzn.ac.za

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