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Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations

1
Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico
2
Data First Consulting, Inc., Sebastopol, CA 95472, USA
3
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
4
IrsiCaixa AIDS Research Institute, Badalona, 08916 Catalonia, Spain
5
Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA 94305, USA
6
National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
7
Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
8
Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(6), 617; https://doi.org/10.3390/v12060617
Received: 1 May 2020 / Revised: 22 May 2020 / Accepted: 27 May 2020 / Published: 5 June 2020
(This article belongs to the Special Issue Next Generation Sequencing for HIV Drug Resistance Testing)
Higher accessibility and decreasing costs of next generation sequencing (NGS), availability of commercial kits, and development of dedicated analysis pipelines, have allowed an increasing number of laboratories to adopt this technology for HIV drug resistance (HIVDR) genotyping. Conventional HIVDR genotyping is traditionally carried out using population-based Sanger sequencing, which has a limited capacity for reliable detection of variants present at intra-host frequencies below a threshold of approximately 20%. NGS has the potential to improve sensitivity and quantitatively identify low-abundance variants, improving efficiency and lowering costs. However, some challenges exist for the standardization and quality assurance of NGS-based HIVDR genotyping. In this paper, we highlight considerations of these challenges as related to laboratory, clinical, and implementation of NGS for HIV drug resistance testing. Several sources of variation and bias occur in each step of the general NGS workflow, i.e., starting material, sample type, PCR amplification, library preparation method, instrument and sequencing chemistry-inherent errors, and data analysis options and limitations. Additionally, adoption of NGS-based HIVDR genotyping, especially for clinical care, poses pressing challenges, especially for resource-poor settings, including infrastructure and equipment requirements and cost, logistic and supply chains, instrument service availability, personnel training, validated laboratory protocols, and standardized analysis outputs. The establishment of external quality assessment programs may help to address some of these challenges and is needed to proceed with NGS-based HIVDR genotyping adoption. View Full-Text
Keywords: HIV drug resistance; next-generation sequencing; low/medium-income countries; implementation; low-abundance variants HIV drug resistance; next-generation sequencing; low/medium-income countries; implementation; low-abundance variants
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MDPI and ACS Style

Ávila-Ríos, S.; Parkin, N.; Swanstrom, R.; Paredes, R.; Shafer, R.; Ji, H.; Kantor, R. Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations. Viruses 2020, 12, 617. https://doi.org/10.3390/v12060617

AMA Style

Ávila-Ríos S, Parkin N, Swanstrom R, Paredes R, Shafer R, Ji H, Kantor R. Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations. Viruses. 2020; 12(6):617. https://doi.org/10.3390/v12060617

Chicago/Turabian Style

Ávila-Ríos, Santiago; Parkin, Neil; Swanstrom, Ronald; Paredes, Roger; Shafer, Robert; Ji, Hezhao; Kantor, Rami. 2020. "Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations" Viruses 12, no. 6: 617. https://doi.org/10.3390/v12060617

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