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Tebit DM, Nickel G, Gibson R, Rodriguez M, Hathaway NJ, Bain K, Reyes-Rodriguez AL, Ondoa P, Heeney JL, Li Y, Bongorno J, Canaday D, McDonald D, Bailey JA, Arts EJ. Replicative fitness and pathogenicity of primate lentiviruses in lymphoid tissue, primary human and chimpanzee cells: relation to possible jumps to humans. EBioMedicine 2024; 100:104965. [PMID: 38215691 PMCID: PMC10827413 DOI: 10.1016/j.ebiom.2023.104965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only originated from a primate lentivirus over 100 years ago. METHODS This study examined the replicative fitness, transmission, restriction, and cytopathogenicity of 22 primate lentiviruses in primary human lymphoid tissue and both primary human and chimpanzee peripheral blood mononuclear cells. FINDINGS Pairwise competitions revealed that SIV from chimpanzees (cpz) had the highest replicative fitness in human or chimpanzee peripheral blood mononuclear cells, even higher fitness than HIV-1 group M strains responsible for worldwide epidemic. The SIV strains belonging to the "HIV-2 lineage" (including SIVsmm, SIVmac, SIVagm) had the lowest replicative fitness. SIVcpz strains were less inhibited by human restriction factors than the "HIV-2 lineage" strains. SIVcpz efficiently replicated in human tonsillar tissue but did not deplete CD4+ T-cells, consistent with the slow or nonpathogenic disease observed in most chimpanzees. In contrast, HIV-1 isolates and SIV of the HIV-2 lineage were pathogenic to the human tonsillar tissue, almost independent of the level of virus replication. INTERPRETATION Of all primate lentiviruses, SIV from chimpanzees appears most capable of infecting and replicating in humans, establishing HIV-1. SIV from other Old World monkeys, e.g. the progenitor of HIV-2, replicate slowly in humans due in part to restriction factors. Nonetheless, many of these SIV strains were more pathogenic than SIVcpz. Either SIVcpz evolved into a more pathogenic virus while in humans or a rare SIVcpz, possibly extinct in chimpanzees, was pathogenic immediately following the jump into human. FUNDING Support for this study to E.J.A. was provided by the NIH/NIAID R01 AI49170 and CIHR project grant 385787. Infrastructure support was provided by the NIH CFAR AI36219 and Canadian CFI/Ontario ORF 36287. Efforts of J.A.B. and N.J.H. was provided by NIH AI099473 and for D.H.C., by VA and NIH AI AI080313.
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Affiliation(s)
- Denis M Tebit
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Global Biomed Scientific, LLC, P.O. Box 2368, Forest, VA, USA
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard Gibson
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Myriam Rodriguez
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nicolas J Hathaway
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Katie Bain
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Angel L Reyes-Rodriguez
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pascal Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia; Department of Global Health, Institute of Global Health and Development, University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yue Li
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Jennifer Bongorno
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - David Canaday
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David McDonald
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Eric J Arts
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Microbiology and Immunology, Western University, Ontario, Canada.
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Barr KA, Rhodes KL, Gilad Y. The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees. Genome Biol 2023; 24:207. [PMID: 37697401 PMCID: PMC10496171 DOI: 10.1186/s13059-023-03019-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/21/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees. RESULTS We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes. CONCLUSIONS Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.
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Affiliation(s)
- Kenneth A Barr
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | | | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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3
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Ahuja SK, Manoharan MS, Lee GC, McKinnon LR, Meunier JA, Steri M, Harper N, Fiorillo E, Smith AM, Restrepo MI, Branum AP, Bottomley MJ, Orrù V, Jimenez F, Carrillo A, Pandranki L, Winter CA, Winter LA, Gaitan AA, Moreira AG, Walter EA, Silvestri G, King CL, Zheng YT, Zheng HY, Kimani J, Blake Ball T, Plummer FA, Fowke KR, Harden PN, Wood KJ, Ferris MT, Lund JM, Heise MT, Garrett N, Canady KR, Abdool Karim SS, Little SJ, Gianella S, Smith DM, Letendre S, Richman DD, Cucca F, Trinh H, Sanchez-Reilly S, Hecht JM, Cadena Zuluaga JA, Anzueto A, Pugh JA, Agan BK, Root-Bernstein R, Clark RA, Okulicz JF, He W. Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection. Nat Commun 2023; 14:3286. [PMID: 37311745 PMCID: PMC10264401 DOI: 10.1038/s41467-023-38238-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/17/2023] [Indexed: 06/15/2023] Open
Abstract
Some people remain healthier throughout life than others but the underlying reasons are poorly understood. Here we hypothesize this advantage is attributable in part to optimal immune resilience (IR), defined as the capacity to preserve and/or rapidly restore immune functions that promote disease resistance (immunocompetence) and control inflammation in infectious diseases as well as other causes of inflammatory stress. We gauge IR levels with two distinct peripheral blood metrics that quantify the balance between (i) CD8+ and CD4+ T-cell levels and (ii) gene expression signatures tracking longevity-associated immunocompetence and mortality-associated inflammation. Profiles of IR metrics in ~48,500 individuals collectively indicate that some persons resist degradation of IR both during aging and when challenged with varied inflammatory stressors. With this resistance, preservation of optimal IR tracked (i) a lower risk of HIV acquisition, AIDS development, symptomatic influenza infection, and recurrent skin cancer; (ii) survival during COVID-19 and sepsis; and (iii) longevity. IR degradation is potentially reversible by decreasing inflammatory stress. Overall, we show that optimal IR is a trait observed across the age spectrum, more common in females, and aligned with a specific immunocompetence-inflammation balance linked to favorable immunity-dependent health outcomes. IR metrics and mechanisms have utility both as biomarkers for measuring immune health and for improving health outcomes.
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Affiliation(s)
- Sunil K Ahuja
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA.
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA.
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Muthu Saravanan Manoharan
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Grace C Lee
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Pharmacotherapy Education and Research Center, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Lyle R McKinnon
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Justin A Meunier
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Nathan Harper
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Alisha M Smith
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Marcos I Restrepo
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anne P Branum
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Matthew J Bottomley
- Transplantation Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
- Oxford Kidney Unit, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Fabio Jimenez
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Andrew Carrillo
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Lavanya Pandranki
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Caitlyn A Winter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Lauryn A Winter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Alvaro A Gaitan
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Alvaro G Moreira
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Elizabeth A Walter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Guido Silvestri
- Department of Pathology, Emory University School of Medicine & Emory National Primate Research Center, Atlanta, GA, 30322, USA
| | - Christopher L King
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- National Resource Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
| | - Hong-Yi Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- National Resource Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
| | - Joshua Kimani
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - T Blake Ball
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Keith R Fowke
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Paul N Harden
- Oxford Kidney Unit, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Kathryn J Wood
- Transplantation Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jennifer M Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Kristen R Canady
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Susan J Little
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sara Gianella
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Davey M Smith
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, 92161, USA
| | - Scott Letendre
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
| | - Douglas D Richman
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, 07100, Italy
| | - Hanh Trinh
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Sandra Sanchez-Reilly
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Joan M Hecht
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Jose A Cadena Zuluaga
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Antonio Anzueto
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jacqueline A Pugh
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Brian K Agan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | | | - Robert A Clark
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Jason F Okulicz
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Department of Medicine, Infectious Diseases Service, Brooke Army Medical Center, San Antonio, TX, 78234, USA
| | - Weijing He
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
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Jasinska AJ, Apetrei C, Pandrea I. Walk on the wild side: SIV infection in African non-human primate hosts-from the field to the laboratory. Front Immunol 2023; 13:1060985. [PMID: 36713371 PMCID: PMC9878298 DOI: 10.3389/fimmu.2022.1060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
HIV emerged following cross-species transmissions of simian immunodeficiency viruses (SIVs) that naturally infect non-human primates (NHPs) from Africa. While HIV replication and CD4+ T-cell depletion lead to increased gut permeability, microbial translocation, chronic immune activation, and systemic inflammation, the natural hosts of SIVs generally avoid these deleterious consequences when infected with their species-specific SIVs and do not progress to AIDS despite persistent lifelong high viremia due to long-term coevolution with their SIV pathogens. The benign course of natural SIV infection in the natural hosts is in stark contrast to the experimental SIV infection of Asian macaques, which progresses to simian AIDS. The mechanisms of non-pathogenic SIV infections are studied mainly in African green monkeys, sooty mangabeys, and mandrills, while progressing SIV infection is experimentally modeled in macaques: rhesus macaques, pigtailed macaques, and cynomolgus macaques. Here, we focus on the distinctive features of SIV infection in natural hosts, particularly (1): the superior healing properties of the intestinal mucosa, which enable them to maintain the integrity of the gut barrier and prevent microbial translocation, thus avoiding excessive/pathologic immune activation and inflammation usually perpetrated by the leaking of the microbial products into the circulation; (2) the gut microbiome, the disruption of which is an important factor in some inflammatory diseases, yet not completely understood in the course of lentiviral infection; (3) cell population shifts resulting in target cell restriction (downregulation of CD4 or CCR5 surface molecules that bind to SIV), control of viral replication in the lymph nodes (expansion of natural killer cells), and anti-inflammatory effects in the gut (NKG2a/c+ CD8+ T cells); and (4) the genes and biological pathways that can shape genetic adaptations to viral pathogens and are associated with the non-pathogenic outcome of the natural SIV infection. Deciphering the protective mechanisms against SIV disease progression to immunodeficiency, which have been established through long-term coevolution between the natural hosts and their species-specific SIVs, may prompt the development of novel therapeutic interventions, such as drugs that can control gut inflammation, enhance gut healing capacities, or modulate the gut microbiome. These developments can go beyond HIV infection and open up large avenues for correcting gut damage, which is common in many diseases.
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Affiliation(s)
- Anna J. Jasinska
- Division of Infectious Diseases, Department of Medicine (DOM), School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine (DOM), School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ivona Pandrea
- Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States,Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,*Correspondence: Ivona Pandrea,
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5
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Pawar H, Ostridge HJ, Schmidt JM, Andrés AM. Genetic adaptations to SIV across chimpanzee populations. PLoS Genet 2022; 18:e1010337. [PMID: 36007015 PMCID: PMC9467346 DOI: 10.1371/journal.pgen.1010337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 09/12/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
Central and eastern chimpanzees are infected with Simian Immunodeficiency Virus (SIV) in the wild, typically without developing acute immunodeficiency. Yet the recent zoonotic transmission of chimpanzee SIV to humans, which were naïve to the virus, gave rise to the Human Immunodeficiency Virus (HIV), which causes AIDS and is responsible for one of the deadliest pandemics in human history. Chimpanzees have likely been infected with SIV for tens of thousands of years and have likely evolved to reduce its pathogenicity, becoming semi-natural hosts that largely tolerate the virus. In support of this view, central and eastern chimpanzees show evidence of positive selection in genes involved in SIV/HIV cell entry and immune response to SIV, respectively. We hypothesise that the population first infected by SIV would have experienced the strongest selective pressure to control the lethal potential of zoonotic SIV, and that population genetics will reveal those first critical adaptations. With that aim we used population genetics to investigate signatures of positive selection in the common ancestor of central-eastern chimpanzees. The genes with signatures of positive selection in the ancestral population are significantly enriched in SIV-related genes, especially those involved in the immune response to SIV and those encoding for host genes that physically interact with SIV/HIV (VIPs). This supports a scenario where SIV first infected the central-eastern ancestor and where this population was under strong pressure to adapt to zoonotic SIV. Interestingly, integrating these genes with candidates of positive selection in the two infected subspecies reveals novel patterns of adaptation to SIV. Specifically, we observe evidence of positive selection in numerous steps of the biological pathway responsible for T-helper cell differentiation, including CD4 and multiple genes that SIV/HIV use to infect and control host cells. This pathway is active only in CD4+ cells which SIV/HIV infects, and it plays a crucial role in shaping the immune response so it can efficiently control the virus. Our results confirm the importance of SIV as a selective factor, identify specific genetic changes that may have allowed our closest living relatives to reduce SIV’s pathogenicity, and demonstrate the potential of population genomics to reveal the evolutionary mechanisms used by naïve hosts to reduce the pathogenicity of zoonotic pathogens. Chimpanzees are at the origin of HIV-1, a virus that generates an incurable disease and that generated a pandemic that has claimed 35 million lives. Chimpanzees have evolved to control the pathogenicity of the virus, which does not typically develop into AIDS in the same way as in humans. Identifying the genetic adaptations responsible for this process provides critical knowledge about SIV and HIV. Our analysis of chimpanzee genetic adaptations identified specific genes and molecular pathways involved in adaptation to SIV, providing important insights into the mechanisms that likely allowed our closest living relatives to control SIV/HIV. Further, we establish SIV as a strong and recurrent selective pressure in central and eastern chimpanzees, two important subspecies of large mammals that are currently endangered.
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Affiliation(s)
- Harvinder Pawar
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Harrison J. Ostridge
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Joshua M. Schmidt
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- * E-mail: (JMS); (AMA)
| | - Aida M. Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail: (JMS); (AMA)
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The HLA A03 Supertype and Several Pan Species Major Histocompatibility Complex Class I A Allotypes Share a Preference for Binding Positively Charged Residues in the F Pocket: Implications for Controlling Retroviral Infections. J Virol 2020; 94:JVI.01960-19. [PMID: 32075930 DOI: 10.1128/jvi.01960-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
The major histocompatibility complex (MHC) class I region of humans, chimpanzees (Pan troglodytes), and bonobos (Pan paniscus) is highly similar, and orthologues of HLA-A, -B, and -C are present in both Pan species. Based on functional characteristics, the different HLA-A allotypes are classified into different supertypes. One of them, the HLA A03 supertype, is widely distributed among different human populations. All contemporary known chimpanzee and bonobo MHC class I A allotypes cluster genetically into one of the six HLA-A families, the HLA-A1/A3/A11/A30 family. We report here that the peptide-binding motif of the Patr-A*05:01 allotype, which is commonly present in a cohort of western African chimpanzees, has a strong preference for binding peptides with basic amino acids at the carboxyl terminus. This phenomenon is shared with the family members of the HLA A03 supertype. Based on the chemical similarities in the peptide-binding pocket, we inferred that the preference for binding peptides with basic amino acids at the carboxyl terminus is widely present among the human, chimpanzee, and bonobo MHC-A allotypes. Subsequent in silico peptide-binding predictions illustrated that these allotypes have the capacity to target conserved parts of the proteome of human immunodeficiency virus type 1 (HIV-1) and the simian immunodeficiency virus SIVcpz.IMPORTANCE Most experimentally infected chimpanzees seem to control an HIV-1 infection and are therefore considered to be relatively resistant to developing AIDS. Contemporary free-ranging chimpanzees may carry SIVcpz, and there is evidence for AIDS-like symptoms in these free-ranging animals, whereas SIV infections in bonobos appear to be absent. In humans, the natural control of an HIV-1 infection is strongly associated with the presence of particular HLA class I allotypes. The ancestor of the contemporary living chimpanzees and bonobos survived a selective sweep targeting the MHC class I repertoire. We have put forward a hypothesis that this may have been caused by an ancestral retroviral infection similar to SIVcpz. Characterization of the relevant MHC allotypes may contribute to understanding the shaping of their immune repertoire. The abundant presence of MHC-A allotypes that prefer peptides with basic amino acids at the C termini suggests that these molecules may contribute to the control of retroviral infections in humans, chimpanzees, and bonobos.
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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] [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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Veazey RS, Lackner AA. Nonhuman Primate Models and Understanding the Pathogenesis of HIV Infection and AIDS. ILAR J 2018; 58:160-171. [PMID: 29228218 DOI: 10.1093/ilar/ilx032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/04/2017] [Indexed: 12/16/2022] Open
Abstract
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals. Research in NHP has led to "dogma changing" discoveries in immunology, infectious disease, and even our own genetics. We now know that many of our genes are retroviral remnants, or developed in response to archaic HIV-like retroviral infections. Early studies involving blood from HIV patients and in experiments in cultured tissues contributed to confusion regarding the cause of AIDS and impeded progress in the development of effective interventions. Research on the many retroviruses of different NHP species have broadened our understanding of human immunology and perhaps even our origins and evolution as a species. In combination with recent advances in molecular biology and computational analytics, research in NHPs has unique potential for discoveries that will directly lead to new cures for old human and animal diseases, including HIV/AIDS.
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Affiliation(s)
- Ronald S Veazey
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine.,Department of Pathology and Laboratory Medicine, Tulane University School of Medicine
| | - Andrew A Lackner
- Tulane National Primate Research Center, Tulane University School of Medicine.,Department of Microbiology and Pathology and Laboratory Medicine, Tulane University School of Medicine
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9
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Abstract
Pandemic HIV-1, a human lentivirus, is the result of zoonotic transmission of SIV from chimpanzees (SIVcpz). How SIVcpz established spread in humans after spillover is an outstanding question. Lentiviral cross-species transmissions are exceptionally rare events. Nevertheless, the chimpanzee and the gorilla were part of the transmission chains that resulted in sustained infections that evolved into HIV-1. Although many restriction factors can repress the early stages of lentiviral replication, others target replication during the late phases. In some cases, viruses incorporate host proteins that interfere with subsequent rounds of replication. Though limited and small, HIVs and SIVs, including SIVcpz can use their genome products to modulate and escape some of these barriers and thus establish a chronic infection.
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Affiliation(s)
- Augustin Penda Twizerimana
- Clinic for Gastroenterology, Hepatology & Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Rachel Scheck
- Clinic for Gastroenterology, Hepatology & Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology & Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology & Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
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Experimental Adaptive Evolution of Simian Immunodeficiency Virus SIVcpz to Pandemic Human Immunodeficiency Virus Type 1 by Using a Humanized Mouse Model. J Virol 2018; 92:JVI.01905-17. [PMID: 29212937 DOI: 10.1128/jvi.01905-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/28/2017] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1), the causative agent of AIDS, originated from simian immunodeficiency virus from chimpanzees (SIVcpz), the precursor of the human virus, approximately 100 years ago. This indicates that HIV-1 has emerged through the cross-species transmission of SIVcpz from chimpanzees to humans. However, it remains unclear how SIVcpz has evolved into pandemic HIV-1 in humans. To address this question, we inoculated three SIVcpz strains (MB897, EK505, and MT145), four pandemic HIV-1 strains (NL4-3, NLCSFV3, JRCSF, and AD8), and two nonpandemic HIV-1 strains (YBF30 and DJO0131). Humanized mice infected with SIVcpz strain MB897, a virus phylogenetically similar to pandemic HIV-1, exhibited a peak viral load comparable to that of mice infected with pandemic HIV-1, while peak viral loads of mice infected with SIVcpz strain EK505 or MT145 as well as nonpandemic HIV-1 strains were significantly lower. These results suggest that SIVcpz strain MB897 is preadapted to humans, unlike the other SIVcpz strains. Moreover, viral RNA sequencing of MB897-infected humanized mice identified a nonsynonymous mutation in env, a G413R substitution in gp120. The infectivity of the gp120 G413R mutant of MB897 was significantly higher than that of parental MB897. Furthermore, we demonstrated that the gp120 G413R mutant of MB897 augments the capacity for viral replication in both in vitro cell cultures and humanized mice. Taken together, this is the first experimental investigation to use an animal model to demonstrate a gain-of-function evolution of SIVcpz into pandemic HIV-1.IMPORTANCE From the mid-20th century, humans have been exposed to the menace of infectious viral diseases, such as severe acute respiratory syndrome coronavirus, Ebola virus, and Zika virus. These outbreaks of emerging/reemerging viruses can be triggered by cross-species viral transmission from wild animals to humans, or zoonoses. HIV-1, the causative agent of AIDS, emerged by the cross-species transmission of SIVcpz, the HIV-1 precursor in chimpanzees, around 100 years ago. However, the process by which SIVcpz evolved to become HIV-1 in humans remains unclear. Here, by using a hematopoietic stem cell-transplanted humanized-mouse model, we experimentally recapitulate the evolutionary process of SIVcpz to become HIV-1. We provide evidence suggesting that a strain of SIVcpz, MB897, preadapted to infect humans over other SIVcpz strains. We further demonstrate a gain-of-function evolution of SIVcpz in infected humanized mice. Our study reveals that pandemic HIV-1 has emerged through at least two steps: preadaptation and subsequent gain-of-function mutations.
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11
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [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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van Bolhuis H, Wolters M, de Boer M, Fijnheer R, van Zijll Langhout M, Niphuis H, Eckmann C. Thrombotic thrombocytopenic purpura related to ADAMTS13 deficiency, and successful treatment in a chimpanzee (Pan troglodytes verus). J Med Primatol 2017; 46:267-270. [PMID: 28547839 DOI: 10.1111/jmp.12278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 11/30/2022]
Abstract
A 27-year-old male chimpanzee (Pan troglodytes verus) developed signs of thrombotic thrombocytopenic purpura (TTP). ADAMTS13 deficiency appeared to be the cause of disease. After treatment with high-dose prednisone, haematological values and clinical signs recovered. This is the first description of spontaneous TTP associated with ADAMTS13 deficiency in a non-human primate.
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Affiliation(s)
| | - Marno Wolters
- AAP, Rescue Center for Exotic Animals, Almere, the Netherlands
| | - Mark de Boer
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Rob Fijnheer
- Department of Haematology, Meander Hospital Amersfoort, Amersfoort, the Netherlands
| | | | - Henk Niphuis
- Department of Virology, Biomedical Primate Research Center, Rijswijk, the Netherlands
| | - Carel Eckmann
- Department of Blood Coagulation, Sanquin Diagnostic Services, Amsterdam, the Netherlands
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13
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Kaulfuß M, Wensing I, Windmann S, Hrycak CP, Bayer W. Induction of complex immune responses and strong protection against retrovirus challenge by adenovirus-based immunization depends on the order of vaccine delivery. Retrovirology 2017; 14:8. [PMID: 28166802 PMCID: PMC5294899 DOI: 10.1186/s12977-017-0336-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/31/2017] [Indexed: 01/04/2023] Open
Abstract
Background In the Friend retrovirus mouse model we developed potent adenovirus-based vaccines that were designed to induce either strong Friend virus GagL85–93-specific CD8+ T cell or antibody responses, respectively. To optimize the immunization outcome we evaluated vaccination strategies using combinations of these vaccines. Results While the vaccines on their own confer strong protection from a subsequent Friend virus challenge, the simple combination of the vaccines for the establishment of an optimized immunization protocol did not result in a further improvement of vaccine effectivity. We demonstrate that the co-immunization with GagL85–93/leader-gag encoding vectors together with envelope-encoding vectors abrogates the induction of GagL85–93-specific CD8+ T cells, and in successive immunization protocols the immunization with the GagL85–93/leader-gag encoding vector had to precede the immunization with an envelope encoding vector for the efficient induction of GagL85–93-specific CD8+ T cells. Importantly, the antibody response to envelope was in fact enhanced when the mice were adenovirus-experienced from a prior immunization, highlighting the expedience of this approach. Conclusions To circumvent the immunosuppressive effect of envelope on immune responses to simultaneously or subsequently administered immunogens, we developed a two immunizations-based vaccination protocol that induces strong immune responses and confers robust protection of highly Friend virus-susceptible mice from a lethal Friend virus challenge. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0336-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meike Kaulfuß
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Ina Wensing
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Sonja Windmann
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Camilla Patrizia Hrycak
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Wibke Bayer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany.
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Abstract
PURPOSE OF REVIEW The purpose is to review recent insights into the impact of HIV-associated immune activation on AIDS and non-AIDS morbidity and mortality. RECENT FINDINGS Immune activation has long been recognized as an important consequence of untreated HIV infection and predictor of AIDS progression, which declines but fails to normalize during suppressive antiretroviral therapy, and continues to predict disease in this setting. Thus, a major research agenda is to develop novel therapies to reduce persistent immune activation in treated HIV infection. Yet, the optimal targets for interventions remain unclear. Both the specific root causes of immune activation and the many interconnected pathways of immune activation that are most likely to drive disease risk in HIV-infected individuals remain incompletely characterized, but recent studies have shed new light on these topics. SUMMARY In the context of this review, we will summarize recent evidence helping to elucidate the immunologic pathways that appear most strongly predictive of infectious and noninfectious morbidity. We will also highlight the likelihood that not all root drivers of immune activation - and the discrete immunologic pathways to which they give rise - are likely to produce the same disease manifestations and/or be equally attenuated by early antiretroviral therapy initiation.
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15
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Verstrepen BE, Nieuwenhuis IG, Mooij P, Verschoor EJ, Fagrouch ZC, Kondova I, Boonstra A, Koopman G. Role of microbial translocation in soluble CD14 up-regulation in HIV-, but not in HCV-, infected chimpanzees. J Gen Virol 2016; 97:2599-2607. [PMID: 27534537 DOI: 10.1099/jgv.0.000577] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
During human immunodeficiency virus (HIV) infection, soluble CD14 (sCD14) is up-regulated as a consequence of pathological disruption of the gut epithelial barrier, and subsequent increased microbial translocation. Also in hepatitis C virus (HCV)-infected patients with advanced liver fibrosis, increased levels of sCD14 have been reported. Since the liver plays an important role in clearance of translocated bacterial products, hepatic fibrosis may negatively affect clearance and thus contribute to higher sCD14 levels. Chimpanzees (Pan troglodytes) infected with HCV typically show no signs of liver fibrosis. Here, we have tested the hypothesis that increased levels of sCD14 occur in the absence of hepatic fibrosis or microbial translocation in chimpanzees chronically infected with HCV. sCD14 was up-regulated in both HIV/simian immunodeficiency virus (SIV)- and HCV-infected chimpanzees. In HIV/SIV-infected chimpanzees, intestinal fatty acid-binding protein, a marker for gut perturbation, lipopolysaccharide (LPS)-binding-protein and LPS core antibodies, confirm that sCD14 up-regulation was caused by increased microbial translocation. In HCV-infected chimpanzees, no evidence was found for increased microbial translocation despite up-regulation of sCD14. Additionally, the impact of liver fibrosis on microbial translocation was addressed by direct comparison of chimpanzees with a high HCV load and human patients with advanced fibrosis. These data suggest that only in a small minority of HCV patients, hepatic fibrosis corroborates microbial translocation.
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Affiliation(s)
- Babs E Verstrepen
- Department of Virology, Biomedical Primate Research Centre, 2280 GH Rijswijk, The Netherlands
| | - Ivonne G Nieuwenhuis
- Department of Virology, Biomedical Primate Research Centre, 2280 GH Rijswijk, The Netherlands
| | - Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, 2280 GH Rijswijk, The Netherlands
| | - Ernst J Verschoor
- Department of Virology, Biomedical Primate Research Centre, 2280 GH Rijswijk, The Netherlands
| | - Zahra C Fagrouch
- Department of Virology, Biomedical Primate Research Centre, 2280 GH Rijswijk, The Netherlands
| | - Ivanela Kondova
- Division of Pathology and Microbiology, Biomedical Primate Research Centre, 2280 GH Rijswijk, The Netherlands
| | - André Boonstra
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, 3015 CE Rotterdam, The Netherlands
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, 2280 GH Rijswijk, The Netherlands
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