Higher Genotyping Performance of the Applied Biosystems TaqPath Seq HIV-1 Genotyping Kit Against ViroSeq HIV-1 Genotyping Kit in HIV Protease, Reverse Transcriptase, and Integrase Regions

Ontlametse Thato Choga,1,2 Obiageli Okafor,3 Goitseone Martha Lemogang,1 Wonderful Tatenda Choga,1,2 Gaonyadiwe Muzanywa,1 Andrea E Garcia,3 Sikhulile Moyo,1,2,4– 6 Simani Gaseitsiwe1,4 1Botswana Harvard Health Partnership, Gaborone, Botswana; 2Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana; 3Thermo Fisher Scientific, South San Francisco, CA, USA; 4Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA; 5School of Health Systems and Public Health, Faculty of Health Sciences. University of Pretoria, Pretoria, South Africa; 6Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South AfricaCorrespondence: Simani Gaseitsiwe, Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana, Tel +267 390 2671, Fax +267 390 1284, Email [email protected]: We assessed the performance of Applied Biosystems TaqPath Seq HIV-1 Genotyping Kit (CE-IVD) (TaqPath Kit) against the ViroSeq HIV-1 Genotyping Assays in genotyping HIV protease (PR), reverse transcriptase (RT), and integrase (INI) regions.Methods: The study included 43 HIV-1 plasma specimens: 20 from people living with HIV-1C and 23 well-characterized HIV-positive Virology Quality Assurance (VQA) samples with PR-, RT-, and INI mutations. VQA samples included HIV-1 subtypes A, B, C, D, F, G, CRFO2_AG and URF. HIV-1 RNA extracted from all specimens was tested with both genotyping assays. Known HIV drug resistance mutations (DRMs) were identified using the Stanford HIV drug resistance database. Sequencing success rates, nucleotide identity, and DRMs from the two commercial assays were compared.Results: Of 43 samples, TaqPath Kit amplified 93.0% (40) for HIV PR/RT and 97.7% (42) for HIV INI regions, compared to ViroSeq Assays, which amplified 69.8% (30) and 72.1% (31) for PR/RT and INI, respectively. The TaqPath Kit successfully sequenced 90.0% (36/40) PR/RT and 97.6% (41/42) INI amplicons, while ViroSeq Assays sequenced 53.3% (16/30) PR/RT and 87.1% (27/31) INI amplicons. The mean nucleotide similarity was 98.8% (SD ± 1.30), 99.6% (SD ± 1.32) and 99.2% (SD ± 0.72) for paired RT, PR and INI sequences, respectively. The TaqPath Kit detected 97.2% (35/36) of DRMs identified by the ViroSeq Assays and an additional 83 mutations and polymorphisms in samples that failed genotyping with the ViroSeq Assays. Among these, 85.5% (71/83) were confirmed by the reference sequence, including 39 major DRMs.Conclusion: The TaqPath Kit demonstrated higher genotyping performance compared to the ViroSeq assays. The TaqPath Kit was able to detect DRMs in the PR, RT and INI regions of various HIV-1 subtypes, offering a critical tool to identify and monitor HIV drug resistance to new and existing antiretroviral drugs targeting these regions.Keywords: HIV drug resistance, genotyping assays, sequencing outcome, nucleotide identity scores