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Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants.
Viruses 2019; 11(4)V

Abstract

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.

Authors+Show Affiliations

Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. andybanin@gmail.com. Faculty of Medicine and Biomedical Sciences, Department of Biochemistry, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon. andybanin@gmail.com.Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. Michael.Tuen@nyumc.org.Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. bimelajude@gmail.com. Faculty of Science, Department of Biochemistry, BP 1364 Yaoundé, Cameroon. bimelajude@gmail.com.Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants, BP 906 Yaoundé, Cameroon. marcel.tongo@gmail.com.Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. Paul.Zappile@nyumc.org.Applied Bioinformatics Laboratories (ABL) and Genome Technology Center (GTC), Division of Advanced Research Technologies (DART), New York University Langone Medical Center, New York, NY 10016, USA. Adriana.Heguy@nyumc.org.Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. a_nanfack@yahoo.fr. Medical Diagnostic Center, BP 15810 Yaoundé, Cameroon. a_nanfack@yahoo.fr. Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, BP 3077 Messa Yaoundé, Cameroon. a_nanfack@yahoo.fr.Medical Diagnostic Center, BP 15810 Yaoundé, Cameroon. jmeli_cm@yahoo.fr.Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA. Xiaohong.Wang@va.gov.Faculty of Medicine and Biomedical Sciences, Department of Microbiology, Parasitology and Infectious Diseases, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon. dmbanya1@yahoo.co.uk.Faculty of Medicine and Biomedical Sciences, Department of Biochemistry, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon. alireza.khodadadi-jamayran@nyumc.org.Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. Adriana.Heguy@nyumc.org.Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. camacf01@nyumc.org. Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA. camacf01@nyumc.org.Faculty of Medicine and Biomedical Sciences, Department of Pharmacotoxicology & Pharmacokinetics, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon. charlesfokunang@yahoo.co.uk.Department of Pathology, New York University School of Medicine, New York, NY 10016, USA. Ralf.Duerr@nyumc.org. Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA. Ralf.Duerr@nyumc.org.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30939815

Citation

Banin, Andrew N., et al. "Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants." Viruses, vol. 11, no. 4, 2019.
Banin AN, Tuen M, Bimela JS, et al. Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants. Viruses. 2019;11(4).
Banin, A. N., Tuen, M., Bimela, J. S., Tongo, M., Zappile, P., Khodadadi-Jamayran, A., ... Duerr, R. (2019). Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants. Viruses, 11(4), doi:10.3390/v11040317.
Banin AN, et al. Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants. Viruses. 2019 Apr 1;11(4) PubMed PMID: 30939815.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants. AU - Banin,Andrew N, AU - Tuen,Michael, AU - Bimela,Jude S, AU - Tongo,Marcel, AU - Zappile,Paul, AU - Khodadadi-Jamayran,Alireza, AU - Nanfack,Aubin J, AU - Meli,Josephine, AU - Wang,Xiaohong, AU - Mbanya,Dora, AU - Ngogang,Jeanne, AU - Heguy,Adriana, AU - Nyambi,Phillipe N, AU - Fokunang,Charles, AU - Duerr,Ralf, Y1 - 2019/04/01/ PY - 2019/03/05/received PY - 2019/03/26/revised PY - 2019/03/27/accepted PY - 2019/4/4/entrez PY - 2019/4/4/pubmed PY - 2019/4/4/medline KW - HIV-1 group M subtype-independent approach KW - Near full genome amplification and sequencing KW - bulk sequencing and cloning KW - rational primer design KW - single-genome amplification (SGA) KW - third-generation sequencing (TGS) JF - Viruses JO - Viruses VL - 11 IS - 4 N2 - 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. SN - 1999-4915 UR - https://www.unboundmedicine.com/medline/citation/30939815/Development_of_a_Versatile,_Near_Full_Genome_Amplification_and_Sequencing_Approach_for_a_Broad_Variety_of_HIV-1_Group_M_Variants L2 - http://www.mdpi.com/resolver?pii=v11040317 DB - PRIME DP - Unbound Medicine ER -