Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations
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 g...
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| Format: | Article |
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MDPI AG
2020-06-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/6/617 |
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| author | Santiago Ávila-Ríos Neil Parkin Ronald Swanstrom Roger Paredes Robert Shafer Hezhao Ji Rami Kantor |
| author_facet | Santiago Ávila-Ríos Neil Parkin Ronald Swanstrom Roger Paredes Robert Shafer Hezhao Ji Rami Kantor |
| author_sort | Santiago Ávila-Ríos |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T19:21:39Z |
| format | Article |
| id | doaj.art-421a52ec9e854b92aa788809c3ba3b88 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T19:21:39Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-421a52ec9e854b92aa788809c3ba3b882023-11-20T02:56:16ZengMDPI AGViruses1999-49152020-06-0112661710.3390/v12060617Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation ConsiderationsSantiago Ávila-Ríos0Neil Parkin1Ronald Swanstrom2Roger Paredes3Robert Shafer4Hezhao Ji5Rami Kantor6Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Col. Sección XVI, Mexico City 14080, MexicoData First Consulting, Inc., Sebastopol, CA 95472, USALineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USAIrsiCaixa AIDS Research Institute, Badalona, 08916 Catalonia, SpainDivision of Infectious Diseases, Stanford University School of Medicine, Stanford, CA 94305, USANational HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, CanadaDivision of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USAHigher 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.https://www.mdpi.com/1999-4915/12/6/617HIV drug resistancenext-generation sequencinglow/medium-income countriesimplementationlow-abundance variants |
| spellingShingle | Santiago Ávila-Ríos Neil Parkin Ronald Swanstrom Roger Paredes Robert Shafer Hezhao Ji Rami Kantor Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations Viruses HIV drug resistance next-generation sequencing low/medium-income countries implementation low-abundance variants |
| title | Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations |
| title_full | Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations |
| title_fullStr | Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations |
| title_full_unstemmed | Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations |
| title_short | Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations |
| title_sort | next generation sequencing for hiv drug resistance testing laboratory clinical and implementation considerations |
| topic | HIV drug resistance next-generation sequencing low/medium-income countries implementation low-abundance variants |
| url | https://www.mdpi.com/1999-4915/12/6/617 |
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