HIV-1 low copy viral sequencing-A prototype assay

Abstract

In HIV-1 patients with low viral burden, sequencing is often problematic, yet important. This study presents a sensitive, sub-type independent system for sequencing of low level viremia. Sequencing data from 32 HIV-1 infected patients with low level viremia were collected longitudinally. A combination of ViroSeq® HIV-1 Genotyping System and an in-house nesting protocol was used. Eight sub-types were represented. The success-rate of amplification of both PR and RT in the same sample was 100% in samples with viral loads above 100 copies/ml. Below 100 copies/ml, this study managed to amplify both regions in 7/13 (54%) samples. The assays were able to amplify either PR or RT in all sub-types included but one sub-type A specimen. In conclusion, this study presents a promising, simple assay to increase the ability to perform HIV-1 resistance testing at low level viremia. This is a prototype assay and the method needs further testing to evaluate clinical performance.

Keywords:

• HIV-1
• sequencing
• low level viremia

Acknowledgments

This work was supported by the Swedish Research Council (grant K2011-58P-20931-01-4) and the Gothenburg Medical Society. We would like to thank Ulrika Noborg and Mona Brantefjord in the HIV-team at the Department of Virology at Sahlgrenska University Hospital for the excellent technical work.

Declaration of interest

Dr Tomas Mellberg, Jon Krabbe and Dr Bo Svennerholm have all declared that no competing interests exist. Dr Magnus Gisslén has the following conflicts: Received honorarium from Abbvie, BMS, Gilead, GSK/ViiV and Janssen for participation on scientific advisory boards and educational lectures.