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)
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.
- 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.
KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).