Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants
Near full genome sequencing (NFGS) of HIV-1 is required to assess the genetic composition of HIV-1 strains comprehensively. Population-wide, it enables a determination of the heterogeneity of HIV-1 and the emergence of novel/recombinant strains, while for each individual it constitutes a diagnostic...
| Main Authors: | , , , , , , , , , , , , , , |
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MDPI AG
2019-04-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/11/4/317 |
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| author | Andrew N. Banin Michael Tuen Jude S. Bimela Marcel Tongo Paul Zappile Alireza Khodadadi-Jamayran Aubin J. Nanfack Josephine Meli Xiaohong Wang Dora Mbanya Jeanne Ngogang Adriana Heguy Phillipe N. Nyambi Charles Fokunang Ralf Duerr |
| author_facet | Andrew N. Banin Michael Tuen Jude S. Bimela Marcel Tongo Paul Zappile Alireza Khodadadi-Jamayran Aubin J. Nanfack Josephine Meli Xiaohong Wang Dora Mbanya Jeanne Ngogang Adriana Heguy Phillipe N. Nyambi Charles Fokunang Ralf Duerr |
| author_sort | Andrew N. Banin |
| collection | DOAJ |
| description | Near full genome sequencing (NFGS) of HIV-1 is required to assess the genetic composition of HIV-1 strains comprehensively. Population-wide, it enables a determination of the heterogeneity of HIV-1 and the emergence of novel/recombinant strains, while for each individual it constitutes a diagnostic instrument to assist targeted therapeutic measures against viral components. There is still a lack of robust and adaptable techniques for efficient NFGS from miscellaneous HIV-1 subtypes. Using rational primer design, a broad primer set was developed for the amplification and sequencing of diverse HIV-1 group M variants from plasma. Using pure subtypes as well as diverse, unique recombinant forms (URF), variable amplicon approaches were developed for NFGS comprising all functional genes. Twenty-three different genomes composed of subtypes A (A1), B, F (F2), G, CRF01_AE, CRF02_AG, and CRF22_01A1 were successfully determined. The NFGS approach was robust irrespective of viral loads (≥306 copies/mL) and amplification method. Third-generation sequencing (TGS), single genome amplification (SGA), cloning, and bulk sequencing yielded similar outcomes concerning subtype composition and recombinant breakpoint patterns. The introduction of a simple and versatile near full genome amplification, sequencing, and cloning method enables broad application in phylogenetic studies of diverse HIV-1 subtypes and can contribute to personalized HIV therapy and diagnosis. |
| first_indexed | 2024-12-22T19:13:57Z |
| format | Article |
| id | doaj.art-b904fd66c8774562957b278c6b65051c |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-22T19:13:57Z |
| publishDate | 2019-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-b904fd66c8774562957b278c6b65051c2022-12-21T18:15:34ZengMDPI AGViruses1999-49152019-04-0111431710.3390/v11040317v11040317Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M VariantsAndrew N. Banin0Michael Tuen1Jude S. Bimela2Marcel Tongo3Paul Zappile4Alireza Khodadadi-Jamayran5Aubin J. Nanfack6Josephine Meli7Xiaohong Wang8Dora Mbanya9Jeanne Ngogang10Adriana Heguy11Phillipe N. Nyambi12Charles Fokunang13Ralf Duerr14Department of Pathology, New York University School of Medicine, New York, NY 10016, USADepartment of Pathology, New York University School of Medicine, New York, NY 10016, USADepartment of Pathology, New York University School of Medicine, New York, NY 10016, USACenter of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants, BP 906 Yaoundé, CameroonDepartment of Pathology, New York University School of Medicine, New York, NY 10016, USAApplied Bioinformatics Laboratories (ABL) and Genome Technology Center (GTC), Division of Advanced Research Technologies (DART), New York University Langone Medical Center, New York, NY 10016, USADepartment of Pathology, New York University School of Medicine, New York, NY 10016, USAMedical Diagnostic Center, BP 15810 Yaoundé, CameroonManhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USAFaculty of Medicine and Biomedical Sciences, Department of Microbiology, Parasitology and Infectious Diseases, University of Yaoundé 1, BP 1364 Yaoundé, CameroonFaculty of Medicine and Biomedical Sciences, Department of Biochemistry, University of Yaoundé 1, BP 1364 Yaoundé, CameroonDepartment of Pathology, New York University School of Medicine, New York, NY 10016, USADepartment of Pathology, New York University School of Medicine, New York, NY 10016, USAFaculty of Medicine and Biomedical Sciences, Department of Pharmacotoxicology & Pharmacokinetics, University of Yaoundé 1, BP 1364 Yaoundé, CameroonDepartment of Pathology, New York University School of Medicine, New York, NY 10016, USANear full genome sequencing (NFGS) of HIV-1 is required to assess the genetic composition of HIV-1 strains comprehensively. Population-wide, it enables a determination of the heterogeneity of HIV-1 and the emergence of novel/recombinant strains, while for each individual it constitutes a diagnostic instrument to assist targeted therapeutic measures against viral components. There is still a lack of robust and adaptable techniques for efficient NFGS from miscellaneous HIV-1 subtypes. Using rational primer design, a broad primer set was developed for the amplification and sequencing of diverse HIV-1 group M variants from plasma. Using pure subtypes as well as diverse, unique recombinant forms (URF), variable amplicon approaches were developed for NFGS comprising all functional genes. Twenty-three different genomes composed of subtypes A (A1), B, F (F2), G, CRF01_AE, CRF02_AG, and CRF22_01A1 were successfully determined. The NFGS approach was robust irrespective of viral loads (≥306 copies/mL) and amplification method. Third-generation sequencing (TGS), single genome amplification (SGA), cloning, and bulk sequencing yielded similar outcomes concerning subtype composition and recombinant breakpoint patterns. The introduction of a simple and versatile near full genome amplification, sequencing, and cloning method enables broad application in phylogenetic studies of diverse HIV-1 subtypes and can contribute to personalized HIV therapy and diagnosis.https://www.mdpi.com/1999-4915/11/4/317Near full genome amplification and sequencingHIV-1 group M subtype-independent approachrational primer designsingle-genome amplification (SGA)third-generation sequencing (TGS)bulk sequencing and cloning |
| spellingShingle | Andrew N. Banin Michael Tuen Jude S. Bimela Marcel Tongo Paul Zappile Alireza Khodadadi-Jamayran Aubin J. Nanfack Josephine Meli Xiaohong Wang Dora Mbanya Jeanne Ngogang Adriana Heguy Phillipe N. Nyambi Charles Fokunang Ralf Duerr Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants Viruses Near full genome amplification and sequencing HIV-1 group M subtype-independent approach rational primer design single-genome amplification (SGA) third-generation sequencing (TGS) bulk sequencing and cloning |
| title | Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants |
| title_full | Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants |
| title_fullStr | Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants |
| title_full_unstemmed | Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants |
| title_short | Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants |
| title_sort | development of a versatile near full genome amplification and sequencing approach for a broad variety of hiv 1 group m variants |
| topic | Near full genome amplification and sequencing HIV-1 group M subtype-independent approach rational primer design single-genome amplification (SGA) third-generation sequencing (TGS) bulk sequencing and cloning |
| url | https://www.mdpi.com/1999-4915/11/4/317 |
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