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Thomas J, Mughal F, Roper KJ, Kotsiri A, Albalawi W, Alshehri A, Reddy YBS, Mukherjee S, Pollakis G, Paxton WA, Hoptroff M. Development of a pseudo-typed virus particle based method to determine the efficacy of virucidal agents. Sci Rep 2024; 14:2174. [PMID: 38273020 PMCID: PMC10810821 DOI: 10.1038/s41598-024-52177-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
The ongoing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has highlighted the threat that viral outbreaks pose to global health. A key tool in the arsenal to prevent and control viral disease outbreaks is disinfection of equipment and surfaces with formulations that contain virucidal agents (VA). However, assessment of the efficacy of virus inactivation often requires live virus assays or surrogate viruses such as Modified Vaccinia Virus Ankara (MVA), which can be expensive, time consuming and technically challenging. Therefore, we have developed a pseudo-typed virus (PV) based approach to assess the inactivation of enveloped viruses with a fast and quantitative output that can be adapted to emerging viruses. Additionally, we have developed a method to completely remove the cytotoxicity of virucidal agents while retaining the required sensitivity to measure PV infectivity. Our results indicated that the removal of cytotoxicity was an essential step to accurately measure virus inactivation. Further, we demonstrated that there was no difference in susceptibility to virus inactivation between PVs that express the envelopes of HIV-1, SARS-CoV-2, and Influenza A/Indonesia. Therefore, we have developed an effective and safe alternative to live virus assays that enables the rapid assessment of virucidal activity for the development and optimization of virucidal reagents.
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK.
| | - Farah Mughal
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Kelly J Roper
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Aurelia Kotsiri
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Wejdan Albalawi
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Abdullateef Alshehri
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Yugandhar B S Reddy
- Unilever Research & Development Centre, 64 Main Road, Whitefield, Bangalore, Karnataka, 560066, India
| | - Sayandip Mukherjee
- Unilever Research & Development Centre, 64 Main Road, Whitefield, Bangalore, Karnataka, 560066, India
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK.
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK.
| | - Michael Hoptroff
- Unilever Research & Development, Port Sunlight, Bebington, Wirral, CH63 3JW, UK.
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Roper KJ, Thomas J, Albalawi W, Maddocks E, Dobson S, Alshehri A, Barone FG, Baltazar M, Semple MG, Ho A, Turtle L, Paxton WA, Pollakis G. Quantifying neutralising antibody responses against SARS-CoV-2 in dried blood spots (DBS) and paired sera. Sci Rep 2023; 13:15014. [PMID: 37697014 PMCID: PMC10495436 DOI: 10.1038/s41598-023-41928-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
The ongoing SARS-CoV-2 pandemic was initially managed by non-pharmaceutical interventions such as diagnostic testing, isolation of positive cases, physical distancing and lockdowns. The advent of vaccines has provided crucial protection against SARS-CoV-2. Neutralising antibody (nAb) responses are a key correlate of protection, and therefore measuring nAb responses is essential for monitoring vaccine efficacy. Fingerstick dried blood spots (DBS) are ideal for use in large-scale sero-surveillance because they are inexpensive, offer the option of self-collection and can be transported and stored at ambient temperatures. Such advantages also make DBS appealing to use in resource-limited settings and in potential future pandemics. In this study, nAb responses in sera, venous blood and fingerstick blood stored on filter paper were measured. Samples were collected from SARS-CoV-2 acutely infected individuals, SARS-CoV-2 convalescent individuals and SARS-CoV-2 vaccinated individuals. Good agreement was observed between the nAb responses measured in eluted DBS and paired sera. Stability of nAb responses was also observed in sera stored on filter paper at room temperature for 28 days. Overall, this study provides support for the use of filter paper as a viable sample collection method to study nAb responses.
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Affiliation(s)
- Kelly J Roper
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Wejdan Albalawi
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Emily Maddocks
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Susan Dobson
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Abdullateef Alshehri
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Francesco G Barone
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, L69 3BX, UK
| | - Murielle Baltazar
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Malcolm G Semple
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Lance Turtle
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK.
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.
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Heeregrave EJ, Thomas J, van Capel TM, de Jong EC, Pollakis G, Paxton WA. Glycan dependent phenotype differences of HIV-1 generated from macrophage versus CD4 + T helper cell populations. Front Immunol 2023; 14:1107349. [PMID: 37415979 PMCID: PMC10320205 DOI: 10.3389/fimmu.2023.1107349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is able to infect a variety of cell types with differences in entry efficiency and replication kinetics determined by the host cell type or the viral phenotype. The phenotype of the virus produced from these various cell types, including infectivity, co-receptor usage and neutralisation sensitivity, may also be affected by the characteristics of the producing cell. This can be due to incorporation of variant cell-specific molecules or differences in post-translational modifications of the gp41/120 envelope. In this study we produced genetically identical virus strains from macrophages, CD4-enriched lymphocytes as well as Th1 and Th2 CD4+ cell lines and compared each different virus stock for their infectivity in various cell types and sensitivity to neutralisation. In order to study the effect of the producer host cell on the virus phenotype, virus stocks were normalised on infectivity and were sequenced to confirm env gene homogeneity. Virus production by Th1 or Th2 cells did not compromise infectivity of the variant cell types tested. We observed no difference in sensitivity to co-receptor blocking agents upon viral passage through Th1 and Th2 CD4+ cell lineages nor did this affect DC-SIGN-mediated viral capture as measured in a transfer assay to CD4+ lymphocytes. Virus produced by macrophages was comparably sensitive to CC-chemokine inhibition as was virus generated from the array of CD4+ lymphocytes. We identified that virus produced from macrophages was fourteen times more resistant to 2G12 neutralisation than virus produced from CD4+ lymphocytes. Macrophage-produced dual-tropic (R5/X4) virus was six times more efficiently transmitted to CD4+ cells than lymphocyte-derived HIV-1 (p<0.0001) after DCSIGN capture. These results provide further insights to what extent the host cell influences viral phenotype and thereby various aspects of HIV-1 pathogenesis but suggest that viruses generated from Th1 versus Th2 cells are consistent in phenotype.
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Affiliation(s)
- Edwin J. Heeregrave
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Toni M. van Capel
- Department of Experimental Immunology, University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Esther C. de Jong
- Department of Experimental Immunology, University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Georgios Pollakis
- Department of Experimental Immunology, University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Eser TM, Baranov O, Huth M, Ahmed MIM, Deák F, Held K, Lin L, Pekayvaz K, Leunig A, Nicolai L, Pollakis G, Buggert M, Price DA, Rubio-Acero R, Reich J, Falk P, Markgraf A, Puchinger K, Castelletti N, Olbrich L, Vanshylla K, Klein F, Wieser A, Hasenauer J, Kroidl I, Hoelscher M, Geldmacher C. Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion. Nat Commun 2023; 14:2952. [PMID: 37225706 DOI: 10.1038/s41467-023-38020-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/12/2023] [Indexed: 05/26/2023] Open
Abstract
Despite intensive research since the emergence of SARS-CoV-2, it has remained unclear precisely which components of the early immune response protect against the development of severe COVID-19. Here, we perform a comprehensive immunogenetic and virologic analysis of nasopharyngeal and peripheral blood samples obtained during the acute phase of infection with SARS-CoV-2. We find that soluble and transcriptional markers of systemic inflammation peak during the first week after symptom onset and correlate directly with upper airways viral loads (UA-VLs), whereas the contemporaneous frequencies of circulating viral nucleocapsid (NC)-specific CD4+ and CD8+ T cells correlate inversely with various inflammatory markers and UA-VLs. In addition, we show that high frequencies of activated CD4+ and CD8+ T cells are present in acutely infected nasopharyngeal tissue, many of which express genes encoding various effector molecules, such as cytotoxic proteins and IFN-γ. The presence of IFNG mRNA-expressing CD4+ and CD8+ T cells in the infected epithelium is further linked with common patterns of gene expression among virus-susceptible target cells and better local control of SARS-CoV-2. Collectively, these results identify an immune correlate of protection against SARS-CoV-2, which could inform the development of more effective vaccines to combat the acute and chronic illnesses attributable to COVID-19.
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Affiliation(s)
- Tabea M Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Olga Baranov
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Manuel Huth
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748, Garching, Germany
| | - Mohammed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Flora Deák
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Luming Lin
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kami Pekayvaz
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Alexander Leunig
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Leo Nicolai
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE, UK
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, CF14 4XN, UK
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Jakob Reich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Philine Falk
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Alissa Markgraf
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Kerstin Puchinger
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, LMU Munich, 81377, Munich, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748, Garching, Germany
- Faculty of Mathematics and Natural Sciences, University of Bonn, 53113, Bonn, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany.
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Fisher AM, Airey G, Liu Y, Gemmell M, Thomas J, Bentley EG, Whitehead MA, Paxton WA, Pollakis G, Paterson S, Viney M. The Ecology of Viruses in Urban Rodents with a Focus on SARS-CoV-2. Emerg Microbes Infect 2023:2217940. [PMID: 37219409 DOI: 10.1080/22221751.2023.2217940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Wild animals are naturally infected with a range of viruses, some of which may be zoonotic for humans. During the human COVID pandemic there was also the possibility of rodents acquiring SARS-CoV-2 from people, so-called reverse zoonoses. To investigate this we sampled rats (Rattus norvegicus) and mice (Apodemus sylvaticus) from urban environments in 2020 during the human COVID-19 pandemic. We metagenomically sequenced lung and gut tissue and faeces for viruses, PCR screened for SARS-CoV-2, and serologically surveyed for anti-SARS-CoV-2 Spike antibodies. We describe the range of viruses that we found in these two rodent species. We found no molecular evidence of SARS-CoV-2 infection, though in rats we found lung antibody responses and evidence of neutralisation ability, that are consistent with rats being exposed to SARS-CoV-2 and / or exposed to other viruses that result in cross-reactive antibodies.
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Affiliation(s)
- Adam M Fisher
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
- These authors contributed equally to this work
- Current address, School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - George Airey
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
- These authors contributed equally to this work
| | - Yuchen Liu
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - Matthew Gemmell
- Centre for Genomic Research, University of Liverpool, L69 7ZB, UK
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7BE, UK
| | - Eleanor G Bentley
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - Mark A Whitehead
- Centre for Genomic Research, University of Liverpool, L69 7ZB, UK
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7BE, UK
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7BE, UK
| | - Steve Paterson
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
- Centre for Genomic Research, University of Liverpool, L69 7ZB, UK
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
- To whom correspondence should be addressed
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Parker E, Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, Davis C, Vink E, McDonald SE, Moore SC, Dicks S, Jegatheesan K, Cook NJ, Hope J, Cherepanov P, McClure MO, Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G. SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study. Front Immunol 2023; 14:1146702. [PMID: 37056776 PMCID: PMC10087108 DOI: 10.3389/fimmu.2023.1146702] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured via DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.
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Affiliation(s)
- Eleanor Parker
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jordan Thomas
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kelly J. Roper
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Samreen Ijaz
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, London, United Kingdom
| | - Tansy Edwards
- Medical Research Council (MRC) International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Federica Marchesin
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ksenia Katsanovskaja
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lauren Lett
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Christopher Jones
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hayley E. Hardwick
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Chris Davis
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Elen Vink
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sarah E. McDonald
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shona C. Moore
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Steve Dicks
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, London, United Kingdom
- National Health Service (NHS) Blood and Transplant, London, United Kingdom
| | - Keerthana Jegatheesan
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, London, United Kingdom
- National Health Service (NHS) Blood and Transplant, London, United Kingdom
| | - Nicola J. Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Joshua Hope
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Myra O. McClure
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | | | - Lance Turtle
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Antonia Ho
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Malcolm G. Semple
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - William A. Paxton
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Richard S. Tedder
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Georgios Pollakis
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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7
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Donnellan S, Pennington SH, Ruggiero A, Martinez-Rodriguez C, Pouget M, Thomas J, Ward SA, Pollakis G, Biagini GA, Paxton WA. A Quantitative Method for the Study of HIV-1 and Mycobacterium tuberculosis Coinfection. J Infect Dis 2023; 227:708-713. [PMID: 36537213 PMCID: PMC9978310 DOI: 10.1093/infdis/jiac491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis and human immunodeficiency virus-1 (HIV-1) syndemic interactions are a major global health concern. Despite the clinical significance of coinfection, our understanding of the cellular pathophysiology and the therapeutic pharmacodynamic impact of coinfection is limited. Here, we use single-round infectious HIV-1 pseudotyped viral particles expressing green fluorescent protein alongside M. tuberculosis expressing mCherry to study pathogenesis and treatment. We report that HIV-1 infection inhibited intracellular replication of M. tuberculosis and demonstrate the therapeutic activity of antiviral treatment (efavirenz) and antimicrobial treatment (rifampicin). The described method could be applied for detailed mechanistic studies to inform the development of novel treatment strategies.
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Affiliation(s)
- Samantha Donnellan
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Shaun H Pennington
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology, and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Department of Neuroscience, Biomedicine, and Movement Sciences, University of Verona, Verona, Italy
| | - Carmen Martinez-Rodriguez
- Department of Clinical Infection, Microbiology, and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Marion Pouget
- Department of Clinical Infection, Microbiology, and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology, and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Steve A Ward
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology, and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Giancarlo A Biagini
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - William A Paxton
- Department of Clinical Infection, Microbiology, and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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8
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Ijaz S, Dicks S, Jegatheesan K, Parker E, Katsanovskaja K, Vink E, McClure MO, Shute J, Hope J, Cook N, Cherepanov P, Turtle L, Paxton WA, Pollakis G, Ho A, Openshaw PJM, Baillie JK, Semple MG, Tedder RS. Mapping of SARS-CoV-2 IgM and IgG in gingival crevicular fluid: Antibody dynamics and linkage to severity of COVID-19 in hospital inpatients. J Infect 2022; 85:152-160. [PMID: 35667482 PMCID: PMC9163047 DOI: 10.1016/j.jinf.2022.05.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/19/2022] [Accepted: 05/29/2022] [Indexed: 02/06/2023]
Affiliation(s)
- Samreen Ijaz
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK.
| | - Steve Dicks
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK; NHS Blood and Transplant, London, UK
| | - Keerthana Jegatheesan
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK; NHS Blood and Transplant, London, UK
| | - Eleanor Parker
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Elen Vink
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Myra O McClure
- Department of Infectious Disease, Imperial College London, London, UK
| | - J Shute
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Joshua Hope
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Nicola Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Peter Cherepanov
- Department of Infectious Disease, Imperial College London, London, UK; Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - William A Paxton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Georgios Pollakis
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Richard S Tedder
- Department of Infectious Disease, Imperial College London, London, UK
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9
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McKay LGA, Thomas J, Albalawi W, Fattaccioli A, Dieu M, Ruggiero A, McKeating JA, Ball JK, Tarr AW, Renard P, Pollakis G, Paxton WA. The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway. Front Immunol 2022; 13:831695. [PMID: 35371105 PMCID: PMC8964954 DOI: 10.3389/fimmu.2022.831695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Following acute HCV infection, the virus establishes a chronic disease in the majority of patients whilst few individuals clear the infection spontaneously. The precise mechanisms that determine chronic HCV infection or spontaneous clearance are not completely understood but are proposed to be driven by host and viral genetic factors as well as HCV encoded immunomodulatory proteins. Using the HIV-1 LTR as a tool to measure NF-κB activity, we identified that the HCV E1E2 glycoproteins and more so the E2 protein down-modulates HIV-1 LTR activation in 293T, TZM-bl and the more physiologically relevant Huh7 liver derived cell line. We demonstrate this effect is specifically mediated through inhibiting NF-κB binding to the LTR and show that this effect was conserved for all HCV genotypes tested. Transcriptomic analysis of 293T cells expressing the HCV glycoproteins identified E1E2 mediated stimulation of the endoplasmic reticulum (ER) stress response pathway and upregulation of stress response genes such as ATF3. Through shRNA mediated inhibition of ATF3, one of the components, we observed that E1E2 mediated inhibitory effects on HIV-1 LTR activity was alleviated. Our in vitro studies demonstrate that HCV Env glycoprotein activates host ER Stress Pathways known to inhibit NF-κB activity. This has potential implications for understanding HCV induced immune activation as well as oncogenesis.
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Affiliation(s)
- Lindsay G. A. McKay
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Wejdan Albalawi
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Antoine Fattaccioli
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Marc Dieu
- MaSUN, Mass Spectrometry Facility, University of Namur (UNamur), Namur, Belgium
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jonathan K. Ball
- Wolfson Centre for Global Virus Research and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- Wolfson Centre for Global Virus Research and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium,MaSUN, Mass Spectrometry Facility, University of Namur (UNamur), Namur, Belgium
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - William A. Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom,*Correspondence: William A. Paxton,
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10
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Fong Y, Markby J, Andreotti M, Beck I, Bourlet T, Brambilla D, Frenkel L, Lira R, Nelson JAE, Pollakis G, Reigadas S, Richman D, Sawadogo S, Waters L, Yang C, Zeh C, Doherty M, Vojnov L. Diagnostic Accuracy of Dried Plasma Spot Specimens for HIV-1 Viral Load Testing: A Systematic Review and Meta-analysis. J Acquir Immune Defic Syndr 2022; 89:261-273. [PMID: 34732684 PMCID: PMC8826610 DOI: 10.1097/qai.0000000000002855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/26/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Dried plasma spot specimens may be a viable alternative to traditional liquid plasma in field settings, but the diagnostic accuracy is not well understood. METHODS Standard databases (PubMed and Medline), conferences, and gray literature were searched until January 2019. The quality of evidence was evaluated using the Standards for Reporting Studies of Diagnostic Accuracy and Quality Assessment of Diagnostic Accuracy Studies-2 criteria. We used univariate and bivariate random effects models to determine misclassification, sensitivity, and specificity across multiple thresholds, overall and for each viral load technology, and to account for between-study variation. RESULTS We identified 23 studies for inclusion in the systematic review that compared the diagnostic accuracy of dried plasma spots with that of plasma. Primary data from 16 of the 23 studies were shared and included in the meta-analysis, representing 18 countries, totaling 1847 paired dried plasma spot:plasma data points. The mean bias of dried plasma spot specimens compared with that of plasma was 0.28 log10 copies/mL, whereas the difference in median viral load was 2.25 log10 copies/mL. More dried plasma spot values were undetectable compared with plasma values (43.6% vs. 29.8%). Analyzing all technologies together, the sensitivity and specificity of dried plasma spot specimens were >92% across all treatment failure thresholds compared and total misclassification <5.4% across all treatment failure thresholds compared. Some technologies had lower sensitivity or specificity; however, the results were typically consistent across treatment failure thresholds. DISCUSSION Overall, dried plasma spot specimens performed relatively well compared with plasma with sensitivity and specificity values greater than 90% and misclassification rates less than 10% across all treatment failure thresholds reviewed.
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Affiliation(s)
- Youyi Fong
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Mauro Andreotti
- National Center for Global Health, Istituto Superiore di Sanita, Rome, Italy
| | - Ingrid Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Thomas Bourlet
- Laboratory of Virology, University Hospital of Saint-Etienne, France
| | | | - Lisa Frenkel
- Departments of Pediatrics and Laboratory Medicine, University of Washington, Seattle, WA
| | - Rosalia Lira
- Unidad de Investigacion Medica en Enfermedades Infecciosas y Parasitarias, UMAE Hospital de Pediatria, CMN Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Julie A. E. Nelson
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Georgios Pollakis
- Department of Human Retrovirology, University of Amsterdam, Amsterdam, the Netherlands
| | - Sandrine Reigadas
- Laboratory of Virology, University Hospital of Bordeaux 33076, Bordeaux, France
| | | | - Souleymane Sawadogo
- Division of Global HIV/AIDS, US Centers for Disease Control and Prevention, Windhoek, Namibia
| | - Laura Waters
- St. Stephens AIDS Trust, Chelsea & Westminster Hospital, London, United Kingdom
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/AIDS and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA
| | - Clement Zeh
- Division of HIV/AIDS Prevention, US Centers for Disease Control and Prevention, Kisumu, Kenya; and
| | - Meg Doherty
- World Health Organization, Geneva, Switzerland
| | - Lara Vojnov
- World Health Organization, Geneva, Switzerland
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11
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Horvath A, Rogers L, Pollakis G, Baranov O, Pieroth N, Joseph S, Chachage M, Heitzer A, Maganga L, Msafiri F, Joachim A, Viegas E, Eller LA, Kibuuka H, Rerks-Ngarm S, Pitisuttithum P, Nitayapan S, Dhitavat J, Premsri N, Fidler S, Shattock RJ, Robb ML, Weber J, McCormack S, Munseri PJ, Lyamuya E, Nilsson C, Kroidl A, Hoelscher M, Wagner R, Geldmacher C, Held K. Systematic comparison of HIV-1 Envelope-specific IgG responses induced by different vaccination regimens: Can we steer IgG recognition towards regions of viral vulnerability? Front Immunol 2022; 13:1075606. [PMID: 36741409 PMCID: PMC9891136 DOI: 10.3389/fimmu.2022.1075606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Immunogens and vaccination regimens can influence patterns of immune-epitope recognition, steering them towards or away from epitopes of potential viral vulnerability. HIV-1 envelope (Env)-specific antibodies targeting variable region 2 (V2) or 3 (V3) correlated with protection during the RV144 trial, however, it was suggested that the immunodominant V3 region might divert antibody responses away from other relevant sites. We mapped IgG responses against linear Env epitopes in five clinical HIV vaccine trials, revealing a specific pattern of Env targeting for each regimen. Notable V2 responses were only induced in trials administering CRF01_AE based immunogens, but targeting of V3 was seen in all trials, with the soluble, trimeric CN54gp140 protein eliciting robust V3 recognition. Strong V3 targeting was linked to greater overall response, increased number of total recognised antigenic regions, and where present, stronger V2 recognition. Hence, strong induction of V3-specific antibodies did not negatively impact the targeting of other linear epitopes in this study, suggesting that the induction of antibodies against V3 and other regions of potential viral vulnerability need not be necessarily mutually exclusive.
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Affiliation(s)
- Augusta Horvath
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Lisa Rogers
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Georgios Pollakis
- Institute of Infection Veterinary and Ecological Sciences (IVES/CIMI), University of Liverpool, Liverpool, United Kingdom
| | - Olga Baranov
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Nora Pieroth
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Sarah Joseph
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, United Kingdom
| | - Mkunde Chachage
- National Institute for Medical Research-Mbeya Medical Research Centre (NIMR-MMRC), Mbeya, Tanzania
| | - Asli Heitzer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Lucas Maganga
- National Institute for Medical Research-Mbeya Medical Research Centre (NIMR-MMRC), Mbeya, Tanzania
| | - Frank Msafiri
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Agricola Joachim
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Edna Viegas
- Instituto Nacional de Saúde, Maputo, Mozambique
| | - Leigh-Anne Eller
- United States Military HIV Research Program, Silver Spring, MD, United States.,Makerere University Walter Reed Project, Kampala, Uganda.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Supachai Rerks-Ngarm
- Department of Disease Control, Ministry of Public Health, Mueang Nonthaburi, Thailand
| | | | | | - Jittima Dhitavat
- Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nakorn Premsri
- Department of Disease Control, Ministry of Public Health, Mueang Nonthaburi, Thailand
| | - Sarah Fidler
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Robin J Shattock
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Merlin Lee Robb
- United States Military HIV Research Program, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Jonathan Weber
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Sheena McCormack
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, United Kingdom
| | | | - Eligius Lyamuya
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Charlotta Nilsson
- Department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden.,The Public Health Agency of Sweden, Solna, Sweden
| | - Arne Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University Regensburg, Regensburg, Germany.,Institute of Clinical Microbiology and Hygiene; University Hospital Regensburg, Regensburg, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
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12
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Malatinkova E, Thomas J, De Spiegelaere W, Rutsaert S, Geretti AM, Pollakis G, Paxton WA, Vandekerckhove L, Ruggiero A. Measuring Proviral HIV-1 DNA: Hurdles and Improvements to an Assay Monitoring Integration Events Utilising Human Alu Repeat Sequences. Life (Basel) 2021; 11:life11121410. [PMID: 34947941 PMCID: PMC8706387 DOI: 10.3390/life11121410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/28/2022] Open
Abstract
Integrated HIV-1 DNA persists despite antiretroviral therapy and can fuel viral rebound following treatment interruption. Hence, methods to specifically measure the integrated HIV-1 DNA portion only are important to monitor the reservoir in eradication trials. Here, we provide an up-to-date overview of the literature on the different approaches used to measure integrated HIV-1 DNA. Further, we propose an implemented standard-curve free assay to quantify integrated HIV-1 DNA, so-called Alu-5LTR PCR, which utilises novel primer combinations. We tested the Alu-5LTR PCR in 20 individuals on suppressive ART for a median of nine years; the results were compared to those produced with the standard-free Alu-gag assay. The numbers of median integrated HIV-1 DNA copies were 5 (range: 1–12) and 14 (5–26) with the Alu-gag and Alu-5LTR, respectively. The ratios between Alu-gag vs Alu-5LTR results were distributed within the cohort as follows: most patients (12/20, 60%) provided ratios between 2–5, with 3/20 (15%) and 5/20 (25%) being below or above this range, respectively. Alu-5LTR assay sensitivity was also determined using an “integrated standard”; the data confirmed the increased sensitivity of the assay, i.e., equal to 0.25 proviruses in 10,000 genomes. This work represents an improvement in the field of measuring proviral HIV-1 DNA that could be employed in future HIV-1 persistence and eradication studies.
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Affiliation(s)
- Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Ward De Spiegelaere
- Laboratory of Veterinary Morphology, Faculty of Veterinary Sciences, Ghent University, B-9820 Ghent, Belgium;
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Anna Maria Geretti
- Fondazione PTV and Faculty of Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
- School of Immunology & Microbial Sciences, King’s College London, London WC2R 2LS, UK
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - William A. Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
- Department Neurosciences, Biomedicine and Movement Sciences, School of Medicine-University of Verona, 37129 Verona, Italy
- Correspondence: ; Tel.: +39-045-802-7190
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13
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Abbas A, Abdukahil SA, Abdulkadir NN, Abe R, Abel L, Absil L, Acharya S, Acker A, Adachi S, Adam E, Adrião D, Ageel SA, Ahmed S, Ain Q, Ainscough K, Aisa T, Ait Hssain A, Ait Tamlihat Y, Akimoto T, Akmal E, Al Qasim E, Alalqam R, Alam T, Al-dabbous T, Alegesan S, Alegre C, Alessi M, Alex B, Alexandre K, Al-Fares A, Alfoudri H, Ali I, Ali Shah N, Alidjnou KE, Aliudin J, Alkhafajee Q, Allavena C, Allou N, Altaf A, Alves J, Alves JM, Alves R, Amaral M, Amira N, Ammerlaan H, Ampaw P, Andini R, Andrejak C, Angheben A, Angoulvant F, Ansart S, Anthonidass S, Antonelli M, Antunes de Brito CA, Anwar KR, Apriyana A, Arabi Y, Aragao I, Arali R, Arancibia F, Araujo C, Arcadipane A, Archambault P, Arenz L, Arlet JB, Arnold-Day C, Aroca A, Arora L, Arora R, Artaud-Macari E, Aryal D, Asaki M, Asensio A, Ashley E, Ashraf M, Ashraf S, Asim M, Assie JB, Asyraf A, Atique A, Attanyake AMUL, Auchabie J, Aumaitre H, Auvet A, Azemar L, Azoulay C, Bach B, Bachelet D, Badr C, Baig N, Baillie JK, Baird JK, Bak 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D, Treoux T, Trieu HT, Tripathy S, Tromeur C, Trontzas I, Trouillon T, Truong J, Tual C, Tubiana S, Tuite H, Turmel JM, Turtle LC, Tveita A, Twardowski P, Uchiyama M, Udayanga PGI, Udy A, Ullrich R, Umer Z, Uribe A, Usman A, Vajdovics C, Val-Flores L, Valle AL, Valran A, Van de Velde S, van den Berge M, van der Feltz M, van der Valk P, Van Der Vekens N, Van der Voort P, Van Der Werf S, van Dyk M, van Gulik L, Van Hattem J, van Lelyveld S, van Netten C, Van Twillert G, van Veen I, Vanel N, Vanoverschelde H, Varghese P, Varrone M, Vasudayan SR, Vauchy C, Vaughan H, Veeran S, Veislinger A, Vencken S, Ventura S, Verbon A, Vidal JE, Vieira C, Vijayan D, Villanueva JA, Villar J, Villeneuve PM, Villoldo A, Vinh Chau NV, Visseaux B, Visser H, Vitiello C, Vonkeman H, Vuotto F, Wahab NH, Wahab SA, Wahid NA, Wainstein M, Wan Muhd Shukeri WF, Wang CH, Webb SA, Wei J, Weil K, Wen TP, Wesselius S, West TE, Wham M, Whelan B, White N, Wicky PH, Wiedemann A, Wijaya SO, Wille K, Willems S, Williams V, Wils EJ, Wing Yiu N, Wong C, Wong TF, Wong XC, Wong YS, Xian GE, Xian LS, Xuan KP, Xynogalas I, Yacoub S, Yakop SRBM, Yamazaki M, Yazdanpanah Y, Yee Liang Hing N, Yelnik C, Yeoh CH, Yerkovich S, Yokoyama T, Yonis H, Yousif O, Yuliarto S, Zaaqoq A, Zabbe M, Zacharowski K, Zahid M, Zahran M, Zaidan NZB, Zambon M, Zambrano M, Zanella A, Zawadka K, Zaynah N, Zayyad H, Zoufaly A, Zucman D. The value of open-source clinical science in pandemic response: lessons from ISARIC. Lancet Infect Dis 2021; 21:1623-1624. [PMID: 34619109 PMCID: PMC8489876 DOI: 10.1016/s1473-3099(21)00565-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/16/2021] [Indexed: 12/31/2022]
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14
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Hauser A, Carnell G, Held K, Sulbaran G, Tischbierek N, Rogers L, Pollakis G, Tonks P, Hoelscher M, Ding S, Sanders RW, Geldmacher C, Sattentau Q, Weissenhorn W, Heeney JL, Peterhoff D, Wagner R. Stepwise Conformational Stabilization of a HIV-1 Clade C Consensus Envelope Trimer Immunogen Impacts the Profile of Vaccine-Induced Antibody Responses. Vaccines (Basel) 2021; 9:750. [PMID: 34358165 PMCID: PMC8310183 DOI: 10.3390/vaccines9070750] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/16/2023] Open
Abstract
Stabilization of the HIV-1 Envelope glycoprotein trimer (Env) in its native pre-fusion closed conformation is regarded as one of several requirements for the induction of neutralizing antibody (nAb) responses, which, in turn, will most likely be a prerequisite for the development of an efficacious preventive vaccine. Here, we systematically analyzed how the stepwise stabilization of a clade C consensus (ConC) Env immunogen impacts biochemical and biophysical protein traits such as antigenicity, thermal stability, structural integrity, and particle size distribution. The increasing degree of conformational rigidification positively correlates with favorable protein characteristics, leading to optimized homogeneity of the protein preparations, increased thermal stability, and an overall favorable binding profile of structure-dependent broadly neutralizing antibodies (bnAbs) and non-neutralizing antibodies (non-nAbs). We confirmed that increasing the structural integrity and stability of the Env trimers positively correlates with the quality of induced antibody responses by the immunogens. These and other data contribute to the selection of ConCv5 KIKO as novel Env immunogens for use within the European Union's H2020 Research Consortium EHVA (European HIV Alliance) for further preclinical analysis and phase 1 clinical development.
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Affiliation(s)
- Alexandra Hauser
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Guidenn Sulbaran
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France; (G.S.); (W.W.)
| | - Nadine Tischbierek
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
| | - Lisa Rogers
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology, and Immunology (CIMI), University of Liverpool, Liverpool L69 7BE, UK;
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU EZI), Liverpool L69 7BE, UK
| | - Paul Tonks
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Song Ding
- EuroVacc Foundation, 1105 BP Amsterdam, The Netherlands;
| | - Rogier W. Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Quentin Sattentau
- The Sir Willian Dunn School of Pathology, The University of Oxford, Oxford OX1 3RE, UK;
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France; (G.S.); (W.W.)
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
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15
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Pouget M, Coussens AK, Ruggiero A, Koch A, Thomas J, Besra GS, Wilkinson RJ, Bhatt A, Pollakis G, Paxton WA. Generation of Liposomes to Study the Effect of Mycobacterium Tuberculosis Lipids on HIV-1 cis- and trans-Infections. Int J Mol Sci 2021; 22:ijms22041945. [PMID: 33669411 PMCID: PMC7920488 DOI: 10.3390/ijms22041945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/01/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death among HIV-1-infected individuals and Mycobacterium tuberculosis (Mtb) co-infection is an early precipitate to AIDS. We aimed to determine whether Mtb strains differentially modulate cellular susceptibility to HIV-1 infection (cis- and trans-infection), via surface receptor interaction by their cell envelope lipids. Total lipids from pathogenic (lineage 4 Mtb H37Rv, CDC1551 and lineage 2 Mtb HN878, EU127) and non-pathogenic (Mycobacterium bovis BCG and Mycobacterium smegmatis) Mycobacterium strains were integrated into liposomes mimicking the lipid distribution and antigen accessibility of the mycobacterial cell wall. The resulting liposomes were tested for modulating in vitro HIV-1 cis- and trans-infection of TZM-bl cells using single-cycle infectious virus particles. Mtb glycolipids did not affect HIV-1 direct infection however, trans-infection of both R5 and X4 tropic HIV-1 strains were impaired in the presence of glycolipids from M. bovis, Mtb H37Rv and Mtb EU127 strains when using Raji-DC-SIGN cells or immature and mature dendritic cells (DCs) to capture virus. SL1, PDIM and TDM lipids were identified to be involved in DC-SIGN recognition and impairment of HIV-1 trans-infection. These findings indicate that variant strains of Mtb have differential effect on HIV-1 trans-infection with the potential to influence HIV-1 disease course in co-infected individuals.
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Affiliation(s)
- Marion Pouget
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (M.P.); (A.R.); (J.T.)
- UCD Centre for Experimental Pathogen Host Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Anna K. Coussens
- Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa; (A.K.C.); (A.K.); (R.J.W.)
- Walter and Eliza Hall Institute of Medical Research, Parkville 3279, Australia
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (M.P.); (A.R.); (J.T.)
- Academic Department of Pediatrics (DPUO), IRCCS Ospedale Pediatrico Bambino Gesù, Piazza S. Onofrio 4, 00165 Rome, Italy
| | - Anastasia Koch
- Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa; (A.K.C.); (A.K.); (R.J.W.)
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (M.P.); (A.R.); (J.T.)
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK; (G.S.B.); (A.B.)
| | - Robert J. Wilkinson
- Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa; (A.K.C.); (A.K.); (R.J.W.)
- Department of Infectious Diseases, Imperial College, London W2 1PG, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Apoorva Bhatt
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK; (G.S.B.); (A.B.)
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (M.P.); (A.R.); (J.T.)
- Correspondence: (G.P.); (W.A.P.); Tel.: +44-151-795-9681 (G.P.); +44-151-795-9605 (W.A.P.)
| | - William A. Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (M.P.); (A.R.); (J.T.)
- Correspondence: (G.P.); (W.A.P.); Tel.: +44-151-795-9681 (G.P.); +44-151-795-9605 (W.A.P.)
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16
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Dong X, Munoz-Basagoiti J, Rickett NY, Pollakis G, Paxton WA, Günther S, Kerber R, Ng LFP, Elmore MJ, Magassouba N, Carroll MW, Matthews DA, Hiscox JA. Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease. Genome Biol 2020; 21:238. [PMID: 32894206 PMCID: PMC7475720 DOI: 10.1186/s13059-020-02148-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Viral load is a major contributor to outcome in patients with Ebola virus disease (EVD), with high values leading to a fatal outcome. Evidence from the 2013-2016 Ebola virus (EBOV) outbreak indicated that different genotypes of the virus can have different phenotypes in patients. Additionally, due to the error-prone nature of viral RNA synthesis in an individual patient, the EBOV genome exists around a dominant viral genome sequence. The minor variants within a patient may contribute to the overall phenotype in terms of viral protein function. To investigate the effects of these minor variants, blood samples from patients with acute EVD were deeply sequenced. RESULTS We examine the minor variant frequency between patients with acute EVD who survived infection with those who died. Non-synonymous differences in viral proteins were identified that have implications for viral protein function. The greatest frequency of substitution was identified at three codon sites in the L gene-which encodes the viral RNA-dependent RNA polymerase (RdRp). Recapitulating this in an assay for virus replication, these substitutions result in aberrant viral RNA synthesis and correlate with patient outcome. CONCLUSIONS Together, these findings support the notion that in patients who survived EVD, in some cases, the genetic variability of the virus resulted in deleterious mutations that affected viral protein function, leading to reduced viral load. Such mutations may also lead to persistent strains of the virus and be associated with recrudescent infections.
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Affiliation(s)
- Xiaofeng Dong
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jordana Munoz-Basagoiti
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Natasha Y Rickett
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Georgios Pollakis
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - William A Paxton
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Romy Kerber
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Lisa F P Ng
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.,Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | - N'faly Magassouba
- Laboratoire des fièvres hémorragiques en Guinée, Université Gamal Abdel Nasser de Conakry, Conakry, Guinea
| | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.,Public Health England, Salisbury, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Singapore, Singapore
| | - Julian A Hiscox
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK. .,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK. .,Singapore Immunology Network, A*STAR, Singapore, Singapore.
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17
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Joachim A, Ahmed MIM, Pollakis G, Rogers L, Hoffmann VS, Munseri P, Aboud S, Lyamuya EF, Bakari M, Robb ML, Wahren B, Sandstrom E, Nilsson C, Biberfeld G, Geldmacher C, Held K. Induction of Identical IgG HIV-1 Envelope Epitope Recognition Patterns After Initial HIVIS-DNA/MVA-CMDR Immunization and a Late MVA-CMDR Boost. Front Immunol 2020; 11:719. [PMID: 32411138 PMCID: PMC7198863 DOI: 10.3389/fimmu.2020.00719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/30/2020] [Indexed: 01/16/2023] Open
Abstract
In the RV144 trial, to date the only HIV-1 vaccine efficacy trial demonstrating a modestly reduced risk of HIV-1 acquisition, antibody responses toward the HIV Envelope protein (Env) variable (V) 2 and V3 regions were shown to be correlated with a reduced risk of infection. These potentially protective antibody responses, in parallel with the vaccine efficacy, however, waned quickly. Dissecting vaccine-induced IgG recognition of antigenic regions and their variants within the HIV-1 Env from different vaccine trials will aid in designing future HIV-1 immunogens and vaccination schedules. We, therefore, analyzed the IgG response toward linear HIV-1 Env epitopes elicited by a multi-clade, multigene HIVIS-DNA priming, and heterologous recombinant modified vaccinia virus Ankara (MVA-CMDR) boosting regimen (HIVIS03) and assessed whether a late MVA-CMDR boost 3 years after completion of the initial vaccination schedule (HIVIS06) restored antibody responses toward these epitopes. Here we report that vaccination schedule in the HIVIS03 trial elicited IgG responses against linear epitopes within the V2 and V3 tip as well as against the gp41 immunodominant region in a high proportion of vaccinees. Antibodies against the V2 and gp41 Env regions were restricted to variants with close homology to the MVA-CMDR immunogen sequence, while V3 responses were more cross-reactive. Boosting with a late third MVA-CMDR after 3 years effectively restored waned IgG responses to linear Env epitopes and induced targeting of identical antigenic regions and variants comparable to the previous combined HIVIS-DNA/MVA-CMDR regimen. Our findings support the notion that anti-HIV-1 Env responses, associated with a reduced risk of infection in RV144, could be maintained by regular boosting with a single dose of MVA-CMDR.
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Affiliation(s)
- Agricola Joachim
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Mohamed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Georgios Pollakis
- Faculty of Health and Life Science, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU EZI), Liverpool, United Kingdom
| | - Lisa Rogers
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Verena S Hoffmann
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology, LMU Munich, Munich, Germany
| | - Patricia Munseri
- Department of Internal Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Said Aboud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Eligius F Lyamuya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Muhammad Bakari
- Tanzania Ministry of Health, Community Development, Gender, Elderly, and Children, Dodoma, Tanzania
| | - Merlin L Robb
- Walter Reed Army Institute of Research (WRAIR), Rockville, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Britta Wahren
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eric Sandstrom
- Department of Clinical Science and Education, Karolinska Institutet, Sodersjukhuset, Stockholm, Sweden
| | - Charlotta Nilsson
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden.,The Public Health Agency of Sweden, Solna, Sweden
| | - Gunnel Biberfeld
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
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18
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Abstract
HIV-1 eradication strategies aim to achieve viral remission in the absence of antiretroviral therapy (ART). The development of an HIV-1 cure remains challenging due to the latent reservoir (LR): long-lived CD4 T cells that harbor transcriptionally silent HIV-1 provirus. The LR is stable despite years of suppressive ART and is the source of rebound viremia following therapy interruption. Cure strategies such as "shock and kill" aim to eliminate or reduce the LR by reversing latency, exposing the infected cells to clearance via the immune response or the viral cytopathic effect. Alternative strategies include therapeutic vaccination, which aims to prime the immune response to facilitate control of the virus in the absence of ART. Despite promising advances, these strategies have been unable to significantly reduce the LR or increase the time to viral rebound but have provided invaluable insight in the field of HIV-1 eradication. The development and assessment of an HIV-1 cure requires robust assays that can measure the LR with sufficient sensitivity to detect changes that may occur following treatment. The viral outgrowth assay (VOA) is considered the gold standard method for LR quantification due to its ability to distinguish intact and defective provirus. However, the VOA is time consuming and resource intensive, therefore several alternative assays have been developed to bridge the gap between practicality and accuracy. Whilst a cure for HIV-1 infection remains elusive, recent advances in our understanding of the LR and methods for its eradication have offered renewed hope regarding achieving ART free viral remission.
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Immune and Infectious Disease Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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19
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Steba GS, Koekkoek SM, Prins M, Brinkman K, Kwa D, van der Meer JTM, van der Valk M, Molenkamp R, Pollakis G, Schinkel J, Paxton WA. Bile-salt stimulated lipase polymorphisms do not associate with HCV susceptibility. Virus Res 2019; 274:197715. [PMID: 31622635 DOI: 10.1016/j.virusres.2019.197715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/05/2019] [Accepted: 08/12/2019] [Indexed: 12/01/2022]
Abstract
Bile-salt stimulate lipase (BSSL) is a glycoprotein found in human milk and blood that can potently bind DC-SIGN. The BSSL gene is highly polymorphic with a variant number of O-linked glycosylated 11 amino acid repeats at the C-terminus of the protein, encoded in exon 11 of the gene. It has been shown that certain BSSL genotypes associate with decreased HIV-1 transmission in vitro and decreased HIV-1 disease progression. The protein forms dimers and individuals possessing one high (typically 14-21) and one low (typically 7-11) number of repeat domains has been shown to have stronger binding of BSSL to DC-SIGN and HIV-1 inhibitory activity in vitro. Since we previously demonstrated that SNPs within the DC-SIGN gene can associate with risk of HCV sexual transmission and which can be linked to diminished DC-SIGN gene expression we aimed to identify whether BSSL polymorphisms associated similarly through differential binding to DC-SIGN. DNA was isolated from the HIV-1 infected MSM cohort (MOSAIC) composed of HCV multiple exposed uninfected (MEU) (N = 30) and multiple exposed HCV infected (MEI) (N = 32) individuals and from the Amsterdam cohort studies (ACS) intravenous drug using (IDU) cohort (22 MEI and 40 MEU). The numbers of repeats in exon 11 were determined by PCR with repeat distributions compared between MEI and MEU. No statistical significant difference in the copy number of exon 11 repeats, or combinations of, in the BSSL gene was observed when comparing HCV infected MEI with MEU, thus the exon 11 repeat copy number in the BSSL gene does not affect HCV susceptibility.
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Affiliation(s)
- Gaby S Steba
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Sylvie M Koekkoek
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Maria Prins
- Department of Infectious Diseases Research and Prevention, Public Health Service of Amsterdam, Amsterdam, the Netherlands; Division of Infectious Diseases, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Kees Brinkman
- Department of Internal Medicine, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands
| | - David Kwa
- Department of Microbiology, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands
| | - Jan T M van der Meer
- Division of Infectious Diseases, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marc van der Valk
- Division of Infectious Diseases, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Richard Molenkamp
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Georgios Pollakis
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Clinical Infection, Microbiology and Immunology Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Janke Schinkel
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - William A Paxton
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Clinical Infection, Microbiology and Immunology Institute of Infection and Global Health, University of Liverpool, United Kingdom.
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20
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Aljabr W, Armstrong S, Rickett NY, Pollakis G, Touzelet O, Cloutman-Green E, Matthews DA, Hiscox JA. High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo. Viruses 2019; 11:v11100926. [PMID: 31658630 PMCID: PMC6832471 DOI: 10.3390/v11100926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/27/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of pediatric infection and also causes disease in the elderly and those with underlying respiratory problems. There is no vaccine for HRSV and anti-viral therapeutics are not broadly applicable. To investigate the effect of HRSV biology in children, nasopharyngeal aspirates were taken from children with different viral loads and a combined high throughput RNAseq and label free quantitative proteomics approach was used to characterize the nucleic acid and proteins in these samples. HRSV proteins were identified in the nasopharyngeal aspirates from infected children, and their abundance correlated with viral load (Ct value), confirming HRSV infection. Analysis of the HRSV genome indicated that the children were infected with sub-group A virus and that minor variants in nucleotide frequency occurred in discrete clusters along the HRSV genome, and within a patient clustered distinctly within the glycoprotein gene. Data from the samples were binned into four groups; no-HRSV infection (control), high viral load (Ct < 20), medium viral load (Ct = 20-25), and low viral load (Ct > 25). Cellular proteins associated with the anti-viral response (e.g., ISG15) were identified in the nasopharyngeal aspirates and their abundance was correlated with viral load. These combined approaches have not been used before to study HRSV biology in vivo and can be readily applied to the study the variation of virus host interactions.
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Affiliation(s)
- Waleed Aljabr
- King Fahad Medical City, Research Center, 59046 Riyadh 11525, Saudi Arabia.
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
| | - Natasha Y Rickett
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
| | - Olivier Touzelet
- School of Medicine, Dentistry & Biomedical Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
| | | | - David A Matthews
- School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
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21
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Mouser EEIM, Pollakis G, Smits HH, Thomas J, Yazdanbakhsh M, de Jong EC, Paxton WA. Schistosoma mansoni soluble egg antigen (SEA) and recombinant Omega-1 modulate induced CD4+ T-lymphocyte responses and HIV-1 infection in vitro. PLoS Pathog 2019; 15:e1007924. [PMID: 31487324 PMCID: PMC6728022 DOI: 10.1371/journal.ppat.1007924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023] Open
Abstract
Parasitic helminths evade, skew and dampen human immune responses through numerous mechanisms. Such effects will likely have consequences for HIV-1 transmission and disease progression. Here we analyzed the effects that soluble egg antigen (SEA) from Schistosoma mansoni had on modulating HIV-1 infection and cytokine/chemokine production in vitro. We determined that SEA, specifically through kappa-5, can potently bind to DC-SIGN and thereby blocks DC-SIGN mediated HIV-1 trans-infection (p<0.05) whilst not interfering with cis-infection. DCs exposed to SEA whilst maturing under Th2 promoting conditions, will upon co-culture with naïve T-cells induce a T-cell population that was less susceptible to HIV-1 R5 infection (p<0.05) compared to DCs unexposed to SEA, whereas HIV-1 X4 virus infection was unaffected. This was not observed for DCs exposed to SEA while maturing under Th1 or Th1/Th2 (Tmix) promoting conditions. All T-cell populations induced by SEA exposed DCs demonstrate a reduced capacity to produce IFN-γ and MIP-1β. The infection profile of T-cells infected with HIV-1 R5 was not associated with down-modulation of CCR5 cell surface expression. We further show that DCs maturing under Tmix conditions exposed to plant recombinant omega-1 protein (rω-1), which demonstrates similar functions to natural ω-1, induced T-cell populations that were less sensitive for HIV-1 R5 infection (p<0.05), but not for X4 virus infection. This inhibition associated again with a reduction in IFN-γ and MIP-1β expression, but additionally correlated with reduced CCR5 expression. We have shown that SEA parasite antigens and more specifically rω-1 can modulate HIV-1 infectivity with the potential to influence disease course in co-infected individuals. Parasitic helminths have developed a number of strategies to evade, skew and dampen human immune responses. Such effects will likely have consequences for HIV-1 transmission and disease progression. Here we analyzed the effect that soluble egg antigen (SEA) from Schistosoma mansoni had on HIV-1 infection in vitro. We determined that SEA, through kappa-5, can potently block DC-SIGN mediated HIV-1 trans-infection of CD4+ T-lymphocytes, but not block cis-infection. Dendritic cells (DC) exposed to SEA during maturation under Th2 skewing conditions, induce T-cell populations that are less susceptible to HIV-1 R5 infection compared to cells induced by unexposed DCs. HIV-1 X4 infection was unaffected. This restricted infection profile was not associated with down-modulation of CCR5 surface expression or observed differences in cytokine/chemokine production. Using recombinant omega-1, an abundant component of SEA, HIV-1 R5 infection was similarly inhibited with no effect on HIV-1 X4 infection levels. Hence SEA possesses antigens, namely omega-1, that can modulate HIV-1 infection and potentially influence disease course in co-infected individuals.
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Affiliation(s)
- Emily EIM Mouser
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Hermelijn H. Smits
- Department of Parasitology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Esther C. de Jong
- Department of Cell Biology and Histology, Amsterdam UMC, Location Academic Medical Center, Amsterdam, the Netherlands
- Department of Experimental Immunology, Amsterdam UMC, Location Academic Medical Center, Amsterdam, the Netherlands
- * E-mail: (ECdJ); (WAP)
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- * E-mail: (ECdJ); (WAP)
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22
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Nadai Y, Held K, Joseph S, Ahmed MIM, Hoffmann VS, Peterhoff D, Missanga M, Bauer A, Joachim A, Reimer U, Zerweck J, McCormack S, Cope AV, Tatoud R, Shattock RJ, Robb ML, Sandstroem EG, Hoelscher M, Maboko L, Bakari M, Kroidl A, Wagner R, Weber J, Pollakis G, Geldmacher C. Envelope-Specific Recognition Patterns of HIV Vaccine-Induced IgG Antibodies Are Linked to Immunogen Structure and Sequence. Front Immunol 2019; 10:717. [PMID: 31105688 PMCID: PMC6492543 DOI: 10.3389/fimmu.2019.00717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/18/2019] [Indexed: 11/13/2022] Open
Abstract
Background: A better understanding of the parameters influencing vaccine-induced IgG recognition of individual antigenic regions and their variants within the HIV Envelope protein (Env) can help to improve design of preventive HIV vaccines. Methods: Env-specific IgG responses were mapped in samples of the UKHVC003 Standard Group (UK003SG, n = 11 from UK) and TaMoVac01 (TMV01, n = 17 from Tanzania) HIV vaccine trials. Both trials consisted of three immunizations with DNA, followed by two boosts with recombinant Modified Vaccinia Virus Ankara (MVA), either mediating secretion of gp120 (UK003SG) or the presentation of cell membrane bound gp150 envelopes (TMV01) from infected cells, and an additional two boosts with 5 μg of CN54gp140 protein adjuvanted with glucopyranosyl lipid adjuvant (GLA). Env immunogen sequences in UK003SG were solely based on the clade C isolate CN54, whereas in TMV01 these were based on clades A, C, B, and CRF01AE. The peptide microarray included 8 globally representative Env sequences, CN54gp140 and the MVA-encoded Env immunogens from both trials, as well as additional peptide variants for hot spots of immune recognition. Results: After the second MVA boost, UK003SG vaccinees almost exclusively targeted linear, non-glycosylated antigenic regions located in the inter-gp120 interface. In contrast, TMV01 recipients most strongly targeted the V2 region and an immunodominant region in gp41. The V3 region was frequently targeted in both trials, with a higher recognition magnitude for diverse antigenic variants observed in the UK003SG (p < 0.0001). After boosting with CN54gp140/GLA, the overall response magnitude increased with a more comparable recognition pattern of antigenic regions and variants between the two trials. Recognition of most immunodominant regions within gp120 remained significantly stronger in UK003SG, whereas V2-region recognition was not boosted in either group. Conclusions: IgG recognition of linear antigenic Env regions differed between the two trials particularly after the second MVA boost. Structural features of the MVA-encoded immunogens, such as secreted, monomeric gp120 vs. membrane-anchored, functional gp150, and differences in prime-boost immunogen sequence variability most probably contributed to these differences. Prime-boosting with multivalent Env immunogens during TMV01 did not improve variant cross-recognition of immunodominant peptide variants in the V3 region.
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Affiliation(s)
- Yuka Nadai
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Sarah Joseph
- MRC Clinical Trials Unit at UCL, London, United Kingdom
| | - Mohamed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Verena S Hoffmann
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, University Regensburg, Regensburg, Germany
| | | | - Asli Bauer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Agricola Joachim
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ulf Reimer
- JPT Peptide Technologies, Berlin, Germany
| | | | | | - Alethea V Cope
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Roger Tatoud
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Robin J Shattock
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Merlin Lee Robb
- US Military HIV Research Program, Silver Spring, MD, United States
| | - Eric G Sandstroem
- Department of Clinical Science and Education, Karolinska Institutet at Södersjukhuset, Stockholm, Sweden
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | | | - Muhammad Bakari
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Arne Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University Regensburg, Regensburg, Germany.,Institute of Clinical Microbiology and Hygiene, University Hospital, Regensburg, Germany
| | - Jonathan Weber
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Georgios Pollakis
- Institute of Global Health (CIMI), University of Liverpool, Liverpool, United Kingdom
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
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23
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Steba GS, Koekkoek SM, Tanck MWT, Vanhommerig JW, van der Meer JTM, Kwa D, Brinkman K, Prins M, Berkhout B, Pollakis G, Molenkamp R, Schinkel J, Paxton WA. SNP rs688 within the low-density lipoprotein receptor (LDL-R) gene associates with HCV susceptibility. Liver Int 2019; 39:463-469. [PMID: 30260075 PMCID: PMC6588020 DOI: 10.1111/liv.13978] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Despite high-risk behaviour, 10%-20% of HCV multiple exposed individuals remain uninfected (MEU), whilst the remainder become infected (MEI). We hypothesize that host factors play a role in HCV susceptibility. We aimed to identify polymorphisms in host genes that encode for proteins involved in viral entry: CD81, Scavenger receptor 1 (SR-1), Low-density lipoprotein receptor (LDL-R), Claudin-1 (CLDN1), Occludin (OCLN) and Niemann-Pick C1-like 1 (NPC1L1). METHODS Multiple exposed infected and MEU from two observational cohorts were selected. From the MSM study of acute infection with HCV (MOSAIC), HIV-1 infected MEU cases (n = 30) and HIV-1 infected MEI controls (n = 32) were selected based on reported high-risk behaviour. From the Amsterdam Cohorts Studies (ACS) injecting drug users (IDU) cohort, MEU cases (n = 40) and MEI controls (n = 22) were selected who injected drugs for ≥2 years, in the nineties, when HCV incidence was high. Selected single nucleotide polymorphisms (SNPs) were determined by sequencing or SNP assays. RESULTS No associations were found for SNPs within genes coding for CD81, SR-1, Claudin-1 or Occludin between the MEU and MEI individuals from either cohort. We did observe a significant association for rs688 within the LDL-R gene with HCV infection (OR: 0.41 P = 0.001), however, LDL cholesterol levels did not vary between individuals carrying the differential SNPs. Additionally, a marginal significant effect was found for rs217434 and rs2072183 (OR: 2.07 P = 0.032 and OR: 1.76 P = 0.039, respectively) within NPC1L1. CONCLUSIONS Our results demonstrate that the rs688 SNP within the LDL-R gene associates with HCV susceptibility through mucosal as well as intravenous exposure.
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Affiliation(s)
- Gaby S. Steba
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Sylvie M. Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Michael W. T. Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics (CEBB), Amsterdam UMCAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Joost W. Vanhommerig
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Infectious DiseasesPublic Health Service of AmsterdamAmsterdamThe Netherlands
| | - Jan T. M. van der Meer
- Division of Infectious Diseases, Tropical Medicine and AIDS, Department of Internal Medicine, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - David Kwa
- Department of MicrobiologyOnze Lieve Vrouwe GasthuisAmsterdamThe Netherlands
| | - Kees Brinkman
- Department of Internal MedicineOnze Lieve Vrouwe GasthuisAmsterdamThe Netherlands
| | - Maria Prins
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Clinical Epidemiology, Biostatistics and Bioinformatics (CEBB), Amsterdam UMCAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and ImmunologyInstitute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
| | - Richard Molenkamp
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - William A. Paxton
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Clinical Infection, Microbiology and ImmunologyInstitute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
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24
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van Montfort T, van der Sluis R, Darcis G, Beaty D, Groen K, Pasternak AO, Pollakis G, Vink M, Westerhout EM, Hamdi M, Bakker M, van der Putten B, Jurriaans S, Prins JH, Jeeninga R, Thomas AAM, Speijer D, Berkhout B. Dendritic cells potently purge latent HIV-1 beyond TCR-stimulation, activating the PI3K-Akt-mTOR pathway. EBioMedicine 2019; 42:97-108. [PMID: 30824386 PMCID: PMC6491380 DOI: 10.1016/j.ebiom.2019.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/01/2019] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background The latent HIV-1 reservoir in treated patients primarily consists of resting memory CD4+ T cells. Stimulating the T-cell receptor (TCR), which facilitates transition of resting into effector T cells, is the most effective strategy to purge these latently infected cells. Here we supply evidence that TCR-stimulated effector T cells still frequently harbor latent HIV-1. Methods Primary HIV-1 infected cells were used in a latency assay with or without dendritic cells (DCs) and reversion of HIV-1 latency was determined, in the presence or absence of specific pathway inhibitors. Findings Renewed TCR-stimulation or subsequent activation with latency reversing agents (LRAs) did not overcome latency. However, interaction of infected effector cells with DCs triggered further activation of latent HIV-1. When compared to TCR-stimulation only, CD4+ T cells from aviremic patients receiving TCR + DC-stimulation reversed latency more frequently. Such a “one-two punch” strategy seems ideal for purging the reservoir. We determined that DC contact activates the PI3K-Akt-mTOR pathway in CD4+ T cells. Interpretation This insight could facilitate the development of a novel class of potent LRAs that purge latent HIV beyond levels reached by T-cell activation.
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Affiliation(s)
- Thijs van Montfort
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands.
| | - Renée van der Sluis
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Gilles Darcis
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands; Department of Infectious Diseases, Liege University Hospital, Liege, Belgium
| | - Doyle Beaty
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Kevin Groen
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Alexander O Pasternak
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), University of Liverpool, Liverpool, 8 West Derby Street, United Kingdom
| | - Monique Vink
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Ellen M Westerhout
- Department of Oncogenomics, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Mohamed Hamdi
- Department of Oncogenomics, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Margreet Bakker
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Boas van der Putten
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Suzanne Jurriaans
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Jan H Prins
- Department of Internal Medicine, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Rienk Jeeninga
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Adri A M Thomas
- Department Developmental Biology, Faculty Beta-Science, Utrecht, Padualaan 8, 3584, CH, the Netherlands
| | - Dave Speijer
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam University Medical Centers, Amsterdam, Meibergdreef 15, 1105AZ, the Netherlands
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25
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Thomas J, Ruggiero A, Procopio FA, Pantaleo G, Paxton WA, Pollakis G. Comparative analysis and generation of a robust HIV-1 DNA quantification assay. J Virol Methods 2018; 263:24-31. [PMID: 30326210 DOI: 10.1016/j.jviromet.2018.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 12/18/2022]
Abstract
HIV-1 infection cannot be cured due to the presence of the latent reservoir (LR). Novel cure or treatment strategies, such as "shock and kill" or therapeutic vaccination, aim to reduce or eradicate the LR. Cure strategies utilise robust DNA quantification assays to measure the change in the LR in low copy scenarios. No standard assay exists, which impedes the reliable comparison of results from different therapy and vaccine trials and HIV-1 total DNA quantification methods have not been previously compared. The HIV-1 long terminal repeat (LTR) has been shown to be the best target for DNA quantification. We have analysed two HIV-1 quantification assays, both able to differentiate between the variant HIV-1 DNA forms via the use of pre-amplification and primers targeting LTR. We identify a strong correlation (r=0.9759, P<0.0001) between assays which is conserved in low copy samples (r=0.8220, P<0.0001) indicating that these assays may be used interchangeably. The RvS assay performed significantly (P=0.0021) better than the CV assay when quantifying HIV-1 total DNA in patient CD4+ T lymphocytes. Sequence analysis demonstrated that viral diversity can limit DNA quantification, however in silico analysis of the primers indicated that within the target region nucleotide miss-matches appear infrequently. Further in silico analysis using up to-date sequence information led to the improvement of primers and enabled us to establish a more broadly specific assay with significantly higher HIV-1 DNA quantification capacity in patient samples (p=0.0057, n=17).
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Francesco A Procopio
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom.
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26
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Tedder RS, Samuel D, Dicks S, Scott JT, Ijaz S, Smith CC, Adaken C, Cole C, Baker S, Edwards T, Kamara P, Kargbo O, Niazi S, Nwakanma D, d'Alessandro U, Burch G, Doughty H, Brown CS, Andrews N, Glynn JR, van Griensven J, Pollakis G, Paxton WA, Semple MG. Detection, characterization, and enrollment of donors of Ebola convalescent plasma in Sierra Leone. Transfusion 2018; 58:1289-1298. [PMID: 29572862 PMCID: PMC5947131 DOI: 10.1111/trf.14580] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/05/2018] [Accepted: 01/15/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Passive therapy with convalescent plasma provides an early opportunity to intervene in Ebola virus disease (EVD). Methods for field screening and selection of potential donors and quantifying plasma antibody are needed. STUDY DESIGN AND METHODS Recombinant Ebola virus glycoprotein (EBOV GP) was formatted into immunoglobulin G‐capture, competitive, and double‐antigen bridging enzyme immunoassays (EIAs). EVD survivors in Freetown, Sierra Leone, were recruited as potential plasma donors and assessed locally using sera alone and/or paired sera and oral fluids (ORFs). Uninfected controls comprised unexposed Gambians and communities in Western Area, Sierra Leone. Antibody neutralization in selected sera was measured retrospectively in a pseudotype virus assay. RESULTS A total of 115 potential donors were considered for enrollment: 110 plasma samples were concordantly reactive in the three EIAs; three were concordantly unreactive and two were reactive in two of three EIAs (98.2% agreement; 95% confidence interval [CI], 93.9%‐99.8%). In 88 donors with paired ORF and plasma, G‐capture EIA reactivity correlated well in the two analytes (R2 = 0.795). Plasma and ORF from 44 Gambians were unreactive. ORF samples from 338 of 339 unexposed Western Area community controls were unreactive (specificity, 99.7%; 95% CI, 98.4%‐99.7%); ORF samples from 113 of 116 Kerry Town EVD survivors were reactive (sensitivity, 97.4%; 95% CI, 92.5%‐99.5%). Strong reactivity in G‐capture and/or competitive EIAs identified donors with high plasma EBOV GP antibody levels in the double‐antigen bridging assay, correlating with high levels of neutralizing antibody. CONCLUSIONS In‐field testing can qualify convalescent donors for providing high‐titer antibody.
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Affiliation(s)
- Richard S Tedder
- Blood Borne Virus Unit.,Transfusion Microbiology, National Health Service Blood and Transplant.,Division of Infection and Immunity, University College London, London, UK
| | - Dhan Samuel
- Serology Development Unit, Virus Reference Department, National Infection Service, Public Health England
| | - Steve Dicks
- Blood Borne Virus Unit.,Transfusion Microbiology, National Health Service Blood and Transplant
| | | | | | - Catherine C Smith
- Travel Medicine and International Health Team, Health Protection Scotland, Glasgow, UK
| | - Charlene Adaken
- Institute of Infection and Global Health, National Institute for Health Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | | | - Samuel Baker
- National Safe Blood Service, Connaught Hospital, Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Tansy Edwards
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine
| | - Philip Kamara
- National Safe Blood Service, Connaught Hospital, Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Osman Kargbo
- National Safe Blood Service, Connaught Hospital, Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | | | - Umberto d'Alessandro
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Medical Research Council, Fajara, Banjul, The Gambia
| | - Graham Burch
- DiaSorin S.p.A, Biotechnology Manufacturing, Dartford, UK
| | - Heidi Doughty
- National Health Service Blood and Transplant.,College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Colin S Brown
- King's Sierra Leone Partnership, King's Centre for Global Health, King's Health Partners and King's College London.,Reference Microbiology, National Infection Service
| | - Nick Andrews
- Statistics, Modelling and Economics Department, Public Health England, London, UK
| | - Judith R Glynn
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine
| | - Johan van Griensven
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Georgios Pollakis
- Institute of Infection and Global Health, National Institute for Health Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - William A Paxton
- Institute of Infection and Global Health, National Institute for Health Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
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Banga R, Procopio FA, Ruggiero A, Noto A, Ohmiti K, Cavassini M, Corpataux JM, Paxton WA, Pollakis G, Perreau M. Blood CXCR3 + CD4 T Cells Are Enriched in Inducible Replication Competent HIV in Aviremic Antiretroviral Therapy-Treated Individuals. Front Immunol 2018; 9:144. [PMID: 29459864 PMCID: PMC5807378 DOI: 10.3389/fimmu.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/17/2018] [Indexed: 01/14/2023] Open
Abstract
We recently demonstrated that lymph nodes (LNs) PD-1+/T follicular helper (Tfh) cells from antiretroviral therapy (ART)-treated HIV-infected individuals were enriched in cells containing replication competent virus. However, the distribution of cells containing inducible replication competent virus has been only partially elucidated in blood memory CD4 T-cell populations including the Tfh cell counterpart circulating in blood (cTfh). In this context, we have investigated the distribution of (1) total HIV-infected cells and (2) cells containing replication competent and infectious virus within various blood and LN memory CD4 T-cell populations of conventional antiretroviral therapy (cART)-treated HIV-infected individuals. In the present study, we show that blood CXCR3-expressing memory CD4 T cells are enriched in cells containing inducible replication competent virus and contributed the most to the total pool of cells containing replication competent and infectious virus in blood. Interestingly, subsequent proviral sequence analysis did not indicate virus compartmentalization between blood and LN CD4 T-cell populations, suggesting dynamic interchanges between the two compartments. We then investigated whether the composition of blood HIV reservoir may reflect the polarization of LN CD4 T cells at the time of reservoir seeding and showed that LN PD-1+ CD4 T cells of viremic untreated HIV-infected individuals expressed significantly higher levels of CXCR3 as compared to CCR4 and/or CCR6, suggesting that blood CXCR3-expressing CD4 T cells may originate from LN PD-1+ CD4 T cells. Taken together, these results indicate that blood CXCR3-expressing CD4 T cells represent the major blood compartment containing inducible replication competent virus in treated aviremic HIV-infected individuals.
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Affiliation(s)
- Riddhima Banga
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Francesco A Procopio
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Noto
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Khalid Ohmiti
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Matthias Cavassini
- Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jean-Marc Corpataux
- Vascular Surgery, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, Liverpool, United Kingdom
| | - Matthieu Perreau
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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28
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Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, Di Caro A, Diclaro J, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kargbo B, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll M, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 2017; 544:309-315. [PMID: 28405027 PMCID: PMC5712493 DOI: 10.1038/nature22040] [Citation(s) in RCA: 242] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023]
Abstract
The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.
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Affiliation(s)
- Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Luiz Max Carvalho
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew J. Tatem
- WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- Flowminder Foundation, Stockholm, Sweden
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Daniel J. Park
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jason T. Ladner
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Armando Arias
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark
| | - Danny Asogun
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
| | - Filip Bielejec
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Sarah L. Caddy
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | - Matthew Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Jonathan D’Ambrozio
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Simon Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Antonino Di Caro
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- National Institute for Infectious Diseases ”L. Spallanzani” – IRCCS, Via Portuense 292, 00149 Rome, Italy
| | - JosephW. Diclaro
- Naval Medical Research Unit 3, 3A Imtidad Ramses Street, Cairo, 11517, Egypt
| | - Sophie Duraffour
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Michael J. Elmore
- National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK
| | | | - Ousmane Faye
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal
| | - Merle L. Gilbert
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | - Stephen Gire
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Andreas Gnirke
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Julian A. Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, UK
| | - Umaru Jah
- University of Makeni, Makeni, Sierra Leone
| | - Brima Kargbo
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Jeffrey R. Kugelman
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Di Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia Lu
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | | | - Suzanne Mate
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | | | - Luke W. Meredith
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- University of Makeni, Makeni, Sierra Leone
| | - James Qu
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Suzan D. Pas
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - My VT Phan
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK
| | - Chantal B. Reusken
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | - John S. Schieffelin
- Department of Pediatrics, Section of Infectious Diseases, New Orleans, LA 70112, USA
| | - Rachel S. Sealfon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Etienne Simon-Loriere
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Génétique Fonctionelle des Maladies Infectieuses, CNRS URA3012, Paris 75015, France
| | - Saskia L. Smits
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Kilian Stoecker
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany
| | - Lucy Thorne
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | - Ekaete Alice Tobin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
| | - Mohamed A. Vandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Simon J. Watson
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kendra West
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | - Michael R. Wiley
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- University of Nebraska Medical Center, Omaha, NE, USA
| | - Sarah M. Winnicki
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shirlee Wohl
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Roman Wölfel
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany
| | - Nathan L. Yozwiak
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kristian G. Andersen
- The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, CA 92037, USA
- Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Sylvia O. Blyden
- Ministry of Social Welfare, Gender and Children’s Affairs, New Englandville, Freetown, Sierra Leone
| | - Fatorma Bolay
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | - MilesW. Carroll
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, UK
- University of Southampton, South General Hospital, Southampton SO16 6YD, UK
| | | | | | | | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George F. Gao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Robert F. Garry
- Department of Microbiology and Immunology, New Orleans, LA 70112, USA
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- University of Makeni, Makeni, Sierra Leone
| | - Stephan Günther
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Christian T. Happi
- Department of Biological Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney, NSW 2006, Australia
| | - Brima Kargbo
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | | | - Paul Kellam
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Division of Infectious Diseases, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - N’Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | | | - Stuart T. Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | | | - Gustavo Palacios
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Pardis C. Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amadou Sall
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal
| | - Ute Ströher
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | - Isatta Wurie
- University of Sierra Leone, Freetown, Sierra Leone
| | - Marc A. Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Biomathematics David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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29
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Banga R, Procopio FA, Noto A, Pollakis G, Cavassini M, Ohmiti K, Corpataux JM, de Leval L, Pantaleo G, Perreau M. PD-1+ and follicular helper T cells are responsible for persistent HIV-1 transcription in treated aviremic individuals. Nat Med 2016; 22:754-61. [DOI: 10.1038/nm.4113] [Citation(s) in RCA: 316] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/26/2016] [Indexed: 12/13/2022]
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30
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Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, Hewson R, García-Dorival I, Bore JA, Koundouno R, Abdellati S, Afrough B, Aiyepada J, Akhilomen P, Asogun D, Atkinson B, Badusche M, Bah A, Bate S, Baumann J, Becker D, Becker-Ziaja B, Bocquin A, Borremans B, Bosworth A, Boettcher JP, Cannas A, Carletti F, Castilletti C, Clark S, Colavita F, Diederich S, Donatus A, Duraffour S, Ehichioya D, Ellerbrok H, Fernandez-Garcia MD, Fizet A, Fleischmann E, Gryseels S, Hermelink A, Hinzmann J, Hopf-Guevara U, Ighodalo Y, Jameson L, Kelterbaum A, Kis Z, Kloth S, Kohl C, Korva M, Kraus A, Kuisma E, Kurth A, Liedigk B, Logue CH, Lüdtke A, Maes P, McCowen J, Mély S, Mertens M, Meschi S, Meyer B, Michel J, Molkenthin P, Muñoz-Fontela C, Muth D, Newman ENC, Ngabo D, Oestereich L, Okosun J, Olokor T, Omiunu R, Omomoh E, Pallasch E, Pályi B, Portmann J, Pottage T, Pratt C, Priesnitz S, Quartu S, Rappe J, Repits J, Richter M, Rudolf M, Sachse A, Schmidt KM, Schudt G, Strecker T, Thom R, Thomas S, Tobin E, Tolley H, Trautner J, Vermoesen T, Vitoriano I, Wagner M, Wolff S, Yue C, Capobianchi MR, Kretschmer B, Hall Y, Kenny JG, Rickett NY, Dudas G, Coltart CEM, Kerber R, Steer D, Wright C, Senyah F, Keita S, Drury P, Diallo B, de Clerck H, Van Herp M, Sprecher A, Traore A, Diakite M, Konde MK, Koivogui L, Magassouba N, Avšič-Županc T, Nitsche A, Strasser M, Ippolito G, Becker S, Stoecker K, Gabriel M, Raoul H, Di Caro A, Wölfel R, Formenty P, Günther S. Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature 2015; 524:97-101. [PMID: 26083749 PMCID: PMC10601607 DOI: 10.1038/nature14594] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/01/2015] [Indexed: 01/17/2023]
Abstract
West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.
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Affiliation(s)
- Miles W. Carroll
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- University of Southampton, South General Hospital, Southampton, SO16 6YD UK
| | - David A. Matthews
- Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD UK
| | - Julian A. Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | | | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 2FL UK
- Fogarty International Center, National Institutes of Health, Bethesda, 20892 Maryland USA
- Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 2FL UK
| | - Roger Hewson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Isabel García-Dorival
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Joseph Akoi Bore
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Raymond Koundouno
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Saïd Abdellati
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Tropical Medicine, Antwerp, B-2000 Belgium
| | - Babak Afrough
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - John Aiyepada
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Patience Akhilomen
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Danny Asogun
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Barry Atkinson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Marlis Badusche
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Amadou Bah
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Swiss Tropical and Public Health Institute, University of Basel, Basel, CH-4002 Switzerland
| | - Simon Bate
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Jan Baumann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Dirk Becker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Beate Becker-Ziaja
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Anne Bocquin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Benny Borremans
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Department of Biology, University of Antwerp, Antwerp, B-2020 Belgium
| | - Andrew Bosworth
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Jan Peter Boettcher
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Angela Cannas
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Fabrizio Carletti
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Concetta Castilletti
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Simon Clark
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Francesca Colavita
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Sandra Diederich
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, 17493 Insel Riems Germany
| | - Adomeh Donatus
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Sophie Duraffour
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- KU Leuven Rega institute, Leuven, B-3000 Belgium
| | - Deborah Ehichioya
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Redeemer’s University, Osun State Nigeria
| | - Heinz Ellerbrok
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Maria Dolores Fernandez-Garcia
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, 28029 Spain
| | - Alexandra Fizet
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, 69365 France
| | - Erna Fleischmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Sophie Gryseels
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Department of Biology, University of Antwerp, Antwerp, B-2020 Belgium
| | - Antje Hermelink
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Julia Hinzmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Ute Hopf-Guevara
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Yemisi Ighodalo
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Lisa Jameson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Anne Kelterbaum
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Zoltan Kis
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Center for Epidemiology, National Biosafety Laboratory, Budapest, H-1097 Hungary
| | - Stefan Kloth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Claudia Kohl
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Miša Korva
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000 Slovenia
| | - Annette Kraus
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Public Health Agency of Sweden, Solna, 171 82 Sweden
| | - Eeva Kuisma
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Andreas Kurth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Britta Liedigk
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Christopher H. Logue
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Anja Lüdtke
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, 20251 Germany
| | - Piet Maes
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- KU Leuven Rega institute, Leuven, B-3000 Belgium
| | - James McCowen
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Stéphane Mély
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Marc Mertens
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, 17493 Insel Riems Germany
| | - Silvia Meschi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Benjamin Meyer
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, University of Bonn, Bonn, 53127 Germany
| | - Janine Michel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Peter Molkenthin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - César Muñoz-Fontela
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, 20251 Germany
| | - Doreen Muth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, University of Bonn, Bonn, 53127 Germany
| | - Edmund N. C. Newman
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Didier Ngabo
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Lisa Oestereich
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Jennifer Okosun
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Thomas Olokor
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Racheal Omiunu
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Emmanuel Omomoh
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Elisa Pallasch
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Bernadett Pályi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Center for Epidemiology, National Biosafety Laboratory, Budapest, H-1097 Hungary
| | - Jasmine Portmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Federal Office for Civil Protection, Spiez Laboratory, Spiez, CH-3700 Switzerland
| | - Thomas Pottage
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Catherine Pratt
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Simone Priesnitz
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bundeswehr Hospital, Hamburg, 22049 Germany
| | - Serena Quartu
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Julie Rappe
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Virology and Immunology, Mittelhäusern, CH-3147 Switzerland
| | - Johanna Repits
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Janssen-Cilag, Sollentuna, SE-192 07 Sweden
| | - Martin Richter
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Martin Rudolf
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Andreas Sachse
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Kristina Maria Schmidt
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Gordian Schudt
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Thomas Strecker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Ruth Thom
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Stephen Thomas
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Ekaete Tobin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Howard Tolley
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Jochen Trautner
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Thünen Institute, Hamburg, D-22767 Germany
| | - Tine Vermoesen
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Tropical Medicine, Antwerp, B-2000 Belgium
| | - Inês Vitoriano
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Matthias Wagner
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Svenja Wolff
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Constanze Yue
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Maria Rosaria Capobianchi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Birte Kretschmer
- Eurice - European Research and Project Office GmbH, Berlin, 10115 Germany
| | - Yper Hall
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
| | - John G. Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Natasha Y. Rickett
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 2FL UK
| | - Cordelia E. M. Coltart
- Department of Infection and Population Health, University College London, London, WC1E 6JB UK
| | - Romy Kerber
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Damien Steer
- Research IT, University of Bristol, Bristol, BS8 1HH UK
| | - Callum Wright
- Advanced Computing Research Centre, University of Bristol, Bristol, BS8 1HH UK
| | - Francis Senyah
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
| | | | - Patrick Drury
- World Health Organization, Geneva 27, 1211 Switzerland
| | | | | | | | | | - Alexis Traore
- Section Prévention et Lutte contre la Maladie à la Direction Préfectorale de la Santé de Guéckédou, Guéckédou, Guinea
| | - Mandiou Diakite
- Université Gamal Abdel Nasser de Conakry, CHU Donka, Conakry, Guinea
| | | | | | - N’Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Tatjana Avšič-Županc
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000 Slovenia
| | - Andreas Nitsche
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Marc Strasser
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Federal Office for Civil Protection, Spiez Laboratory, Spiez, CH-3700 Switzerland
| | - Giuseppe Ippolito
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Stephan Becker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Kilian Stoecker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Martin Gabriel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Hervé Raoul
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Antonino Di Caro
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Roman Wölfel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | | | - Stephan Günther
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
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Ruggiero A, De Spiegelaere W, Cozzi-Lepri A, Kiselinova M, Pollakis G, Beloukas A, Vandekerckhove L, Strain M, Richman D, Phillips A, Geretti AM. During Stably Suppressive Antiretroviral Therapy Integrated HIV-1 DNA Load in Peripheral Blood is Associated with the Frequency of CD8 Cells Expressing HLA-DR/DP/DQ. EBioMedicine 2015; 2:1153-9. [PMID: 26498496 PMCID: PMC4588402 DOI: 10.1016/j.ebiom.2015.07.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/13/2015] [Accepted: 07/17/2015] [Indexed: 11/26/2022] Open
Abstract
Background Characterising the correlates of HIV persistence improves understanding of disease pathogenesis and guides the design of curative strategies. This study investigated factors associated with integrated HIV-1 DNA load during consistently suppressive first-line antiretroviral therapy (ART). Method Total, integrated, and 2-long terminal repeats (LTR) circular HIV-1 DNA, residual plasma HIV-1 RNA, T-cell activation markers, and soluble CD14 (sCD14) were measured in peripheral blood of 50 patients that had received 1–14 years of efavirenz-based or nevirapine-based therapy. Results Integrated HIV-1 DNA load (per 106 peripheral blood mononuclear cells) was median 1.9 log10 copies (interquartile range 1.7–2.2) and showed a mean difference of 0.2 log10 copies per 10 years of suppressive ART (95% confidence interval − 0.2, 0.6; p = 0.28). It was positively correlated with total HIV-1 DNA load and frequency of CD8+HLA-DR/DP/DQ+ cells, and was also higher in subjects with higher sCD14 levels, but showed no correlation with levels of 2-LTR circular HIV-1 DNA and residual plasma HIV-1 RNA, or the frequency of CD4+CD38+ and CD8+CD38+ cells. Adjusting for pre-ART viral load, duration of suppressive ART, CD4 cell counts, residual plasma HIV-1 RNA levels, and sCD14 levels, integrated HIV-1 DNA load was mean 0.5 log10 copies higher for each 50% higher frequency of CD8+HLA-DR/DP/DQ+ cells (95% confidence interval 0.2, 0.9; p = 0.01). Conclusions The observed positive association between integrated HIV-1 DNA load and frequency of CD8+DR/DP/DQ+ cells indicates that a close correlation between HIV persistence and immune activation continues during consistently suppressive therapy. The inducers of the distinct activation profile warrant further investigation. Data from a homogenously treated population with consistent virological suppression Integrated HIV-1 DNA load did not vary significantly by duration of therapy Integrated HIV-1 DNA load was not associated with markers of recent virus replication Integrated HIV-1 DNA load and CD8+HLA-DR/DP/DQ+ frequency were positively associated Subjects with top quartile integrated HIV-1 DNA load showed high sCD14 levels
Integrated HIV-1 DNA load remains constant in the peripheral blood of individuals receiving long-term suppressive antiretroviral therapy (ART). However, the mechanisms preventing decay of the reservoir remain unclear. We studied a cross-sectional population, defined by the duration of suppressive ART. Integrated HIV-1 DNA load did not differ significantly according to the duration of suppressive ART, and showed no association with direct or indirect markers of ongoing virus replication. Rather, there was an independent, positive association between integrated HIV-1 DNA load and the frequency of CD8 cells expressing the activation marker HLA-DR/DP/DQ. These cells appear to have important regulatory and effector function. Our findings add to growing evidence that immune activation sustains the HIV-1 reservoir during long-term suppressive ART.
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Key Words
- 2-LTR, 2-long terminal repeats
- ART, Anti-retroviral therapy
- Activation
- CMV, cytomegalovirus virus
- CRN, Clinical Research Network
- EBV, Epstein-Bar virus
- ELISA, enzyme-linked immune-enzymatic assay
- HIC, HIV-1 controllers
- HIV-1 VL, HIV-1 viral load
- HIV-1, Human Immunodeficiency Virus type 1
- HLA, Human Leukocyte Antigen
- Integration
- LPS, lipopolysaccharide
- NIHR, National Institute for Health Research
- NNRTI, Non-nucleoside reverse-transcriptase inhibitors
- NRTI, nucleoside/nucleotide reverse transcriptase inhibitors
- PBMCs, Peripheral blood mononuclear cells
- PCR, Polymerase chain reaction
- PFA, paraformaldehyde
- Persistence
- Reservoir
- Suppression
- VLS, Viral Load Suppression
- WHO, World Health Organisation
- sCD14, soluble CD14
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Affiliation(s)
- Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, 8 West Derby Street, Liverpool L697BE, United Kingdom
| | - Ward De Spiegelaere
- HIV Translational Research Unit, Department of Internal Medicine, Ghent University and University Hospital Ghent, De Pintelaan 1859000, Ghent, Belgium
| | - Alessandro Cozzi-Lepri
- Department of Infection and Population Health, University College London, Royal Free Campus, Rowland Hill Street, London, NW32PF, United Kingdom
| | - Maja Kiselinova
- HIV Translational Research Unit, Department of Internal Medicine, Ghent University and University Hospital Ghent, De Pintelaan 1859000, Ghent, Belgium
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, 8 West Derby Street, Liverpool L697BE, United Kingdom
| | - Apostolos Beloukas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, 8 West Derby Street, Liverpool L697BE, United Kingdom
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Ghent University and University Hospital Ghent, De Pintelaan 1859000, Ghent, Belgium
| | - Matthew Strain
- VA San Diego Healthcare System and Center for AIDS Research, University of California San Diego, La Jolla, CA 92093, United States
| | - Douglas Richman
- VA San Diego Healthcare System and Center for AIDS Research, University of California San Diego, La Jolla, CA 92093, United States
| | - Andrew Phillips
- Department of Infection and Population Health, University College London, Royal Free Campus, Rowland Hill Street, London, NW32PF, United Kingdom
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection and Global Health (IGH), University of Liverpool, 8 West Derby Street, Liverpool L697BE, United Kingdom
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Bracke L, Willems E, Gall A, Kellam P, Coppens S, Meehan C, Pollakis G, Berkhout B, Vanham G, Cornelissen M, Heyndrickx L, Ariën K. Characterisation of Transmitted and Non-transmitted HIV in Index-recipient Transmission Pairs. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5491.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lotte Bracke
- Institute of Tropical Medicine, Department of Biomedical Sciences, Virology Unit, Antwerp, Belgium
| | - Elisabeth Willems
- Institute of Tropical Medicine, Department of Biomedical Sciences, Virology Unit, Antwerp, Belgium
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Sandra Coppens
- Institute of Tropical Medicine, Department of Biomedical Sciences, Virology Unit, Antwerp, Belgium
| | - Conor Meehan
- Institute of Tropical Medicine, Department of Biomedical Sciences, Mycobacteriology Unit, Antwerp, Belgium
| | - Georgios Pollakis
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Institute of Infection and Global Health/CIMI, University of Liverpool, Liverpool, United Kingdom
| | - Ben Berkhout
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Guido Vanham
- Institute of Tropical Medicine, Department of Biomedical Sciences, Virology Unit, Antwerp, Belgium
| | - Marion Cornelissen
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Leo Heyndrickx
- Institute of Tropical Medicine, Department of Biomedical Sciences, Virology Unit, Antwerp, Belgium
| | - Kevin Ariën
- Institute of Tropical Medicine, Department of Biomedical Sciences, Virology Unit, Antwerp, Belgium
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Span P, Pollakis G, Paxton W, Sweep F, Foekens J, Martens J, Sieuwerts A, van Laarhoven H. Improved metastasis-free survival in nonadjuvantly treated postmenopausal breast cancer patients with chemokine receptor 5 del32 frameshift mutations. Int J Cancer 2014; 136:91-7. [DOI: 10.1002/ijc.28962] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/24/2014] [Indexed: 11/10/2022]
Affiliation(s)
- P.N. Span
- Department of Radiation Oncology; Radboud University Medical Center; Nijmegen The Netherlands
| | - G. Pollakis
- Laboratory of Experimental Virology; Academic Medical Center, University of Amsterdam; Amsterdam The Netherlands
- Department of Clinical Infection Microbiology and Immunology; IGH, University of Liverpool; Liverpool United Kingdom
| | - W.A. Paxton
- Laboratory of Experimental Virology; Academic Medical Center, University of Amsterdam; Amsterdam The Netherlands
- Department of Clinical Infection Microbiology and Immunology; IGH, University of Liverpool; Liverpool United Kingdom
| | - F.C.G.J. Sweep
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
| | - J.A. Foekens
- Department of Medical Oncology; Erasmus MC Cancer Institute, Erasmus University Medical Center, and Cancer Genomics Netherlands; Rotterdam The Netherlands
| | - J.W.M. Martens
- Department of Medical Oncology; Erasmus MC Cancer Institute, Erasmus University Medical Center, and Cancer Genomics Netherlands; Rotterdam The Netherlands
| | - A.M. Sieuwerts
- Department of Medical Oncology; Erasmus MC Cancer Institute, Erasmus University Medical Center, and Cancer Genomics Netherlands; Rotterdam The Netherlands
| | - H.W.M. van Laarhoven
- Department of Medical Oncology; Academic Medical Center, University of Amsterdam; Amsterdam The Netherlands
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Pollakis G, Richel O, Vis JD, Prins JM, Paxton WA, de Vries HJC. Increased HIV-1 activity in anal high-grade squamous intraepithelial lesions compared with unaffected anal mucosa in men who have sex with men. Clin Infect Dis 2014; 58:1634-7. [PMID: 24604897 DOI: 10.1093/cid/ciu133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We studied 3 patients with focal intra-anal tissue high-grade squamous intraepithelial lesions (HSILs). All had increased human immunodeficiency virus type 1 (HIV-1) RNA and DNA in lesions compared with that in healthy mucosa. HIV-1 RNA and HIV-1 episomal DNA were indicative of ongoing viral replication, more so in anal HSILs.
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Affiliation(s)
- Georgios Pollakis
- Institute of Infection and Global Health/CIMI, University of Liverpool, United Kingdom
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35
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van der Sluis RM, van Montfort T, Pollakis G, Sanders RW, Speijer D, Berkhout B, Jeeninga RE. Dendritic cell-induced activation of latent HIV-1 provirus in actively proliferating primary T lymphocytes. PLoS Pathog 2013; 9:e1003259. [PMID: 23555263 PMCID: PMC3605277 DOI: 10.1371/journal.ppat.1003259] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 02/05/2013] [Indexed: 12/31/2022] Open
Abstract
HIV-1 latency remains a formidable barrier towards virus eradication as therapeutic attempts to purge these reservoirs are so far unsuccessful. The pool of transcriptionally silent proviruses is established early in infection and persists for a lifetime, even when viral loads are suppressed below detection levels using anti-retroviral therapy. Upon therapy interruption the reservoir can re-establish systemic infection. Different cellular reservoirs that harbor latent provirus have been described. In this study we demonstrate that HIV-1 can also establish a silent integration in actively proliferating primary T lymphocytes. Co-culturing of these proliferating T lymphocytes with dendritic cells (DCs) activated the provirus from latency. Activation did not involve DC-mediated C-type lectin DC-SIGN signaling or TCR-stimulation but was mediated by DC-secreted component(s) and cell-cell interaction between DC and T lymphocyte that could be inhibited by blocking ICAM-1 dependent adhesion. These results imply that circulating DCs could purge HIV-1 from latency and re-initiate virus replication. Moreover, our data show that viral latency can be established early after infection and supports the idea that actively proliferating T lymphocytes with an effector phenotype contribute to the latent viral reservoir. Unraveling this physiologically relevant purging mechanism could provide useful information for the development of new therapeutic strategies that aim at the eradication of HIV-1 reservoirs.
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Affiliation(s)
- Renée M. van der Sluis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Thijs van Montfort
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Rienk E. Jeeninga
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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36
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Schopman NC, van Montfort T, Willemsen M, Knoepfel SA, Pollakis G, van Kampen A, Sanders RW, Haasnoot J, Berkhout B. Selective packaging of cellular miRNAs in HIV-1 particles. Virus Res 2012; 169:438-47. [DOI: 10.1016/j.virusres.2012.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/07/2012] [Accepted: 06/12/2012] [Indexed: 01/21/2023]
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37
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van der Sluis RM, van Montfort T, Centlivre M, Schopman NCT, Cornelissen M, Sanders RW, Berkhout B, Jeeninga RE, Paxton WA, Pollakis G. Quantitation of HIV-1 DNA with a sensitive TaqMan assay that has broad subtype specificity. J Virol Methods 2012; 187:94-102. [PMID: 23059551 DOI: 10.1016/j.jviromet.2012.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 09/04/2012] [Accepted: 09/10/2012] [Indexed: 11/30/2022]
Abstract
The increasing diversity of HIV-1 isolates makes virus quantitation challenging, especially when diverse isolates co-circulate in a geographical area. Measuring the HIV-1 DNA levels in cells has become a valuable practical tool for fundamental and clinical research. A quantitative HIV-1 DNA assay was developed based on TaqMan(®) technology. Primers that target the highly conserved LTR region were designed to detect a broad array of HIV-1 variants, including viral isolates from many subtypes, with high sensitivity. Introduction of a pre-amplification step prior to the TaqMan(®) reaction allowed the specific amplification of fully reverse transcribed viral DNA. Execution of the pre-amplification step with a second primer set enables for the exclusive quantitation of the 2-LTR circular HIV-1 DNA form.
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Affiliation(s)
- Renée M van der Sluis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, Amsterdam, The Netherlands
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38
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Baan E, van der Sluis RM, Bakker ME, Bekker V, Pajkrt D, Jurriaans S, Kuijpers TW, Berkhout B, Wolthers KC, Paxton WA, Pollakis G. Human immunodeficiency virus type 1 gp120 envelope characteristics associated with disease progression differ in family members infected with genetically similar viruses. J Gen Virol 2012; 94:20-29. [PMID: 23015744 DOI: 10.1099/vir.0.046185-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) envelope protein provides the primary contact between the virus and host, and is the main target of the adaptive humoral immune response. The length of gp120 variable loops and the number of N-linked glycosylation events are key determinants for virus infectivity and immune escape, while the V3 loop overall positive charge is known to affect co-receptor tropism. We selected two families in which both parents and two children had been infected with HIV-1 for nearly 10 years, but who demonstrated variable parameters of disease progression. We analysed the gp120 envelope sequence and compared individuals that progressed to those that did not in order to decipher evolutionary alterations that are associated with disease progression when individuals are infected with genetically related virus strains. The analysis of the V3-positive charge demonstrated an association between higher V3-positive charges with disease progression. The ratio between the amino acid length and the number of potential N-linked glycosylation sites was also shown to be associated with disease progression with the healthier family members having a lower ratio. In conclusion in individuals initially infected with genetically linked virus strains the V3-positive charges and N-linked glycosylation are associated with HIV-1 disease progression and follow varied evolutionary paths for individuals with varied disease progression.
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Affiliation(s)
- Elly Baan
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Renée M van der Sluis
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Margreet E Bakker
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Vincent Bekker
- Emma Children's Hospital, Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Dasja Pajkrt
- Emma Children's Hospital, Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Suzanne Jurriaans
- Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Taco W Kuijpers
- Emma Children's Hospital, Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Katja C Wolthers
- Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - William A Paxton
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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Baan E, de Ronde A, Luchters S, Vyankandondera J, Lange JM, Pollakis G, Paxton WA. HIV type 1 mother-to-child transmission facilitated by distinctive glycosylation sites in the gp120 envelope glycoprotein. AIDS Res Hum Retroviruses 2012; 28:715-24. [PMID: 21916748 DOI: 10.1089/aid.2011.0023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) characteristics associated with mother-to-child transmission (MTCT) are still poorly understood. We studied a cohort of 30 mothers from Rwanda infected with HIV-1 subtype A or C viruses of whom seven infected their children either during gestation or soon after birth. CD4 counts and viral load did not significantly differ between nontransmitting mother (NTM) versus transmitting mother (TM) groups. In contrast to earlier studies we not only analyzed and compared the genotypic characteristics of the V1-V5 region of the gp120 envelope of viruses found in TM and their infected children, but also included data from the NTM. No differences were found with respect to length and number of potential N-glycosylation sites (PNGS) in the V1-V2 and the V1-V5 region. We identified that viruses with a PNGS on positions AA234 and AA339 were preferably transmitted and that viruses with PNGS-N295 showed a disadvantage in transmission. We also showed that the frequency of PNGS-N339 in the viruses of TM and infected children was significantly higher than the frequency in NTM in our cohort and in viruses undergoing sexual transmission while the frequency of PNGS-N295 in children was significantly lower than the frequency in TM and acute horizontal infections. Collectively, our results provide evidence that the presence of the PNGS-N339 site and absence of the PNGS-N295 site in the gp120 envelope confers an advantage to HIV-1 when considering MTCT.
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Affiliation(s)
- Elly Baan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands
| | - Anthony de Ronde
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands
| | - Stanley Luchters
- IATEC, International Antiviral Therapy Evaluation Center, Amsterdam, the Netherlands
| | - Joseph Vyankandondera
- CHUK, Centre Hospitalier Universitaire de Kigali and Belgian Technical Cooperation, Kigali, Rwanda
| | - Joep M. Lange
- IATEC, International Antiviral Therapy Evaluation Center, Amsterdam, the Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands
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Stax MJ, Kootstra NA, van 't Wout AB, Tanck MWT, Bakker M, Pollakis G, Paxton WA. HIV-1 disease progression is associated with bile-salt stimulated lipase (BSSL) gene polymorphism. PLoS One 2012; 7:e32534. [PMID: 22412885 PMCID: PMC3295759 DOI: 10.1371/journal.pone.0032534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/01/2012] [Indexed: 01/25/2023] Open
Abstract
Background DC-SIGN expressed by dendritic cells captures HIV-1 resulting in trans-infection of CD4+ T-lymphocytes. However, BSSL (bile-salt stimulated lipase) binding to DC-SIGN interferes with HIV-1 capture. DC-SIGN binding properties of BSSL associate with the polymorphic repeated motif of BSSL exon 11. Furthermore, BSSL binds to HIV-1 co-receptor CXCR4. We hypothesized that BSSL modulates HIV-1 disease progression and emergence of CXCR4 using HIV-1 (X4) variants. Results The relation between BSSL genotype and HIV-1 disease progression and emergence of X4 variants was studied using Kaplan Meier and multivariate Cox proportional hazard analysis in a cohort of HIV-1 infected men having sex with men (n = 334, with n = 130 seroconverters). We analyzed the association of BSSL genotype with set-point viral load and CD4 cell count, both pre-infection and post-infection at viral set-point. The number of repeats in BSSL exon 11 were highly variable ranging from 10 to 18 in seropositive individuals and from 5–17 in HRSN with 16 repeats being dominant (>80% carry at least one allele with 16 repeats). We defined 16 to 18 repeats as high (H) and less than 16 repeats as low (L) repeat numbers. Homozygosity for the high (H) repeat number BSSL genotype (HH) correlated with high CD4 cell numbers prior to infection (p = 0.007). In HIV-1 patients, delayed disease progression was linked to the HH BSSL genotype (RH = 0.462 CI = 0.282–0.757, p = 0.002) as was delayed emergence of X4 variants (RH = 0.525, 95% CI = 0.290–0.953, p = 0.034). The LH BSSL genotype, previously found to be associated with enhanced DC-SIGN binding of human milk, was identified to correlate with accelerated disease progression in our cohort of HIV-1 infected MSM (RH = 0.517, 95% CI = 0.328–0.818, p = 0.005). Conclusion We identify BSSL as a marker for HIV-1 disease progression and emergence of X4 variants. Additionally, we identified a relation between BSSL genotype and CD4 cell counts prior to infection.
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Affiliation(s)
- Martijn J. Stax
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and CINIMA at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van 't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and CINIMA at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Michael W. T. Tanck
- Department Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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van Werkhoven MB, Baan E, Bakker M, Jurriaans S, Paxton WA, Pollakis G. Transmission of two distinct HIV type 1 strains to an individual that were harbored for many years by another. AIDS Res Hum Retroviruses 2012; 28:225-7. [PMID: 21790473 DOI: 10.1089/aid.2011.0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The concept of transmission bottlenecks in HIV-1 infection is well established. Coinfections and superinfections have been increasingly documented and provide a founding cause for the expansion of viral diversity through recombination. It is still relatively unclear how HIV-1 will propagate and evolve in individuals infected with more than one viral strain. Here we report on the parallel transmission of genetically distant viral strains cocirculating in one individual over many years to a single recipient.
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Affiliation(s)
- Maaike B. van Werkhoven
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Elly Baan
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Suzanne Jurriaans
- Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - William A Paxton
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Stax MJ, Naarding MA, Tanck MWT, Lindquist S, Hernell O, Lyle R, Brandtzaeg P, Eggesbø M, Pollakis G, Paxton WA. Binding of human milk to pathogen receptor DC-SIGN varies with bile salt-stimulated lipase (BSSL) gene polymorphism. PLoS One 2011; 6:e17316. [PMID: 21386960 PMCID: PMC3046167 DOI: 10.1371/journal.pone.0017316] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 01/27/2011] [Indexed: 11/22/2022] Open
Abstract
Objective Dendritic cells bind an array of antigens and DC-SIGN has been postulated to act as a receptor for mucosal pathogen transmission. Bile salt-stimulated lipase (BSSL) from human milk potently binds DC-SIGN and blocks DC-SIGN mediated trans-infection of CD4+ T-lymphocytes with HIV-1. Objective was to study variation in DC-SIGN binding properties and the relation between DC-SIGN binding capacity of milk and BSSL gene polymorphisms. Study Design ELISA and PCR were used to study DC-SIGN binding properties and BSSL exon 11 size variation for human milk derived from 269 different mothers distributed over 4 geographical regions. Results DC-SIGN binding properties were highly variable for milks derived from different mothers and between samplings from different geographical regions. Differences in DC-SIGN binding were correlated with a genetic polymorphism in BSSL which is related to the number of 11 amino acid repeats at the C-terminus of the protein. Conclusion The observed variation in DC-SIGN binding properties among milk samples may have implications for the risk of mucosal transmission of pathogens during breastfeeding.
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Affiliation(s)
- Martijn J. Stax
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Marloes A. Naarding
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael W. T. Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne Lindquist
- Pediatrics Unit, Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Olle Hernell
- Pediatrics Unit, Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Per Brandtzaeg
- LIIPAT, Centre for Immune Regulation, University of Oslo, and Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Merete Eggesbø
- Division of Epidemiology, Department of Genes and Environment, Norwegian Institute of Public Health, Oslo, Norway
| | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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43
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Centlivre M, Legrand N, Steingrover R, van der Sluis R, Grijsen ML, Bakker M, Jurriaans S, Berkhout B, Paxton WA, Prins JM, Pollakis G. Altered dynamics and differential infection profiles of lymphoid and myeloid cell subsets during acute and chronic HIV-1 infection. J Leukoc Biol 2011; 89:785-95. [PMID: 21310820 DOI: 10.1189/jlb.0410231] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The dynamics of immune cell populations during acute HIV-1 infection are not fully deciphered, especially for non-T cells. In this study, we tested whether specific cellular subsets of the innate arm of the immune response are affected early after HIV-1 infection. Using a cohort of HIV-1-infected individuals, we have monitored the relative frequency of blood T lymphocytes, monocytes, and DCs at various infection stages and measured their respective intracellular HIV-1 DNA loads. The HIV-1 DNA load in naive CD4(+) T lymphocytes, which are lost very early during acute infection, was ten- to 100-fold lower than in CD57(-) and CD57(+) memory CD4(+) T lymphocytes. We observed that despite rapid, persistent loss after HIV-1 infection, pDCs represented a non-negligible HIV-1 DNA reservoir. CD16(+) proinflammatory cDCs and monocytes accumulated gradually, and HIV-infected CD16(+) monocytes contained higher HIV-1 DNA loads than their CD16(-) counterpart during acute infection. During chronic infection, CD16(+) cDCs exhibited higher HIV-1 DNA loads than the CD16(-) population. Overall, our results demonstrate that non-T cell compartments are a major HIV-1 DNA reservoir, and CD16(+) monocytes and CD16(+) cDCs potentially play an important role in HIV-1 dissemination.
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Affiliation(s)
- Mireille Centlivre
- Laboratories of Experimental Virology, Department of Medical Microbiology, Center for Infection andImmunity Amsterdam, Tropical Medicine and AIDS, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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44
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Geldmacher C, Ngwenyama N, Schuetz A, Petrovas C, Reither K, Heeregrave EJ, Casazza JP, Ambrozak DR, Louder M, Ampofo W, Pollakis G, Hill B, Sanga E, Saathoff E, Maboko L, Roederer M, Paxton WA, Hoelscher M, Koup RA. Preferential infection and depletion of Mycobacterium tuberculosis-specific CD4 T cells after HIV-1 infection. ACTA ACUST UNITED AC 2010; 207:2869-81. [PMID: 21115690 PMCID: PMC3005236 DOI: 10.1084/jem.20100090] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
HIV-1 preferentially infects M. tuberculosis-specific CD4+ T cells due to their increased production of IL-2. HIV-1 infection results in the progressive loss of CD4 T cells. In this study, we address how different pathogen-specific CD4 T cells are affected by HIV infection and the cellular parameters involved. We found striking differences in the depletion rates between CD4 T cells to two common opportunistic pathogens, cytomegalovirus (CMV) and Mycobacterium tuberculosis (MTB). CMV-specific CD4 T cells persisted after HIV infection, whereas MTB-specific CD4 T cells were depleted rapidly. CMV-specific CD4 T cells expressed a mature phenotype and produced very little IL-2, but large amounts of MIP-1β. In contrast, MTB-specific CD4 T cells were less mature, and most produced IL-2 but not MIP-1β. Staphylococcal enterotoxin B–stimulated IL-2–producing cells were more susceptible to HIV infection in vitro than MIP-1β–producing cells. Moreover, IL-2 production was associated with expression of CD25, and neutralization of IL-2 completely abrogated productive HIV infection in vitro. HIV DNA was found to be most abundant in IL-2–producing cells, and least abundant in MIP-1β–producing MTB-specific CD4 T cells from HIV-infected subjects with active tuberculosis. These data support the hypothesis that differences in function affect the susceptibility of pathogen-specific CD4 T cells to HIV infection and depletion in vivo, providing a potential mechanism to explain the rapid loss of MTB-specific CD4 T cells after HIV infection.
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Affiliation(s)
- Christof Geldmacher
- Immunology Laboratory, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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45
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Pollakis G, A Paxton W. HIV-1 (co)Receptors: Implications for Vaccine and Therapy Design. Curr Pharm Des 2010; 16:3701-15. [DOI: 10.2174/138161210794079146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 10/15/2010] [Indexed: 11/22/2022]
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46
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Heeregrave EJ, Ampofo WK, Tetteh JKA, Ofori M, Ofori SB, Shah AS, Pollakis G, Paxton WA. Generation of HIV-1 primary isolates representative of plasma variants using the U87.CD4 cell line. J Virol Methods 2010; 169:341-50. [PMID: 20705104 DOI: 10.1016/j.jviromet.2010.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/28/2010] [Accepted: 08/03/2010] [Indexed: 11/26/2022]
Abstract
In order to obtain HIV-1 primary isolates in settings with limited access to donor PBMCs, a culture method was developed where patient PBMCs infected with HIV-1 were cultured together with U87.CD4 cells. Using this non-laborious method, it is possible to harvest virus solely on the basis of syncytia formation and circumventing monitoring of viral replication by CA-p24 ELISA. Primary isolates from 23 out of 33 patients (70%) were isolated successfully. From PCR amplification and sequencing of the V1V5 region of the viral gp120 envelope gene, primary isolates were compared with variants obtained from plasma and PBMCs of 13 patients. The primary isolates of seven patients (54%) resembled closely the plasma viral quasispecies, whereas different variants were isolated from the other patients (46%). Three patients harboured a dual infection, while this remained unnoticed from sequencing the plasma or PBMC compartment. The primary isolates were highly infectious for TZM-bl cells and could infect CD4-enriched lymphocytes. This study demonstrates that it is possible to grow viral isolates using a non-laborious and simple method. These isolates may be used in the field for studies on antiretroviral therapy or for vaccine trials.
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Affiliation(s)
- Edwin J Heeregrave
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
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47
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Ayele W, Mekonnen Y, Messele T, Mengistu Y, Tsegaye A, Bakker M, Berkhout B, Dorigo-Zetsma W, Wolday D, Goudsmit J, Coutinho R, de Baar M, Paxton WA, Pollakis G. Differences in HIV type 1 RNA plasma load profile of closely related cocirculating Ethiopian subtype C strains: C and C'. AIDS Res Hum Retroviruses 2010; 26:805-13. [PMID: 20624072 DOI: 10.1089/aid.2009.0152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Two HIV-1 subtype C subclusters have been identified in Ethiopia (C and C') with little knowledge regarding their biological or clinical differences. We longitudinally monitored HIV-1 viral loads and CD4(+) T cell counts for 130 subtype C-infected individuals from Ethiopia over 5 years. The genetic subclusters C and C' were determined and comparisons were made between the groups. None of the study individuals received antiretroviral therapy. Subcluster C' was found to be the more prevalent (72.3%) genotype circulating. Individuals infected with subcluster C' harbored higher viral loads in comparison to subcluster C-infected individuals when the CD4(+) T cell counts were high (500-900 cells/mm(3)), whereas at low CD4(+) T cell counts (0-150 cells/mm(3)) individuals infected with subcluster C viruses showed higher viral loads. We identified a greater number of deaths among individuals infected with subcluster C viruses in comparison to C'. Our results indicate that infection with subcluster C viruses leads to a more rapid onset of disease, despite the initial lower HIV-1 RNA plasma loads. Additionally, the higher viral loads seen for HIV-1 subcluster C' infections at higher CD4(+) T cell counts can help explain the higher prevalence of this subtype in Ethiopia.
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Affiliation(s)
- Workenesh Ayele
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | - Yared Mekonnen
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | - Tsehaynesh Messele
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | - Yohannes Mengistu
- Department of Microbiology, Immunology and Parasitology, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aster Tsegaye
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | - Margreet Bakker
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology–Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology–Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Wendelien Dorigo-Zetsma
- Regional Microbiological and Serological Laboratory, Hospital Hilversum, Hilversum, The Netherlands
| | - Dawit Wolday
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | | | - Roel Coutinho
- Rijksinstituut voor Volksgezondheid en Milieu (RIVM), 3721 MA Bilthoven, The Netherlands
| | | | - William A. Paxton
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology–Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology–Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Heeregrave EJ, Geels MJ, Brenchley JM, Baan E, Ambrozak DR, van der Sluis RM, Bennemeer R, Douek DC, Goudsmit J, Pollakis G, Koup RA, Paxton WA. Lack of in vivo compartmentalization among HIV-1 infected naïve and memory CD4+ T cell subsets. Virology 2009; 393:24-32. [PMID: 19698967 PMCID: PMC2753733 DOI: 10.1016/j.virol.2009.07.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 06/29/2009] [Accepted: 07/13/2009] [Indexed: 11/28/2022]
Abstract
Viral compartmentalization between naïve and memory CD4(+) T cell subsets has been described, but only for individuals who were receiving antiretroviral therapy (ART). We present here an extensive analysis of the viral quasispecies residing in the naïve, central and effector memory CD4(+) T cell subsets in a number of therapy naïve individuals and representing an array of HIV-1 subtypes. We longitudinally analyzed subset-specific infection and evolution in a subtype B infected individual who switches from CCR5 to dual CCR5/CXCR4 coreceptor usage. We show that the central memory subset, the predominantly infected subset, harbors a more diverse viral population compared to the others. Through sequence analysis of the env C2V3 region we demonstrate a lack of viral compartmentalization among all subsets. Upon coreceptor switch we observe a pronounced increase in the infection level of the naïve population. Our findings emphasize the importance of all CD4(+) T cell subsets to viral evolution.
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Affiliation(s)
- Edwin J. Heeregrave
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Mark J. Geels
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Jason M. Brenchley
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - Elly Baan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - David R. Ambrozak
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - Renee M. van der Sluis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Rune Bennemeer
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | | | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Richard A. Koup
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
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Stax MJ, Pollakis G, Sprenger RR, Melchers M, van Montfort T, Sanders RW, Speijer D, Paxton WA. P07-10. Natural compounds in bodily fluids which bind DC-SIGN and prevent HIV-1 capture and transfer to CD4 cells. Retrovirology 2009. [PMCID: PMC2767591 DOI: 10.1186/1742-4690-6-s3-p108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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50
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Stax MJ, van Montfort T, Sprenger RR, Melchers M, Sanders RW, van Leeuwen E, Repping S, Pollakis G, Speijer D, Paxton WA. Mucin 6 in seminal plasma binds DC-SIGN and potently blocks dendritic cell mediated transfer of HIV-1 to CD4(+) T-lymphocytes. Virology 2009; 391:203-11. [PMID: 19682628 DOI: 10.1016/j.virol.2009.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 04/03/2009] [Accepted: 06/06/2009] [Indexed: 10/20/2022]
Abstract
Many viruses transmitted via the genital or oral mucosa have the potential to interact with dendritic cell-specific intercellular adhesion molecule-3 grabbing non integrin (DC-SIGN) expressed on immature dendritic cells (iDCs) that lie below the mucosal surface. These cells have been postulated to capture and disseminate human immunodeficiency virus type-1 (HIV-1) to CD4(+) lymphocytes, potentially through breaches in the mucosal lining. We have previously described that BSSL (bile salt-stimulated lipase) in human milk can bind DC-SIGN and block transfer. Here we demonstrate that seminal plasma has similar DC-SIGN blocking properties as BSSL in human milk. Using comparative SDS-PAGE and Western blotting combined with mass spectrometry we identified mucin 6 as the DC-SIGN binding component in seminal plasma. Additionally, we demonstrate that purified mucin 6 binds DC-SIGN and successfully inhibits viral transfer. Mucin 6 in seminal plasma may therefore interfere with the sexual transmission of HIV-1 and other DC-SIGN co-opting viruses.
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Affiliation(s)
- Martijn J Stax
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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