Comparison of an in-house ‘home-brew’ and commercial ViroSeq integrase genotyping assays on HIV-1 subtype C samples


Autoři: Kaelo K. Seatla aff001;  Wonderful T. Choga aff003;  Mompati Mogwele aff001;  Thabo Diphoko aff001;  Dorcas Maruapula aff001;  Lucy Mupfumi aff001;  Rosemary M. Musonda aff001;  Christopher F. Rowley aff004;  Ava Avalos aff001;  Ishmael Kasvosve aff002;  Sikhulile Moyo aff001;  Simani Gaseitsiwe aff001
Působiště autorů: Botswana Harvard AIDS Institute Partnership Gaborone, Botswana aff001;  Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana aff002;  Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa aff003;  Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America aff004;  Careena Centre for Health, Gaborone, Botswana aff005;  Ministry of Health and Wellness, Gaborone, Botswana aff006
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0224292

Souhrn

Background

Roll-out of Integrase Strand Transfer Inhibitors (INSTIs) such as dolutegravir for HIV combination antiretroviral therapy (cART) in sub-Saharan Africa necessitates the development of affordable HIV drug resistance (HIVDR) assays targeting the Integrase gene. We optimised and evaluated an in-house integrase HIV-1 drug resistance assay (IH-Int) and compared it to a commercially available assay, ViroSeq Integrase Genotyping kit (VS-Int) amongst HIV-1 clade C infected individuals.

Methods

We used 54 plasma samples from treatment naïve participants and one plasma sample from a patient failing INSTI based cART. Specimens were genotyped using both the VS-Int and IH-Int assays. Stanford HIV drug resistance database were used for integrase resistance interpretation. We compared the major and minor resistance mutations, pairwise nucleotide and amino-acid identity, costs and assay time.

Results

Among 55 specimens tested with IH-Int, 53 (96.4%) successfully amplified compared to 45/55 (81.8%) for the VS-Int assay. The mean nucleotide and amino acid similarity from 33 paired sequences was 99.8% (SD ± 0.30) and 99.8% (SD ± 0.39) for the IH-Int and VS-Int assay respectively. The reagent cost/sample were 32 USD and 147 USD for IH-Int and VS-Int assay, respectively. All sequenced samples were confirmed as HIV-1 subtype C.

Conclusions

The IH-Int assay had a high amplification success rate and high concordance with the commercial assay. It is significantly cheaper compared to the commercial assay. Our assay has the needed specifications for routine monitoring of participants on Dolutegravir based regimens in Botswana.

Klíčová slova:

Antimicrobial resistance – Drug screening – Genotyping – HIV-1 – Nucleotide sequencing – Reverse transcriptase-polymerase chain reaction – Viral load


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2019 Číslo 11