1
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Plenderleith LJ, Liu W, Learn GH, Loy DE, Speede S, Sanz CM, Morgan DB, Bertolani P, Hart JA, Hart TB, Hahn BH, Sharp PM. Ancient Introgression between Two Ape Malaria Parasite Species. Genome Biol Evol 2020; 11:3269-3274. [PMID: 31697367 PMCID: PMC7145702 DOI: 10.1093/gbe/evz244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2019] [Indexed: 01/13/2023] Open
Abstract
The Laverania clade comprises the human malaria parasite Plasmodium falciparum as well as at least seven additional parasite species that infect wild African apes. A recent analysis of Laverania genome sequences (Otto TD, et al. 2018. Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. Nat Microbiol. 3: 687–697) reported three instances of interspecies gene transfer, one of which had previously been described. Generating gene sequences from additional ape parasites and re-examining sequencing reads generated in the Otto et al. study, we identified one of the newly described gene transfers as an assembly artifact of sequences derived from a sample coinfected by two parasite species. The second gene transfer between ancestors of two divergent chimpanzee parasite lineages was confirmed, but involved a much larger number of genes than originally described, many of which encode exported proteins that remodel, or bind to, erythrocytes. Because successful hybridization between Laverania species is very rare, it will be important to determine to what extent these gene transfers have shaped their host interactions.
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Affiliation(s)
- Lindsey J Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania
| | | | - Dorothy E Loy
- Department of Medicine, University of Pennsylvania.,Department of Microbiology, University of Pennsylvania
| | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, International Development Association-Africa, Portland, Oregon
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis.,Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo
| | - David B Morgan
- Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo.,Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois
| | - Paco Bertolani
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, Kinshasa, Democratic Republic of the Congo
| | - Terese B Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, Kinshasa, Democratic Republic of the Congo
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania.,Department of Microbiology, University of Pennsylvania
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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2
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Paes W, Leonov G, Partridge T, Chikata T, Murakoshi H, Frangou A, Brackenridge S, Nicastri A, Smith AG, Learn GH, Li Y, Parker R, Oka S, Pellegrino P, Williams I, Haynes BF, McMichael AJ, Shaw GM, Hahn BH, Takiguchi M, Ternette N, Borrow P. Contribution of proteasome-catalyzed peptide cis-splicing to viral targeting by CD8 + T cells in HIV-1 infection. Proc Natl Acad Sci U S A 2019; 116:24748-24759. [PMID: 31748275 PMCID: PMC6900506 DOI: 10.1073/pnas.1911622116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Peptides generated by proteasome-catalyzed splicing of noncontiguous amino acid sequences have been shown to constitute a source of nontemplated human leukocyte antigen class I (HLA-I) epitopes, but their role in pathogen-specific immunity remains unknown. CD8+ T cells are key mediators of HIV type 1 (HIV-1) control, and identification of novel epitopes to enhance targeting of infected cells is a priority for prophylactic and therapeutic strategies. To explore the contribution of proteasome-catalyzed peptide splicing (PCPS) to HIV-1 epitope generation, we developed a broadly applicable mass spectrometry-based discovery workflow that we employed to identify spliced HLA-I-bound peptides on HIV-infected cells. We demonstrate that HIV-1-derived spliced peptides comprise a relatively minor component of the HLA-I-bound viral immunopeptidome. Although spliced HIV-1 peptides may elicit CD8+ T cell responses relatively infrequently during infection, CD8+ T cells primed by partially overlapping contiguous epitopes in HIV-infected individuals were able to cross-recognize spliced viral peptides, suggesting a potential role for PCPS in restricting HIV-1 escape pathways. Vaccine-mediated priming of responses to spliced HIV-1 epitopes could thus provide a novel means of exploiting epitope targets typically underutilized during natural infection.
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Affiliation(s)
- Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom;
| | - German Leonov
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Takayuki Chikata
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hayato Murakoshi
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Anna Frangou
- Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Andrew G Smith
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert Parker
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Shinichi Oka
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
- AIDS Clinical Centre, National Centre for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Pierre Pellegrino
- Centre for Sexual Health and HIV Research, University College London, London WC1E 6JB, United Kingdom
| | - Ian Williams
- Centre for Sexual Health and HIV Research, University College London, London WC1E 6JB, United Kingdom
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom;
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3
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Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B. HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design. Cell Host Microbe 2019; 26:296. [PMID: 31415756 PMCID: PMC6706656 DOI: 10.1016/j.chom.2019.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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4
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Kinchen VJ, Zahid MN, Flyak AI, Soliman MG, Learn GH, Wang S, Davidson E, Doranz BJ, Ray SC, Cox AL, Crowe JE, Bjorkman PJ, Shaw GM, Bailey JR. Broadly Neutralizing Antibody Mediated Clearance of Human Hepatitis C Virus Infection. Cell Host Microbe 2019; 24:717-730.e5. [PMID: 30439341 DOI: 10.1016/j.chom.2018.10.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/17/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022]
Abstract
The role that broadly neutralizing antibodies (bNAbs) play in natural clearance of human hepatitis C virus (HCV) infection and the underlying mechanisms remain unknown. Here, we investigate the mechanism by which bNAbs, isolated from two humans who spontaneously cleared HCV infection, contribute to HCV control. Using viral gene sequences amplified from longitudinal plasma of the two subjects, we found that these bNAbs, which target the front layer of the HCV envelope protein E2, neutralized most autologous HCV strains. Acquisition of resistance to bNAbs by some autologous strains was accompanied by progressive loss of E2 protein function, and temporally associated with HCV clearance. These data demonstrate that bNAbs can mediate clearance of human HCV infection by neutralizing infecting strains and driving escaped viruses to an unfit state. These immunopathologic events distinguish HCV from HIV-1 and suggest that development of an HCV vaccine may be achievable.
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Affiliation(s)
- Valerie J Kinchen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Muhammad N Zahid
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew I Flyak
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mary G Soliman
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - Stuart C Ray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrea L Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Justin R Bailey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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5
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Zahid MN, Wang S, Learn GH, Abt PL, Blumberg EA, Reese PP, Goldberg DS, Shaw GM, Bar KJ. High multiplicity infection following transplantation of hepatitis C virus-positive organs. J Clin Invest 2019; 129:3134-3139. [PMID: 31112523 DOI: 10.1172/jci127203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Highly effective direct-acting antivirals against Hepatitis C virus (HCV) have created an opportunity to transplant organs from HCV-positive individuals into HCV-negative recipients, since de novo infection can be routinely cured. As this procedure is performed more widely, it becomes increasingly important to understand the biological underpinnings of virus transmission, especially the multiplicity of infection. Here, we used single genome sequencing of plasma virus in four genotype 1a HCV-positive organ donors and their seven organ recipients to assess the genetic bottleneck associated with HCV transmission following renal and cardiac transplantation. In all recipients, de novo infection was established by multiple genetically distinct viruses that reflect the full phylogenetic spectrum of replication-competent virus circulating in donor plasma. This was true in renal and cardiac transplantation and in recipients with peak viral loads ranging between 2.9 and 6.6 log10 IU/mL. The permissive transmission process characterized here contrasts sharply with sexual or injection-related transmission, which occurs less frequently per exposure and is generally associated with a stringent genetic bottleneck. These findings highlight the effectiveness of current anti-HCV regimens, while raising caution regarding the substantially higher multiplicity of infection seen in organ transplantation-associated HCV acquisition.
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6
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Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B. HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design. Cell Host Microbe 2019; 25:59-72.e8. [PMID: 30629920 PMCID: PMC6331341 DOI: 10.1016/j.chom.2018.12.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/06/2018] [Accepted: 11/14/2018] [Indexed: 12/26/2022]
Abstract
Eliciting HIV-1-specific broadly neutralizing antibodies (bNAbs) remains a challenge for vaccine development, and the potential of passively delivered bNAbs for prophylaxis and therapeutics is being explored. We used neutralization data from four large virus panels to comprehensively map viral signatures associated with bNAb sensitivity, including amino acids, hypervariable region characteristics, and clade effects across four different classes of bNAbs. The bNAb signatures defined for the variable loop 2 (V2) epitope region of HIV-1 Env were then employed to inform immunogen design in a proof-of-concept exploration of signature-based epitope targeted (SET) vaccines. V2 bNAb signature-guided mutations were introduced into Env 459C to create a trivalent vaccine, and immunization of guinea pigs with V2-SET vaccines resulted in increased breadth of NAb responses compared with Env 459C alone. These data demonstrate that bNAb signatures can be utilized to engineer HIV-1 Env vaccine immunogens capable of eliciting antibody responses with greater neutralization breadth. HIV-1 bNAb sensitivity signatures from 4 large virus panels mapped across 4 Ab classes Non-contact hypervariable region characteristics are critical for bNAb sensitivity HIV-1 Env 459C used alone as a vaccine can elicit modest tier 2 NAbs in guinea pigs V2 bNAb signature-guided modifications in 459C enhanced neutralization breadth
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Affiliation(s)
- Christine A Bricault
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | | | - Peter Hraber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Edward F Kreider
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Johannes F Scheid
- Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02114, USA
| | - James M Kovacs
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Departments of Chemistry and Biochemistry, University of Colorado, Colorado Springs, CO 80918, USA
| | - Jennifer L Shields
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Christy L Lavine
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Fadi Ghantous
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Michael Rist
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Madeleine G Bayne
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - George H Neubauer
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Coraline Chéneau
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Jennifer J Jones
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jie Zeng
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christina Ochsenbauer
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA
| | - Bing Chen
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - S Gnanakaran
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - LaTonya D Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA.
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
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7
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Bibollet-Ruche F, Russell RM, Liu W, Stewart-Jones GBE, Sherrill-Mix S, Li Y, Learn GH, Smith AG, Gondim MVP, Plenderleith LJ, Decker JM, Easlick JL, Wetzel KS, Collman RG, Ding S, Finzi A, Ayouba A, Peeters M, Leendertz FH, van Schijndel J, Goedmakers A, Ton E, Boesch C, Kuehl H, Arandjelovic M, Dieguez P, Murai M, Colin C, Koops K, Speede S, Gonder MK, Muller MN, Sanz CM, Morgan DB, Atencia R, Cox D, Piel AK, Stewart FA, Ndjango JBN, Mjungu D, Lonsdorf EV, Pusey AE, Kwong PD, Sharp PM, Shaw GM, Hahn BH. CD4 receptor diversity in chimpanzees protects against SIV infection. Proc Natl Acad Sci U S A 2019; 116:3229-3238. [PMID: 30718403 PMCID: PMC6386711 DOI: 10.1073/pnas.1821197116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human and simian immunodeficiency viruses (HIV/SIVs) use CD4 as the primary receptor to enter target cells. Here, we show that the chimpanzee CD4 is highly polymorphic, with nine coding variants present in wild populations, and that this diversity interferes with SIV envelope (Env)-CD4 interactions. Testing the replication fitness of SIVcpz strains in CD4+ T cells from captive chimpanzees, we found that certain viruses were unable to infect cells from certain hosts. These differences were recapitulated in CD4 transfection assays, which revealed a strong association between CD4 genotypes and SIVcpz infection phenotypes. The most striking differences were observed for three substitutions (Q25R, Q40R, and P68T), with P68T generating a second N-linked glycosylation site (N66) in addition to an invariant N32 encoded by all chimpanzee CD4 alleles. In silico modeling and site-directed mutagenesis identified charged residues at the CD4-Env interface and clashes between CD4- and Env-encoded glycans as mechanisms of inhibition. CD4 polymorphisms also reduced Env-mediated cell entry of monkey SIVs, which was dependent on at least one D1 domain glycan. CD4 allele frequencies varied among wild chimpanzees, with high diversity in all but the western subspecies, which appeared to have undergone a selective sweep. One allele was associated with lower SIVcpz prevalence rates in the wild. These results indicate that substitutions in the D1 domain of the chimpanzee CD4 can prevent SIV cell entry. Although some SIVcpz strains have adapted to utilize these variants, CD4 diversity is maintained, protecting chimpanzees against infection with SIVcpz and other SIVs to which they are exposed.
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Affiliation(s)
| | - Ronnie M Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew G Smith
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Julie M Decker
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Juliet L Easlick
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Katherine S Wetzel
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Shilei Ding
- Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du Centre Hospitalier de L'Université de Montréal, Montréal, QC H2X0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Andrés Finzi
- Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du Centre Hospitalier de L'Université de Montréal, Montréal, QC H2X0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Ahidjo Ayouba
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Fabian H Leendertz
- Research Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, 13353 Berlin, Germany
| | - Joost van Schijndel
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Chimbo Foundation, 1011 PW Amsterdam, The Netherlands
| | | | - Els Ton
- Chimbo Foundation, 1011 PW Amsterdam, The Netherlands
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Hjalmar Kuehl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Paula Dieguez
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mizuki Murai
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christelle Colin
- Projet Primates France, Centre de Conservation pour Chimpanzés, BP 36 Faranah, Republic of Guinea
| | - Kathelijne Koops
- Department of Anthropology, University of Zurich, CH-8006 Zurich, Switzerland
| | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, In Defense of Animals-Africa, Portland, OR 97204
| | - Mary K Gonder
- Department of Biology, Drexel University, Philadelphia, PA 19104
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, St Louis, MO 63130
- Congo Program, Wildlife Conservation Society, BP 14537 Brazzaville, Republic of the Congo
| | - David B Morgan
- Congo Program, Wildlife Conservation Society, BP 14537 Brazzaville, Republic of the Congo
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL 60614
| | - Rebecca Atencia
- Tchimpounga Chimpanzee Rehabilitation Center, The Jane Goodall Institute-Congo, BP 1206 Pointe Noire, Republic of Congo
| | - Debby Cox
- Tchimpounga Chimpanzee Rehabilitation Center, The Jane Goodall Institute-Congo, BP 1206 Pointe Noire, Republic of Congo
- Africa Programs, The Jane Goodall Institute, Vienna, VA 22182
| | - Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Fiona A Stewart
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, BP 2012 Kisangani, Democratic Republic of the Congo
| | - Deus Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute, Kigoma, Tanzania
| | | | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
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8
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Loy DE, Plenderleith LJ, Sundararaman SA, Liu W, Gruszczyk J, Chen YJ, Trimboli S, Learn GH, MacLean OA, Morgan ALK, Li Y, Avitto AN, Giles J, Calvignac-Spencer S, Sachse A, Leendertz FH, Speede S, Ayouba A, Peeters M, Rayner JC, Tham WH, Sharp PM, Hahn BH. Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites. Proc Natl Acad Sci U S A 2018; 115:E8450-E8459. [PMID: 30127015 PMCID: PMC6130405 DOI: 10.1073/pnas.1810053115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Wild-living African apes are endemically infected with parasites that are closely related to human Plasmodium vivax, a leading cause of malaria outside Africa. This finding suggests that the origin of P. vivax was in Africa, even though the parasite is now rare in humans there. To elucidate the emergence of human P. vivax and its relationship to the ape parasites, we analyzed genome sequence data of P. vivax strains infecting six chimpanzees and one gorilla from Cameroon, Gabon, and Côte d'Ivoire. We found that ape and human parasites share nearly identical core genomes, differing by only 2% of coding sequences. However, compared with the ape parasites, human strains of P. vivax exhibit about 10-fold less diversity and have a relative excess of nonsynonymous nucleotide polymorphisms, with site-frequency spectra suggesting they are subject to greatly relaxed purifying selection. These data suggest that human P. vivax has undergone an extreme bottleneck, followed by rapid population expansion. Investigating potential host-specificity determinants, we found that ape P. vivax parasites encode intact orthologs of three reticulocyte-binding protein genes (rbp2d, rbp2e, and rbp3), which are pseudogenes in all human P. vivax strains. However, binding studies of recombinant RBP2e and RBP3 proteins to human, chimpanzee, and gorilla erythrocytes revealed no evidence of host-specific barriers to red blood cell invasion. These data suggest that, from an ancient stock of P. vivax parasites capable of infecting both humans and apes, a severely bottlenecked lineage emerged out of Africa and underwent rapid population growth as it spread globally.
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Affiliation(s)
- Dorothy E Loy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Sesh A Sundararaman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jakub Gruszczyk
- Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia
| | - Yi-Jun Chen
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3010, Australia
| | - Stephanie Trimboli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Oscar A MacLean
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Alex L K Morgan
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexa N Avitto
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jasmin Giles
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | | | | | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, International Development Association-Africa, Portland, OR 97208
| | - Ahidjo Ayouba
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, United Kingdom
| | - Wai-Hong Tham
- Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3010, Australia
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
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9
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Salantes DB, Zheng Y, Mampe F, Srivastava T, Beg S, Lai J, Li JZ, Tressler RL, Koup RA, Hoxie J, Abdel-Mohsen M, Sherrill-Mix S, McCormick K, Overton ET, Bushman FD, Learn GH, Siliciano RF, Siliciano JM, Tebas P, Bar KJ. HIV-1 latent reservoir size and diversity are stable following brief treatment interruption. J Clin Invest 2018; 128:3102-3115. [PMID: 29911997 PMCID: PMC6026010 DOI: 10.1172/jci120194] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/24/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The effect of a brief analytical treatment interruption (ATI) on the HIV-1 latent reservoir of individuals who initiate antiretroviral therapy (ART) during chronic infection is unknown. METHODS We evaluated the impact of transient viremia on the latent reservoir in participants who underwent an ATI and at least 6 months of subsequent viral suppression in a clinical trial testing the effect of passive infusion of the broadly neutralizing Ab VRC01 during ATI. RESULTS Measures of total HIV-1 DNA, cell-associated RNA, and infectious units per million cells (IUPM) (measured by quantitative viral outgrowth assay [QVOA]) were not statistically different before or after ATI. Phylogenetic analyses of HIV-1 env sequences from QVOA and proviral DNA demonstrated little change in the composition of the virus populations comprising the pre- and post-ATI reservoir. Expanded clones were common in both QVOA and proviral DNA sequences. The frequency of clonal populations differed significantly between QVOA viruses, proviral DNA sequences, and the viruses that reactivated in vivo. CONCLUSIONS The results indicate that transient viremia from ATI does not substantially alter measures of the latent reservoir, that clonal expansion is prevalent within the latent reservoir, and that characterization of latent viruses that can reactivate in vivo remains challenging. TRIAL REGISTRATION ClinicalTrials.gov NCT02463227FUNDING. Funding was provided by the NIH.
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Affiliation(s)
| | - Yu Zheng
- Harvard University, Cambridge, Massachusetts, USA
| | - Felicity Mampe
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Subul Beg
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Randall L. Tressler
- Division of AIDS (DAIDS), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | | | - James Hoxie
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | | | | - Robert F. Siliciano
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Pablo Tebas
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Joas S, Parrish EH, Gnanadurai CW, Lump E, Stürzel CM, Parrish NF, Learn GH, Sauermann U, Neumann B, Rensing KM, Fuchs D, Billingsley JM, Bosinger SE, Silvestri G, Apetrei C, Huot N, Garcia-Tellez T, Müller-Trutwin M, Hotter D, Sauter D, Stahl-Hennig C, Hahn BH, Kirchhoff F. Species-specific host factors rather than virus-intrinsic virulence determine primate lentiviral pathogenicity. Nat Commun 2018; 9:1371. [PMID: 29636452 PMCID: PMC5893559 DOI: 10.1038/s41467-018-03762-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/07/2018] [Indexed: 12/23/2022] Open
Abstract
HIV-1 causes chronic inflammation and AIDS in humans, whereas related simian immunodeficiency viruses (SIVs) replicate efficiently in their natural hosts without causing disease. It is currently unknown to what extent virus-specific properties are responsible for these different clinical outcomes. Here, we incorporate two putative HIV-1 virulence determinants, i.e., a Vpu protein that antagonizes tetherin and blocks NF-κB activation and a Nef protein that fails to suppress T cell activation via downmodulation of CD3, into a non-pathogenic SIVagm strain and test their impact on viral replication and pathogenicity in African green monkeys. Despite sustained high-level viremia over more than 4 years, moderately increased immune activation and transcriptional signatures of inflammation, the HIV-1-like SIVagm does not cause immunodeficiency or any other disease. These data indicate that species-specific host factors rather than intrinsic viral virulence factors determine the pathogenicity of primate lentiviruses.
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Affiliation(s)
- Simone Joas
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Erica H Parrish
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 372327, USA
| | - Clement W Gnanadurai
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
- Department of Veterinary Pathology, University of Georgia, Athens, GA, 30602, USA
| | - Edina Lump
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Nicholas F Parrish
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | | | | | - Dietmar Fuchs
- Division of Biological Chemistry, Biocenter Innsbruck Medical University, Center for Chemistry and Biomedicine, A-6020, Innsbruck, Austria
| | - James M Billingsley
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Steven E Bosinger
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Guido Silvestri
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Cristian Apetrei
- WA Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nicolas Huot
- Institut Pasteur, Unité HIV, Inflammation and Persistence, Paris, 75015, France
- Vaccine Research Institute, Hôpital Henri Mondor, Créteil, 94010, France
| | | | | | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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11
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Loy DE, Rubel MA, Avitto AN, Liu W, Li Y, Learn GH, Ranciaro A, Mbunwe E, Fokunang C, Njamnshi AK, Sharp PM, Tishkoff SA, Hahn BH. Investigating zoonotic infection barriers to ape Plasmodium parasites using faecal DNA analysis. Int J Parasitol 2018; 48:531-542. [PMID: 29476866 DOI: 10.1016/j.ijpara.2017.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/09/2017] [Accepted: 12/15/2017] [Indexed: 01/17/2023]
Abstract
African apes are endemically infected with numerous Plasmodium spp. including close relatives of human Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, and Plasmodium malariae. Although these ape parasites are not believed to pose a zoonotic threat, their ability to colonise humans has not been fully explored. In particular, it remains unknown whether ape parasites are able to initiate exo-erythrocytic replication in human hepatocytes following the bite of an infective mosquito. Since animal studies have shown that liver stage infection can result in the excretion of parasite nucleic acids into the bile, we screened faecal samples from 504 rural Cameroonians for Plasmodium DNA. Using pan-Laverania as well as P. malariae- and P. vivax-specific primer sets, we amplified human P. falciparum (n = 14), P. malariae (n = 1), and P. ovale wallikeri (n = 1) mitochondrial sequences from faecal DNA of 15 individuals. However, despite using an intensified PCR screening approach we failed to detect ape Laverania, ape P. vivax or ape P. malariae parasites in these same subjects. One faecal sample from a hunter-gatherer contained a sequence closely related to the porcupine parasite Plasmodium atheruri. Since this same faecal sample also contained porcupine mitochondrial DNA, but a matching blood sample was Plasmodium-negative, it is likely that this hunter-gatherer consumed Plasmodium-infected bushmeat. Faecal Plasmodium detection was not secondary to intestinal bleeding and/or infection with gastrointestinal parasites, but indicative of blood parasitaemia. Quantitative PCR identified 26-fold more parasite DNA in the blood of faecal Plasmodium-positive than faecal Plasmodium-negative individuals (P = 0.01). However, among blood-positive individuals only 10% - 20% had detectable Plasmodium sequences in their stool. Thus, faecal screening of rural Cameroonians failed to uncover abortive ape Plasmodium infections, but detected infection with human parasites, albeit with reduced sensitivity compared with blood analysis.
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Affiliation(s)
- Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexa N Avitto
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Mbunwe
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K Njamnshi
- Department of Neurology, Faculty of Medicine and Biomedical Sciences, Central Hospital Yaoundé, University of Yaoundé I, Yaoundé, Cameroon
| | - Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Liu W, Sherrill-Mix S, Learn GH, Scully EJ, Li Y, Avitto AN, Loy DE, Lauder AP, Sundararaman SA, Plenderleith LJ, Ndjango JBN, Georgiev AV, Ahuka-Mundeke S, Peeters M, Bertolani P, Dupain J, Garai C, Hart JA, Hart TB, Shaw GM, Sharp PM, Hahn BH. Wild bonobos host geographically restricted malaria parasites including a putative new Laverania species. Nat Commun 2017; 8:1635. [PMID: 29158512 PMCID: PMC5696340 DOI: 10.1038/s41467-017-01798-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/16/2017] [Indexed: 02/01/2023] Open
Abstract
Malaria parasites, though widespread among wild chimpanzees and gorillas, have not been detected in bonobos. Here, we show that wild-living bonobos are endemically Plasmodium infected in the eastern-most part of their range. Testing 1556 faecal samples from 11 field sites, we identify high prevalence Laverania infections in the Tshuapa-Lomami-Lualaba (TL2) area, but not at other locations across the Congo. TL2 bonobos harbour P. gaboni, formerly only found in chimpanzees, as well as a potential new species, Plasmodium lomamiensis sp. nov. Rare co-infections with non-Laverania parasites were also observed. Phylogenetic relationships among Laverania species are consistent with co-divergence with their gorilla, chimpanzee and bonobo hosts, suggesting a timescale for their evolution. The absence of Plasmodium from most field sites could not be explained by parasite seasonality, nor by bonobo population structure, diet or gut microbiota. Thus, the geographic restriction of bonobo Plasmodium reflects still unidentified factors that likely influence parasite transmission.
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Affiliation(s)
- Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erik J Scully
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexa N Avitto
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dorothy E Loy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Abigail P Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sesh A Sundararaman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, BP 2012, Kisangani, Democratic Republic of the Congo
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomedicale, University of Kinshasa, BP 1197, Kinshasa, Democratic Republic of the Congo
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier 1, BP 5045, Montpellier, 34394, France
| | - Paco Bertolani
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, CB2 1QH, UK
| | - Jef Dupain
- African Wildlife Foundation Conservation Centre, P.O. Box 310, 00502, Nairobi, Kenya
| | - Cintia Garai
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Terese B Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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13
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Piel AK, Stewart FA, Pintea L, Li Y, Ramirez MA, Loy DE, Crystal PA, Learn GH, Knapp LA, Sharp PM, Hahn BH. Correction: The Malagarasi River Does Not Form an Absolute Barrier to Chimpanzee Movement in Western Tanzania. PLoS One 2017; 12:e0182723. [PMID: 28763511 PMCID: PMC5538667 DOI: 10.1371/journal.pone.0182723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0058965.].
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14
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Barbian HJ, Jackson-Jewett R, Brown CS, Bibollet-Ruche F, Learn GH, Decker T, Kreider EF, Li Y, Denny TN, Sharp PM, Shaw GM, Lifson J, Acosta EP, Saag MS, Bar KJ, Hahn BH. Effective treatment of SIVcpz-induced immunodeficiency in a captive western chimpanzee. Retrovirology 2017; 14:35. [PMID: 28576126 PMCID: PMC5457593 DOI: 10.1186/s12977-017-0359-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/25/2017] [Indexed: 01/20/2023] Open
Abstract
Background Simian immunodeficiency virus of chimpanzees (SIVcpz), the progenitor of human immunodeficiency virus type 1 (HIV-1), is associated with increased mortality and AIDS-like immunopathology in wild-living chimpanzees (Pan troglodytes). Surprisingly, however, similar findings have not been reported for chimpanzees experimentally infected with SIVcpz in captivity, raising questions about the intrinsic pathogenicity of this lentivirus. Findings Here, we report progressive immunodeficiency and clinical disease in a captive western chimpanzee (P. t. verus) infected twenty years ago by intrarectal inoculation with an SIVcpz strain (ANT) from a wild-caught eastern chimpanzee (P. t. schweinfurthii). With sustained plasma viral loads of 105 to 106 RNA copies/ml for the past 15 years, this chimpanzee developed CD4+ T cell depletion (220 cells/μl), thrombocytopenia (90,000 platelets/μl), and persistent soft tissue infections refractory to antibacterial therapy. Combination antiretroviral therapy consisting of emtricitabine (FTC), tenofovir disoproxil fumarate (TDF), and dolutegravir (DTG) decreased plasma viremia to undetectable levels (<200 copies/ml), improved CD4+ T cell counts (509 cell/μl), and resulted in the rapid resolution of all soft tissue infections. However, initial lack of adherence and/or differences in pharmacokinetics led to low plasma drug concentrations, which resulted in transient rebound viremia and the emergence of FTC resistance mutations (M184V/I) identical to those observed in HIV-1 infected humans. Conclusions These data demonstrate that SIVcpz can cause immunodeficiency and other hallmarks of AIDS in captive chimpanzees, including P. t. verus apes that are not naturally infected with this virus. Moreover, SIVcpz-associated immunodeficiency can be effectively treated with antiretroviral therapy, although sufficiently high plasma concentrations must be maintained to prevent the emergence of drug resistance. These findings extend a growing body of evidence documenting the immunopathogenicity of SIVcpz and suggest that experimentally infected chimpanzees may benefit from clinical monitoring and therapeutic intervention.
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Affiliation(s)
- Hannah J Barbian
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | | | | | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Timothy Decker
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Edward F Kreider
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - George M Shaw
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Jeffrey Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Edward P Acosta
- Department of Medicine and Center for AIDS Research, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael S Saag
- Department of Medicine and Center for AIDS Research, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Katharine J Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Beatrice H Hahn
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
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15
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Learn GH, Schaal BA. POPULATION SUBDIVISION FOR RIBOSOMAL DNA REPEAT VARIANTS IN
CLEMATIS FREMONTII. Evolution 2017; 41:433-438. [DOI: 10.1111/j.1558-5646.1987.tb05809.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/1986] [Accepted: 11/11/1986] [Indexed: 11/30/2022]
Affiliation(s)
- Gerald H. Learn
- Department of Biology Washington University St. Louis MO 63130
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16
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Bailey JR, Flyak AI, Cohen VJ, Li H, Wasilewski LN, Snider AE, Wang S, Learn GH, Kose N, Loerinc L, Lampley R, Cox AL, Pfaff JM, Doranz BJ, Shaw GM, Ray SC, Crowe JE. Broadly neutralizing antibodies with few somatic mutations and hepatitis C virus clearance. JCI Insight 2017; 2:92872. [PMID: 28469084 PMCID: PMC5414559 DOI: 10.1172/jci.insight.92872] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/21/2017] [Indexed: 01/15/2023] Open
Abstract
Here, we report the isolation of broadly neutralizing mAbs (bNAbs) from persons with broadly neutralizing serum who spontaneously cleared hepatitis C virus (HCV) infection. We found that bNAbs from two donors bound the same epitope and were encoded by the same germline heavy chain variable gene segment. Remarkably, these bNAbs were encoded by antibody variable genes with sparse somatic mutations. For one of the most potent bNAbs, these somatic mutations were critical for antibody neutralizing breadth and for binding to autologous envelope variants circulating late in infection. However, somatic mutations were not necessary for binding of the bNAb unmutated ancestor to envelope proteins of early autologous transmitted/founder viruses. This study identifies a public B cell clonotype favoring early recognition of a conserved HCV epitope, proving that anti-HCV bNAbs can achieve substantial neutralizing breadth with relatively few somatic mutations, and identifies HCV envelope variants that favored selection and maturation of an anti-HCV bNAb in vivo. These data provide insight into the molecular mechanisms of immune-mediated clearance of HCV infection and present a roadmap to guide development of a vaccine capable of stimulating anti-HCV bNAbs with a physiologic number of somatic mutations characteristic of vaccine responses.
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Affiliation(s)
- Justin R Bailey
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew I Flyak
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Valerie J Cohen
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lisa N Wasilewski
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Anna E Snider
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Leah Loerinc
- Vanderbilt Vaccine Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Rebecca Lampley
- Vanderbilt Vaccine Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Andrea L Cox
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stuart C Ray
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland, USA
| | - James E Crowe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Vaccine Center, Vanderbilt University, Nashville, Tennessee, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
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17
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Mack K, Starz K, Sauter D, Langer S, Bibollet-Ruche F, Learn GH, Stürzel CM, Leoz M, Plantier JC, Geyer M, Hahn BH, Kirchhoff F. Efficient Vpu-Mediated Tetherin Antagonism by an HIV-1 Group O Strain. J Virol 2017; 91:e02177-16. [PMID: 28077643 PMCID: PMC5331793 DOI: 10.1128/jvi.02177-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/22/2016] [Indexed: 11/20/2022] Open
Abstract
Simian immunodeficiency viruses (SIVs) use their Nef proteins to counteract the restriction factor tetherin. However, a deletion in human tetherin prevents antagonism by the Nef proteins of SIVcpz and SIVgor, which represent the ape precursors of human immunodeficiency virus type 1 (HIV-1). To promote virus release from infected cells, pandemic HIV-1 group M strains evolved Vpu as a tetherin antagonist, while the Nef protein of less widespread HIV-1 group O strains acquired the ability to target a region adjacent to this deletion. In this study, we identified an unusual HIV-1 group O strain (RBF206) that evolved Vpu as an effective antagonist of human tetherin. While both RBF206 Vpu and Nef exert anti-tetherin activity in transient-transfection assays, mainly Vpu promotes RBF206 release in infected CD4+ T cells. Although mutations distinct from the adaptive changes observed in group M Vpus (M-Vpus) were critical for the acquisition of its anti-tetherin activity, RBF206 O-Vpu potently suppresses NF-κB activation and reduces CD4 cell surface expression. Interestingly, RBF206 Vpu counteracts tetherin in a largely species-independent manner, degrading both the long and short isoforms of human tetherin. Downmodulation of CD4, but not counteraction of tetherin, by RBF206 Vpu was dependent on the cellular ubiquitin ligase machinery. Our data present the first example of an HIV-1 group O Vpu that efficiently antagonizes human tetherin and suggest that counteraction by O-Nefs may be suboptimal.IMPORTANCE Previous studies showed that HIV-1 groups M and O evolved two alternative strategies to counteract the human ortholog of the restriction factor tetherin. While HIV-1 group M switched from Nef to Vpu due to a deletion in the cytoplasmic domain of human tetherin, HIV-1 group O, which lacks Vpu-mediated anti-tetherin activity, acquired a Nef protein that is able to target a region adjacent to the deletion. Here we report an unusual exception, identifying a strain of HIV-1 group O (RBF206) whose Vpu protein evolved an effective antagonism of human tetherin. Interestingly, the adaptive changes in RBF206 Vpu are distinct from those found in M-Vpus and mediate efficient counteraction of both the long and short isoforms of this restriction factor. Our results further illustrate the enormous flexibility of HIV-1 in counteracting human defense mechanisms.
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Affiliation(s)
- Katharina Mack
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Kathrin Starz
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Simon Langer
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Marie Leoz
- Laboratoire de Virologie, CHU Charles Nicolle, Rouen, France
- EA 2656 GRAM Université de Rouen, Rouen, France
| | - Jean-Christophe Plantier
- Laboratoire de Virologie, CHU Charles Nicolle, Rouen, France
- EA 2656 GRAM Université de Rouen, Rouen, France
- Laboratoire associé au Centre National de Référence du VIH, CHU Charles Nicolle, Rouen, France
| | - Matthias Geyer
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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18
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Caskey M, Schoofs T, Gruell H, Settler A, Karagounis T, Kreider EF, Murrell B, Pfeifer N, Nogueira L, Oliveira TY, Learn GH, Cohen YZ, Lehmann C, Gillor D, Shimeliovich I, Unson-O’Brien C, Weiland D, Robles A, Kümmerle T, Wyen C, Levin R, Witmer-Pack M, Eren K, Ignacio C, Kiss S, West AP, Mouquet H, Zingman BS, Gulick RM, Keler T, Bjorkman PJ, Seaman MS, Hahn BH, Fätkenheuer G, Schlesinger SJ, Nussenzweig MC, Klein F. Antibody 10-1074 suppresses viremia in HIV-1-infected individuals. Nat Med 2017; 23:185-191. [PMID: 28092665 PMCID: PMC5467219 DOI: 10.1038/nm.4268] [Citation(s) in RCA: 338] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/13/2016] [Indexed: 02/08/2023]
Abstract
Monoclonal antibody 10-1074 targets the V3 glycan supersite on the HIV-1 envelope (Env) protein. It is among the most potent anti-HIV-1 neutralizing antibodies isolated so far. Here we report on its safety and activity in 33 individuals who received a single intravenous infusion of the antibody. 10-1074 was well tolerated and had a half-life of 24.0 d in participants without HIV-1 infection and 12.8 d in individuals with HIV-1 infection. Thirteen individuals with viremia received the highest dose of 30 mg/kg 10-1074. Eleven of these participants were 10-1074-sensitive and showed a rapid decline in viremia by a mean of 1.52 log10 copies/ml. Virologic analysis revealed the emergence of multiple independent 10-1074-resistant viruses in the first weeks after infusion. Emerging escape variants were generally resistant to the related V3-specific antibody PGT121, but remained sensitive to antibodies targeting nonoverlapping epitopes, such as the anti-CD4-binding-site antibodies 3BNC117 and VRC01. The results demonstrate the safety and activity of 10-1074 in humans and support the idea that antibodies targeting the V3 glycan supersite might be useful for the treatment and prevention of HIV-1 infection.
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Affiliation(s)
- Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Till Schoofs
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Henning Gruell
- Laboratory of Experimental Immunology, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, Cologne, Germany
| | - Allison Settler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Theodora Karagounis
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Edward F. Kreider
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, San Diego, California, USA
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Thiago Y. Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Gerald H. Learn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yehuda Z. Cohen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Clara Lehmann
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, Cologne, Germany
| | - Daniel Gillor
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Cecilia Unson-O’Brien
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Daniela Weiland
- Laboratory of Experimental Immunology, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, Cologne, Germany
| | - Alexander Robles
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Tim Kümmerle
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
| | - Christoph Wyen
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
| | - Rebeka Levin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Maggi Witmer-Pack
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Kemal Eren
- Department of Biomedical Informatics and
- Bioinformatics and System Biology, University of California, San Diego, San Diego, California, USA
| | - Caroline Ignacio
- Department of Medicine, University of California, San Diego, San Diego, California, USA
| | - Szilard Kiss
- Department of Ophthalmology, Weill Cornell Medical College of Cornell University, New York, New York, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Hugo Mouquet
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris, France
| | - Barry S. Zingman
- Division of Infectious Diseases, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, New York, USA
- Einstein/CUNY/Rockefeller Center for AIDS Research, Bronx, New York, New York, USA
| | - Roy M. Gulick
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Tibor Keler
- Celldex Therapeutics, Inc., Hampton, New Jersey, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gerd Fätkenheuer
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, Cologne, Germany
| | - Sarah J. Schlesinger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, Cologne, Germany
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19
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Iyer SS, Bibollet-Ruche F, Sherrill-Mix S, Learn GH, Plenderleith L, Smith AG, Barbian HJ, Russell RM, Gondim MVP, Bahari CY, Shaw CM, Li Y, Decker T, Haynes BF, Shaw GM, Sharp PM, Borrow P, Hahn BH. Resistance to type 1 interferons is a major determinant of HIV-1 transmission fitness. Proc Natl Acad Sci U S A 2017; 114:E590-E599. [PMID: 28069935 PMCID: PMC5278458 DOI: 10.1073/pnas.1620144114] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Sexual transmission of HIV-1 is an inefficient process, with only one or few variants of the donor quasispecies establishing the new infection. A critical, and as yet unresolved, question is whether the mucosal bottleneck selects for viruses with increased transmission fitness. Here, we characterized 300 limiting dilution-derived virus isolates from the plasma, and in some instances genital secretions, of eight HIV-1 donor and recipient pairs. Although there were no differences in the amount of virion-associated envelope glycoprotein, recipient isolates were on average threefold more infectious (P = 0.0001), replicated to 1.4-fold higher titers (P = 0.004), were released from infected cells 4.2-fold more efficiently (P < 0.00001), and were significantly more resistant to type I IFNs than the corresponding donor isolates. Remarkably, transmitted viruses exhibited 7.8-fold higher IFNα2 (P < 0.00001) and 39-fold higher IFNβ (P < 0.00001) half-maximal inhibitory concentrations (IC50) than did donor isolates, and their odds of replicating in CD4+ T cells at the highest IFNα2 and IFNβ doses were 35-fold (P < 0.00001) and 250-fold (P < 0.00001) greater, respectively. Interestingly, pretreatment of CD4+ T cells with IFNβ, but not IFNα2, selected donor plasma isolates that exhibited a transmitted virus-like phenotype, and such viruses were also detected in the donor genital tract. These data indicate that transmitted viruses are phenotypically distinct, and that increased IFN resistance represents their most distinguishing property. Thus, the mucosal bottleneck selects for viruses that are able to replicate and spread efficiently in the face of a potent innate immune response.
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Affiliation(s)
- Shilpa S Iyer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lindsey Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Andrew G Smith
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Hannah J Barbian
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ronnie M Russell
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcos V P Gondim
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Catherine Y Bahari
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christiana M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Timothy Decker
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Barton F Haynes
- Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710
- Department of Medicine, Duke University Medical Center, Durham, NC 27710
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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20
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Bar KJ, Sneller MC, Harrison LJ, Justement JS, Overton ET, Petrone ME, Salantes DB, Seamon CA, Scheinfeld B, Kwan RW, Learn GH, Proschan MA, Kreider EF, Blazkova J, Bardsley M, Refsland EW, Messer M, Clarridge KE, Tustin NB, Madden PJ, Oden K, O'Dell SJ, Jarocki B, Shiakolas AR, Tressler RL, Doria-Rose NA, Bailer RT, Ledgerwood JE, Capparelli EV, Lynch RM, Graham BS, Moir S, Koup RA, Mascola JR, Hoxie JA, Fauci AS, Tebas P, Chun TW. Effect of HIV Antibody VRC01 on Viral Rebound after Treatment Interruption. N Engl J Med 2016; 375:2037-2050. [PMID: 27959728 PMCID: PMC5292134 DOI: 10.1056/nejmoa1608243] [Citation(s) in RCA: 341] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND The discovery of potent and broadly neutralizing antibodies (bNAbs) against human immunodeficiency virus (HIV) has made passive immunization a potential strategy for the prevention and treatment of HIV infection. We sought to determine whether passive administration of VRC01, a bNAb targeting the HIV CD4-binding site, can safely prevent or delay plasma viral rebound after the discontinuation of antiretroviral therapy (ART). METHODS We conducted two open-label trials (AIDS Clinical Trials Group [ACTG] A5340 and National Institutes of Health [NIH] 15-I-0140) of the safety, side-effect profile, pharmacokinetic properties, and antiviral activity of VRC01 in persons with HIV infection who were undergoing interruption of ART. RESULTS A total of 24 participants were enrolled, and one serious alcohol-related adverse event occurred. Viral rebound occurred despite plasma VRC01 concentrations greater than 50 μg per milliliter. The median time to rebound was 4 weeks in the A5340 trial and 5.6 weeks in the NIH trial. Study participants were more likely than historical controls to have viral suppression at week 4 (38% vs. 13%, P=0.04 by a two-sided Fisher's exact test in the A5340 trial; and 80% vs. 13%, P<0.001 by a two-sided Fisher's exact test in the NIH trial) but the difference was not significant at week 8. Analyses of virus populations before ART as well as before and after ART interruption showed that VRC01 exerted pressure on rebounding virus, resulting in restriction of recrudescent viruses and selection for preexisting and emerging antibody neutralization-resistant virus. CONCLUSIONS VRC01 slightly delayed plasma viral rebound in the trial participants, as compared with historical controls, but it did not maintain viral suppression by week 8. In the small number of participants enrolled in these trials, no safety concerns were identified with passive immunization with a single bNAb (VRC01). (Funded by the National Institute of Allergy and Infectious Diseases and others; ACTG A5340 and NIH 15-I-0140 ClinicalTrials.gov numbers, NCT02463227 and NCT02471326 .).
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Affiliation(s)
- Katharine J Bar
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Michael C Sneller
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Linda J Harrison
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - J Shawn Justement
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Edgar T Overton
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Mary E Petrone
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - D Brenda Salantes
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Catherine A Seamon
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Benjamin Scheinfeld
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Richard W Kwan
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Gerald H Learn
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Michael A Proschan
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Edward F Kreider
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Jana Blazkova
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Mark Bardsley
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Eric W Refsland
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Michael Messer
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Katherine E Clarridge
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Nancy B Tustin
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Patrick J Madden
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - KaSaundra Oden
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Sijy J O'Dell
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Bernadette Jarocki
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Andrea R Shiakolas
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Randall L Tressler
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Nicole A Doria-Rose
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Robert T Bailer
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Julie E Ledgerwood
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Edmund V Capparelli
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Rebecca M Lynch
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Barney S Graham
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Susan Moir
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Richard A Koup
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - John R Mascola
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - James A Hoxie
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Anthony S Fauci
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Pablo Tebas
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
| | - Tae-Wook Chun
- From the University of Pennsylvania (K.J.B., D.B.S., B.S., G.H.L., E.F.K., M.B., J.A.H., P.T.) and Children's Hospital of Philadelphia (N.B.T.) - both in Philadelphia; the Laboratory of Immunoregulation (M.C.S., J.S.J., M.E.P., J.B., E.W.R., K.E.C., S.M., A.S.F., T.-W.C.), Biostatistics Research Branch (M.A.P.), Vaccine Research Center (P.J.M., S.J.O., A.R.S., N.A.D.-R., R.T.B., J.E.L., R.M.L., B.S.G., R.A.K., J.R.M.), and Division of AIDS (R.L.T.), National Institute of Allergy and Infectious Diseases and National Institutes of Health (NIH), and the Critical Care Medicine Department, Clinical Center, NIH (C.A.S., R.W.K.), Bethesda, the AIDS Clinical Trials Group, Silver Spring (K.O.), and Columbus Technologies and Services, Greenbelt (R.L.T.) - all in Maryland; Harvard T.H. Chan School of Public Health, Boston (L.J.H.); the University of Alabama at Birmingham, Birmingham (E.T.O., M.M.); Frontier Science and Technology Research Foundation, Amherst, NY (B.J.); and the University of California, San Diego, La Jolla (E.V.C.)
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Salazar-Gonzalez JF, Salazar MG, Tully DC, Ogilvie CB, Learn GH, Allen TM, Heath SL, Goepfert P, Bar KJ. Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes. Pathog Immun 2016; 1:129-153. [PMID: 27819061 PMCID: PMC5096837 DOI: 10.20411/pai.v1i1.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background: Identification of HIV-1 genomes responsible for establishing clinical infection in newly infected individuals is fundamental to prevention and pathogenesis research. Processing, storage, and transportation of the clinical samples required to perform these virologic assays in resource-limited settings requires challenging venipuncture and cold chain logistics. Here, we validate the use of dried-blood spots (DBS) as a simple and convenient alternative to collecting and storing frozen plasma. Methods: We performed parallel nucleic acid extraction, single genome amplification (SGA), next generation sequencing (NGS), and phylogenetic analyses on plasma and DBS. Results: We demonstrated the capacity to extract viral RNA from DBS and perform SGA to infer the complete nucleotide sequence of the transmitted/founder (TF) HIV-1 envelope gene and full-length genome in two acutely infected individuals. Using both SGA and NGS methodologies, we showed that sequences generated from DBS and plasma display comparable phylogenetic patterns in both acute and chronic infection. SGA was successful on samples with a range of plasma viremia, including samples as low as 1,700 copies/ml and an estimated ~50 viral copies per blood spot. Further, we demonstrated reproducible efficiency in gp160 env sequencing in DBS stored at ambient temperature for up to three weeks or at -20°C for up to five months. Conclusions: These findings support the use of DBS as a practical and cost-effective alternative to frozen plasma for clinical trials and translational research conducted in resource-limited settings.
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Affiliation(s)
| | - Maria G Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Damien C Tully
- Ragon Institute of MHG, MIT, and Harvard, Boston, MA, USA
| | | | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Todd M Allen
- Ragon Institute of MHG, MIT, and Harvard, Boston, MA, USA
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Katharine J Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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22
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Liu W, Sundararaman SA, Loy DE, Learn GH, Li Y, Plenderleith LJ, Ndjango JBN, Speede S, Atencia R, Cox D, Shaw GM, Ayouba A, Peeters M, Rayner JC, Hahn BH, Sharp PM. Multigenomic Delineation of Plasmodium Species of the Laverania Subgenus Infecting Wild-Living Chimpanzees and Gorillas. Genome Biol Evol 2016; 8:1929-39. [PMID: 27289102 PMCID: PMC4943199 DOI: 10.1093/gbe/evw128] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2016] [Indexed: 12/15/2022] Open
Abstract
Plasmodium falciparum, the major cause of malaria morbidity and mortality worldwide, is only distantly related to other human malaria parasites and has thus been placed in a separate subgenus, termed Laverania Parasites morphologically similar to P. falciparum have been identified in African apes, but only one other Laverania species, Plasmodium reichenowi from chimpanzees, has been formally described. Although recent studies have pointed to the existence of additional Laverania species, their precise number and host associations remain uncertain, primarily because of limited sampling and a paucity of parasite sequences other than from mitochondrial DNA. To address this, we used limiting dilution polymerase chain reaction to amplify additional parasite sequences from a large number of chimpanzee and gorilla blood and fecal samples collected at two sanctuaries and 30 field sites across equatorial Africa. Phylogenetic analyses of more than 2,000 new sequences derived from the mitochondrial, nuclear, and apicoplast genomes revealed six divergent and well-supported clades within the Laverania parasite group. Although two of these clades exhibited deep subdivisions in phylogenies estimated from organelle gene sequences, these sublineages were geographically defined and not present in trees from four unlinked nuclear loci. This greatly expanded sequence data set thus confirms six, and not seven or more, ape Laverania species, of which P. reichenowi, Plasmodium gaboni, and Plasmodium billcollinsi only infect chimpanzees, whereas Plasmodium praefalciparum, Plasmodium adleri, and Pladmodium blacklocki only infect gorillas. The new sequence data also confirm the P. praefalciparum origin of human P. falciparum.
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Affiliation(s)
- Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Sesh A Sundararaman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom
| | | | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, IDA-Africa, Portland, Oregon
| | - Rebeca Atencia
- Tchimpounga Chimpanzee Rehabilitation Center, Pointe-Noire, Republic of the Congo
| | - Debby Cox
- Tchimpounga Chimpanzee Rehabilitation Center, Pointe-Noire, Republic of the Congo Africa Programmes, Jane Goodall Institute, Vienna, Virginia
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Ahidjo Ayouba
- UMI 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, and University of Montpellier, France
| | - Martine Peeters
- UMI 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, and University of Montpellier, France
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom
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23
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Loy DE, Liu W, Li Y, Learn GH, Plenderleith LJ, Sundararaman SA, Sharp PM, Hahn BH. Out of Africa: origins and evolution of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Int J Parasitol 2016; 47:87-97. [PMID: 27381764 DOI: 10.1016/j.ijpara.2016.05.008] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/25/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022]
Abstract
Plasmodium falciparum and Plasmodium vivax account for more than 95% of all human malaria infections, and thus pose a serious public health challenge. To control and potentially eliminate these pathogens, it is important to understand their origins and evolutionary history. Until recently, it was widely believed that P. falciparum had co-evolved with humans (and our ancestors) over millions of years, whilst P. vivax was assumed to have emerged in southeastern Asia following the cross-species transmission of a parasite from a macaque. However, the discovery of a multitude of Plasmodium spp. in chimpanzees and gorillas has refuted these theories and instead revealed that both P. falciparum and P. vivax evolved from parasites infecting wild-living African apes. It is now clear that P. falciparum resulted from a recent cross-species transmission of a parasite from a gorilla, whilst P. vivax emerged from an ancestral stock of parasites that infected chimpanzees, gorillas and humans in Africa, until the spread of the protective Duffy-negative mutation eliminated P. vivax from human populations there. Although many questions remain concerning the biology and zoonotic potential of the P. falciparum- and P. vivax-like parasites infecting apes, comparative genomics, coupled with functional parasite and vector studies, are likely to yield new insights into ape Plasmodium transmission and pathogenesis that are relevant to the treatment and prevention of human malaria.
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Affiliation(s)
- Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sesh A Sundararaman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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24
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Li H, Wang S, Kong R, Ding W, Lee FH, Parker Z, Kim E, Learn GH, Hahn P, Policicchio B, Brocca-Cofano E, Deleage C, Hao X, Chuang GY, Gorman J, Gardner M, Lewis MG, Hatziioannou T, Santra S, Apetrei C, Pandrea I, Alam SM, Liao HX, Shen X, Tomaras GD, Farzan M, Chertova E, Keele BF, Estes JD, Lifson JD, Doms RW, Montefiori DC, Haynes BF, Sodroski JG, Kwong PD, Hahn BH, Shaw GM. Envelope residue 375 substitutions in simian-human immunodeficiency viruses enhance CD4 binding and replication in rhesus macaques. Proc Natl Acad Sci U S A 2016; 113:E3413-22. [PMID: 27247400 PMCID: PMC4914158 DOI: 10.1073/pnas.1606636113] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Most simian-human immunodeficiency viruses (SHIVs) bearing envelope (Env) glycoproteins from primary HIV-1 strains fail to infect rhesus macaques (RMs). We hypothesized that inefficient Env binding to rhesus CD4 (rhCD4) limits virus entry and replication and could be enhanced by substituting naturally occurring simian immunodeficiency virus Env residues at position 375, which resides at a critical location in the CD4-binding pocket and is under strong positive evolutionary pressure across the broad spectrum of primate lentiviruses. SHIVs containing primary or transmitted/founder HIV-1 subtype A, B, C, or D Envs with genotypic variants at residue 375 were constructed and analyzed in vitro and in vivo. Bulky hydrophobic or basic amino acids substituted for serine-375 enhanced Env affinity for rhCD4, virus entry into cells bearing rhCD4, and virus replication in primary rhCD4 T cells without appreciably affecting antigenicity or antibody-mediated neutralization sensitivity. Twenty-four RMs inoculated with subtype A, B, C, or D SHIVs all became productively infected with different Env375 variants-S, M, Y, H, W, or F-that were differentially selected in different Env backbones. Notably, SHIVs replicated persistently at titers comparable to HIV-1 in humans and elicited autologous neutralizing antibody responses typical of HIV-1. Seven animals succumbed to AIDS. These findings identify Env-rhCD4 binding as a critical determinant for productive SHIV infection in RMs and validate a novel and generalizable strategy for constructing SHIVs with Env glycoproteins of interest, including those that in humans elicit broadly neutralizing antibodies or bind particular Ig germ-line B-cell receptors.
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Affiliation(s)
- Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Rui Kong
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Wenge Ding
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Fang-Hua Lee
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Zahra Parker
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Eunlim Kim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ben Policicchio
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | | | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Xingpei Hao
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Matthew Gardner
- Department of Infectious Disease, Scripps Research Institute, Jupiter, FL 33458
| | | | | | - Sampa Santra
- Center of Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | - Ivona Pandrea
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | - S Munir Alam
- Department of Medicine, Duke University, Durham, NC 27710
| | - Hua-Xin Liao
- Department of Medicine, Duke University, Durham, NC 27710
| | - Xiaoying Shen
- Department of Medicine, Duke University, Durham, NC 27710
| | | | - Michael Farzan
- Department of Infectious Disease, Scripps Research Institute, Jupiter, FL 33458
| | - Elena Chertova
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Jacob D Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Robert W Doms
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | | | | | - Joseph G Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
| | - Peter D Kwong
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
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25
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Schoofs T, Klein F, Braunschweig M, Kreider EF, Feldmann A, Nogueira L, Oliveira T, Lorenzi JCC, Parrish EH, Learn GH, West AP, Bjorkman PJ, Schlesinger SJ, Seaman MS, Czartoski J, McElrath MJ, Pfeifer N, Hahn BH, Caskey M, Nussenzweig MC. HIV-1 therapy with monoclonal antibody 3BNC117 elicits host immune responses against HIV-1. Science 2016; 352:997-1001. [PMID: 27199429 DOI: 10.1126/science.aaf0972] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/14/2016] [Indexed: 01/07/2023]
Abstract
3BNC117 is a broad and potent neutralizing antibody to HIV-1 that targets the CD4 binding site on the viral envelope spike. When administered passively, this antibody can prevent infection in animal models and suppress viremia in HIV-1-infected individuals. Here we report that HIV-1 immunotherapy with a single injection of 3BNC117 affects host antibody responses in viremic individuals. In comparison to untreated controls that showed little change in their neutralizing activity over a 6-month period, 3BNC117 infusion significantly improved neutralizing responses to heterologous tier 2 viruses in nearly all study participants. We conclude that 3BNC117-mediated immunotherapy enhances host humoral immunity to HIV-1.
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Affiliation(s)
- Till Schoofs
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Florian Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA. Laboratory of Experimental Immunology, Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany. Department of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, 50937 Cologne, Germany
| | - Malte Braunschweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA. Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Edward F Kreider
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Feldmann
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E14, 66123 Saarbrücken, Germany
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Erica H Parrish
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anthony P West
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah J Schlesinger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Julie Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E14, 66123 Saarbrücken, Germany
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA. Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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26
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Li H, Stoddard MB, Wang S, Giorgi EE, Blair LM, Learn GH, Hahn BH, Alter HJ, Busch MP, Fierer DS, Ribeiro RM, Perelson AS, Bhattacharya T, Shaw GM. Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification. J Virol 2016; 90:152-66. [PMID: 26468546 PMCID: PMC4702571 DOI: 10.1128/jvi.02156-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/02/2015] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED Despite the recent development of highly effective anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and development of an effective vaccine. A precise molecular identification of transmitted/founder (T/F) HCV genomes that lead to productive clinical infection could play a critical role in vaccine research, as it has for HIV-1. However, the replication schema of these two RNA viruses differ substantially, as do viral responses to innate and adaptive host defenses. These differences raise questions as to the certainty of T/F HCV genome inferences, particularly in cases where multiple closely related sequence lineages have been observed. To clarify these issues and distinguish between competing models of early HCV diversification, we examined seven cases of acute HCV infection in humans and chimpanzees, including three examples of virus transmission between linked donors and recipients. Using single-genome sequencing (SGS) of plasma vRNA, we found that inferred T/F sequences in recipients were identical to viral sequences in their respective donors. Early in infection, HCV genomes generally evolved according to a simple model of random evolution where the coalescent corresponded to the T/F sequence. Closely related sequence lineages could be explained by high multiplicity infection from a donor whose viral sequences had undergone a pretransmission bottleneck due to treatment, immune selection, or recent infection. These findings validate SGS, together with mathematical modeling and phylogenetic analysis, as a novel strategy to infer T/F HCV genome sequences. IMPORTANCE Despite the recent development of highly effective, interferon-sparing anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and the development of an effective vaccine, which could be facilitated by a precise molecular identification of transmitted/founder (T/F) viral genomes and their progeny. We used single-genome sequencing to show that inferred HCV T/F sequences in recipients were identical to viral sequences in their respective donors and that viral genomes generally evolved early in infection according to a simple model of random sequence evolution. Altogether, the findings validate T/F genome inferences and illustrate how T/F sequence identification can illuminate studies of HCV transmission, immunopathogenesis, drug resistance development, and vaccine protection, including sieving effects on breakthrough virus strains.
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Affiliation(s)
- Hui Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mark B Stoddard
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elena E Giorgi
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lily M Blair
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Department of Biology, Stanford University, Stanford, California, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Harvey J Alter
- Department of Transfusion Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael P Busch
- Blood Systems Research Institute, University of California San Francisco, San Francisco, California, USA
| | - Daniel S Fierer
- Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruy M Ribeiro
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Tanmoy Bhattacharya
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Santa Fe Institute, Santa Fe, New Mexico, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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27
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Langer SM, Hopfensperger K, Iyer SS, Kreider EF, Learn GH, Lee LH, Hahn BH, Sauter D. A Naturally Occurring rev1-vpu Fusion Gene Does Not Confer a Fitness Advantage to HIV-1. PLoS One 2015; 10:e0142118. [PMID: 26554585 PMCID: PMC4640844 DOI: 10.1371/journal.pone.0142118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Pandemic strains of HIV-1 (group M) encode a total of nine structural (gag, pol, env), regulatory (rev, tat) and accessory (vif, vpr, vpu, nef) genes. However, some subtype A and C viruses exhibit an unusual gene arrangement in which the first exon of rev (rev1) and the vpu gene are placed in the same open reading frame. Although this rev1-vpu gene fusion is present in a considerable fraction of HIV-1 strains, its functional significance is unknown. RESULTS Examining infectious molecular clones (IMCs) of HIV-1 that encode the rev1-vpu polymorphism, we show that a fusion protein is expressed in infected cells. Due to the splicing pattern of viral mRNA, however, these same IMCs also express a regular Vpu protein, which is produced at much higher levels. To investigate the function of the fusion gene, we characterized isogenic IMC pairs differing only in their ability to express a Rev1-Vpu protein. Analysis in transfected HEK293T and infected CD4+ T cells showed that all of these viruses were equally active in known Vpu functions, such as down-modulation of CD4 or counteraction of tetherin. Furthermore, the polymorphism did not affect Vpu-mediated inhibition of NF-кB activation or Rev-dependent nuclear export of incompletely spliced viral mRNAs. There was also no evidence for enhanced replication of Rev1-Vpu expressing viruses in primary PBMCs or ex vivo infected human lymphoid tissues. Finally, the frequency of HIV-1 quasispecies members that encoded a rev1-vpu fusion gene did not change in HIV-1 infected individuals over time. CONCLUSIONS Expression of a rev1-vpu fusion gene does not affect regular Rev and Vpu functions or alter HIV-1 replication in primary target cells. Since there is no evidence for increased replication fitness of rev1-vpu encoding viruses, this polymorphism likely emerged in the context of other mutations within and/or outside the rev1-vpu intergenic region, and may have a neutral phenotype.
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Affiliation(s)
- Simon M. Langer
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Shilpa S. Iyer
- Departments of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Edward F. Kreider
- Departments of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Gerald H. Learn
- Departments of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Lan-Hui Lee
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
- Department of Laboratory, Kunming Branch, Taipei City Hospital, 10844, Taipei, Taiwan
| | - Beatrice H. Hahn
- Departments of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
- * E-mail:
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28
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Cohn LB, Silva IT, Oliveira TY, Rosales RA, Parrish EH, Learn GH, Hahn BH, Czartoski JL, McElrath MJ, Lehmann C, Klein F, Caskey M, Walker BD, Siliciano JD, Siliciano RF, Jankovic M, Nussenzweig MC. HIV-1 integration landscape during latent and active infection. Cell 2015; 160:420-32. [PMID: 25635456 DOI: 10.1016/j.cell.2015.01.020] [Citation(s) in RCA: 338] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/18/2014] [Accepted: 01/12/2015] [Indexed: 11/15/2022]
Abstract
The barrier to curing HIV-1 is thought to reside primarily in CD4(+) T cells containing silent proviruses. To characterize these latently infected cells, we studied the integration profile of HIV-1 in viremic progressors, individuals receiving antiretroviral therapy, and viremic controllers. Clonally expanded T cells represented the majority of all integrations and increased during therapy. However, none of the 75 expanded T cell clones assayed contained intact virus. In contrast, the cells bearing single integration events decreased in frequency over time on therapy, and the surviving cells were enriched for HIV-1 integration in silent regions of the genome. Finally, there was a strong preference for integration into, or in close proximity to, Alu repeats, which were also enriched in local hotspots for integration. The data indicate that dividing clonally expanded T cells contain defective proviruses and that the replication-competent reservoir is primarily found in CD4(+) T cells that remain relatively quiescent.
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Affiliation(s)
- Lillian B Cohn
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Israel T Silva
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; National Institute of Science and Technology in Stem Cell and Cell Therapy and Center for Cell Based Therapy, Rua Catão Roxo, 2501, Ribeirão Preto CEP 14051-140, Brazil
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Rafael A Rosales
- Departamento de Computação e Matemática, Universidade de São Paulo. Av. Bandeirantes, 3900, Ribeirão Preto CEP 14049-901, Brazil
| | - Erica H Parrish
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julie L Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Clara Lehmann
- Department I of Internal Medicine, University Hospital of Cologne, 50924 Cologne, Germany; German Centre for Infection Research, partner site Bonn-Cologne, 50924 Cologne, Germany
| | - Florian Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Bruce D Walker
- Ragon Institute of MGH, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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29
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Barbian HJ, Decker JM, Bibollet-Ruche F, Galimidi RP, West AP, Learn GH, Parrish NF, Iyer SS, Li Y, Pace CS, Song R, Huang Y, Denny TN, Mouquet H, Martin L, Acharya P, Zhang B, Kwong PD, Mascola JR, Verrips CT, Strokappe NM, Rutten L, McCoy LE, Weiss RA, Brown CS, Jackson R, Silvestri G, Connors M, Burton DR, Shaw GM, Nussenzweig MC, Bjorkman PJ, Ho DD, Farzan M, Hahn BH. Neutralization properties of simian immunodeficiency viruses infecting chimpanzees and gorillas. mBio 2015; 6:e00296-15. [PMID: 25900654 PMCID: PMC4453581 DOI: 10.1128/mbio.00296-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Broadly cross-reactive neutralizing antibodies (bNabs) represent powerful tools to combat human immunodeficiency virus type 1 (HIV-1) infection. Here, we examined whether HIV-1-specific bNabs are capable of cross-neutralizing distantly related simian immunodeficiency viruses (SIVs) infecting central (Pan troglodytes troglodytes) (SIVcpzPtt) and eastern (Pan troglodytes schweinfurthii) (SIVcpzPts) chimpanzees (n = 11) as well as western gorillas (Gorilla gorilla gorilla) (SIVgor) (n = 1). We found that bNabs directed against the CD4 binding site (n = 10), peptidoglycans at the base of variable loop 3 (V3) (n = 5), and epitopes at the interface of surface (gp120) and membrane-bound (gp41) envelope glycoproteins (n = 5) failed to neutralize SIVcpz and SIVgor strains. In addition, apex V2-directed bNabs (n = 3) as well as llama-derived (heavy chain only) antibodies (n = 6) recognizing both the CD4 binding site and gp41 epitopes were either completely inactive or neutralized only a fraction of SIVcpzPtt strains. In contrast, one antibody targeting the membrane-proximal external region (MPER) of gp41 (10E8), functional CD4 and CCR5 receptor mimetics (eCD4-Ig, eCD4-Ig(mim2), CD4-218.3-E51, and CD4-218.3-E51-mim2), as well as mono- and bispecific anti-human CD4 (iMab and LM52) and CCR5 (PRO140, PRO140-10E8) receptor antibodies neutralized >90% of SIVcpz and SIVgor strains with low-nanomolar (0.13 to 8.4 nM) potency. Importantly, the latter antibodies blocked virus entry not only in TZM-bl cells but also in Cf2Th cells expressing chimpanzee CD4 and CCR5 and neutralized SIVcpz in chimpanzee CD4(+) T cells, with 50% inhibitory concentrations (IC50s) ranging from 3.6 to 40.5 nM. These findings provide new insight into the protective capacity of anti-HIV-1 bNabs and identify candidates for further development to combat SIVcpz infection. IMPORTANCE SIVcpz is widespread in wild-living chimpanzees and can cause AIDS-like immunopathology and clinical disease. HIV-1 infection of humans can be controlled by antiretroviral therapy; however, treatment of wild-living African apes with current drug regimens is not feasible. Nonetheless, it may be possible to curb the spread of SIVcpz in select ape communities using vectored immunoprophylaxis and/or therapy. Here, we show that antibodies and antibody-like inhibitors developed to combat HIV-1 infection in humans are capable of neutralizing genetically diverse SIVcpz and SIVgor strains with considerable breadth and potency, including in primary chimpanzee CD4(+) T cells. These reagents provide an important first step toward translating intervention strategies currently developed to treat and prevent AIDS in humans to SIV-infected apes.
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Affiliation(s)
- Hannah J Barbian
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie M Decker
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rachel P Galimidi
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - Anthony P West
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas F Parrish
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shilpa S Iyer
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yingying Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Ruijiang Song
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Loic Martin
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Gif-sur-Yvette, France
| | - Priyamvada Acharya
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Nika M Strokappe
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Lucy Rutten
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Robin A Weiss
- Division of Infection and Immunity, University College London, London, United Kingdom
| | | | | | - Guido Silvestri
- Yerkes Regional Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Michael Farzan
- Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Kluge SF, Mack K, Iyer SS, Pujol FM, Heigele A, Learn GH, Usmani SM, Sauter D, Joas S, Hotter D, Bibollet-Ruche F, Plenderleith LJ, Peeters M, Geyer M, Sharp PM, Fackler OT, Hahn BH, Kirchhoff F. Nef proteins of epidemic HIV-1 group O strains antagonize human tetherin. Cell Host Microbe 2014; 16:639-50. [PMID: 25525794 DOI: 10.1016/j.chom.2014.10.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/13/2014] [Accepted: 09/18/2014] [Indexed: 01/06/2023]
Abstract
Most simian immunodeficiency viruses use their Nef protein to antagonize the host restriction factor tetherin. A deletion in human tetherin confers Nef resistance, representing a hurdle to successful zoonotic transmission. HIV-1 group M evolved to utilize the viral protein U (Vpu) to counteract tetherin. Although HIV-1 group O has spread epidemically in humans, it has not evolved a Vpu-based tetherin antagonism. Here we show that HIV-1 group O Nef targets a region adjacent to this deletion to inhibit transport of human tetherin to the cell surface, enhances virion release, and increases viral resistance to inhibition by interferon-α. The Nef protein of the inferred common ancestor of group O viruses is also active against human tetherin. Thus, Nef-mediated antagonism of human tetherin evolved prior to the spread of HIV-1 group O and likely facilitated secondary virus transmission. Our results may explain the epidemic spread of HIV-1 group O.
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Affiliation(s)
- Silvia F Kluge
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Katharina Mack
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Shilpa S Iyer
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - François M Pujol
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Anke Heigele
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Shariq M Usmani
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Simone Joas
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | - Martine Peeters
- UMI233, TransVIHMI, Institut de Recherche pour le Développement (IRD) and Université Montpellier, Montpellier 34394, France
| | - Matthias Geyer
- Group Physical Biochemistry, Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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Sterrett S, Learn GH, Edlefsen PT, Haynes BF, Hahn BH, Shaw GM, Bar KJ. Low Multiplicity of HIV-1 Infection and No Vaccine Enhancement in VAX003 Injection Drug Users. Open Forum Infect Dis 2014; 1:ofu056. [PMID: 25734126 PMCID: PMC4281816 DOI: 10.1093/ofid/ofu056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/23/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND We performed human immunodeficiency virus type 1 (HIV-1) transmitted/founder (T/F) virus analysis of the VAX003 vaccine efficacy trial participants to characterize the transmission bottleneck and test for vaccine-associated reduction or enhancement of infection in this injection drug user (IDU) cohort. METHODS We performed single genome sequencing of plasma vRNA from 50 subjects sampled in early HIV infection. Sequences were analyzed phylogenetically, T/F viruses enumerated, and a sieve analysis performed. RESULTS Eight of 19 (42%) placebo recipients were productively infected by more than 1 virus (range 1-5, median 1, mean 1.7). This frequency of multiple virus transmission was greater than reported for heterosexual cohorts (19%, P = .03) but not statistically different from vaccine recipients (22.6%, P > .05), where the range was 1-3, median 1, and mean 1.3 (P > .05 for all comparisons). An atypical sieve effect was detected in Env V2 but was not associated with reduction or enhancement of virus acquisition. CONCLUSIONS The number of T/F viruses in IDUs was surprising low, with 95% of individuals infected by only 1-3 viruses. This finding suggests that a successful vaccine or other prevention modality generally needs to protect against only one or a few viruses regardless of risk behavior. T/F analysis identified an atypical genetic sieve in the V2 region of Envelope and found no evidence for vaccine-mediated enhancement in VAX003.
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Affiliation(s)
| | - Gerald H Learn
- Perelman School of Medicine , University of Pennsylvania , Philadelphia
| | - Paul T Edlefsen
- Fred Hutchinson Cancer Research Center , Seattle, Washington
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center , Durham, North Carolina
| | - Beatrice H Hahn
- Perelman School of Medicine , University of Pennsylvania , Philadelphia
| | - George M Shaw
- Perelman School of Medicine , University of Pennsylvania , Philadelphia
| | - Katharine J Bar
- Perelman School of Medicine , University of Pennsylvania , Philadelphia
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Permar SR, Salazar MG, Gao F, Cai F, Learn GH, Kalilani L, Hahn BH, Shaw GM, Salazar-Gonzalez JF. Clonal amplification and maternal-infant transmission of nevirapine-resistant HIV-1 variants in breast milk following single-dose nevirapine prophylaxis. Retrovirology 2013; 10:88. [PMID: 23941304 PMCID: PMC3765243 DOI: 10.1186/1742-4690-10-88] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/06/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Intrapartum administration of single-dose nevirapine (sdNVP) reduces perinatal HIV-1 transmission in resource-limiting settings by half. Yet this strategy has limited effect on subsequent breast milk transmission, making the case for new treatment approaches to extend maternal/infant antiretroviral prophylaxis through the period of lactation. Maternal and transmitted infant HIV-1 variants frequently develop NVP resistance mutations following sdNVP, complicating subsequent treatment/prophylaxis regimens. However, it is not clear whether NVP-resistant viruses are transmitted via breastfeeding or arise de novo in the infant. FINDINGS We performed a detailed HIV genetic analysis using single genome sequencing to identify the origin of drug-resistant variants in an sdNVP-treated postnatally-transmitting mother-infant pair. Phylogenetic analysis of HIV sequences from the child revealed low-diversity variants indicating infection by a subtype C single transmitted/founder virus that shared full-length sequence identity with a clonally-amplified maternal breast milk virus variant harboring the K103N NVP resistance mutation. CONCLUSION In this mother/child pair, clonal amplification of maternal NVP-resistant HIV variants present in systemic and mammary gland compartments following intrapartum sdNVP represents one source of transmitted NVP-resistant variants that is responsible for the acquisition of drug resistant virus by the breastfeeding infant. This finding emphasizes the need for combination antiretroviral prophylaxis to prevent mother-to-child HIV transmission.
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Affiliation(s)
- Sallie R Permar
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
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33
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Piel AK, Stewart FA, Pintea L, Li Y, Ramirez MA, Loy DE, Crystal PA, Learn GH, Knapp LA, Sharp PM, Hahn BH. The malagarasi river does not form an absolute barrier to chimpanzee movement in Western Tanzania. PLoS One 2013; 8:e58965. [PMID: 23536841 PMCID: PMC3594223 DOI: 10.1371/journal.pone.0058965] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Malagarasi River has long been thought to be a barrier to chimpanzee movements in western Tanzania. This potential geographic boundary could affect chimpanzee ranging behavior, population connectivity and pathogen transmission, and thus has implications for conservation strategies and government policy. Indeed, based on mitochondrial DNA sequence comparisons it was recently argued that chimpanzees from communities to the north and to the south of the Malagarasi are surprisingly distantly related, suggesting that the river prevents gene flow. To investigate this, we conducted a survey along the Malagarasi River. We found a ford comprised of rocks that researchers could cross on foot. On a trail leading to this ford, we collected 13 fresh fecal samples containing chimpanzee DNA, two of which tested positive for SIVcpz. We also found chimpanzee feces within the riverbed. Taken together, this evidence suggests that the Malagarasi River is not an absolute barrier to chimpanzee movements and communities from the areas to the north and south should be considered a single population. These results have important consequences for our understanding of gene flow, disease dynamics and conservation management.
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Affiliation(s)
- Alex K Piel
- Department of Anthropology, University of California San Diego, San Diego, California, United States of America.
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34
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Baalwa J, Wang S, Parrish NF, Decker JM, Keele BF, Learn GH, Yue L, Ruzagira E, Ssemwanga D, Kamali A, Amornkul PN, Price MA, Kappes JC, Karita E, Kaleebu P, Sanders E, Gilmour J, Allen S, Hunter E, Montefiori DC, Haynes BF, Cormier E, Hahn BH, Shaw GM. Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones. Virology 2012; 436:33-48. [PMID: 23123038 DOI: 10.1016/j.virol.2012.10.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 09/25/2012] [Accepted: 10/05/2012] [Indexed: 11/18/2022]
Abstract
We report the molecular identification, cloning and initial biological characterization of 12 full-length HIV-1 subtype A, D and A/D recombinant transmitted/founder (T/F) genomes. T/F genomes contained intact canonical open reading frames and all T/F viruses were replication competent in primary human T-cells, although subtype D virus replication was more efficient (p<0.05). All 12 viruses utilized CCR5 but not CXCR4 as a co-receptor for entry and exhibited a neutralization profile typical of tier 2 primary virus strains, with significant differences observed between subtype A and D viruses with respect to sensitivity to monoclonal antibodies VRC01, PG9 and PG16 and polyclonal subtype C anti-HIV IgG (p<0.05 for each). The present report doubles the number of T/F HIV-1 clones available for pathogenesis and vaccine research and extends their representation to include subtypes A, B, C and D.
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Affiliation(s)
- Joshua Baalwa
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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35
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Ribeiro RM, Li H, Wang S, Stoddard MB, Learn GH, Korber BT, Bhattacharya T, Guedj J, Parrish EH, Hahn BH, Shaw GM, Perelson AS. Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate. PLoS Pathog 2012; 8:e1002881. [PMID: 22927817 PMCID: PMC3426522 DOI: 10.1371/journal.ppat.1002881] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 07/12/2012] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) is present in the host with multiple variants generated by its error prone RNA-dependent RNA polymerase. Little is known about the initial viral diversification and the viral life cycle processes that influence diversity. We studied the diversification of HCV during acute infection in 17 plasma donors, with frequent sampling early in infection. To analyze these data, we developed a new stochastic model of the HCV life cycle. We found that the accumulation of mutations is surprisingly slow: at 30 days, the viral population on average is still 46% identical to its transmitted viral genome. Fitting the model to the sequence data, we estimate the median in vivo viral mutation rate is 2.5×10−5 mutations per nucleotide per genome replication (range 1.6–6.2×10−5), about 5-fold lower than previous estimates. To confirm these results we analyzed the frequency of stop codons (N = 10) among all possible non-sense mutation targets (M = 898,335), and found a mutation rate of 2.8–3.2×10−5, consistent with the estimate from the dynamical model. The slow accumulation of mutations is consistent with slow turnover of infected cells and replication complexes within infected cells. This slow turnover is also inferred from the viral load kinetics. Our estimated mutation rate, which is similar to that of other RNA viruses (e.g., HIV and influenza), is also compatible with the accumulation of substitutions seen in HCV at the population level. Our model identifies the relevant processes (long-lived cells and slow turnover of replication complexes) and parameters involved in determining the rate of HCV diversification. Hepatitis C virus (HCV) is a RNA virus that infects over 170 million people across the world. It leads to a chronic infection in the majority of people who are infected (>70%). Most people only discover that they are infected long after initial infection. Thus, it is difficult to study the very early events in infection. Here we study 17 individuals during the earliest possible stages of infection, from before the virus is detectable in the plasma to around 35 days post-infection. We focus on understanding the viral kinetics and the diversification of HCV during this acute phase of infection. During chronic infection HCV is present in the host as a swarm of multiple variants generated by its error prone copying. We studied the early diversification of HCV during acute infection using a new mathematical model of HCV replication. We found that after a phase of fast increase in viral load, accompanied by viral diversification, there is a stabilization of viral load and diversity levels. Using our model, we were able to estimate for the first time the HCV mutation rate during acute infection. We estimated the median in vivo viral mutation rate is 2.5×10−5 mutations per nucleotide per genome replication (range 1.6–6.2×10−5), about 5-fold lower than previous estimates. We also used a different approach, based on results of classical genetics, to calculate HCV's mutation rate and obtained consistent results (2.8–3.2×10−5).
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Affiliation(s)
- Ruy M. Ribeiro
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shuyi Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark B. Stoddard
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gerald H. Learn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Bette T. Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jeremie Guedj
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Erica H. Parrish
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Beatrice H. Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alan S. Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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36
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Li H, Stoddard MB, Wang S, Blair LM, Giorgi EE, Parrish EH, Learn GH, Hraber P, Goepfert PA, Saag MS, Denny TN, Haynes BF, Hahn BH, Ribeiro RM, Perelson AS, Korber BT, Bhattacharya T, Shaw GM. Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. PLoS Pathog 2012; 8:e1002880. [PMID: 22927816 PMCID: PMC3426529 DOI: 10.1371/journal.ppat.1002880] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 06/27/2012] [Indexed: 02/07/2023] Open
Abstract
A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures. Hepatitis C virus infects as many as 170 million people worldwide. Globally, there are seven major genotypes of HCV that differ by approximately 30% in nucleotide sequence. Importantly, the natural history of HCV infection is variable, ranging from spontaneous resolution to persistent viremia and chronic disease. Factors responsible for this variability in clinical outcome are unknown but likely involve a combination of viral and host determinants. To this end, a precise molecular identification of transmitted HCV genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of plasma viral RNA to identify transmitted viral genomes and their progeny in 17 subjects with acute infection. Numbers of transmitted viruses leading to productive clinical infection ranged from 1 to 37 or more (median = 4). Surprisingly, we found evidence of high multiplicity acute-to-acute HCV transmission in 3 of 17 subjects, which suggests that clinical transmission of HCV, like that of HIV-1, may be enhanced in early infection when virus titers are highest and neutralizing antibodies are absent. These results provide novel insight into HCV transmission and early virus diversification key to our understanding of virus natural history and response to drug selection and immune pressure.
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Affiliation(s)
- Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark B. Stoddard
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shuyi Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lily M. Blair
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Elena E. Giorgi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Erica H. Parrish
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gerald H. Learn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Peter Hraber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Paul A. Goepfert
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Saag
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Thomas N. Denny
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Beatrice H. Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ruy M. Ribeiro
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bette T. Korber
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Rudicell RS, Piel AK, Stewart F, Moore DL, Learn GH, Li Y, Takehisa J, Pintea L, Shaw GM, Moore J, Sharp PM, Hahn BH. High prevalence of simian immunodeficiency virus infection in a community of savanna chimpanzees. J Virol 2011; 85:9918-28. [PMID: 21775446 PMCID: PMC3196395 DOI: 10.1128/jvi.05475-11] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/13/2011] [Indexed: 12/27/2022] Open
Abstract
Simian immunodeficiency virus of chimpanzees (SIVcpz) has a significant negative impact on the health, reproduction, and life span of chimpanzees, yet the prevalence and distribution of this virus in wild-living populations are still only poorly understood. Here, we show that savanna chimpanzees, who live in ecologically marginal habitats at 10- to 50-fold lower population densities than forest chimpanzees, can be infected with SIVcpz at high prevalence rates. Fecal samples were collected from nonhabituated eastern chimpanzees (Pan troglodytes schweinfurthii) in the Issa Valley (n = 375) and Shangwa River (n = 6) areas of the Masito-Ugalla region in western Tanzania, genotyped to determine the number of sampled individuals, and tested for SIVcpz-specific antibodies and nucleic acids. None of 5 Shangwa River apes tested positive for SIVcpz; however, 21 of 67 Issa Valley chimpanzees were SIVcpz infected, indicating a prevalence rate of 31% (95% confidence interval, 21% to 44%). Two individuals became infected during the 14-month observation period, documenting continuing virus spread in this community. To characterize the newly identified SIVcpz strains, partial and full-length viral sequences were amplified from fecal RNA of 10 infected chimpanzees. Phylogenetic analyses showed that the Ugalla viruses formed a monophyletic lineage most closely related to viruses endemic in Gombe National Park, also located in Tanzania, indicating a connection between these now separated communities at some time in the past. These findings document that SIVcpz is more widespread in Tanzania than previously thought and that even very low-density chimpanzee populations can be infected with SIVcpz at high prevalence rates. Determining whether savanna chimpanzees, who face much more extreme environmental conditions than forest chimpanzees, are more susceptible to SIVcpz-associated morbidity and mortality will have important scientific and conservation implications.
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Affiliation(s)
| | - Alex K. Piel
- Department of Anthropology, University of California at San Diego, La Jolla, California 92093
| | - Fiona Stewart
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, United Kingdom
| | - Deborah L. Moore
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas 78249
| | - Gerald H. Learn
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Yingying Li
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jun Takehisa
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Lilian Pintea
- The Jane Goodall Institute, Arlington, Virginia 22203
| | - George M. Shaw
- Departments of Microbiology
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jim Moore
- Department of Anthropology, University of California at San Diego, La Jolla, California 92093
| | - Paul M. Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Beatrice H. Hahn
- Departments of Microbiology
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
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Liu W, Li Y, Learn GH, Rudicell RS, Robertson JD, Keele BF, Ndjango JBN, Sanz CM, Morgan DB, Locatelli S, Gonder MK, Kranzusch PJ, Walsh PD, Delaporte E, Mpoudi-Ngole E, Georgiev AV, Muller MN, Shaw GM, Peeters M, Sharp PM, Rayner JC, Hahn BH. Origin of the human malaria parasite Plasmodium falciparum in gorillas. Malar J 2010. [PMCID: PMC2963212 DOI: 10.1186/1475-2875-9-s2-i6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Rudicell RS, Holland Jones J, Wroblewski EE, Learn GH, Li Y, Robertson JD, Greengrass E, Grossmann F, Kamenya S, Pintea L, Mjungu DC, Lonsdorf EV, Mosser A, Lehman C, Collins DA, Keele BF, Goodall J, Hahn BH, Pusey AE, Wilson ML. Impact of simian immunodeficiency virus infection on chimpanzee population dynamics. PLoS Pathog 2010; 6:e1001116. [PMID: 20886099 PMCID: PMC2944804 DOI: 10.1371/journal.ppat.1001116] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 08/20/2010] [Indexed: 11/30/2022] Open
Abstract
Like human immunodeficiency virus type 1 (HIV-1), simian immunodeficiency virus of chimpanzees (SIVcpz) can cause CD4+ T cell loss and premature death. Here, we used molecular surveillance tools and mathematical modeling to estimate the impact of SIVcpz infection on chimpanzee population dynamics. Habituated (Mitumba and Kasekela) and non-habituated (Kalande) chimpanzees were studied in Gombe National Park, Tanzania. Ape population sizes were determined from demographic records (Mitumba and Kasekela) or individual sightings and genotyping (Kalande), while SIVcpz prevalence rates were monitored using non-invasive methods. Between 2002–2009, the Mitumba and Kasekela communities experienced mean annual growth rates of 1.9% and 2.4%, respectively, while Kalande chimpanzees suffered a significant decline, with a mean growth rate of −6.5% to −7.4%, depending on population estimates. A rapid decline in Kalande was first noted in the 1990s and originally attributed to poaching and reduced food sources. However, between 2002–2009, we found a mean SIVcpz prevalence in Kalande of 46.1%, which was almost four times higher than the prevalence in Mitumba (12.7%) and Kasekela (12.1%). To explore whether SIVcpz contributed to the Kalande decline, we used empirically determined SIVcpz transmission probabilities as well as chimpanzee mortality, mating and migration data to model the effect of viral pathogenicity on chimpanzee population growth. Deterministic calculations indicated that a prevalence of greater than 3.4% would result in negative growth and eventual population extinction, even using conservative mortality estimates. However, stochastic models revealed that in representative populations, SIVcpz, and not its host species, frequently went extinct. High SIVcpz transmission probability and excess mortality reduced population persistence, while intercommunity migration often rescued infected communities, even when immigrating females had a chance of being SIVcpz infected. Together, these results suggest that the decline of the Kalande community was caused, at least in part, by high levels of SIVcpz infection. However, population extinction is not an inevitable consequence of SIVcpz infection, but depends on additional variables, such as migration, that promote survival. These findings are consistent with the uneven distribution of SIVcpz throughout central Africa and explain how chimpanzees in Gombe and elsewhere can be at equipoise with this pathogen. It is now well established that human immunodeficiency virus type 1 (HIV-1), which causes acquired immune deficiency syndrome (AIDS), emerged following cross-species transmission of a simian immunodeficiency virus that infects chimpanzees (SIVcpz). Although SIVcpz was originally believed not to be pathogenic, a recent study conducted in Gombe National Park, Tanzania, found that infected chimpanzees can develop AIDS-like symptoms and have a high mortality. To examine the impact of SIVcpz on chimpanzee survival, we examined and then modeled the effect of virus infection on chimpanzee population growth. We studied three communities, including the little-studied Kalande community, located in the south of the park. We found that 46% of Kalande apes were infected with SIVcpz, compared to less than 13% of the other communities. Interestingly, the communities with lower infection rates grew, while Kalande suffered a catastrophic decline. Mathematical modeling indicated that chimpanzee populations infected with SIVcpz are likely to decline, although intercommunity migration counteracted this negative effect, allowing many simulated populations to persist. These results suggest that SIVcpz infection, together with other variables, contributed to the Kalande population decline. However, population extinction is not a necessary consequence of SIVcpz infection, but can be counteracted by other factors, such as migration, that promote population survival. These findings are consistent with the uneven distribution of SIVcpz across Africa and may explain how chimpanzees as a species have survived this pathogen.
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Affiliation(s)
- Rebecca S. Rudicell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - James Holland Jones
- Department of Anthropology, Stanford University, Stanford, California, United States of America
- Woods Institute for the Environment, Stanford University, Stanford, California, United States of America
| | - Emily E. Wroblewski
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Gerald H. Learn
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yingying Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joel D. Robertson
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | | | - Falk Grossmann
- Africa Program, Wildlife Conservation Society, Bronx, New York, United States of America
| | - Shadrack Kamenya
- Gombe Stream Research Centre, The Jane Goodall Institute, Kigoma, Tanzania
| | - Lilian Pintea
- The Jane Goodall Institute, Arlington, Virginia, United States of America
| | - Deus C. Mjungu
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Elizabeth V. Lonsdorf
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois, United States of America
| | - Anna Mosser
- Gombe Stream Research Centre, The Jane Goodall Institute, Kigoma, Tanzania
| | - Clarence Lehman
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - D. Anthony Collins
- Gombe Stream Research Centre, The Jane Goodall Institute, Kigoma, Tanzania
| | - Brandon F. Keele
- The AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Jane Goodall
- The Jane Goodall Institute, Arlington, Virginia, United States of America
| | - Beatrice H. Hahn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Michael L. Wilson
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
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Rolland M, Carlson JM, Manocheewa S, Swain JV, Lanxon-Cookson E, Deng W, Rousseau CM, Raugi DN, Learn GH, Maust BS, Coovadia H, Ndung'u T, Goulder PJR, Walker BD, Brander C, Heckerman DE, Mullins JI. Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics. PLoS One 2010; 5. [PMID: 20824187 PMCID: PMC2931691 DOI: 10.1371/journal.pone.0012463] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 07/30/2010] [Indexed: 11/19/2022] Open
Abstract
Background Despite high potential for HIV-1 genetic variation, the emergence of some mutations is constrained by fitness costs, and may be associated with compensatory amino acid (AA) co-variation. To characterize the interplay between Cytotoxic T Lymphocyte (CTL)-mediated pressure and HIV-1 evolutionary pathways, we investigated AA co-variation in Gag sequences obtained from 449 South African individuals chronically infected with HIV-1 subtype C. Methodology/Principal Findings Individuals with CTL responses biased toward Gag presented lower viral loads than individuals with under-represented Gag-specific CTL responses. Using methods that account for founder effects and HLA linkage disequilibrium, we identified 35 AA sites under Human Leukocyte Antigen (HLA)-restricted CTL selection pressure and 534 AA-to-AA interactions. Analysis of two-dimensional distances between co-varying residues revealed local stabilization mechanisms since 40% of associations involved neighboring residues. Key features of our co-variation analysis included sites with a high number of co-varying partners, such as HLA-associated sites, which had on average 55% more connections than other co-varying sites. Conclusions/Significance Clusters of co-varying AA around HLA-associated sites (especially at typically conserved sites) suggested that cooperative interactions act to preserve the local structural stability and protein function when CTL escape mutations occur. These results expose HLA-imprinted HIV-1 polymorphisms and their interlinked mutational paths in Gag that are likely due to opposite selective pressures from host CTL-mediated responses and viral fitness constraints.
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Affiliation(s)
- Morgane Rolland
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America.
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Sauter D, Schindler M, Specht A, Landford WN, Münch J, Kim KA, Votteler J, Schubert U, Bibollet-Ruche F, Keele BF, Takehisa J, Ogando Y, Ochsenbauer C, Kappes JC, Ayouba A, Peeters M, Learn GH, Shaw G, Sharp PM, Bieniasz P, Hahn BH, Hatziioannou T, Kirchhoff F. Tetherin-driven adaptation of Vpu and Nef function and the evolution of pandemic and nonpandemic HIV-1 strains. Cell Host Microbe 2010; 6:409-21. [PMID: 19917496 DOI: 10.1016/j.chom.2009.10.004] [Citation(s) in RCA: 334] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 09/06/2009] [Accepted: 10/12/2009] [Indexed: 02/01/2023]
Abstract
Vpu proteins of pandemic HIV-1 M strains degrade the viral receptor CD4 and antagonize human tetherin to promote viral release and replication. We show that Vpus from SIVgsn, SIVmus, and SIVmon infecting Cercopithecus primate species also degrade CD4 and antagonize tetherin. In contrast, SIVcpz, the immediate precursor of HIV-1, whose Vpu shares a common ancestry with SIVgsn/mus/mon Vpu, uses Nef rather than Vpu to counteract chimpanzee tetherin. Human tetherin, however, is resistant to Nef and thus poses a significant barrier to zoonotic transmission of SIVcpz to humans. Remarkably, Vpus from nonpandemic HIV-1 O strains are poor tetherin antagonists, whereas those from the rare group N viruses do not degrade CD4. Thus, only HIV-1 M evolved a fully functional Vpu following the three independent cross-species transmissions that resulted in HIV-1 groups M, N, and O. This may explain why group M viruses are almost entirely responsible for the global HIV/AIDS pandemic.
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Affiliation(s)
- Daniel Sauter
- Institute of Molecular Virology, Universitätsklinikum, 89081 Ulm, Germany
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42
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Li H, Bar KJ, Wang S, Decker JM, Chen Y, Sun C, Salazar-Gonzalez JF, Salazar MG, Learn GH, Morgan CJ, Schumacher JE, Hraber P, Giorgi EE, Bhattacharya T, Korber BT, Perelson AS, Eron JJ, Cohen MS, Hicks CB, Haynes BF, Markowitz M, Keele BF, Hahn BH, Shaw GM. High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. PLoS Pathog 2010; 6:e1000890. [PMID: 20485520 PMCID: PMC2869329 DOI: 10.1371/journal.ppat.1000890] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/01/2010] [Indexed: 11/18/2022] Open
Abstract
Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies. To this end, single genome amplification (SGA) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous identification of transmitted/founder viruses and a precise estimation of their numbers. Here, we applied this approach to HIV-1 env analyses in a cohort of acutely infected men who have sex with men (MSM) and found that a high proportion (10 of 28; 36%) had been productively infected by more than one virus. In subjects with multivariant transmission, the minimum number of transmitted viruses ranged from 2 to 10 with viral recombination leading to rapid and extensive genetic shuffling among virus lineages. A combined analysis of these results, together with recently published findings based on identical SGA methods in largely heterosexual (HSX) cohorts, revealed a significantly higher frequency of multivariant transmission in MSM than in HSX [19 of 50 subjects (38%) versus 34 of 175 subjects (19%); Fisher's exact p = 0.008]. To further evaluate the SGA strategy for identifying transmitted/founder viruses, we analyzed 239 overlapping 5′ and 3′ half genome or env-only sequences from plasma viral RNA (vRNA) and blood mononuclear cell DNA in an MSM subject who had a particularly well-documented virus exposure history 3–6 days before symptom onset and 14–17 days before peak plasma viremia (47,600,000 vRNA molecules/ml). All 239 sequences coalesced to a single transmitted/founder virus genome in a time frame consistent with the clinical history, and a molecular clone of this genome encoded replication competent virus in accord with model predictions. Higher multiplicity of HIV-1 infection in MSM compared with HSX is consistent with the demonstrably higher epidemiological risk of virus acquisition in MSM and could indicate a greater challenge for HIV-1 vaccines than previously recognized. Understanding the biology of sexual transmission of HIV-1 could contribute importantly to the development of effective prevention measures. However, different routes of virus transmission (vaginal, rectal, penile or oral) and inaccessibility of tissues at or near the time of virus transmission make this goal elusive. Here, we apply single genome amplification and sequencing of plasma HIV-1 and a model of random virus evolution to a cohort of acutely infected men who have sex with men (MSM) and find that MSM are twice as likely as heterosexuals to become infected by multiple viruses as opposed to a single virus. Some MSM subjects were infected by as many as 7 to 10 or more genetically distinct viruses as a consequence of a single exposure event. We go on to molecularly clone the first full-length transmitted/founder subtype B HIV-1 virus and show that it is highly replicative in human CD4+ T-cells but not macrophages. Our study provides the first comparative, quantitative analysis of the multiplicity of HIV-1 infection in the two primary risk groups—MSM and heterosexuals—driving the global pandemic, and we discuss the implications of the findings to HIV-1 vaccine development and prevention research.
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Affiliation(s)
- Hui Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Katharine J. Bar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Shuyi Wang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Julie M. Decker
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yalu Chen
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chuanxi Sun
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jesus F. Salazar-Gonzalez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Maria G. Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Gerald H. Learn
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Charity J. Morgan
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joseph E. Schumacher
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter Hraber
- Theoretical Biology and Biophysics (T6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Elena E. Giorgi
- Theoretical Biology and Biophysics (T6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Tanmoy Bhattacharya
- Nuclear and Particle Physics, Astrophysics and Cosmology (T-2), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Bette T. Korber
- Theoretical Biology and Biophysics (T6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics (T6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Joseph J. Eron
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Myron S. Cohen
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Charles B. Hicks
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, New York, New York, United States of America
- Rockefeller University, New York, New York, United States of America
| | - Brandon F. Keele
- SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
| | - Beatrice H. Hahn
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - George M. Shaw
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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43
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Permar SR, Kang HH, Wilks AB, Mach LV, Carville A, Mansfield KG, Learn GH, Hahn BH, Letvin NL. Local replication of simian immunodeficiency virus in the breast milk compartment of chronically-infected, lactating rhesus monkeys. Retrovirology 2010; 7:7. [PMID: 20122164 PMCID: PMC2825190 DOI: 10.1186/1742-4690-7-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 02/01/2010] [Indexed: 11/22/2022] Open
Abstract
Breast milk transmission remains a major mode of infant HIV acquisition, yet anatomic and immunologic forces shaping virus quasispecies in milk are not well characterized. In this study, phylogenic analysis of envelope sequences of milk SIV variants revealed groups of nearly identical viruses, indicating local virus production. However, comparison of the patterns and rates of CTL escape of blood and milk virus demonstrated only subtle differences between the compartments. These findings suggest that a substantial fraction of milk viruses are produced by locally-infected cells, but are shaped by cellular immune pressures similar to that in the blood.
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Affiliation(s)
- Sallie R Permar
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA.
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44
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Liu MK, Ferrari G, Salazar J, Keele B, Tanner RL, Hraber P, Giorgi E, Ganusov VV, Learn GH, Salazar MG, Moore SR, Digleria K, Yu Z, Rostron T, DeBoer C, Williams A, Margaret C, Kopycinski J, Campion SL, Bourne VE, Brackenridge S, Hahn B, Cohen M, Borrow P, Weinhold K, Perelson A, Shaw G, Korber BT, Goonetilleke N, McMichael AJ. OA06-04. The role of early T-cell responses in subjects with acute HIV-1 infection. Retrovirology 2009. [PMCID: PMC2767563 DOI: 10.1186/1742-4690-6-s3-o40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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45
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Keele BF, Jones JH, Terio KA, Estes JD, Rudicell RS, Wilson ML, Li Y, Learn GH, Beasley TM, Schumacher-Stankey J, Wroblewski E, Mosser A, Raphael J, Kamenya S, Lonsdorf EV, Travis DA, Mlengeya T, Kinsel MJ, Else JG, Silvestri G, Goodall J, Sharp PM, Shaw GM, Pusey AE, Hahn BH. Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz. Nature 2009; 460:515-9. [PMID: 19626114 DOI: 10.1038/nature08200] [Citation(s) in RCA: 247] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 06/05/2009] [Indexed: 12/14/2022]
Abstract
African primates are naturally infected with over 40 different simian immunodeficiency viruses (SIVs), two of which have crossed the species barrier and generated human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2). Unlike the human viruses, however, SIVs do not generally cause acquired immunodeficiency syndrome (AIDS) in their natural hosts. Here we show that SIVcpz, the immediate precursor of HIV-1, is pathogenic in free-ranging chimpanzees. By following 94 members of two habituated chimpanzee communities in Gombe National Park, Tanzania, for over 9 years, we found a 10- to 16-fold higher age-corrected death hazard for SIVcpz-infected (n = 17) compared to uninfected (n = 77) chimpanzees. We also found that SIVcpz-infected females were less likely to give birth and had a higher infant mortality rate than uninfected females. Immunohistochemistry and in situ hybridization of post-mortem spleen and lymph node samples from three infected and two uninfected chimpanzees revealed significant CD4(+) T-cell depletion in all infected individuals, with evidence of high viral replication and extensive follicular dendritic cell virus trapping in one of them. One female, who died within 3 years of acquiring SIVcpz, had histopathological findings consistent with end-stage AIDS. These results indicate that SIVcpz, like HIV-1, is associated with progressive CD4(+) T-cell loss, lymphatic tissue destruction and premature death. These findings challenge the prevailing view that all natural SIV infections are non-pathogenic and suggest that SIVcpz has a substantial negative impact on the health, reproduction and lifespan of chimpanzees in the wild.
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Affiliation(s)
- Brandon F Keele
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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46
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Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, Parrish NF, Shaw KS, Guffey MB, Bar KJ, Davis KL, Ochsenbauer-Jambor C, Kappes JC, Saag MS, Cohen MS, Mulenga J, Derdeyn CA, Allen S, Hunter E, Markowitz M, Hraber P, Perelson AS, Bhattacharya T, Haynes BF, Korber BT, Hahn BH, Shaw GM. Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. ACTA ACUST UNITED AC 2009; 206:1273-89. [PMID: 19487424 PMCID: PMC2715054 DOI: 10.1084/jem.20090378] [Citation(s) in RCA: 602] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Identification of full-length transmitted HIV-1 genomes could be instrumental in HIV-1 pathogenesis, microbicide, and vaccine research by enabling the direct analysis of those viruses actually responsible for productive clinical infection. We show in 12 acutely infected subjects (9 clade B and 3 clade C) that complete HIV-1 genomes of transmitted/founder viruses can be inferred by single genome amplification and sequencing of plasma virion RNA. This allowed for the molecular cloning and biological analysis of transmitted/founder viruses and a comprehensive genome-wide assessment of the genetic imprint left on the evolving virus quasispecies by a composite of host selection pressures. Transmitted viruses encoded intact canonical genes (gag-pol-vif-vpr-tat-rev-vpu-env-nef) and replicated efficiently in primary human CD4+ T lymphocytes but much less so in monocyte-derived macrophages. Transmitted viruses were CD4 and CCR5 tropic and demonstrated concealment of coreceptor binding surfaces of the envelope bridging sheet and variable loop 3. 2 mo after infection, transmitted/founder viruses in three subjects were nearly completely replaced by viruses differing at two to five highly selected genomic loci; by 12–20 mo, viruses exhibited concentrated mutations at 17–34 discrete locations. These findings reveal viral properties associated with mucosal HIV-1 transmission and a limited set of rapidly evolving adaptive mutations driven primarily, but not exclusively, by early cytotoxic T cell responses.
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Goonetilleke N, Liu MKP, Salazar-Gonzalez JF, Ferrari G, Giorgi E, Ganusov VV, Keele BF, Learn GH, Turnbull EL, Salazar MG, Weinhold KJ, Moore S, Letvin N, Haynes BF, Cohen MS, Hraber P, Bhattacharya T, Borrow P, Perelson AS, Hahn BH, Shaw GM, Korber BT, McMichael AJ. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. ACTA ACUST UNITED AC 2009; 206:1253-72. [PMID: 19487423 PMCID: PMC2715063 DOI: 10.1084/jem.20090365] [Citation(s) in RCA: 498] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identification of the transmitted/founder virus makes possible, for the first time, a genome-wide analysis of host immune responses against the infecting HIV-1 proteome. A complete dissection was made of the primary HIV-1–specific T cell response induced in three acutely infected patients. Cellular assays, together with new algorithms which identify sites of positive selection in the virus genome, showed that primary HIV-1–specific T cells rapidly select escape mutations concurrent with falling virus load in acute infection. Kinetic analysis and mathematical modeling of virus immune escape showed that the contribution of CD8 T cell–mediated killing of productively infected cells was earlier and much greater than previously recognized and that it contributed to the initial decline of plasma virus in acute infection. After virus escape, these first T cell responses often rapidly waned, leaving or being succeeded by T cell responses to epitopes which escaped more slowly or were invariant. These latter responses are likely to be important in maintaining the already established virus set point. In addition to mutations selected by T cells, there were other selected regions that accrued mutations more gradually but were not associated with a T cell response. These included clusters of mutations in envelope that were targeted by NAbs, a few isolated sites that reverted to the consensus sequence, and bystander mutations in linkage with T cell–driven escape.
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Affiliation(s)
- Nilu Goonetilleke
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, England, UK
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48
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Keele BF, Li H, Learn GH, Hraber P, Giorgi EE, Grayson T, Sun C, Chen Y, Yeh WW, Letvin NL, Mascola JR, Nabel GJ, Haynes BF, Bhattacharya T, Perelson AS, Korber BT, Hahn BH, Shaw GM. Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. ACTA ACUST UNITED AC 2009; 206:1117-34. [PMID: 19414559 PMCID: PMC2715022 DOI: 10.1084/jem.20082831] [Citation(s) in RCA: 262] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We recently developed a novel strategy to identify transmitted HIV-1 genomes in acutely infected humans using single-genome amplification and a model of random virus evolution. Here, we used this approach to determine the molecular features of simian immunodeficiency virus (SIV) transmission in 18 experimentally infected Indian rhesus macaques. Animals were inoculated intrarectally (i.r.) or intravenously (i.v.) with stocks of SIVmac251 or SIVsmE660 that exhibited sequence diversity typical of early-chronic HIV-1 infection. 987 full-length SIV env sequences (median of 48 per animal) were determined from plasma virion RNA 1–5 wk after infection. i.r. inoculation was followed by productive infection by one or a few viruses (median 1; range 1–5) that diversified randomly with near starlike phylogeny and a Poisson distribution of mutations. Consensus viral sequences from ramp-up and peak viremia were identical to viruses found in the inocula or differed from them by only one or a few nucleotides, providing direct evidence that early plasma viral sequences coalesce to transmitted/founder viruses. i.v. infection was >2,000-fold more efficient than i.r. infection, and viruses transmitted by either route represented the full genetic spectra of the inocula. These findings identify key similarities in mucosal transmission and early diversification between SIV and HIV-1, and thus validate the SIV–macaque mucosal infection model for HIV-1 vaccine and microbicide research.
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Affiliation(s)
- Brandon F Keele
- University of Alabama at Birmingham, Birmingham, AL 35223, USA
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Rousseau CM, Lockhart DW, Listgarten J, Maley SN, Kadie C, Learn GH, Nickle DC, Heckerman DE, Deng W, Brander C, Ndung'u T, Coovadia H, Goulder PJ, Korber BT, Walker BD, Mullins JI. Rare HLA drive additional HIV evolution compared to more frequent alleles. AIDS Res Hum Retroviruses 2009; 25:297-303. [PMID: 19327049 DOI: 10.1089/aid.2008.0208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
HIV-1 can evolve HLA-specific escape variants in response to HLA-mediated cellular immunity. HLA alleles that are common in the host population may increase the frequency of such escape variants at the population level. When loss of viral fitness is caused by immune escape variation, these variants may revert upon infection of a new host who does not have the corresponding HLA allele. Furthermore, additional escape variants may appear in response to the nonconcordant HLA alleles. Because individuals with rare HLA alleles are less likely to be infected by a partner with concordant HLA alleles, viral populations infecting hosts with rare HLA alleles may undergo a greater amount of evolution than those infecting hosts with common alleles due to the loss of preexisting escape variants followed by new immune escape. This hypothesis was evaluated using maximum likelihood phylogenetic trees of each gene from 272 full-length HIV-1 sequences. Recent viral evolution, as measured by the external branch length, was found to be inversely associated with HLA frequency in nef (p < 0.02), env (p < 0.03), and pol (p < or = 0.05), suggesting that rare HLA alleles provide a disproportionate force driving viral evolution compared to common alleles, likely due to the loss of preexisting escape variants during early stages postinfection.
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Affiliation(s)
| | - David W. Lockhart
- Department of Biostatistics, University of Washington, Seattle Washington 98103
| | | | - Stephen N. Maley
- Department of Microbiology, University of Washington, Seattle Washington 98103
| | - Carl Kadie
- eScience Research Group, Microsoft Research, Redmond, Washington 98052
| | - Gerald H. Learn
- Department of Microbiology, University of Washington, Seattle Washington 98103
| | - David C. Nickle
- Department of Microbiology, University of Washington, Seattle Washington 98103
| | | | - Wenjie Deng
- Department of Microbiology, University of Washington, Seattle Washington 98103
| | - Christian Brander
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Thumbi Ndung'u
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
- HIV Pathogenesis Program, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Hoosen Coovadia
- HIV Pathogenesis Program, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Philip J.R. Goulder
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
- HIV Pathogenesis Program, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Pediatrics, Nuffield Department of Medicine, Oxford, England
| | - Bette T. Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico 87544
- Santa Fe Institute, Santa Fe, New Mexico 87501
| | - Bruce D. Walker
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
- HIV Pathogenesis Program, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle Washington 98103
- Department of Medicine, University of Washington, Seattle, Washington 98103
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Takehisa J, Kraus MH, Ayouba A, Bailes E, Van Heuverswyn F, Decker JM, Li Y, Rudicell RS, Learn GH, Neel C, Ngole EM, Shaw GM, Peeters M, Sharp PM, Hahn BH. Origin and biology of simian immunodeficiency virus in wild-living western gorillas. J Virol 2009; 83:1635-48. [PMID: 19073717 PMCID: PMC2643789 DOI: 10.1128/jvi.02311-08] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 12/02/2008] [Indexed: 01/17/2023] Open
Abstract
Western lowland gorillas (Gorilla gorilla gorilla) are infected with a simian immunodeficiency virus (SIVgor) that is closely related to chimpanzee and human immunodeficiency viruses (SIVcpz and HIV-1, respectively) in west central Africa. Although existing data suggest a chimpanzee origin for SIVgor, a paucity of available sequences has precluded definitive conclusions. Here, we report the molecular characterization of one partial (BQ664) and three full-length (CP684, CP2135, and CP2139) SIVgor genomes amplified from fecal RNAs of wild-living gorillas at two field sites in Cameroon. Phylogenetic analyses showed that all SIVgor strains clustered together, forming a monophyletic lineage throughout their genomes. Interestingly, the closest relatives of SIVgor were not SIVcpzPtt strains from west central African chimpanzees (Pan troglodytes troglodytes) but human viruses belonging to HIV-1 group O. In trees derived from most genomic regions, SIVgor and HIV-1 group O formed a sister clade to the SIVcpzPtt lineage. However, in a tree derived from 5' pol sequences ( approximately 900 bp), SIVgor and HIV-1 group O fell within the SIVcpzPtt radiation. The latter was due to two SIVcpzPtt strains that contained mosaic pol sequences, pointing to the existence of a divergent SIVcpzPtt lineage that gave rise to SIVgor and HIV-1 group O. Gorillas appear to have acquired this lineage at least 100 to 200 years ago. To examine the biological properties of SIVgor, we synthesized a full-length provirus from fecal consensus sequences. Transfection of the resulting clone (CP2139.287) into 293T cells yielded infectious virus that replicated efficiently in both human and chimpanzee CD4(+) T cells and used CCR5 as the coreceptor for viral entry. Together, these results provide strong evidence that P. t. troglodytes apes were the source of SIVgor. These same apes may also have spawned the group O epidemic; however, the possibility that gorillas served as an intermediary host cannot be excluded.
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Affiliation(s)
- Jun Takehisa
- Department of Medicine, University of Alabama at Birmingham, AL 35294, USA
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