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Song H, Giorgi EE, Ganusov VV, Cai F, Athreya G, Yoon H, Carja O, Hora B, Hraber P, Romero-Severson E, Jiang C, Li X, Wang S, Li H, Salazar-Gonzalez JF, Salazar MG, Goonetilleke N, Keele BF, Montefiori DC, Cohen MS, Shaw GM, Hahn BH, McMichael AJ, Haynes BF, Korber B, Bhattacharya T, Gao F. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat Commun 2018; 9:1928. [PMID: 29765018 PMCID: PMC5954121 DOI: 10.1038/s41467-018-04217-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 04/10/2018] [Indexed: 11/29/2022] Open
Abstract
Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of within-host diversification is less understood. Here we develop a novel computational tool (RAPR (Recombination Analysis PRogram)) to enable a detailed view of in vivo viral recombination during early infection, and we apply it to near-full-length HIV-1 genome sequences from longitudinal samples. Recombinant genomes rapidly replace transmitted/founder (T/F) lineages, with a median half-time of 27 days, increasing the genetic complexity of the viral population. We identify recombination hot and cold spots that differ from those observed in inter-subtype recombinants. Furthermore, RAPR analysis of longitudinal samples from an individual with well-characterized neutralizing antibody responses shows that recombination helps carry forward resistance-conferring mutations in the diversifying quasispecies. These findings provide insight into molecular mechanisms by which viral recombination contributes to HIV-1 persistence and immunopathogenesis and have implications for studies of HIV transmission and evolution in vivo.
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Affiliation(s)
- Hongshuo Song
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Elena E Giorgi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Fangping Cai
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Gayathri Athreya
- Office for Research & Discovery, University of Arizona, Tucson, AZ, 85721, USA
| | - Hyejin Yoon
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Oana Carja
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Peter Hraber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | | | - Chunlai Jiang
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, 130012, China
| | - Xiaojun Li
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jesus F Salazar-Gonzalez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- MRC/UVRI and LSHTM Uganda Research Unit, Plot 51-57, Nakiwogo Road, Entebbe, Uganda
| | - Maria G Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Nilu Goonetilleke
- Departments of Microbiology and Immunology & Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - David C Montefiori
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Myron S Cohen
- Departments of Microbiology and Immunology & Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew J McMichael
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Barton F Haynes
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Bette Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Feng Gao
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, 130012, China.
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