1
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Nemphos SM, Green HC, Prusak JE, Fell SL, Goff K, Varnado M, Didier K, Guy N, Moström MJ, Tatum C, Massey C, Barnes MB, Rowe LA, Allers C, Blair RV, Embers ME, Maness NJ, Marx PA, Grasperge B, Kaur A, De Paris K, Shaffer JG, Hensley-McBain T, Londono-Renteria B, Manuzak JA. Elevated Inflammation Associated with Markers of Neutrophil Function and Gastrointestinal Disruption in Pilot Study of Plasmodium fragile Co-Infection of ART-Treated SIVmac239+ Rhesus Macaques. Viruses 2024; 16:1036. [PMID: 39066199 PMCID: PMC11281461 DOI: 10.3390/v16071036] [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: 05/16/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Human immunodeficiency virus (HIV) and malaria, caused by infection with Plasmodium spp., are endemic in similar geographical locations. As a result, there is high potential for HIV/Plasmodium co-infection, which increases the pathology of both diseases. However, the immunological mechanisms underlying the exacerbated disease pathology observed in co-infected individuals are poorly understood. Moreover, there is limited data available on the impact of Plasmodium co-infection on antiretroviral (ART)-treated HIV infection. Here, we used the rhesus macaque (RM) model to conduct a pilot study to establish a model of Plasmodium fragile co-infection during ART-treated simian immunodeficiency virus (SIV) infection, and to begin to characterize the immunopathogenic effect of co-infection in the context of ART. We observed that P. fragile co-infection resulted in parasitemia and anemia, as well as persistently detectable viral loads (VLs) and decreased absolute CD4+ T-cell counts despite daily ART treatment. Notably, P. fragile co-infection was associated with increased levels of inflammatory cytokines, including monocyte chemoattractant protein 1 (MCP-1). P. fragile co-infection was also associated with increased levels of neutrophil elastase, a plasma marker of neutrophil extracellular trap (NET) formation, but significant decreases in markers of neutrophil degranulation, potentially indicating a shift in the neutrophil functionality during co-infection. Finally, we characterized the levels of plasma markers of gastrointestinal (GI) barrier permeability and microbial translocation and observed significant correlations between indicators of GI dysfunction, clinical markers of SIV and Plasmodium infection, and neutrophil frequency and function. Taken together, these pilot data verify the utility of using the RM model to examine ART-treated SIV/P. fragile co-infection, and indicate that neutrophil-driven inflammation and GI dysfunction may underlie heightened SIV/P. fragile co-infection pathogenesis.
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Affiliation(s)
- Sydney M. Nemphos
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Hannah C. Green
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - James E. Prusak
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Sallie L. Fell
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Kelly Goff
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Megan Varnado
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Kaitlin Didier
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Natalie Guy
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Matilda J. Moström
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Coty Tatum
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Chad Massey
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Mary B. Barnes
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Lori A. Rowe
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Carolina Allers
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Robert V. Blair
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Monica E. Embers
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Nicholas J. Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Preston A. Marx
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA
- Department of Tropical Medicine and Infectious Disease, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA;
| | - Brooke Grasperge
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Amitinder Kaur
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Kristina De Paris
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27559, USA
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | | | - Berlin Londono-Renteria
- Department of Tropical Medicine and Infectious Disease, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA;
| | - Jennifer A. Manuzak
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Department of Tropical Medicine and Infectious Disease, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA;
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2
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Khanal S, Fennessey CM, O'Brien SP, Thorpe A, Reid C, Immonen TT, Smith R, Bess JW, Swanstrom AE, Del Prete GQ, Davenport MP, Okoye AA, Picker LJ, Lifson JD, Keele BF. In Vivo Validation of the Viral Barcoding of Simian Immunodeficiency Virus SIVmac239 and the Development of New Barcoded SIV and Subtype B and C Simian-Human Immunodeficiency Viruses. J Virol 2019; 94:e01420-19. [PMID: 31597757 PMCID: PMC6912102 DOI: 10.1128/jvi.01420-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/30/2019] [Indexed: 12/21/2022] Open
Abstract
Genetically barcoded viral populations are powerful tools for evaluating the overall viral population structure as well as assessing the dynamics and evolution of individual lineages in vivo over time. Barcoded viruses are generated by inserting a small, genetically unique tag into the viral genome, which is retained in progeny virus. We recently reported barcoding the well-characterized molecular clone simian immunodeficiency virus (SIV) SIVmac239, resulting in a synthetic swarm (SIVmac239M) containing approximately 10,000 distinct viral clonotypes for which all genetic differences were within a 34-base barcode that could be tracked using next-generation deep sequencing. Here, we assessed the population size, distribution, and authenticity of individual viral clonotypes within this synthetic swarm using samples from 120 rhesus macaques infected intravenously. The number of replicating barcodes in plasma correlated with the infectious inoculum dose, and the primary viral growth rate was similar in all infected animals regardless of the inoculum size. Overall, 97% of detectable clonotypes in the viral stock were identified in the plasma of at least one infected animal. Additionally, we prepared a second-generation barcoded SIVmac239 stock (SIVmac239M2) with over 16 times the number of barcoded variants of the original stock and an additional barcoded stock with suboptimal nucleotides corrected (SIVmac239Opt5M). We also generated four barcoded stocks from subtype B and C simian-human immunodeficiency virus (SHIV) clones. These new SHIV clones may be particularly valuable models to evaluate Env-targeting approaches to study viral transmission or viral reservoir clearance. Overall, this work further establishes the reliability of the barcoded virus approach and highlights the feasibility of adapting this technique to other viral clones.IMPORTANCE We recently developed and published a description of a barcoded simian immunodeficiency virus that has a short random sequence inserted directly into the viral genome. This allows for the tracking of individual viral lineages with high fidelity and ultradeep sensitivity. This virus was used to infect 120 rhesus macaques, and we report here the analysis of the barcodes of these animals during primary infection. We found that the vast majority of barcodes were functional in vivo We then expanded the barcoding approach in a second-generation SIVmac239 stock (SIVmac239M2) with over 16 times the number of barcoded variants of the original stock and a barcoded stock of SIVmac239Opt5M whose sequence had 5 changes from the wild-type SIVmac239 sequence. We also generated 4 barcoded stocks from subtype B and C SHIV clones each containing a human immunodeficiency virus (HIV) type 1 envelope. These virus models are functional and can be useful for studying viral transmission and HIV cure/reservoir research.
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Affiliation(s)
- Sirish Khanal
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Sean P O'Brien
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Abigail Thorpe
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Carolyn Reid
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Taina T Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Rodman Smith
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Julian W Bess
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Adrienne E Swanstrom
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Miles P Davenport
- Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia
| | - Afam A Okoye
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Louis J Picker
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, USA
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3
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Iwamoto N, Mason RD, Song K, Gorman J, Welles HC, Arthos J, Cicala C, Min S, King HAD, Belli AJ, Reimann KA, Foulds KE, Kwong PD, Lifson JD, Keele BF, Roederer M. Blocking α 4β 7 integrin binding to SIV does not improve virologic control. Science 2019; 365:1033-1036. [PMID: 31488690 PMCID: PMC9513815 DOI: 10.1126/science.aaw7765] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/26/2019] [Indexed: 07/31/2023]
Abstract
A study in nonhuman primates reported that infusions of an antibody against α4β7 integrin, in combination with antiretroviral therapy, showed consistent, durable control of simian immunodeficiency virus (SIV) in rhesus macaques. The antibody used has pleiotropic effects, so we set out to gain insight into the underlying mechanism by comparing this treatment to treatment with non-neutralizing monoclonal antibodies against the SIV envelope glycoprotein that only block α4β7 binding to SIV Env but have no other host-directed effects. Similar to the initial study, we used an attenuated strain of SIV containing a stop codon in nef. The study used 30 macaques that all began antiretroviral therapy and then were divided into five groups to receive different antibody treatments. Unlike the published report, we found no sustained virologic control by these treatments in vivo.
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Affiliation(s)
- Nami Iwamoto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kaimei Song
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hugh C Welles
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - James Arthos
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Susie Min
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Hannah A D King
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Aaron J Belli
- MassBiologics, University of Massachusetts Medical School, Boston, MA, USA
| | - Keith A Reimann
- MassBiologics, University of Massachusetts Medical School, Boston, MA, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
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4
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Zhou M, Humbert M, Mukhtar MM, Scinto HB, Vyas HK, Lakhashe SK, Byrareddy SN, Maurer G, Thorat S, Owuor J, Lai Z, Chen Y, Griffiths A, Chenine AL, Gumber S, Villinger F, Montefiori D, Ruprecht RM. Adaptation of an R5 Simian-Human Immunodeficiency Virus Encoding an HIV Clade A Envelope with or without Ablation of Adaptive Host Immunity: Differential Selection of Viral Mutants. J Virol 2019; 93:e02267-18. [PMID: 30760566 PMCID: PMC6475780 DOI: 10.1128/jvi.02267-18] [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: 12/19/2018] [Accepted: 02/05/2019] [Indexed: 11/20/2022] Open
Abstract
Simian-human immunodeficiency virus (SHIV) infection in rhesus macaques (RMs) resembles human immunodeficiency virus type 1 (HIV-1) infection in humans and serves as a tool to evaluate candidate AIDS vaccines. HIV-1 clade A (HIV-A) predominates in parts of Africa. We constructed an R5 clade A SHIV (SHIV-A; strain SHIV-KNH1144) carrying env from a Kenyan HIV-A. SHIV-A underwent rapid serial passage through six RMs. To allow unbridled replication without adaptive immunity, we simultaneously ablated CD8+ and B cells with cytotoxic monoclonal antibodies in the next RM, resulting in extremely high viremia and CD4+ T-cell loss. Infected blood was then transferred into two non-immune-depleted RMs, where progeny SHIV-A showed increased replicative capacity and caused AIDS. We reisolated SHIV-KNH1144p4, which was replication competent in peripheral blood mononuclear cells (PBMC) of all RMs tested. Next-generation sequencing of early- and late-passage SHIV-A strains identified mutations that arose due to "fitness" virus optimization in the former and mutations exhibiting signatures typical for adaptive host immunity in the latter. "Fitness" mutations are best described as mutations that allow for better fit of the HIV-A Env with SIV-derived virion building blocks or host proteins and mutations in noncoding regions that accelerate virus replication, all of which result in the outgrowth of virus variants in the absence of adaptive T-cell and antibody-mediated host immunity.IMPORTANCE In this study, we constructed a simian-human immunodeficiency virus carrying an R5 Kenyan HIV-1 clade A env (SHIV-A). To bypass host immunity, SHIV-A was rapidly passaged in naive macaques or animals depleted of both CD8+ and B cells. Next-generation sequencing identified different mutations that resulted from optimization of viral replicative fitness either in the absence of adaptive immunity or due to pressure from adaptive immune responses.
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Affiliation(s)
- Mingkui Zhou
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Humbert
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Muhammad M Mukhtar
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanna B Scinto
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Hemant K Vyas
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Samir K Lakhashe
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Siddappa N Byrareddy
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregor Maurer
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- VetCore, Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Swati Thorat
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua Owuor
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | - Agnès-Laurence Chenine
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Henry M. Jackson Foundation, Bethesda, Maryland, USA
- Military HIV Research Program, Silver Spring, Maryland, USA
| | - Sanjeev Gumber
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - François Villinger
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ruth M Ruprecht
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Southwest National Primate Research Center, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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5
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Lopker MJ, Del Prete GQ, Estes JD, Li H, Reid C, Newman L, Lipkey L, Camus C, Easlick JL, Wang S, Decker JM, Bar KJ, Learn G, Pal R, Weiss DE, Hahn BH, Lifson JD, Shaw GM, Keele BF. Derivation and Characterization of Pathogenic Transmitted/Founder Molecular Clones from Simian Immunodeficiency Virus SIVsmE660 and SIVmac251 following Mucosal Infection. J Virol 2016; 90:8435-53. [PMID: 27412591 PMCID: PMC5021393 DOI: 10.1128/jvi.00718-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/06/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Currently available simian immunodeficiency virus (SIV) infectious molecular clones (IMCs) and isolates used in nonhuman primate (NHP) models of AIDS were originally derived from infected macaques during chronic infection or end stage disease and may not authentically recapitulate features of transmitted/founder (T/F) genomes that are of particular interest in transmission, pathogenesis, prevention, and treatment studies. We therefore generated and characterized T/F IMCs from genetically and biologically heterogeneous challenge stocks of SIVmac251 and SIVsmE660. Single-genome amplification (SGA) was used to identify full-length T/F genomes present in plasma during acute infection resulting from atraumatic rectal inoculation of Indian rhesus macaques with low doses of SIVmac251 or SIVsmE660. All 8 T/F clones yielded viruses that were infectious and replication competent in vitro, with replication kinetics similar to those of the widely used chronic-infection-derived IMCs SIVmac239 and SIVsmE543. Phenotypically, the new T/F virus strains exhibited a range of neutralization sensitivity profiles. Four T/F virus strains were inoculated into rhesus macaques, and each exhibited typical SIV replication kinetics. The SIVsm T/F viruses were sensitive to TRIM5α restriction. All T/F viruses were pathogenic in rhesus macaques, resulting in progressive CD4(+) T cell loss in gastrointestinal tissues, peripheral blood, and lymphatic tissues. The animals developed pathological immune activation; lymphoid tissue damage, including fibrosis; and clinically significant immunodeficiency leading to AIDS-defining clinical endpoints. These T/F clones represent a new molecular platform for the analysis of virus transmission and immunopathogenesis and for the generation of novel "bar-coded" challenge viruses and next-generation simian-human immunodeficiency viruses that may advance the HIV/AIDS vaccine agenda. IMPORTANCE Nonhuman primate research has relied on only a few infectious molecular clones for a myriad of diverse research projects, including pathogenesis, preclinical vaccine evaluations, transmission, and host-versus-pathogen interactions. With new data suggesting a selected phenotype of the virus that causes infection (i.e., the transmitted/founder virus), we sought to generate and characterize infectious molecular clones from two widely used simian immunodeficiency virus lineages (SIVmac251 and SIVsmE660). Although the exact requirements necessary to be a T/F virus are not yet fully understood, we generated cloned viruses with all the necessary characteristic of a successful T/F virus. The cloned viruses revealed typical acute and set point viral-load dynamics with pathological immune activation, lymphoid tissue damage progressing to significant immunodeficiency, and AIDS-defining clinical endpoints in some animals. These T/F clones represent a new molecular platform for studies requiring authentic T/F viruses.
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Affiliation(s)
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jacob D Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carolyn Reid
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Laura Newman
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Celine Camus
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Shuyi Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie M Decker
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Katharine J Bar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gerald Learn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ranajit Pal
- Advanced BioScience Laboratories, Inc., Rockville, Maryland, USA
| | | | - Beatrice H Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
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6
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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: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [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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Berkhout B, Das AT. On the primer binding site mutation that appears and disappears during HIV and SIV replication. Retrovirology 2015; 12:75. [PMID: 26303815 PMCID: PMC4549124 DOI: 10.1186/s12977-015-0201-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022] Open
Abstract
A recent study by Fennessey et al. (Retrovirology 12:49, 2015) described the optimization of a popular SIV clone by removal of four suboptimal point mutations. One of these mutations is present in a non-coding part of the viral genome and is probed in that study in more detail because of some fascinating properties. This primer binding site (PBS) mutation reverts rapidly to the wild-type sequence, which the authors interpret as indicating that this mutation exerts a profound fitness impact. The authors proposed the involvement of a cellular DNA repair mechanism in the reversion. Furthermore, it was suggested that premature termination of reverse transcription can explain why some of the viral progeny still contained the mutant sequence. However, we argue that all these special properties are a direct consequence of the unique nature of the viral PBS motif. The PBS binds the tRNA primer for reverse transcription and the viral progeny inherits either the sequence of the cellular tRNA or the PBS sequence of the viral RNA genome. The presence of a variant tRNA species explains the rapid appearance and disappearance of a variant PBS sequence.
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Affiliation(s)
- Ben Berkhout
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| | - Atze T Das
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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