MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors
by
Shambhu G. Aralaguppe 1,*,†, Anoop T. Ambikan 1,†, Manickam Ashokkumar 1,2
, Milner M. Kumar 3, Luke Elizabeth Hanna 2, Wondwossen Amogne 4, Anders Sönnerborg 1,5 and Ujjwal Neogi 1
Shambhu G. Aralaguppe 1,*,†, Anoop T. Ambikan 1,†, Manickam Ashokkumar 1,2, Milner M. Kumar 3, Luke Elizabeth Hanna 2, Wondwossen Amogne 4, Anders Sönnerborg 1,5 and Ujjwal Neogi 1
1
Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, 14186 Stockholm, Sweden
2
Department of HIV/AIDS, National Institute for Research in Tuberculosis, Indian Council of Medical Research, Chennai 600031, India
3
Blackbuck Technologies, Porur, Chennai 600116, India
4
Department of Internal Medicine, School of Medicine, Addis Ababa University, 2380 Addis Ababa, Ethiopia
5
Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, 14186 Stockholm, Sweden
*
Author to whom correspondence should be addressed.
†
Equal contribution.
Viruses 2019, 11(9), 806; https://doi.org/10.3390/v11090806
Received: 15 August 2019 / Accepted: 24 August 2019 / Published: 30 August 2019
(This article belongs to the Special Issue Computational Biology of Viruses: From Molecules to Epidemics)
The detection of drug resistance mutations (DRMs) in minor viral populations is of potential clinical importance. However, sophisticated computational infrastructure and competence for analysis of high-throughput sequencing (HTS) data lack at most diagnostic laboratories. Thus, we have proposed a new pipeline, MiDRMpol, to quantify DRM from the HIV-1 pol region. The gag-vpu region of 87 plasma samples from HIV-infected individuals from three cohorts was amplified and sequenced by Illumina HiSeq2500. The sequence reads were adapter-trimmed, followed by analysis using in-house scripts. Samples from Swedish and Ethiopian cohorts were also sequenced by Sanger sequencing. The pipeline was validated against the online tool PASeq (Polymorphism Analysis by Sequencing). Based on an error rate of <1%, a value of >1% was set as reliable to consider a minor variant. Both pipelines detected the mutations in the dominant viral populations, while discrepancies were observed in minor viral populations. In five HIV-1 subtype C samples, minor mutations were detected at the <5% level by MiDRMpol but not by PASeq. MiDRMpol is a computationally as well as labor efficient bioinformatics pipeline for the detection of DRM from HTS data. It identifies minor viral populations (<20%) of DRMs. Our method can be incorporated into large-scale surveillance of HIV-1 DRM.
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Keywords:
MiDRMpol; high-throughput sequencing; drug resistance mutation; antiretroviral therapy; surveillance
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MDPI and ACS Style
Aralaguppe, S.G.; Ambikan, A.T.; Ashokkumar, M.; Kumar, M.M.; Hanna, L.E.; Amogne, W.; Sönnerborg, A.; Neogi, U. MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors. Viruses 2019, 11, 806.
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