1
|
Chowdhury S, Latham KA, Tran AC, Carroll CJ, Stanton RJ, Weekes MP, Neil SJD, Swanson CM, Strang BL. Inhibition of human cytomegalovirus replication by interferon alpha can involve multiple anti-viral factors. J Gen Virol 2023; 104:001929. [PMID: 38063292 PMCID: PMC10770924 DOI: 10.1099/jgv.0.001929] [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: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The shortcomings of current direct-acting anti-viral therapy against human cytomegalovirus (HCMV) has led to interest in host-directed therapy. Here we re-examine the use of interferon proteins to inhibit HCMV replication utilizing both high and low passage strains of HCMV. Pre-treatment of cells with interferon alpha (IFNα) was required for robust and prolonged inhibition of both low and high passage HCMV strains, with no obvious toxicity, and was associated with an increased anti-viral state in HCMV-infected cells. Pre-treatment of cells with IFNα led to poor expression of HCMV immediate-early proteins from both high and low passage strains, which was associated with the presence of the anti-viral factor SUMO-PML. Inhibition of HCMV replication in the presence of IFNα involving ZAP proteins was HCMV strain-dependent, wherein a high passage HCMV strain was obviously restricted by ZAP and a low passage strain was not. This suggested that strain-specific combinations of anti-viral factors were involved in inhibition of HCMV replication in the presence of IFNα. Overall, this work further supports the development of strategies involving IFNα that may be useful to inhibit HCMV replication and highlights the complexity of the anti-viral response to HCMV in the presence of IFNα.
Collapse
Affiliation(s)
- Shabab Chowdhury
- Institute of Infection & Immunity, St George’s, University of London, London, UK
| | - Katie A. Latham
- Institute of Infection & Immunity, St George’s, University of London, London, UK
| | - Andy C. Tran
- Institute of Infection & Immunity, St George’s, University of London, London, UK
| | - Christopher J. Carroll
- Institute of Molecular & Cellular Sciences, St George’s, University of London, London, UK
| | - Richard J. Stanton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Blair L. Strang
- Institute of Infection & Immunity, St George’s, University of London, London, UK
| |
Collapse
|
2
|
Alcolea-Medina A, Snell LB, Alder C, Charalampous T, Williams TGS, Tan MKI, Al-Yaakoubi N, Humayun G, Newsholme W, Goldenberg S, Nebbia G, Neil SJD, Batra R, Edgeworth JD. The ongoing Streptococcus pyogenes (Group A Streptococcus) outbreak in London, United Kingdom, in December 2022: a molecular epidemiology study. Clin Microbiol Infect 2023; 29:887-890. [PMID: 36925107 PMCID: PMC10769882 DOI: 10.1016/j.cmi.2023.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 01/06/2023] [Revised: 02/27/2023] [Accepted: 03/05/2023] [Indexed: 03/17/2023]
Abstract
OBJECTIVES Epidemiological and whole-genome sequencing analysis of an ongoing outbreak of Streptococcus pyogenes (Group A Streptococcus) in London (United Kingdom). METHODS Prospective identification of Group A Streptococcus cases from a diagnostic laboratory serving central and south London between 27 November and 10 December 2022. Case notes were reviewed and isolates were retrieved. Case numbers were compared with the previous 5 years. Whole-genome sequencing was performed with long-read, nanopore technology for emm typing and identification of superantigen genes. Associations of pathogen-related factors with an invasive disease were assessed by single-variable and multi-variable logistic regression. RESULTS Case numbers began increasing in October 2022 from a baseline of 2.0 cases per day, and in December 2022, the average daily case numbers reached 10.8 cases per day, four-fold the number usually seen in winter. A total of 113 cases were identified during the prospective study period. Three quarters (86/113, 76%) were paediatric cases, including 2 deaths. Of 113 cases, 11 (10%) were invasive. In total, 56 isolates were successfully sequenced, including 10 of 11 (91%) invasive isolates. The emm12 (33/56, 59%) and emm1 (9/56, 16%) types were predominant, with 7 of 9 (78%) emm1 isolates being from the M1uk clone. The majority of invasive isolates had superantigen genes spea (7/10, 70%) and spej (8/10, 80%), whereas, in non-invasive isolates, these superantigen genes were found less frequently (spea: 5/46, 11% and spej: 7/46, 15%). By multivariable analysis of pathogen-related factors, spea (OR 8.9, CI 1.4-57, p 0.020) and spej (OR 12, CI 1.8-78, p 0.011) were associated with invasive disease. CONCLUSIONS emm12 and emm1 types predominate in the ongoing outbreak, which mainly affects children. In this outbreak, the spea and spej superantigen genes are associated with the severity of presentation.
Collapse
Affiliation(s)
- Adela Alcolea-Medina
- Department of Infectious Diseases, King's College London, London, UK; Infection Sciences, Synnovis, London, UK
| | - Luke B Snell
- Department of Infectious Diseases, King's College London, London, UK; Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK.
| | - Christopher Alder
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | | | - Tom G S Williams
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Mark K I Tan
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Noor Al-Yaakoubi
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Gul Humayun
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - William Newsholme
- Department of Infection, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Simon Goldenberg
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK; Department of Infection, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, London, UK
| | - Rahul Batra
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, King's College London, London, UK; Centre for Clinical Diagnostics & Infectious Disease Research, Guy's & St. Thomas' NHS Foundation Trust, London, UK
| |
Collapse
|
3
|
Lista MJ, Witney AA, Nichols J, Davison AJ, Wilson H, Latham KA, Ravenhill BJ, Nightingale K, Stanton RJ, Weekes MP, Neil SJD, Swanson CM, Strang BL. Strain-Dependent Restriction of Human Cytomegalovirus by Zinc Finger Antiviral Proteins. J Virol 2023; 97:e0184622. [PMID: 36916924 PMCID: PMC10062169 DOI: 10.1128/jvi.01846-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/29/2022] [Accepted: 02/16/2023] [Indexed: 03/15/2023] Open
Abstract
Cellular antiviral factors that recognize viral nucleic acid can inhibit virus replication. These include the zinc finger antiviral protein (ZAP), which recognizes high CpG dinucleotide content in viral RNA. Here, we investigated the ability of ZAP to inhibit the replication of human cytomegalovirus (HCMV). Depletion of ZAP or its cofactor KHNYN increased the titer of the high-passage HCMV strain AD169 but had little effect on the titer of the low-passage strain Merlin. We found no obvious difference in expression of several viral proteins between AD169 and Merlin in ZAP knockdown cells, but observed a larger increase in infectious virus in AD169 compared to Merlin in the absence of ZAP, suggesting that ZAP inhibited events late in AD169 replication. In addition, there was no clear difference in the CpG abundance of AD169 and Merlin RNAs, indicating that genomic content of the two virus strains was unlikely to be responsible for differences in their sensitivity to ZAP. Instead, we observed less ZAP expression in Merlin-infected cells late in replication compared to AD169-infected cells, which may be related to different abilities of the two virus strains to regulate interferon signaling. Therefore, there are strain-dependent differences in the sensitivity of HCMV to ZAP, and the ability of low-passage HCMV strain Merlin to evade inhibition by ZAP is likely related to its ability to regulate interferon signaling, not the CpG content of RNAs produced from its genome. IMPORTANCE Determining the function of cellular antiviral factors can inform our understanding of virus replication. The zinc finger antiviral protein (ZAP) can inhibit the replication of diverse viruses. Here, we examined ZAP interaction with the DNA virus human cytomegalovirus (HCMV). We found HCMV strain-dependent differences in the ability of ZAP to influence HCMV replication, which may be related to the interaction of HCMV strains with the type I interferon system. These observations affect our current understanding of how ZAP restricts HCMV and how HCMV interacts with the type I interferon system.
Collapse
Affiliation(s)
- Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Adam A. Witney
- Institute of Infection & Immunity, St George’s, University of London, London, United Kingdom
| | - Jenna Nichols
- MRC–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Andrew J. Davison
- MRC–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Katie A. Latham
- Institute of Infection & Immunity, St George’s, University of London, London, United Kingdom
| | - Benjamin J. Ravenhill
- Cambridge Institute for Medical Research, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Katie Nightingale
- Cambridge Institute for Medical Research, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Richard J. Stanton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Blair L. Strang
- Institute of Infection & Immunity, St George’s, University of London, London, United Kingdom
| |
Collapse
|
4
|
Snell LB, Alcolea-Medina A, Charalampous T, Alder C, Williams TGS, Flaviani F, Batra R, Bakrania P, Thangarajah R, Neil SJD, van Nispen Tot Pannerden C, Botgros A, Aarons E, Douthwaite ST, Edgeworth JD, Nebbia G. Real-Time Whole Genome Sequencing to Guide Patient-Tailored Therapy of Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Clin Infect Dis 2023; 76:1125-1128. [PMID: 36327795 PMCID: PMC10029986 DOI: 10.1093/cid/ciac864] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022] Open
Abstract
The management of coronavirus disease 2019 has become more complex due to the expansion of available therapies. The presence of severe acute respiratory syndrome coronavirus 2 variants and mutations further complicates treatment due to their differing susceptibilities to therapies. Here we outline the use of real-time whole genome sequencing to detect persistent infection, evaluate for mutations confering resistance to treatments, and guide treatment decisions.
Collapse
Affiliation(s)
- Luke B Snell
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | | | - Christopher Alder
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Tom G S Williams
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Flavia Flaviani
- National Institute for Health Research Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Prijay Bakrania
- Department of Pharmacy, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rajeni Thangarajah
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Department of Pharmacy, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, United Kingdom
| | | | - Alina Botgros
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Emma Aarons
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Samuel T Douthwaite
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | - Gaia Nebbia
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King's College London, United Kingdom
| |
Collapse
|
5
|
Lista MJ, Ficarelli M, Wilson H, Kmiec D, Youle RL, Wanford J, Winstone H, Odendall C, Taylor IA, Neil SJD, Swanson CM. A Nuclear Export Signal in KHNYN Required for Its Antiviral Activity Evolved as ZAP Emerged in Tetrapods. J Virol 2023; 97:e0087222. [PMID: 36633408 PMCID: PMC9888277 DOI: 10.1128/jvi.00872-22] [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: 06/06/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
The zinc finger antiviral protein (ZAP) inhibits viral replication by directly binding CpG dinucleotides in cytoplasmic viral RNA to inhibit protein synthesis and target the RNA for degradation. ZAP evolved in tetrapods and there are clear orthologs in reptiles, birds, and mammals. When ZAP emerged, other proteins may have evolved to become cofactors for its antiviral activity. KHNYN is a putative endoribonuclease that is required for ZAP to restrict retroviruses. To determine its evolutionary path after ZAP emerged, we compared KHNYN orthologs in mammals and reptiles to those in fish, which do not encode ZAP. This identified residues in KHNYN that are highly conserved in species that encode ZAP, including several in the CUBAN domain. The CUBAN domain interacts with NEDD8 and Cullin-RING E3 ubiquitin ligases. Deletion of the CUBAN domain decreased KHNYN antiviral activity, increased protein expression and increased nuclear localization. However, mutation of residues required for the CUBAN domain-NEDD8 interaction increased KHNYN abundance but did not affect its antiviral activity or cytoplasmic localization, indicating that Cullin-mediated degradation may control its homeostasis and regulation of protein turnover is separable from its antiviral activity. By contrast, the C-terminal residues in the CUBAN domain form a CRM1-dependent nuclear export signal (NES) that is required for its antiviral activity. Deletion or mutation of the NES increased KHNYN nuclear localization and decreased its interaction with ZAP. The final 2 positions of this NES are not present in fish KHNYN orthologs and we hypothesize their evolution allowed KHNYN to act as a ZAP cofactor. IMPORTANCE The interferon system is part of the innate immune response that inhibits viruses and other pathogens. This system emerged approximately 500 million years ago in early vertebrates. Since then, some genes have evolved to become antiviral interferon-stimulated genes (ISGs) while others evolved so their encoded protein could interact with proteins encoded by ISGs and contribute to their activity. However, this remains poorly characterized. ZAP is an ISG that arose during tetrapod evolution and inhibits viral replication. Because KHNYN interacts with ZAP and is required for its antiviral activity against retroviruses, we conducted an evolutionary analysis to determine how specific amino acids in KHNYN evolved after ZAP emerged. This identified a nuclear export signal that evolved in tetrapods and is required for KHNYN to traffic in the cell and interact with ZAP. Overall, specific residues in KHNYN evolved to allow it to act as a cofactor for ZAP antiviral activity.
Collapse
Affiliation(s)
- Maria J. Lista
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Mattia Ficarelli
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Harry Wilson
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Dorota Kmiec
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Rebecca L. Youle
- King’s College London, Department of Infectious Diseases, London, United Kingdom
- The Francis Crick Institute, Macromolecular Structure Laboratory, London, United Kingdom
| | - Joseph Wanford
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Helena Winstone
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Charlotte Odendall
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Ian A. Taylor
- The Francis Crick Institute, Macromolecular Structure Laboratory, London, United Kingdom
| | - Stuart J. D. Neil
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Chad M. Swanson
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| |
Collapse
|
6
|
Lista MJ, Winstone H, Wilson HD, Dyer A, Pickering S, Galao RP, De Lorenzo G, Cowton VM, Furnon W, Suarez N, Orton R, Palmarini M, Patel AH, Snell L, Nebbia G, Swanson C, Neil SJD. The P681H Mutation in the Spike Glycoprotein of the Alpha Variant of SARS-CoV-2 Escapes IFITM Restriction and Is Necessary for Type I Interferon Resistance. J Virol 2022; 96:e0125022. [PMID: 36350154 PMCID: PMC9749455 DOI: 10.1128/jvi.01250-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
The appearance of new dominant variants of concern (VOC) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the coronavirus disease 2019 (COVID-19) pandemic. Of these, the alpha variant (also known as B.1.1.7), which appeared initially in the United Kingdom, became the dominant variant in much of Europe and North America in the first half of 2021. The spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation adjacent to the polybasic cleavage site, which has been suggested to enhance S cleavage. Here, we show that the alpha spike protein confers a level of resistance to beta interferon (IFN-β) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN-β and context-dependent resistance to IFITMs in the alpha S. P681H reduces dependence on endosomal cathepsins, consistent with enhanced cell surface entry. However, reversion of H681 does not reduce cleaved spike incorporation into particles, indicating that it exerts its effect on entry and IFN-β downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOC may well also confer a replication and/or transmission advantage through adaptation to resist innate immune mechanisms. IMPORTANCE Accumulating evidence suggests that variants of concern (VOC) of SARS-CoV-2 evolve to evade the human immune response, with much interest focused on mutations in the spike protein that escape from antibodies. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here, we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type I interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2 and enhancement by its paralogue IFITM3. The key determinant of this is a proline-to-histidine change at position 681 in S adjacent to the furin cleavage site, which in the context of the alpha spike modulates cell entry pathways of SARS-CoV-2. Reversion of the mutation is sufficient to restore interferon and IFITM2 sensitivity, highlighting the dynamic nature of the SARS CoV-2 as it adapts to both innate and adaptive immunity in the humans.
Collapse
Affiliation(s)
- Maria Jose Lista
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Helena Winstone
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Adam Dyer
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Rui Pedro Galao
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicolas Suarez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Luke Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Chad Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| |
Collapse
|
7
|
Galão RP, Wilson H, Schierhorn KL, Debeljak F, Bodmer BS, Goldhill D, Hoenen T, Wilson SJ, Swanson CM, Neil SJD. TRIM25 and ZAP target the Ebola virus ribonucleoprotein complex to mediate interferon-induced restriction. PLoS Pathog 2022; 18:e1010530. [PMID: 35533151 PMCID: PMC9119685 DOI: 10.1371/journal.ppat.1010530] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 05/19/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Ebola virus (EBOV) causes highly pathogenic disease in primates. Through screening a library of human interferon-stimulated genes (ISGs), we identified TRIM25 as a potent inhibitor of EBOV transcription-and-replication-competent virus-like particle (trVLP) propagation. TRIM25 overexpression inhibited the accumulation of viral genomic and messenger RNAs independently of the RNA sensor RIG-I or secondary proinflammatory gene expression. Deletion of TRIM25 strongly attenuated the sensitivity of trVLPs to inhibition by type-I interferon. The antiviral activity of TRIM25 required ZAP and the effect of type-I interferon was modulated by the CpG dinucleotide content of the viral genome. We find that TRIM25 interacts with the EBOV vRNP, resulting in its autoubiquitination and ubiquitination of the viral nucleoprotein (NP). TRIM25 is recruited to incoming vRNPs shortly after cell entry and leads to dissociation of NP from the vRNA. We propose that TRIM25 targets the EBOV vRNP, exposing CpG-rich viral RNA species to restriction by ZAP.
Collapse
Affiliation(s)
- Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Kristina L. Schierhorn
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Franka Debeljak
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Bianca S. Bodmer
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Daniel Goldhill
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Thomas Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Sam J. Wilson
- MRC Centre for Virus Research, University of Glasgow, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| |
Collapse
|
8
|
Snell LB, Fisher CL, Taj U, Stirrup O, Merrick B, Alcolea-Medina A, Charalampous T, Signell AW, Wilson HD, Betancor G, Kia Ik MT, Cunningham E, Cliff PR, Pickering S, Galao RP, Batra R, Neil SJD, Malim MH, Doores KJ, Douthwaite ST, Nebbia G, Edgeworth JD, Awan AR. Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission. Clin Microbiol Infect 2022; 28:93-100. [PMID: 34400345 PMCID: PMC8361005 DOI: 10.1016/j.cmi.2021.07.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/28/2021] [Accepted: 07/31/2021] [Indexed: 01/24/2023]
Abstract
OBJECTIVES To analyse nosocomial transmission in the early stages of the coronavirus 2019 (COVID-19) pandemic at a large multisite healthcare institution. Nosocomial incidence is linked with infection control interventions. METHODS Viral genome sequence and epidemiological data were analysed for 574 consecutive patients, including 86 nosocomial cases, with a positive PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the first 19 days of the pandemic. RESULTS Forty-four putative transmission clusters were found through epidemiological analysis; these included 234 cases and all 86 nosocomial cases. SARS-CoV-2 genome sequences were obtained from 168/234 (72%) of these cases in epidemiological clusters, including 77/86 nosocomial cases (90%). Only 75/168 (45%) of epidemiologically linked, sequenced cases were not refuted by applying genomic data, creating 14 final clusters accounting for 59/77 sequenced nosocomial cases (77%). Viral haplotypes from these clusters were enriched 1-14x (median 4x) compared to the community. Three factors implicated unidentified cases in transmission: (a) community-onset or indeterminate cases were absent in 7/14 clusters (50%), (b) four clusters (29%) had additional evidence of cryptic transmission, and (c) in three clusters (21%) diagnosis of the earliest case was delayed, which may have facilitated transmission. Nosocomial cases decreased to low levels (0-2 per day) despite continuing high numbers of admissions of community-onset SARS-CoV-2 cases (40-50 per day) and before the impact of introducing universal face masks and banning hospital visitors. CONCLUSION Genomics was necessary to accurately resolve transmission clusters. Our data support unidentified cases-such as healthcare workers or asymptomatic patients-as important vectors of transmission. Evidence is needed to ascertain whether routine screening increases case ascertainment and limits nosocomial transmission.
Collapse
Affiliation(s)
- Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, UK; Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Chloe L Fisher
- Genomics Innovation Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Usman Taj
- Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, UK; Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, UK
| | | | - Harry D Wilson
- Department of Infectious Diseases, School of Immunological and Microbial Sciences, King's College London, UK
| | - Gilberto Betancor
- Department of Infectious Diseases, School of Immunological and Microbial Sciences, King's College London, UK
| | - Mark Tan Kia Ik
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, UK
| | - Emma Cunningham
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK
| | | | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunological and Microbial Sciences, King's College London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunological and Microbial Sciences, King's College London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, UK; Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunological and Microbial Sciences, King's College London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunological and Microbial Sciences, King's College London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunological and Microbial Sciences, King's College London, UK
| | - Sam T Douthwaite
- Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, UK; Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, UK; Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Ali R Awan
- Genomics Innovation Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK.
| |
Collapse
|
9
|
Khan H, Winstone H, Jimenez-Guardeño JM, Graham C, Doores KJ, Goujon C, Matthews DA, Davidson AD, Rihn SJ, Palmarini M, Neil SJD, Malim MH. TMPRSS2 promotes SARS-CoV-2 evasion from NCOA7-mediated restriction. PLoS Pathog 2021; 17:e1009820. [PMID: 34807954 PMCID: PMC8648102 DOI: 10.1371/journal.ppat.1009820] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/06/2021] [Accepted: 11/09/2021] [Indexed: 12/18/2022] Open
Abstract
Interferons play a critical role in regulating host immune responses to SARS-CoV-2, but the interferon (IFN)-stimulated gene (ISG) effectors that inhibit SARS-CoV-2 are not well characterized. The IFN-inducible short isoform of human nuclear receptor coactivator 7 (NCOA7) inhibits endocytic virus entry, interacts with the vacuolar ATPase, and promotes endo-lysosomal vesicle acidification and lysosomal protease activity. Here, we used ectopic expression and gene knockout to demonstrate that NCOA7 inhibits infection by SARS-CoV-2 as well as by lentivirus particles pseudotyped with SARS-CoV-2 Spike in lung epithelial cells. Infection with the highly pathogenic, SARS-CoV-1 and MERS-CoV, or seasonal, HCoV-229E and HCoV-NL63, coronavirus Spike-pseudotyped viruses was also inhibited by NCOA7. Importantly, either overexpression of TMPRSS2, which promotes plasma membrane fusion versus endosomal fusion of SARS-CoV-2, or removal of Spike's polybasic furin cleavage site rendered SARS-CoV-2 less sensitive to NCOA7 restriction. Collectively, our data indicate that furin cleavage sensitizes SARS-CoV-2 Spike to the antiviral consequences of endosomal acidification by NCOA7, and suggest that the acquisition of furin cleavage may have favoured the co-option of cell surface TMPRSS proteases as a strategy to evade the suppressive effects of IFN-induced endo-lysosomal dysregulation on virus infection.
Collapse
Affiliation(s)
- Hataf Khan
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Jose M. Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | | | - David A. Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, United Kingdom
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, United Kingdom
| | - Suzannah J. Rihn
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| |
Collapse
|
10
|
Kmiec D, Lista MJ, Ficarelli M, Swanson CM, Neil SJD. S-farnesylation is essential for antiviral activity of the long ZAP isoform against RNA viruses with diverse replication strategies. PLoS Pathog 2021; 17:e1009726. [PMID: 34695163 PMCID: PMC8568172 DOI: 10.1371/journal.ppat.1009726] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/04/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
The zinc finger antiviral protein (ZAP) is a broad inhibitor of virus replication. Its best-characterized function is to bind CpG dinucleotides present in viral RNAs and, through the recruitment of TRIM25, KHNYN and other cofactors, target them for degradation or prevent their translation. The long and short isoforms of ZAP (ZAP-L and ZAP-S) have different intracellular localization and it is unclear how this regulates their antiviral activity against viruses with different sites of replication. Using ZAP-sensitive and ZAP-insensitive human immunodeficiency virus type I (HIV-1), which transcribe the viral RNA in the nucleus and assemble virions at the plasma membrane, we show that the catalytically inactive poly-ADP-ribose polymerase (PARP) domain in ZAP-L is essential for CpG-specific viral restriction. Mutation of a crucial cysteine in the C-terminal CaaX box that mediates S-farnesylation and, to a lesser extent, the residues in place of the catalytic site triad within the PARP domain, disrupted the activity of ZAP-L. Addition of the CaaX box to ZAP-S partly restored antiviral activity, explaining why ZAP-S lacks antiviral activity for CpG-enriched HIV-1 despite conservation of the RNA-binding domain. Confocal microscopy confirmed the CaaX motif mediated localization of ZAP-L to vesicular structures and enhanced physical association with intracellular membranes. Importantly, the PARP domain and CaaX box together jointly modulate the interaction between ZAP-L and its cofactors TRIM25 and KHNYN, implying that its proper subcellular localisation is required to establish an antiviral complex. The essential contribution of the PARP domain and CaaX box to ZAP-L antiviral activity was further confirmed by inhibition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication, which replicates in double-membrane vesicles derived from the endoplasmic reticulum. Thus, compartmentalization of ZAP-L on intracellular membranes provides an essential effector function in ZAP-L-mediated antiviral activity against divergent viruses with different subcellular replication sites.
Collapse
Affiliation(s)
- Dorota Kmiec
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - María José Lista
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Mattia Ficarelli
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| |
Collapse
|
11
|
Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang X, Leibowitz JL, Neil SJD, Skern T, Weiss SR, Worobey M, Andersen KG, Garry RF, Rambaut A. The origins of SARS-CoV-2: A critical review. Cell 2021; 184:4848-4856. [PMID: 34480864 PMCID: PMC8373617 DOI: 10.1016/j.cell.2021.08.017] [Citation(s) in RCA: 260] [Impact Index Per Article: 86.7] [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: 07/10/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 01/11/2023]
Abstract
Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.
Collapse
Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94704, USA
| | - Joel O Wertheim
- Department of Medicine, University of California-San Diego, La Jolla, CA 92093, USA
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College, London W2 1PG, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter C Doherty
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | | | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand; Institute of Environmental Science and Research, Wellington 5022, New Zealand
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University (XJTLU), Suzhou, China
| | - Julian L Leibowitz
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX 77807, USA
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Tim Skern
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Zalgen Labs, Germantown, MD 20876, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.
| |
Collapse
|
12
|
Pickering S, Batra R, Merrick B, Snell LB, Nebbia G, Douthwaite S, Reid F, Patel A, Kia Ik MT, Patel B, Charalampous T, Alcolea-Medina A, Lista MJ, Cliff PR, Cunningham E, Mullen J, Doores KJ, Edgeworth JD, Malim MH, Neil SJD, Galão RP. Comparative performance of SARS-CoV-2 lateral flow antigen tests and association with detection of infectious virus in clinical specimens: a single-centre laboratory evaluation study. Lancet Microbe 2021; 2:e461-e471. [PMID: 34226893 PMCID: PMC8245061 DOI: 10.1016/s2666-5247(21)00143-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Lateral flow devices (LFDs) for rapid antigen testing are set to become a cornerstone of SARS-CoV-2 mass community testing, although their reduced sensitivity compared with PCR has raised questions of how well they identify infectious cases. Understanding their capabilities and limitations is, therefore, essential for successful implementation. We evaluated six commercial LFDs and assessed their correlation with infectious virus culture and PCR cycle threshold (Ct) values. METHODS In a single-centre, laboratory evaluation study, we did a head-to-head comparison of six LFDs commercially available in the UK: Innova Rapid SARS-CoV-2 Antigen Test, Spring Healthcare SARS-CoV-2 Antigen Rapid Test Cassette, E25Bio Rapid Diagnostic Test, Encode SARS-CoV-2 Antigen Rapid Test Device, SureScreen COVID-19 Rapid Antigen Test Cassette, and SureScreen COVID-19 Rapid Fluorescence Antigen Test. We estimated the specificities and sensitivities of the LFDs using stored naso-oropharyngeal swabs collected at St Thomas' Hospital (London, UK) for routine diagnostic SARS-CoV-2 testing by real-time RT-PCR (RT-rtPCR). Swabs were from inpatients and outpatients from all departments of St Thomas' Hospital, and from health-care staff (all departments) and their household contacts. SARS-CoV-2-negative swabs from the same population (confirmed by RT-rtPCR) were used for comparative specificity determinations. All samples were collected between March 23 and Oct 27, 2020. We determined the limit of detection (LOD) for each test using viral plaque-forming units (PFUs) and viral RNA copy numbers of laboratory-grown SARS-CoV-2. Additionally, LFDs were selected to assess the correlation of antigen test result with RT-rtPCR Ct values and positive viral culture in Vero E6 cells. This analysis included longitudinal swabs from five infected inpatients with varying disease severities. Furthermore, the sensitivities of available LFDs were assessed in swabs (n=23; collected from Dec 4, 2020, to Jan 12, 2021) confirmed to be positive (RT-rtPCR and whole-genome sequencing) for the B.1.1.7 variant, which was the dominant genotype in the UK at the time of study completion. FINDINGS All LFDs showed high specificity (≥98·0%), except for the E25Bio test (86·0% [95% CI 77·9-99·9]), and most tests reliably detected 50 PFU/test (equivalent SARS-CoV-2 N gene Ct value of 23·7, or RNA copy number of 3 × 106/mL). Sensitivities of the LFDs on clinical samples ranged from 65·0% (55·2-73·6) to 89·0% (81·4-93·8). These sensitivities increased to greater than 90% for samples with Ct values of lower than 25 for all tests except the SureScreen fluorescence (SureScreen-F) test. Positive virus culture was identified in 57 (40·4%) of 141 samples; 54 (94·7%) of the positive cultures were from swabs with Ct values lower than 25. Among the three LFDs selected for detailed comparisons (the tests with highest sensitivity [Innova], highest specificity [Encode], and alternative technology [SureScreen-F]), sensitivity of the LFDs increased to at least 94·7% when only including samples with detected viral growth. Longitudinal studies of RT-rtPCR-positive samples (tested with Innova, Encode, and both SureScreen-F and the SureScreen visual [SureScreen-V] test) showed that most of the tests identified all infectious samples as positive. Test performance (assessed for Innova and SureScreen-V) was not affected when reassessed on swabs positive for the UK variant B.1.1.7. INTERPRETATION In this comprehensive comparison of antigen LFDs and virus infectivity, we found a clear relationship between Ct values, quantitative culture of infectious virus, and antigen LFD positivity in clinical samples. Our data support regular testing of target groups with LFDs to supplement the current PCR testing capacity, which would help to rapidly identify infected individuals in situations in which they would otherwise go undetected. FUNDING King's Together Rapid COVID-19, Medical Research Council, Wellcome Trust, Huo Family Foundation, UK Department of Health, National Institute for Health Research Comprehensive Biomedical Research Centre.
Collapse
Affiliation(s)
- Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sam Douthwaite
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Fiona Reid
- School of Population Health and Environmental Sciences, King's College London, London, UK
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mark Tan Kia Ik
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Bindi Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
- Viapath Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Penelope R Cliff
- Viapath Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Emma Cunningham
- Viapath Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jane Mullen
- Viapath Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| |
Collapse
|
13
|
Abstract
The zinc finger antiviral protein (ZAP) restricts the replication of a broad range of RNA and DNA viruses. ZAP directly binds viral RNA, targeting it for degradation and inhibiting its translation. While the full scope of RNA determinants involved in mediating selective ZAP activity are unclear, ZAP binds CpG dinucleotides, dictating at least part of its target specificity. ZAP interacts with many cellular proteins, although only a few have been demonstrated to be essential for its antiviral activity, including the 3'-5' exoribonuclease exosome complex, TRIM25, and KHNYN. In addition to inhibiting viral gene expression, ZAP also directly and indirectly targets a subset of cellular messenger RNAs to regulate the innate immune response. Overall, ZAP protects a cell from viral infection by restricting viral replication and regulating cellular gene expression. Further understanding of the ZAP antiviral system may allow for novel viral vaccine and anticancer therapy development. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Mattia Ficarelli
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London SE1 9RT, United Kingdom;
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London SE1 9RT, United Kingdom;
| | - Chad M Swanson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London SE1 9RT, United Kingdom;
| |
Collapse
|
14
|
Koller G, Morrell AP, Galão RP, Pickering S, MacMahon E, Johnson J, Ignatyev K, Neil SJD, Elsharkawy S, Fleck R, Machado PMP, Addison O. More than the Eye Can See: Shedding New Light on SARS-CoV-2 Lateral Flow Device-Based Immunoassays. ACS Appl Mater Interfaces 2021; 13:25694-25700. [PMID: 34048220 PMCID: PMC8188736 DOI: 10.1021/acsami.1c04283] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Containing the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been an unprecedented challenge due to high horizontal transmissivity and asymptomatic carriage rates. Lateral flow device (LFD) immunoassays were introduced in late 2020 to detect SARS-CoV-2 infection in asymptomatic or presymptomatic individuals rapidly. While LFD technologies have been used for over 60 years, their widespread use as a public health tool during a pandemic is unprecedented. By the end of 2020, data from studies into the efficacy of the LFDs emerged and showed these point-of-care devices to have very high specificity (ability to identify true negatives) but inadequate sensitivity with high false-negative rates. The low sensitivity (<50%) shown in several studies is a critical public health concern, as asymptomatic or presymptomatic carriers may wrongly be assumed to be noninfectious, posing a significant risk of further spread in the community. Here, we show that the direct visual readout of SARS-CoV-2 LFDs is an inadequate approach to discriminate a potentially infective viral concentration in a biosample. We quantified significant immobilized antigen-antibody-labeled conjugate complexes within the LFDs visually scored as negative using high-sensitivity synchrotron X-ray fluorescence imaging. Correlating quantitative X-ray fluorescence measurements and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) determined numbers of viral copies, we identified that negatively scored samples could contain up to 100 PFU (equivalent here to ∼10 000 RNA copies/test). The study demonstrates where the shortcomings arise in many of the current direct-readout SARS-CoV-2 LFDs, namely, being a deficiency in the readout as opposed to the potential level of detection of the test, which is orders of magnitude higher. The present findings are of importance both to public health monitoring during the Coronavirus Disease 2019 (COVID-19) pandemic and to the rapid refinement of these tools for immediate and future applications.
Collapse
Affiliation(s)
- Garrit Koller
- Centre
for Host Microbiome Interactions, Faculty of Dentistry, Oral &
Craniofacial Sciences, Kingʼs College
London, London, SE1 9RT, United Kingdom
| | - Alexander P. Morrell
- Centre
for Oral, Clinical & Translational Sciences, Faculty of Dentistry,
Oral & Craniofacial Sciences, Kingʼs
College London, London SE1 9RT, United Kingdom.
| | - Rui Pedro Galão
- Department
of Infectious Diseases, School of Immunology & Microbial Sciences, Kingʼs College London, London SE1 9RT, United Kingdom
| | - Suzanne Pickering
- Department
of Infectious Diseases, School of Immunology & Microbial Sciences, Kingʼs College London, London SE1 9RT, United Kingdom
| | - Eithne MacMahon
- Department
of Infectious Diseases, School of Immunology & Microbial Sciences, Kingʼs College London, London SE1 9RT, United Kingdom
- Guyʼs
and St Thomasʼ NHS Foundation Trust, London SE1 9RT, United Kingdom
| | - Joanna Johnson
- Guyʼs
and St Thomasʼ NHS Foundation Trust, London SE1 9RT, United Kingdom
| | | | - Stuart J. D. Neil
- Department
of Infectious Diseases, School of Immunology & Microbial Sciences, Kingʼs College London, London SE1 9RT, United Kingdom
| | - Sherif Elsharkawy
- Centre
for Oral, Clinical & Translational Sciences, Faculty of Dentistry,
Oral & Craniofacial Sciences, Kingʼs
College London, London SE1 9RT, United Kingdom.
| | - Roland Fleck
- Centre for
Ultrastructural Imaging, Kingʼs College
London, London SE1 9RT, United Kingdom
| | | | - Owen Addison
- Centre
for Oral, Clinical & Translational Sciences, Faculty of Dentistry,
Oral & Craniofacial Sciences, Kingʼs
College London, London SE1 9RT, United Kingdom.
| |
Collapse
|
15
|
Graham C, Seow J, Huettner I, Khan H, Kouphou N, Acors S, Winstone H, Pickering S, Galao RP, Dupont L, Lista MJ, Jimenez-Guardeño JM, Laing AG, Wu Y, Joseph M, Muir L, van Gils MJ, Ng WM, Duyvesteyn HME, Zhao Y, Bowden TA, Shankar-Hari M, Rosa A, Cherepanov P, McCoy LE, Hayday AC, Neil SJD, Malim MH, Doores KJ. Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant. Immunity 2021; 54:1276-1289.e6. [PMID: 33836142 PMCID: PMC8015430 DOI: 10.1016/j.immuni.2021.03.023] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [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: 02/03/2021] [Revised: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 01/21/2023]
Abstract
Interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the receptor ACE2 on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies, and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, N-terminal domain (NTD) and S2 subunits of Spike. To understand how these mutations affect Spike antigenicity, we isolated and characterized >100 monoclonal antibodies targeting epitopes on RBD, NTD, and S2 from SARS-CoV-2-infected individuals. Approximately 45% showed neutralizing activity, of which ∼20% were NTD specific. NTD-specific antibodies formed two distinct groups: the first was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Mutations present in B.1.1.7 Spike frequently conferred neutralization resistance to NTD-specific antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes should be considered when investigating antigenic drift in emerging variants.
Collapse
Affiliation(s)
- Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Liane Dupont
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Adam G Laing
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Yin Wu
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Magdalene Joseph
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Luke Muir
- Division of Infection and Immunity, University College London, London, UK
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands
| | - Weng M Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Adrian C Hayday
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK; The Francis Crick Institute, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK; Genotype-to-Phenotype UK National Virology Consortium.
| |
Collapse
|
16
|
Winstone H, Lista MJ, Reid AC, Bouton C, Pickering S, Galao RP, Kerridge C, Doores KJ, Swanson CM, Neil SJD. The Polybasic Cleavage Site in SARS-CoV-2 Spike Modulates Viral Sensitivity to Type I Interferon and IFITM2. J Virol 2021; 95:e02422-20. [PMID: 33563656 PMCID: PMC8104117 DOI: 10.1128/jvi.02422-20] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/03/2021] [Indexed: 12/31/2022] Open
Abstract
The cellular entry of severe acute respiratory syndrome-associated coronaviruses types 1 and 2 (SARS-CoV-1 and -2) requires sequential protease processing of the viral spike glycoprotein. The presence of a polybasic cleavage site in SARS-CoV-2 spike at the S1/S2 boundary has been suggested to be a factor in the increased transmissibility of SARS-CoV-2 compared to SARS-CoV-1 by facilitating maturation of the spike precursor by furin-like proteases in the producer cells rather than endosomal cathepsins in the target. We investigate the relevance of the polybasic cleavage site in the route of entry of SARS-CoV-2 and the consequences this has for sensitivity to interferons (IFNs) and, more specifically, the IFN-induced transmembrane (IFITM) protein family that inhibit entry of diverse enveloped viruses. We found that SARS-CoV-2 is restricted predominantly by IFITM2, rather than IFITM3, and the degree of this restriction is governed by route of viral entry. Importantly, removal of the cleavage site in the spike protein renders SARS-CoV-2 entry highly pH and cathepsin dependent in late endosomes, where, like SARS-CoV-1 spike, it is more sensitive to IFITM2 restriction. Furthermore, we found that potent inhibition of SARS-CoV-2 replication by type I but not type II IFNs is alleviated by targeted depletion of IFITM2 expression. We propose that the polybasic cleavage site allows SARS-CoV-2 to mediate viral entry in a pH-independent manner, in part to mitigate against IFITM-mediated restriction and promote replication and transmission. This suggests that therapeutic strategies that target furin-mediated cleavage of SARS-CoV-2 spike may reduce viral replication through the activity of type I IFNs.IMPORTANCE The furin cleavage site in the spike protein is a distinguishing feature of SARS-CoV-2 and has been proposed to be a determinant for the higher transmissibility between individuals, compared to SARS-CoV-1. One explanation for this is that it permits more efficient activation of fusion at or near the cell surface rather than requiring processing in the endosome of the target cell. Here, we show that SARS-CoV-2 is inhibited by antiviral membrane protein IFITM2 and that the sensitivity is exacerbated by deletion of the furin cleavage site, which restricts viral entry to low pH compartments. Furthermore, we find that IFITM2 is a significant effector of the antiviral activity of type I interferons against SARS-CoV-2 replication. We suggest that one role of the furin cleavage site is to reduce SARS-CoV-2 sensitivity to innate immune restriction, and thus, it may represent a potential therapeutic target for COVID-19 treatment development.
Collapse
Affiliation(s)
- Helena Winstone
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Alisha C Reid
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Clement Bouton
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Claire Kerridge
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Chad M Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| |
Collapse
|
17
|
Sweeney N, Merrick B, Pedro Galão R, Pickering S, Botgros A, Wilson HD, Signell AW, Betancor G, Tan MKI, Ramble J, Kouphou N, Acors S, Graham C, Seow J, MacMahon E, Neil SJD, Malim MH, Doores K, Douthwaite S, Batra R, Nebbia G, Edgeworth JD. Clinical utility of targeted SARS-CoV-2 serology testing to aid the diagnosis and management of suspected missed, late or post-COVID-19 infection syndromes: Results from a pilot service implemented during the first pandemic wave. PLoS One 2021; 16:e0249791. [PMID: 33826651 PMCID: PMC8026061 DOI: 10.1371/journal.pone.0249791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/24/2021] [Indexed: 01/15/2023] Open
Abstract
During the first wave of the global COVID-19 pandemic the clinical utility and indications for SARS-CoV-2 serological testing were not clearly defined. The urgency to deploy serological assays required rapid evaluation of their performance characteristics. We undertook an internal validation of a CE marked lateral flow immunoassay (LFIA) (SureScreen Diagnostics) using serum from SARS-CoV-2 RNA positive individuals and pre-pandemic samples. This was followed by the delivery of a same-day named patient SARS-CoV-2 serology service using LFIA on vetted referrals at central London teaching hospital with clinical interpretation of result provided to the direct care team. Assay performance, source and nature of referrals, feasibility and clinical utility of the service, particularly benefit in clinical decision-making, were recorded. Sensitivity and specificity of LFIA were 96.1% and 99.3% respectively. 113 tests were performed on 108 participants during three-week pilot. 44% participants (n = 48) had detectable antibodies. Three main indications were identified for serological testing; new acute presentations potentially triggered by recent COVID-19 e.g. pulmonary embolism (n = 5), potential missed diagnoses in context of a recent COVID-19 compatible illness (n = 40), and making infection control or immunosuppression management decisions in persistently SARS-CoV-2 RNA PCR positive individuals (n = 6). We demonstrate acceptable performance characteristics, feasibility and clinical utility of using a LFIA that detects anti-spike antibodies to deliver SARS-CoV-2 serology service in adults and children. Greatest benefit was seen where there is reasonable pre-test probability and results can be linked with clinical advice or intervention. Experience from this pilot can help inform practicalities and benefits of rapidly implementing new tests such as LFIAs into clinical service as the pandemic evolves.
Collapse
Affiliation(s)
- Nicola Sweeney
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Blair Merrick
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Alina Botgros
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Adrian W. Signell
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Gilberto Betancor
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Mark Kia Ik Tan
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - John Ramble
- Infection Sciences, Viapath LLP, St Thomas’ Hospital, London, United Kingdom
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Eithne MacMahon
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Katie Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Sam Douthwaite
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rahul Batra
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Gaia Nebbia
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Jonathan D. Edgeworth
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| |
Collapse
|
18
|
Wells PM, Doores KJ, Couvreur S, Nunez RM, Seow J, Graham C, Acors S, Kouphou N, Neil SJD, Tedder RS, Matos PM, Poulton K, Lista MJ, Dickenson RE, Sertkaya H, Maguire TJA, Scourfield EJ, Bowyer RCE, Hart D, O'Byrne A, Steel KJA, Hemmings O, Rosadas C, McClure MO, Capedevilla-Pujol J, Wolf J, Ourselin S, Brown MA, Malim MH, Spector T, Steves CJ. Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England. J Infect 2020; 81:931-936. [PMID: 33068628 PMCID: PMC7557299 DOI: 10.1016/j.jinf.2020.10.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/11/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Understanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. METHODS We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. FINDINGS We demonstrated a seroprevalence of 12% (51 participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. INTERPRETATION Seroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response. FUNDING NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC.
Collapse
Affiliation(s)
- Philippa M Wells
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Simon Couvreur
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Rocio Martinez Nunez
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | | | - Pedro M Matos
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Kate Poulton
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ruth E Dickenson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helin Sertkaya
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Edward J Scourfield
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ruth C E Bowyer
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Deborah Hart
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Aoife O'Byrne
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Kathryn J A Steel
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Oliver Hemmings
- Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Myra O McClure
- Department of Infectious Disease, Imperial College London, UK
| | | | | | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Matthew A Brown
- Department of Medical & Molecular Genetics, Guy's and St Thomas' Hospital NHS Trust and King's College London NIHR Biomedical Research Centre, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Tim Spector
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Claire J Steves
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK.
| |
Collapse
|
19
|
Seow J, Graham C, Merrick B, Acors S, Pickering S, Steel KJA, Hemmings O, O'Byrne A, Kouphou N, Galao RP, Betancor G, Wilson HD, Signell AW, Winstone H, Kerridge C, Huettner I, Jimenez-Guardeño JM, Lista MJ, Temperton N, Snell LB, Bisnauthsing K, Moore A, Green A, Martinez L, Stokes B, Honey J, Izquierdo-Barras A, Arbane G, Patel A, Tan MKI, O'Connell L, O'Hara G, MacMahon E, Douthwaite S, Nebbia G, Batra R, Martinez-Nunez R, Shankar-Hari M, Edgeworth JD, Neil SJD, Malim MH, Doores KJ. Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans. Nat Microbiol 2020; 5:1598-1607. [PMID: 33106674 PMCID: PMC7610833 DOI: 10.1038/s41564-020-00813-8] [Citation(s) in RCA: 876] [Impact Index Per Article: 219.0] [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: 07/08/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023]
Abstract
Antibody responses to SARS-CoV-2 can be detected in most infected individuals 10-15 d after the onset of COVID-19 symptoms. However, due to the recent emergence of SARS-CoV-2 in the human population, it is not known how long antibody responses will be maintained or whether they will provide protection from reinfection. Using sequential serum samples collected up to 94 d post onset of symptoms (POS) from 65 individuals with real-time quantitative PCR-confirmed SARS-CoV-2 infection, we show seroconversion (immunoglobulin (Ig)M, IgA, IgG) in >95% of cases and neutralizing antibody responses when sampled beyond 8 d POS. We show that the kinetics of the neutralizing antibody response is typical of an acute viral infection, with declining neutralizing antibody titres observed after an initial peak, and that the magnitude of this peak is dependent on disease severity. Although some individuals with high peak infective dose (ID50 > 10,000) maintained neutralizing antibody titres >1,000 at >60 d POS, some with lower peak ID50 had neutralizing antibody titres approaching baseline within the follow-up period. A similar decline in neutralizing antibody titres was observed in a cohort of 31 seropositive healthcare workers. The present study has important implications when considering widespread serological testing and antibody protection against reinfection with SARS-CoV-2, and may suggest that vaccine boosters are required to provide long-lasting protection.
Collapse
Affiliation(s)
- Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Kathryn J A Steel
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Oliver Hemmings
- Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aoife O'Byrne
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Gilberto Betancor
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Harry D Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Adrian W Signell
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Claire Kerridge
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Karen Bisnauthsing
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Amelia Moore
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adrian Green
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Lauren Martinez
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Brielle Stokes
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Johanna Honey
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Alba Izquierdo-Barras
- Guy's and St Thomas' R&D Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gill Arbane
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mark Kia Ik Tan
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Lorcan O'Connell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Geraldine O'Hara
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Eithne MacMahon
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sam Douthwaite
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rocio Martinez-Nunez
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK.
| |
Collapse
|
20
|
Nchioua R, Kmiec D, Müller JA, Conzelmann C, Groß R, Swanson CM, Neil SJD, Stenger S, Sauter D, Münch J, Sparrer KMJ, Kirchhoff F. SARS-CoV-2 Is Restricted by Zinc Finger Antiviral Protein despite Preadaptation to the Low-CpG Environment in Humans. mBio 2020; 11:e01930-20. [PMID: 33067384 PMCID: PMC7569149 DOI: 10.1128/mbio.01930-20] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022] Open
Abstract
Recent evidence shows that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is sensitive to interferons (IFNs). However, the most effective types of IFNs and the underlying antiviral effectors remain to be defined. Here, we show that zinc finger antiviral protein (ZAP), which preferentially targets CpG dinucleotides in viral RNA sequences, restricts SARS-CoV-2. We further demonstrate that ZAP and its cofactors KHNYN and TRIM25 are expressed in human lung cells. Type I, II, and III IFNs all strongly inhibited SARS-CoV-2 and further induced ZAP expression. Comprehensive sequence analyses revealed that SARS-CoV-2 and its closest relatives from horseshoe bats showed the strongest CpG suppression among all known human and bat coronaviruses, respectively. Nevertheless, endogenous ZAP expression restricted SARS-CoV-2 replication in human lung cells, particularly upon treatment with IFN-α or IFN-γ. Both the long and the short isoforms of human ZAP reduced SARS-CoV-2 RNA expression levels, but the former did so with greater efficiency. Finally, we show that the ability to restrict SARS-CoV-2 is conserved in ZAP orthologues of the reservoir bat and potential intermediate pangolin hosts of human coronaviruses. Altogether, our results show that ZAP is an important effector of the innate response against SARS-CoV-2, although this pandemic pathogen emerged from zoonosis of a coronavirus that was preadapted to the low-CpG environment in humans.IMPORTANCE Although interferons inhibit SARS-CoV-2 and have been evaluated for treatment of coronavirus disease 2019 (COVID-19), the most effective types and antiviral effectors remain to be defined. Here, we show that IFN-γ is particularly potent in restricting SARS-CoV-2 and in inducing expression of the antiviral factor ZAP in human lung cells. Knockdown experiments revealed that endogenous ZAP significantly restricts SARS-CoV-2. We further show that CpG dinucleotides which are specifically targeted by ZAP are strongly suppressed in the SARS-CoV-2 genome and that the two closest horseshoe bat relatives of SARS-CoV-2 show the lowest genomic CpG content of all coronavirus sequences available from this reservoir host. Nonetheless, both the short and long isoforms of human ZAP reduced SARS-CoV-2 RNA levels, and this activity was conserved in horseshoe bat and pangolin ZAP orthologues. Our findings indicating that type II interferon is particularly efficient against SARS-CoV-2 and that ZAP restricts this pandemic viral pathogen might promote the development of effective immune therapies against COVID-19.
Collapse
Affiliation(s)
- Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Chad M Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Steffen Stenger
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| |
Collapse
|
21
|
Pickering S, Betancor G, Galão RP, Merrick B, Signell AW, Wilson HD, Kia Ik MT, Seow J, Graham C, Acors S, Kouphou N, Steel KJA, Hemmings O, Patel A, Nebbia G, Douthwaite S, O’Connell L, Luptak J, McCoy LE, Brouwer P, van Gils MJ, Sanders RW, Martinez Nunez R, Bisnauthsing K, O’Hara G, MacMahon E, Batra R, Malim MH, Neil SJD, Doores KJ, Edgeworth JD. Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings. PLoS Pathog 2020; 16:e1008817. [PMID: 32970782 PMCID: PMC7514033 DOI: 10.1371/journal.ppat.1008817] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022] Open
Abstract
There is a clear requirement for an accurate SARS-CoV-2 antibody test, both as a complement to existing diagnostic capabilities and for determining community seroprevalence. We therefore evaluated the performance of a variety of antibody testing technologies and their potential use as diagnostic tools. Highly specific in-house ELISAs were developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays-a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs)-on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. There was a wide variation in the performance of the different platforms, with specificity ranging from 82% to 100%, and overall sensitivity from 60.9% to 87.3%. However, the head-to-head comparison of multiple sero-diagnostic assays on identical sample sets revealed that performance is highly dependent on the time of sampling, with sensitivities of over 95% seen in several tests when assessing samples from more than 20 days post onset of symptoms. Furthermore, these analyses identified clear outlying samples that were negative in all tests, but were later shown to be from individuals with mildest disease presentation. Rigorous comparison of antibody testing platforms will inform the deployment of point-of-care technologies in healthcare settings and their use in the monitoring of SARS-CoV-2 infections.
Collapse
Affiliation(s)
- Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Gilberto Betancor
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Adrian W. Signell
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Mark Tan Kia Ik
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Kathryn J. A. Steel
- Centre for Inflammation Biology and Cancer Immunology (CIBCI), Dept of Inflammation Biology, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Oliver Hemmings
- Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Sam Douthwaite
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Lorcan O’Connell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Jakub Luptak
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Laura E. McCoy
- Division of Infection and Immunity, University College London (UCL), London, United Kingdom
| | - Philip Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Rocio Martinez Nunez
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Karen Bisnauthsing
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Geraldine O’Hara
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Eithne MacMahon
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Jonathan D. Edgeworth
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| |
Collapse
|
22
|
Edgeworth JD, Batra R, Nebbia G, Bisnauthsing K, MacMahon E, Sudhanva M, Douthwaite S, Goldenberg S, O’Hara G, Shankar-Hari M, Doores KJ, Martinez-Nunez R, Hemsley C, Price NM, Lockett J, Lechler RI, Neil SJD, Malim MH. Translational Research in the Time of COVID-19-Dissolving Boundaries. PLoS Pathog 2020; 16:e1008898. [PMID: 32997719 PMCID: PMC7526890 DOI: 10.1371/journal.ppat.1008898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Jonathan D. Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Viapath, London, United Kingdom
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Karen Bisnauthsing
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Eithne MacMahon
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Viapath, London, United Kingdom
| | - Malur Sudhanva
- Viapath, London, United Kingdom
- Department of Virology, King’s College Hospital, London, United Kingdom
| | - Sam Douthwaite
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Simon Goldenberg
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Geraldine O’Hara
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Manu Shankar-Hari
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Katie J. Doores
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rocio Martinez-Nunez
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Carolyn Hemsley
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Nicholas M. Price
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | | | | | - Stuart J. D. Neil
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Michael H. Malim
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- King’s Health Partners, London, United Kingdom
| |
Collapse
|
23
|
Prévost J, Edgar CR, Richard J, Trothen SM, Jacob RA, Mumby MJ, Pickering S, Dubé M, Kaufmann DE, Kirchhoff F, Neil SJD, Finzi A, Dikeakos JD. HIV-1 Vpu Downregulates Tim-3 from the Surface of Infected CD4 + T Cells. J Virol 2020; 94:e01999-19. [PMID: 31941771 PMCID: PMC7081912 DOI: 10.1128/jvi.01999-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/12/2020] [Indexed: 01/26/2023] Open
Abstract
Along with other immune checkpoints, T cell immunoglobulin and mucin domain-containing protein 3 (Tim-3) is expressed on exhausted CD4+ and CD8+ T cells and is upregulated on the surface of these cells upon infection by human immunodeficiency virus type 1 (HIV-1). Recent reports have suggested an antiviral role for Tim-3. However, the molecular determinants of HIV-1 which modulate cell surface Tim-3 levels have yet to be determined. Here, we demonstrate that HIV-1 Vpu downregulates Tim-3 from the surface of infected primary CD4+ T cells, thus attenuating HIV-1-induced upregulation of Tim-3. We also provide evidence that the transmembrane domain of Vpu is required for Tim-3 downregulation. Using immunofluorescence microscopy, we determined that Vpu is in close proximity to Tim-3 and alters its subcellular localization by directing it to Rab 5-positive (Rab 5+) vesicles and targeting it for sequestration within the trans- Golgi network (TGN). Intriguingly, Tim-3 knockdown and Tim-3 blockade increased HIV-1 replication in primary CD4+ T cells, thereby suggesting that Tim-3 expression might represent a natural immune mechanism limiting viral spread.IMPORTANCE HIV infection modulates the surface expression of Tim-3, but the molecular determinants remain poorly understood. Here, we show that HIV-1 Vpu downregulates Tim-3 from the surface of infected primary CD4+ T cells through its transmembrane domain and alters its subcellular localization. Tim-3 blockade increases HIV-1 replication, suggesting a potential negative role of this protein in viral spread that is counteracted by Vpu.
Collapse
Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Cassandra R Edgar
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Steven M Trothen
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Rajesh Abraham Jacob
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Mitchell J Mumby
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Suzanne Pickering
- Department of Infectious Disease, King's College London School of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom
| | - Mathieu Dubé
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Stuart J D Neil
- Department of Infectious Disease, King's College London School of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| |
Collapse
|
24
|
Ficarelli M, Antzin-Anduetza I, Hugh-White R, Firth AE, Sertkaya H, Wilson H, Neil SJD, Schulz R, Swanson CM. CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms. J Virol 2020; 94:e01337-19. [PMID: 31748389 PMCID: PMC7158733 DOI: 10.1128/jvi.01337-19] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/06/2019] [Indexed: 02/07/2023] Open
Abstract
CpG dinucleotides are suppressed in the genomes of many vertebrate RNA viruses, including HIV-1. The cellular antiviral protein ZAP (zinc finger antiviral protein) binds CpGs and inhibits HIV-1 replication when CpGs are introduced into the viral genome. However, it is not known if ZAP-mediated restriction is the only mechanism driving CpG suppression. To determine how CpG dinucleotides affect HIV-1 replication, we increased their abundance in multiple regions of the viral genome and analyzed the effect on RNA expression, protein abundance, and infectious-virus production. We found that the antiviral effect of CpGs was not correlated with their abundance. Interestingly, CpGs inserted into some regions of the genome sensitize the virus to ZAP antiviral activity more efficiently than insertions into other regions, and this sensitivity can be modulated by interferon treatment or ZAP overexpression. Furthermore, the sensitivity of the virus to endogenous ZAP was correlated with its sensitivity to the ZAP cofactor KHNYN. Finally, we show that CpGs in some contexts can also inhibit HIV-1 replication by ZAP-independent mechanisms, and one of these is the activation of a cryptic splice site at the expense of a canonical splice site. Overall, we show that the location and sequence context of the CpG in the viral genome determines its antiviral activity.IMPORTANCE Some RNA virus genomes are suppressed in the nucleotide combination of a cytosine followed by a guanosine (CpG), indicating that they are detrimental to the virus. The antiviral protein ZAP binds viral RNA containing CpGs and prevents the virus from multiplying. However, it remains unknown how the number and position of CpGs in viral genomes affect restriction by ZAP and whether CpGs have other antiviral mechanisms. Importantly, manipulating the CpG content in viral genomes could help create new vaccines. HIV-1 shows marked CpG suppression, and by introducing CpGs into its genome, we show that ZAP efficiently targets a specific region of the viral genome, that the number of CpGs does not predict the magnitude of antiviral activity, and that CpGs can inhibit HIV-1 gene expression through a ZAP-independent mechanism. Overall, the position of CpGs in the HIV-1 genome determines the magnitude and mechanism through which they inhibit the virus.
Collapse
Affiliation(s)
- Mattia Ficarelli
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | | | - Rupert Hugh-White
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Andrew E Firth
- Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Helin Sertkaya
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Harry Wilson
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Chad M Swanson
- Department of Infectious Diseases, King's College London, London, United Kingdom
| |
Collapse
|
25
|
Prévost J, Pickering S, Mumby MJ, Medjahed H, Gendron-Lepage G, Delgado GG, Dirk BS, Dikeakos JD, Stürzel CM, Sauter D, Kirchhoff F, Bibollet-Ruche F, Hahn BH, Dubé M, Kaufmann DE, Neil SJD, Finzi A, Richard J. Upregulation of BST-2 by Type I Interferons Reduces the Capacity of Vpu To Protect HIV-1-Infected Cells from NK Cell Responses. mBio 2019; 10:e01113-19. [PMID: 31213558 PMCID: PMC6581860 DOI: 10.1128/mbio.01113-19] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/03/2023] Open
Abstract
The HIV-1 accessory protein Vpu enhances viral release by counteracting the restriction factor BST-2. Furthermore, Vpu promotes NK cell evasion by downmodulating cell surface NTB-A and PVR, known ligands of the NK cell receptors NTB-A and DNAM-1, respectively. While it has been established that Vpu's transmembrane domain (TMD) is required for the interaction and intracellular sequestration of BST-2, NTB-A, and PVR, it remains unclear how Vpu manages to target these proteins simultaneously. In this study, we show that upon upregulation, BST-2 is preferentially downregulated by Vpu over its other TMD substrates. We found that type I interferon (IFN)-mediated BST-2 upregulation greatly impairs the ability of Vpu to downregulate NTB-A and PVR. Our results suggest that occupation of Vpu by BST-2 affects its ability to downregulate other TMD substrates. Accordingly, knockdown of BST-2 increases Vpu's potency to downmodulate NTB-A and PVR in the presence of type I IFN treatment. Moreover, we show that expression of human BST-2, but not that of the macaque orthologue, decreases Vpu's capacity to downregulate NTB-A. Importantly, we show that type I IFNs efficiently sensitize HIV-1-infected cells to NTB-A- and DNAM-1-mediated direct and antibody-dependent NK cell responses. Altogether, our results reveal that type I IFNs decrease Vpu's polyfunctionality, thus reducing its capacity to protect HIV-1-infected cells from NK cell responses.IMPORTANCE The restriction factor BST-2 and the NK cell ligands NTB-A and PVR are among a growing list of membrane proteins found to be downregulated by HIV-1 Vpu. BST-2 antagonism enhances viral release, while NTB-A and PVR downmodulation contributes to NK cell evasion. However, it remains unclear how Vpu can target multiple cellular factors simultaneously. Here we provide evidence that under physiological conditions, BST-2 is preferentially targeted by Vpu over NTB-A and PVR. Specifically, we show that type I IFNs decrease Vpu's polyfunctionality by upregulating BST-2, thus reducing its capacity to protect HIV-1-infected cells from NK cell responses. This indicates that there is a hierarchy of Vpu substrates upon IFN treatment, revealing that for the virus, targeting BST-2 as part of its resistance to IFN takes precedence over evading NK cell responses. This reveals a potential weakness in HIV-1's immunoevasion mechanisms that may be exploited therapeutically to harness NK cell responses against HIV-1.
Collapse
Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec, Canada
| | - Suzanne Pickering
- Department of Infectious Disease, King's College London School of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom
| | - Mitchell J Mumby
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | | | | | | | - Brennan S Dirk
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mathieu Dubé
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA
| | - Stuart J D Neil
- Department of Infectious Disease, King's College London School of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec, Canada
| |
Collapse
|
26
|
Foster TL, Pickering S, Neil SJD. Inhibiting the Ins and Outs of HIV Replication: Cell-Intrinsic Antiretroviral Restrictions at the Plasma Membrane. Front Immunol 2018; 8:1853. [PMID: 29354117 PMCID: PMC5758531 DOI: 10.3389/fimmu.2017.01853] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 09/15/2017] [Accepted: 12/07/2017] [Indexed: 01/01/2023] Open
Abstract
Like all viruses, human immunodeficiency viruses (HIVs) and their primate lentivirus relatives must enter cells in order to replicate and, once produced, new virions need to exit to spread to new targets. These processes require the virus to cross the plasma membrane of the cell twice: once via fusion mediated by the envelope glycoprotein to deliver the viral core into the cytosol; and secondly by ESCRT-mediated scission of budding virions during release. This physical barrier thus presents a perfect location for host antiviral restrictions that target enveloped viruses in general. In this review we will examine the current understanding of innate host antiviral defences that inhibit these essential replicative steps of primate lentiviruses associated with the plasma membrane, the mechanism by which these viruses have adapted to evade such defences, and the role that this virus/host battleground plays in the transmission and pathogenesis of HIV/AIDS.
Collapse
Affiliation(s)
- Toshana L Foster
- Department of Infectious Disease, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Disease, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Stuart J D Neil
- Department of Infectious Disease, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| |
Collapse
|
27
|
Abstract
Ten years ago, while in Paul Bieniasz's group, I determined that an interferon-induced antiviral activity inhibited the release of enveloped viruses by tethering them to the plasma membrane of infected cells. This commentary examines the lead up to this study and how our observations led to the identification of tetherin.
Collapse
Affiliation(s)
- Stuart J D Neil
- Department of Infectious Disease, Faculty of Life Science and Medicine, King's College London, Guy's Hospital, London SE1 9RT, UK.
| |
Collapse
|
28
|
Foster TL, Wilson H, Iyer SS, Coss K, Doores K, Smith S, Kellam P, Finzi A, Borrow P, Hahn BH, Neil SJD. Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction. Cell Host Microbe 2016; 20:429-442. [PMID: 27640936 PMCID: PMC5075283 DOI: 10.1016/j.chom.2016.08.006] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/04/2016] [Accepted: 08/23/2016] [Indexed: 01/13/2023]
Abstract
Interferon-induced transmembrane proteins (IFITMs) restrict the entry of diverse enveloped viruses through incompletely understood mechanisms. While IFITMs are reported to inhibit HIV-1, their in vivo relevance is unclear. We show that IFITM sensitivity of HIV-1 strains is determined by the co-receptor usage of the viral envelope glycoproteins as well as IFITM subcellular localization within the target cell. Importantly, we find that transmitted founder HIV-1, which establishes de novo infections, is uniquely resistant to the antiviral activity of IFITMs. However, viral sensitivity to IFITMs, particularly IFITM2 and IFITM3, increases over the first 6 months of infection, primarily as a result of neutralizing antibody escape mutations. Additionally, the ability to evade IFITM restriction contributes to the different interferon sensitivities of transmitted founder and chronic viruses. Together, these data indicate that IFITMs constitute an important barrier to HIV-1 transmission and that escape from adaptive immune responses exposes the virus to antiviral restriction.
Collapse
Affiliation(s)
- Toshana L Foster
- Department of Infectious Diseases, King's College London Faculty of Life Sciences and Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Harry Wilson
- Department of Infectious Diseases, King's College London Faculty of Life Sciences and Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Shilpa S Iyer
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karen Coss
- Department of Infectious Diseases, King's College London Faculty of Life Sciences and Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Katie Doores
- Department of Infectious Diseases, King's College London Faculty of Life Sciences and Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Sarah Smith
- Wellcome Trust Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
| | - Paul Kellam
- Wellcome Trust Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
| | - Andrés Finzi
- Centre de Recherche du CHUM and Department of Microbiology, Infection, and Immunology, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 2JD, UK
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London Faculty of Life Sciences and Medicine, Guy's Hospital, London SE1 9RT, UK.
| |
Collapse
|
29
|
Matheson NJ, Sumner J, Wals K, Rapiteanu R, Weekes MP, Vigan R, Weinelt J, Schindler M, Antrobus R, Costa ASH, Frezza C, Clish CB, Neil SJD, Lehner PJ. Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef. Cell Host Microbe 2015; 18:409-23. [PMID: 26439863 PMCID: PMC4608997 DOI: 10.1016/j.chom.2015.09.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [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: 07/02/2015] [Revised: 08/30/2015] [Accepted: 09/10/2015] [Indexed: 11/24/2022]
Abstract
Critical cell surface immunoreceptors downregulated during HIV infection have previously been identified using non-systematic, candidate approaches. To gain a comprehensive, unbiased overview of how HIV infection remodels the T cell surface, we took a distinct, systems-level, quantitative proteomic approach. >100 plasma membrane proteins, many without characterized immune functions, were downregulated during HIV infection. Host factors targeted by the viral accessory proteins Vpu or Nef included the amino acid transporter SNAT1 and the serine carriers SERINC3/5. We focused on SNAT1, a β-TrCP-dependent Vpu substrate. SNAT1 antagonism was acquired by Vpu variants from the lineage of SIVcpz/HIV-1 viruses responsible for pandemic AIDS. We found marked SNAT1 induction in activated primary human CD4+ T cells, and used Consumption and Release (CoRe) metabolomics to identify alanine as an endogenous SNAT1 substrate required for T cell mitogenesis. Downregulation of SNAT1 therefore defines a unique paradigm of HIV interference with immunometabolism. Unbiased global analysis of T cell surface proteome remodeling during HIV infection >100 proteins downregulated, including Nef targets SERINC3/5 and Vpu target SNAT1 β-TrCP-dependent SNAT1 downregulation acquired by pandemic SIVcpz/HIV-1 viruses Uptake of exogenous alanine by SNAT1 critical for primary CD4+ T cell mitogenesis
Collapse
Affiliation(s)
- Nicholas J Matheson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
| | - Jonathan Sumner
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Kim Wals
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Radu Rapiteanu
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Raphael Vigan
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Julia Weinelt
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Michael Schindler
- Helmholtz Center Munich, Institute of Virology, 85764 Neuherberg, Germany; Institute of Medical Virology and Epidemiology of Viral Diseases, University Clinic Tübingen, 72076 Tübingen, Germany
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Ana S H Costa
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Christian Frezza
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Clary B Clish
- The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Paul J Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
| |
Collapse
|
30
|
Galão RP, Pickering S, Curnock R, Neil SJD. Retroviral retention activates a Syk-dependent HemITAM in human tetherin. Cell Host Microbe 2015; 16:291-303. [PMID: 25211072 PMCID: PMC4161388 DOI: 10.1016/j.chom.2014.08.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/18/2014] [Accepted: 08/07/2014] [Indexed: 12/27/2022]
Abstract
Tetherin (BST2/CD317) restricts the release of enveloped viral particles from infected cells. Coupled to this virion retention, hominid tetherins induce proinflammatory gene expression via activating NF-κB. We investigated the events initiating this tetherin-induced signaling and show that physical retention of retroviral particles induces the phosphorylation of conserved tyrosine residues in the cytoplasmic tails of tetherin dimers. This phosphorylation induces the recruitment of spleen tyrosine kinase (Syk), which is required for downstream NF-κB activation, indicating that the tetherin cytoplasmic tail resembles the hemi-immunoreceptor tyrosine-based activation motifs (hemITAMs) found in C-type lectin pattern recognition receptors. Retroviral-induced tetherin signaling is coupled to the cortical actin cytoskeleton via the Rac-GAP-containing protein RICH2 (ARHGAP44), and a naturally occurring tetherin polymorphism with reduced RICH2 binding exhibits decreased phosphorylation and NF-κB activation. Thus, upon virion retention, this linkage to the actin cytoskeleton likely triggers tetherin phosphorylation and subsequent signal transduction to induce an antiviral state. A hemITAM in human tetherin is phosphorylated upon viral restriction Tetherin phosphorylation recruits and is dependent upon the kinase Syk The RICH2-tetherin interaction couples tetherin signaling to the actin cytoskeleton A human polymorphism in tetherin abolishes RICH2 interactions and signal transduction
Collapse
Affiliation(s)
- Rui Pedro Galão
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Suzanne Pickering
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Rachel Curnock
- School of Biochemistry, Faculty of Medical and Veterinary Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Stuart J D Neil
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK.
| |
Collapse
|
31
|
Pickering S, Hué S, Kim EY, Reddy S, Wolinsky SM, Neil SJD. Preservation of tetherin and CD4 counter-activities in circulating Vpu alleles despite extensive sequence variation within HIV-1 infected individuals. PLoS Pathog 2014; 10:e1003895. [PMID: 24465210 PMCID: PMC3900648 DOI: 10.1371/journal.ppat.1003895] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 12/06/2013] [Indexed: 01/19/2023] Open
Abstract
The HIV-1 Vpu protein is expressed from a bi-cistronic message late in the viral life cycle. It functions during viral assembly to maximise infectious virus release by targeting CD4 for proteosomal degradation and counteracting the antiviral protein tetherin (BST2/CD317). Single genome analysis of vpu repertoires throughout infection in 14 individuals infected with HIV-1 clade B revealed extensive amino acid diversity of the Vpu protein. For the most part, this variation in Vpu increases over the course of infection and is associated with predicted epitopes of the individual's MHC class I haplotype, suggesting CD8+ T cell pressure is the major driver of Vpu sequence diversity within the host. Despite this variability, the Vpu functions of targeting CD4 and counteracting both physical virus restriction and NF-κB activation by tetherin are rigorously maintained throughout HIV-1 infection. Only a minority of circulating alleles bear lesions in either of these activities at any given time, suggesting functional Vpu mutants are heavily selected against even at later stages of infection. Comparison of Vpu proteins defective for one or several functions reveals novel determinants of CD4 downregulation, counteraction of tetherin restriction, and inhibition of NF-κB signalling. These data affirm the importance of Vpu functions for in vivo persistence of HIV-1 within infected individuals, not simply for transmission, and highlight its potential as a target for antiviral therapy. The accessory protein Vpu, encoded by HIV-1, performs at least two major roles in the virus life cycle, namely the degradation of newly synthesized CD4 molecules and the counteraction of a host antiviral protein, tetherin. These activities promote the release of infectious viruses from host cells, and recent evidence suggests that Vpu function has been crucial for the cross-species transmission of HIV-1 from chimpanzees, and its subsequent pandemic spread in humans. Here we studied the functional variation in Vpu in infected individuals. We found that the Vpu amino acid sequence can be highly variable within an individual, and that this variation is likely to result from host immune responses targeting antigens derived from Vpu. However, despite this variation, Vpu's major functions are preserved, with only a minority of circulating alleles showing defects throughout the course of infection. These data suggest that defective Vpu proteins are selected against within the infected individual, implying that Vpu functions are critical for HIV-1 replication throughout natural infection, not simply at transmission. Therefore Vpu may represent a novel target for antiviral therapy to augment current treatment strategies for HIV/AIDS.
Collapse
Affiliation(s)
- Suzanne Pickering
- Department of Infectious Disease, King's College School of Medicine, Guy's Hospital, London, United Kingdom
| | - Stephane Hué
- MRC Centre for Medical Molecular Virology, University College London, London, United Kingdom
| | - Eun-Young Kim
- Department of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Susheel Reddy
- Department of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Steven M. Wolinsky
- Department of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Stuart J. D. Neil
- Department of Infectious Disease, King's College School of Medicine, Guy's Hospital, London, United Kingdom
- * E-mail:
| |
Collapse
|
32
|
Galão RP, Le Tortorec A, Pickering S, Kueck T, Neil SJD. Innate sensing of HIV-1 assembly by Tetherin induces NFκB-dependent proinflammatory responses. Cell Host Microbe 2013; 12:633-44. [PMID: 23159053 PMCID: PMC3556742 DOI: 10.1016/j.chom.2012.10.007] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 08/04/2012] [Accepted: 10/01/2012] [Indexed: 11/29/2022]
Abstract
Antiviral proteins that recognize pathogen-specific or aberrantly located molecular motifs are perfectly positioned to act as pattern-recognition receptors and signal to the immune system. Here we investigated whether the interferon-induced viral restriction factor tetherin (CD317/BST2), which is known to inhibit HIV-1 particle release by physically tethering virions to the cell surface, has such a signaling role. We find that upon restriction of Vpu-defective HIV-1, tetherin acts as a virus sensor to induce NFκB-dependent proinflammatory gene expression. Signaling requires both tetherin's extracellular domain involved in virion retention and determinants in the cytoplasmic tail, including an endocytic motif, although signaling is independent of virion endocytosis. Furthermore, recruitment of the TNF-receptor-associated factor TRAF6 and activation of the mitogen-activated protein kinase TAK1 are critical for signaling. Human tetherin's ability to mediate efficient signaling may have arisen as a result of a five amino acid deletion that occurred in hominids after their divergence from chimpanzees.
Collapse
Affiliation(s)
- Rui Pedro Galão
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | | | | | | | | |
Collapse
|
33
|
Goujon C, Schaller T, Galão RP, Amie SM, Kim B, Olivieri K, Neil SJD, Malim MH. Evidence for IFNα-induced, SAMHD1-independent inhibitors of early HIV-1 infection. Retrovirology 2013; 10:23. [PMID: 23442224 PMCID: PMC3598776 DOI: 10.1186/1742-4690-10-23] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Type I interferon (IFN) treatment of some cells, including dendritic cells, macrophages and monocytic THP-1 cells, restricts HIV-1 infection and prevents viral cDNA accumulation. Sterile alpha motif and HD domain protein 1 (SAMHD1), a dGTP-regulated deoxynucleotide triphosphohydrolase, reduces HIV-1 infectivity in myeloid cells, likely by limiting dNTPs available for reverse transcription, and has been described as IFNα-inducible. Myeloid cell infection by HIV-1 is enhanced by HIV-2/SIVSM Vpx, which promotes SAMHD1 degradation, or by exogenous deoxyribonucleoside (dN) addition. FINDINGS SAMHD1 expression was not substantially influenced by IFNα treatment of monocyte-derived macrophages or THP-1 cells. The contributions of SAMHD1 to the inhibition of HIV-1 infectivity by IFNα were assessed through the provision of Vpx, exogenous dN addition, or via RNAi-mediated SAMHD1 knock-down. Both Vpx and dN efficiently restored infection in IFNα-treated macrophages, albeit not to the levels seen with these treatments in the absence of IFNα. Similarly using differentiated THP-1 cells, the addition of Vpx or dNs, or SAMHD1 knock-down, also stimulated infection, but failing to match the levels observed without IFNα. Neither Vpx addition nor SAMHD1 knock-down reversed the IFNα-induced blocks to HIV-1 infection seen in dividing U87-MG or THP-1 cells. Therefore, altered SAMHD1 expression or function cannot account for the IFNα-induced restriction to HIV-1 infection seen in many cells and cell lines. CONCLUSION IFNα establishes an anti-HIV-1 phenotype in many cell types, and appears to accomplish this without potentiating SAMHD1 function. We conclude that additional IFNα-induced suppressors of the early stages of HIV-1 infection await identification.
Collapse
Affiliation(s)
- Caroline Goujon
- Department of Infectious Diseases, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London Bridge, London SE1 9RT, UK
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Tavano B, Galao RP, Graham DR, Neil SJD, Aquino VN, Fuchs D, Boasso A. Ig-like transcript 7, but not bone marrow stromal cell antigen 2 (also known as HM1.24, tetherin, or CD317), modulates plasmacytoid dendritic cell function in primary human blood leukocytes. J Immunol 2013; 190:2622-30. [PMID: 23401591 DOI: 10.4049/jimmunol.1202391] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Ig-like transcript (ILT) 7 is a surface molecule selectively expressed by human plasmacytoid dendritic cells (pDCs). ILT7 cross-linking suppresses pDC activation and type I IFN (IFN-I) secretion following TLR7/9 engagement. The bone marrow stromal cell Ag 2 (BST2, aka HM1.24, tetherin, or CD317) is expressed by different cell types upon exposure to IFN-I and is a natural ligand for ILT7. In this study, we show that ILT7 expression decreased spontaneously in pDCs upon in vitro culture, which correlates with pDC differentiation measured as increased side scatter properties and CCR7 expression. TLR7/9 ligands, as well as HIV, induced BST2 upregulation on all tested cell types except T cells, which required TCR stimulation to respond to TLR9L-induced IFN-I. IFN-γ, IL-4, IL-10, and TNF-α had only marginal effects on BST2 expression in blood leukocytes compared with TLR9L. Preincubation with ILT7 cross-linking Ab inhibited IFN-I production in PBMCs treated with TLR7/9L or HIV, whereas BST2 blockade did not affect IFN-I responses even when BST2 upregulation was further boosted with TCR agonists or immunoregulatory cytokines. Our data indicate that BST2-mediated ILT7 cross-linking may act as a homeostatic regulatory mechanism on immature circulating pDC, rather than a negative feedback for activated mature pDCs that have downregulated ILT7.
Collapse
Affiliation(s)
- Barbara Tavano
- Division of Infectious Diseases, Immunology Section, Chelsea and Westminster Hospital, Department of Medicine, Faculty of Medicine, Imperial College, London SW10 9NH, United Kingdom.
| | | | | | | | | | | | | |
Collapse
|
35
|
Abstract
Tetherin (BST2/CD317) has emerged as a key host cell defense molecule, inhibiting the release and spread of diverse enveloped virions from infected cells. In this chapter, I review the molecular and cellular basis for tetherin's antiviral activities and the function of virally encoded countermeasures that disrupt its function. I further describe recent advances in our understanding of tetherin's associated role in viral pattern recognition and the evidence for its role in limiting viral pathogenesis in vivo.
Collapse
Affiliation(s)
- Stuart J D Neil
- Department of Infectious Disease, King's College London School of Medicine, London, UK.
| |
Collapse
|
36
|
Agromayor M, Soler N, Caballe A, Kueck T, Freund SM, Allen MD, Bycroft M, Perisic O, Ye Y, McDonald B, Scheel H, Hofmann K, Neil SJD, Martin-Serrano J, Williams RL. The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain. Structure 2012; 20:414-28. [PMID: 22405001 PMCID: PMC3314968 DOI: 10.1016/j.str.2011.12.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/13/2011] [Accepted: 12/30/2011] [Indexed: 11/23/2022]
Abstract
The endosomal sorting complexes required for transport (ESCRTs) facilitate endosomal sorting of ubiquitinated cargo, MVB biogenesis, late stages of cytokinesis, and retroviral budding. Here we show that ubiquitin associated protein 1 (UBAP1), a subunit of human ESCRT-I, coassembles in a stable 1:1:1:1 complex with Vps23/TSG101, VPS28, and VPS37. The X-ray crystal structure of the C-terminal region of UBAP1 reveals a domain that we describe as a solenoid of overlapping UBAs (SOUBA). NMR analysis shows that each of the three rigidly arranged overlapping UBAs making up the SOUBA interact with ubiquitin. We demonstrate that UBAP1-containing ESCRT-I is essential for degradation of antiviral cell-surface proteins, such as tetherin (BST-2/CD317), by viral countermeasures, namely, the HIV-1 accessory protein Vpu and the Kaposi sarcoma-associated herpesvirus (KSHV) ubiquitin ligase K5.
Collapse
Affiliation(s)
- Monica Agromayor
- Department of Infectious Diseases, King's College London School of Medicine, London SE1 9RT, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Kueck T, Neil SJD. A cytoplasmic tail determinant in HIV-1 Vpu mediates targeting of tetherin for endosomal degradation and counteracts interferon-induced restriction. PLoS Pathog 2012; 8:e1002609. [PMID: 22479182 PMCID: PMC3315493 DOI: 10.1371/journal.ppat.1002609] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 02/11/2012] [Indexed: 01/12/2023] Open
Abstract
The HIV-1 accessory protein Vpu counteracts tetherin (BST-2/CD317) by preventing its incorporation into virions, reducing its surface expression, and ultimately promoting its degradation. Here we characterize a putative trafficking motif, EXXXLV, in the second alpha helix of the subtype-B Vpu cytoplasmic tail as being required for efficient tetherin antagonism. Mutation of this motif prevents ESCRT-dependent degradation of tetherin/Vpu complexes, tetherin cell surface downregulation, but not its physical interaction with Vpu. Importantly, this motif is required for efficient cell-free virion release from CD4+ T cells, particularly after their exposure to type-1 interferon, indicating that the ability to reduce surface tetherin levels and promote its degradation is important to counteract restriction under conditions that the virus likely encounters in vivo. Vpu EXXXLV mutants accumulate with tetherin at the cell surface and in endosomal compartments, but retain the ability to bind both β-TrCP2 and HRS, indicating that this motif is required for a post-binding trafficking event that commits tetherin for ESCRT-dependent degradation and prevents its transit to the plasma membrane and viral budding zones. We further found that while Vpu function is dependent on clathrin, and the entire second alpha helix of the Vpu tail can be functionally complemented by a clathrin adaptor binding peptide derived from HIV-1 Nef, none of the canonical clathrin adaptors nor retromer are required for this process. Finally we show that residual activity of Vpu EXXXLV mutants requires an intact endocytic motif in tetherin, suggesting that physical association of Vpu with tetherin during its recycling may be sufficient to compromise tetherin activity to some degree. Tetherin inhibits the release of several diverse enveloped viruses from infected cells and is counteracted by the HIV-1 accessory gene Vpu. Vpu prevents tetherin's incorporation into nascent viral particles, promotes its downregulation from the cell surface and targets tetherin for degradation. Here we identify a determinant that resembles an acidic-dileucine-based sorting sequence in the Vpu cytoplasmic tail that is required for efficient counteraction of tetherin activity, particularly in CD4+ T cells treated with type-1 interferon. Mutation of this motif prevents cell-surface downregulation and degradation of Vpu/tetherin complexes but does not affect their interaction. Rather, in its absence, Vpu accumulates in early endosomes and at the cell surface where it becomes incorporated into assembling virions with tetherin, indicating that this motif modulates sub-cellular trafficking of tetherin. Furthermore Vpu activity is clathrin-dependent and can be reconstituted by replacing a portion of the cytoplasmic tail encompassing this motif with one derived from HIV-1 Nef that is known to bind several clathrin adaptors. Finally, we demonstrate that residual function of the mutant Vpu requires a trafficking motif in tetherin, suggesting that physical interaction of tetherin with Vpu during its recycling to the cell-surface can interfere with its function to a variable extent.
Collapse
Affiliation(s)
| | - Stuart J. D. Neil
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
- * E-mail:
| |
Collapse
|
38
|
Le Tortorec A, Willey S, Neil SJD. Antiviral inhibition of enveloped virus release by tetherin/BST-2: action and counteraction. Viruses 2011; 3:520-40. [PMID: 21994744 PMCID: PMC3185764 DOI: 10.3390/v3050520] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 04/19/2011] [Accepted: 04/28/2011] [Indexed: 02/06/2023] Open
Abstract
Tetherin (BST2/CD317) has been recently recognized as a potent interferon-induced antiviral molecule that inhibits the release of diverse mammalian enveloped virus particles from infected cells. By targeting an immutable structure common to all these viruses, the virion membrane, evasion of this antiviral mechanism has necessitated the development of specific countermeasures that directly inhibit tetherin activity. Here we review our current understanding of the molecular basis of tetherin's mode of action, the viral countermeasures that antagonize it, and how virus/tetherin interactions may affect viral transmission and pathogenicity.
Collapse
Affiliation(s)
| | | | - Stuart J. D. Neil
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44-207-188-8279
| |
Collapse
|
39
|
Pardieu C, Vigan R, Wilson SJ, Calvi A, Zang T, Bieniasz P, Kellam P, Towers GJ, Neil SJD. The RING-CH ligase K5 antagonizes restriction of KSHV and HIV-1 particle release by mediating ubiquitin-dependent endosomal degradation of tetherin. PLoS Pathog 2010; 6:e1000843. [PMID: 20419159 PMCID: PMC2855335 DOI: 10.1371/journal.ppat.1000843] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 03/03/2010] [Indexed: 12/29/2022] Open
Abstract
Tetherin (CD317/BST2) is an interferon-induced membrane protein that inhibits the release of diverse enveloped viral particles. Several mammalian viruses have evolved countermeasures that inactivate tetherin, with the prototype being the HIV-1 Vpu protein. Here we show that the human herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) is sensitive to tetherin restriction and its activity is counteracted by the KSHV encoded RING-CH E3 ubiquitin ligase K5. Tetherin expression in KSHV-infected cells inhibits viral particle release, as does depletion of K5 protein using RNA interference. K5 induces a species-specific downregulation of human tetherin from the cell surface followed by its endosomal degradation. We show that K5 targets a single lysine (K18) in the cytoplasmic tail of tetherin for ubiquitination, leading to relocalization of tetherin to CD63-positive endosomal compartments. Tetherin degradation is dependent on ESCRT-mediated endosomal sorting, but does not require a tyrosine-based sorting signal in the tetherin cytoplasmic tail. Importantly, we also show that the ability of K5 to substitute for Vpu in HIV-1 release is entirely dependent on K18 and the RING-CH domain of K5. By contrast, while Vpu induces ubiquitination of tetherin cytoplasmic tail lysine residues, mutation of these positions has no effect on its antagonism of tetherin function, and residual tetherin is associated with the trans-Golgi network (TGN) in Vpu-expressing cells. Taken together our results demonstrate that K5 is a mechanistically distinct viral countermeasure to tetherin-mediated restriction, and that herpesvirus particle release is sensitive to this mode of antiviral inhibition.
Collapse
Affiliation(s)
- Claire Pardieu
- MRC Centre for Medical Molecular Virology, University College London, London, United Kingdom
| | - Raphaël Vigan
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
| | - Sam J. Wilson
- MRC Centre for Medical Molecular Virology, University College London, London, United Kingdom
- Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center and Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
| | - Alessandra Calvi
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
| | - Trinity Zang
- Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center and Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
| | - Paul Bieniasz
- Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center and Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
| | - Paul Kellam
- MRC Centre for Medical Molecular Virology, University College London, London, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Greg J. Towers
- MRC Centre for Medical Molecular Virology, University College London, London, United Kingdom
- * E-mail: (GJT); (SJDN)
| | - Stuart J. D. Neil
- Department of Infectious Disease, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
- * E-mail: (GJT); (SJDN)
| |
Collapse
|
40
|
Groom HCT, Yap MW, Galão RP, Neil SJD, Bishop KN. Susceptibility of xenotropic murine leukemia virus-related virus (XMRV) to retroviral restriction factors. Proc Natl Acad Sci U S A 2010; 107:5166-71. [PMID: 20194752 PMCID: PMC2841911 DOI: 10.1073/pnas.0913650107] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [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] [Indexed: 12/31/2022] Open
Abstract
Xenotropic murine leukemia virus-related virus (XMRV) is a recently discovered gammaretrovirus that has been linked to prostate cancer and chronic fatigue syndrome. This virus is therefore an important potential human pathogen and, as such, it is essential to understand its host cell tropism. Intriguingly, infectious virus has been recovered from patient-derived peripheral blood mononuclear cells. These cells express several antiviral restriction factors that are capable of inhibiting the replication of a wide range of retroviruses, including other gamma retroviruses. This raises the possibility that, similar to HIV, XMRV may have acquired resistance to restriction. We therefore investigated the susceptibility of XMRV to a panel of different restriction factors. We found that both human APOBEC3 and tetherin proteins are able to block XMRV replication. Expression of human TRIM5alpha, however, had no effect on viral infectivity. There was no evidence that XMRV expressed countermeasures to overcome restriction. In addition, the virus was inhibited by factors from nonhuman species, including mouse Apobec3, tetherin, and Fv1 proteins. These results have important implications for predicting the natural target cells for XMRV replication, for relating infection to viral pathogenicity and pathology, and for the design of model systems with which to study XMRV-related diseases.
Collapse
Affiliation(s)
- Harriet C. T. Groom
- Division of Virology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom; and
| | - Melvyn W. Yap
- Division of Virology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom; and
| | - Rui Pedro Galão
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Kate N. Bishop
- Division of Virology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom; and
| |
Collapse
|
41
|
McNatt MW, Zang T, Hatziioannou T, Bartlett M, Fofana IB, Johnson WE, Neil SJD, Bieniasz PD. Species-specific activity of HIV-1 Vpu and positive selection of tetherin transmembrane domain variants. PLoS Pathog 2009; 5:e1000300. [PMID: 19214216 PMCID: PMC2633611 DOI: 10.1371/journal.ppat.1000300] [Citation(s) in RCA: 252] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 01/16/2009] [Indexed: 11/19/2022] Open
Abstract
Tetherin/BST-2/CD317 is a recently identified antiviral protein that blocks the release of nascent retrovirus, and other virus, particles from infected cells. An HIV-1 accessory protein, Vpu, acts as an antagonist of tetherin. Here, we show that positive selection is evident in primate tetherin sequences and that HIV-1 Vpu appears to have specifically adapted to antagonize variants of tetherin found in humans and chimpanzees. Tetherin variants found in rhesus macaques (rh), African green monkeys (agm) and mice were able to inhibit HIV-1 particle release, but were resistant to antagonism by HIV-1 Vpu. Notably, reciprocal exchange of transmembrane domains between human and monkey tetherins conferred sensitivity and resistance to Vpu, identifying this protein domain as a critical determinant of Vpu function. Indeed, differences between hu-tetherin and rh-tetherin at several positions in the transmembrane domain affected sensitivity to antagonism by Vpu. Two alterations in the hu-tetherin transmembrane domain, that correspond to differences found in rh- and agm-tetherin proteins, were sufficient to render hu-tetherin completely resistant to HIV-1 Vpu. Interestingly, transmembrane and cytoplasmic domain sequences in primate tetherins exhibit variation at numerous codons that is likely the result of positive selection, and some of these changes coincide with determinants of HIV-1 Vpu sensitivity. Overall, these data indicate that tetherin could impose a barrier to viral zoonosis as a consequence of positive selection that has been driven by ancient viral antagonists, and that the HIV-1 Vpu protein has specialized to target the transmembrane domains found in human/chimpanzee tetherin proteins. Tetherin is a cell surface protein that acts as an antiviral defense. It functions by tethering newly assembled HIV-1 particles to the surface of the infected cell, such that the viral particle is unable to depart and disseminate to other, uninfected cells. HIV-1 possesses an antagonist of tetherin, termed Vpu, that abolishes tetherin function. We found that HIV-1 is an effective antagonist of human and chimpanzee variants of tetherin but is unable to antagonize tetherins from two monkey species. Additionally, we found that sequence differences in a portion of the protein that is embedded in cell membranes determined whether or not it could be antagonized by Vpu. Since the Vpu protein is alsi a membrane embedded protein, this result suggests that Vpu and tetherin interact within cell membranes. We also show that tetherin has been evolving rapidly, and has likely been placed under selective pressure to change sequence. Notably, portions of tetherin that appear to have been placed under selective pressure coincide with positions that influence Vpu antagonism. Therefore, the evolutionary history of primates determines the effectiveness of HIV-1 Vpu in modern species. Thus, tetherin could impose a barrier to cross species transmission of retroviruses.
Collapse
Affiliation(s)
- Matthew W. McNatt
- Aaron Diamond AIDS Research Center and The Rockefeller University, New York, New York, United States of America
| | - Trinity Zang
- Aaron Diamond AIDS Research Center and The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, New York, New York, United States of America
| | - Theodora Hatziioannou
- Aaron Diamond AIDS Research Center and The Rockefeller University, New York, New York, United States of America
| | - Mackenzie Bartlett
- Department of Microbiology and Molecular Genetics, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America
| | - Ismael Ben Fofana
- Department of Microbiology and Molecular Genetics, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America
| | - Welkin E. Johnson
- Department of Microbiology and Molecular Genetics, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America
| | - Stuart J. D. Neil
- Aaron Diamond AIDS Research Center and The Rockefeller University, New York, New York, United States of America
- * E-mail: (SJDN); (PDB)
| | - Paul D. Bieniasz
- Aaron Diamond AIDS Research Center and The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, New York, New York, United States of America
- * E-mail: (SJDN); (PDB)
| |
Collapse
|
42
|
Neil SJD, Sandrin V, Sundquist WI, Bieniasz PD. An interferon-alpha-induced tethering mechanism inhibits HIV-1 and Ebola virus particle release but is counteracted by the HIV-1 Vpu protein. Cell Host Microbe 2007; 2:193-203. [PMID: 18005734 DOI: 10.1016/j.chom.2007.08.001] [Citation(s) in RCA: 210] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 07/03/2007] [Accepted: 08/06/2007] [Indexed: 10/22/2022]
Abstract
Type 1 interferon (IFN) inhibits the release of HIV-1 virus particles via poorly defined mechanisms. Here, we show that IFNalpha induces retention of viral particles on the surface of fibroblasts, T cells, or primary lymphocytes infected with HIV-1 lacking the Vpu protein. Retained particles are tethered to cell surfaces, can be endocytosed, appear fully assembled, exhibit mature morphology, and can be detached by protease. Strikingly, expression of the HIV-1 Vpu protein attenuates the ability of human cells to adhere to, and thereby retain, nascent HIV-1 particles upon IFNalpha treatment. Vpu also counteracts the IFNalpha-induced retention of virus-like particles assembled from the Ebola virus matrix protein. Furthermore, levels of IFNalpha that suppress replication of Vpu-defective HIV-1 have little effect on wild-type HIV-1. Thus, we propose that HIV-1 expresses Vpu to counteract an IFNalpha-induced, general host defense that inhibits dissemination of enveloped virions from the surface of infected cells.
Collapse
Affiliation(s)
- Stuart J D Neil
- Aaron Diamond AIDS Research Center and the Laboratory of Retrovirology, The Rockefeller University, 455 First Avenue, New York, NY 10016, USA
| | | | | | | |
Collapse
|
43
|
Neil SJD, Eastman SW, Jouvenet N, Bieniasz PD. HIV-1 Vpu promotes release and prevents endocytosis of nascent retrovirus particles from the plasma membrane. PLoS Pathog 2006; 2:e39. [PMID: 16699598 PMCID: PMC1458960 DOI: 10.1371/journal.ppat.0020039] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Accepted: 03/30/2006] [Indexed: 12/31/2022] Open
Abstract
The human immunodeficiency virus (HIV) type-1 viral protein U (Vpu) protein enhances the release of diverse retroviruses from human, but not monkey, cells and is thought to do so by ablating a dominant restriction to particle release. Here, we determined how Vpu expression affects the subcellular distribution of HIV-1 and murine leukemia virus (MLV) Gag proteins in human cells where Vpu is, or is not, required for efficient particle release. In HeLa cells, where Vpu enhances HIV-1 and MLV release approximately 10-fold, concentrations of HIV-1 Gag and MLV Gag fused to cyan fluorescent protein (CFP) were initially detected at the plasma membrane, but then accumulated over time in early and late endosomes. Endosomal accumulation of Gag-CFP was prevented by Vpu expression and, importantly, inhibition of plasma membrane to early endosome transport by dominant negative mutants of Rab5a, dynamin, and EPS-15. Additionally, accumulation of both HIV and MLV Gag in endosomes required a functional late-budding domain. In human HOS cells, where HIV-1 and MLV release was efficient even in the absence of Vpu, Gag proteins were localized predominantly at the plasma membrane, irrespective of Vpu expression or manipulation of endocytic transport. While these data indicated that Vpu inhibits nascent virion endocytosis, Vpu did not affect transferrin endocytosis. Moreover, inhibition of endocytosis did not restore Vpu-defective HIV-1 release in HeLa cells, but instead resulted in accumulation of mature virions that could be released from the cell surface by protease treatment. Thus, these findings suggest that a specific activity that is present in HeLa cells, but not in HOS cells, and is counteracted by Vpu, traps assembled retrovirus particles at the cell surface. This entrapment leads to subsequent endocytosis by a Rab5a- and clathrin-dependent mechanism and intracellular sequestration of virions in endosomes.
Collapse
Affiliation(s)
- Stuart J D Neil
- Aaron Diamond AIDS Research Center, Laboratory of Retrovirology, Rockefeller University, New York, New York, USA
| | | | | | | |
Collapse
|
44
|
Marchant D, Neil SJD, McKnight Á. Human immunodeficiency virus types 1 and 2 have different replication kinetics in human primary macrophage culture. J Gen Virol 2006; 87:411-418. [PMID: 16432029 DOI: 10.1099/vir.0.81391-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [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] [Indexed: 12/29/2022] Open
Abstract
This study compares the replication of primary isolates of human immunodeficiency virus type 2 (HIV-2) and type 1 (HIV-1) in monocyte-derived macrophages (MDMs). Eleven HIV-2 and five HIV-1 primary isolates that use CCR5, CXCR4 or both coreceptors to enter cells were included. Regardless of coreceptor preference, 10 of 11 HIV-2 viruses could enter, reverse transcribe and produce fully infectious virus in MDMs with efficiency equal to that in peripheral blood mononuclear cells. However, the kinetics of replication of HIV-2 compared with HIV-1 over time were distinct. HIV-2 had a burst of virus replication 2 days after infection that resolved into an apparent 'latent state' at day 3. HIV-1, however, continued to produce infectious virions at a lower, but steady, rate throughout the course of infection. These results may have implications for the lower pathogenesis and viral-load characteristics of HIV-2 infection.
Collapse
Affiliation(s)
- David Marchant
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, University College London, 46 Cleveland Street, London W1T 4JF, UK
| | - Stuart J D Neil
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, University College London, 46 Cleveland Street, London W1T 4JF, UK
| | - Áine McKnight
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, University College London, 46 Cleveland Street, London W1T 4JF, UK
| |
Collapse
|
45
|
Neil SJD, Aasa-Chapman MMI, Clapham PR, Nibbs RJ, McKnight A, Weiss RA. The promiscuous CC chemokine receptor D6 is a functional coreceptor for primary isolates of human immunodeficiency virus type 1 (HIV-1) and HIV-2 on astrocytes. J Virol 2005; 79:9618-24. [PMID: 16014924 PMCID: PMC1181543 DOI: 10.1128/jvi.79.15.9618-9624.2005] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The role of coreceptors other than CCR5 and CXCR4 in the pathogenesis of human immunodeficiency virus (HIV) disease is controversial. Here we show that a promiscuous CC chemokine receptor, D6, can function as a coreceptor for various primary dual-tropic isolates of HIV type 1 (HIV-1) and HIV-2. Furthermore, D6 usage is common among chimeric HIV-1 constructs bearing the gp120 proteins of isolates from early seroconverting patients. D6 mRNA and immunoreactivity were demonstrated to be expressed in HIV-1 target cells such as macrophages, peripheral blood mononuclear cells, and primary astrocytes. In primary astrocytes, an RNA interference-mediated knockdown of D6 expression inhibited D6-tropic isolate infection. D6 usage may account for some previous observations of alternative receptor tropism for primary human cells. Thus, D6 may be an important receptor for HIV pathogenesis in the brain and for the early dissemination of virus in the host.
Collapse
Affiliation(s)
- Stuart J D Neil
- Wohl Virion Centre, Division of Infection and Immunity, University College London, UK
| | | | | | | | | | | |
Collapse
|
46
|
Marchant D, Neil SJD, Aubin K, Schmitz C, McKnight A. An envelope-determined, pH-independent endocytic route of viral entry determines the susceptibility of human immunodeficiency virus type 1 (HIV-1) and HIV-2 to Lv2 restriction. J Virol 2005; 79:9410-8. [PMID: 16014904 PMCID: PMC1181606 DOI: 10.1128/jvi.79.15.9410-9418.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [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] [Indexed: 01/27/2023] Open
Abstract
We identified a postentry restriction, termed Lv2, which determines the cellular tropism of two related human immunodeficiency virus type 2 (HIV-2) isolates and is dependent on the sequence of the capsid (CA) and envelope (Env) proteins. To explain the reliance on both CA and Env, we proposed that restrictive Envs deliver susceptible capsids to a compartment where Lv2 is active whereas nonrestrictive Envs deliver capsids into a compartment where Lv2 is either absent or less active. To test this model, we used compounds that affect endocytic pathways (ammonium chloride, bafilomycin A1, hypertonic sucrose) or lipid rafts (methyl-beta-cyclodextrin) to treat restrictive cells and show that restricted virus can be rescued from Lv2 if a lipid-raft-dependent, pH-independent endocytic pathway is inhibited. Furthermore, viral entry into HeLa/CD4 cells containing a tailless CD4 receptor, located outside lipid rafts, was fully permissive. Finally, we show that a variety of primary HIV-1 and HIV-2 viruses are susceptible to Lv2. Thus, we show that the route of entry, determined by the viral envelope, can influence cellular tropism by avoiding intracellular blocks to infection.
Collapse
Affiliation(s)
- David Marchant
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, UCL, London, UK
| | | | | | | | | |
Collapse
|
47
|
Neil SJD, McKnight A, Gustafsson K, Weiss RA. HIV-1 incorporates ABO histo-blood group antigens that sensitize virions to complement-mediated inactivation. Blood 2005; 105:4693-9. [PMID: 15728127 DOI: 10.1182/blood-2004-11-4267] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABO histo-blood group antigens have been postulated to modify pathogen spread through the action of natural antibodies and complement. The antigens are generated by a polymorphic glycosyl-transferase encoded by 2 dominant active and a recessive inactive allele. In this study we investigated whether ABO sugars are incorporated into the envelope of HIV-1 virions. HIV vectors derived from cells expressing ABO antigens displayed sensitivity to fresh human serum analogous to ABO incompatibility, and ABO histo-blood group sugars were detected on the viral envelope protein, glycoprotein 120 (gp120). Moreover, lymphocyte-derived virus also displayed serum sensitivity, reflecting the ABO phenotype of the host when cultured in autologous serum due to adsorption of antigens to cell surfaces. Serum sensitivity required both active complement and specific anti-ABO antibodies. Thus, incorporation of ABO antigens by HIV-1 may affect transmission of virus between individuals of discordant blood groups by interaction with host natural antibody and complement.
Collapse
Affiliation(s)
- Stuart J D Neil
- Wohl Virion Centre, Division of Infection and Immunity, University College London, London, United Kingdom
| | | | | | | |
Collapse
|
48
|
Schmitz C, Marchant D, Neil SJD, Aubin K, Reuter S, Dittmar MT, McKnight A. Lv2, a novel postentry restriction, is mediated by both capsid and envelope. J Virol 2004; 78:2006-16. [PMID: 14747565 PMCID: PMC369432 DOI: 10.1128/jvi.78.4.2006-2016.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2003] [Accepted: 11/01/2003] [Indexed: 11/20/2022] Open
Abstract
The characterization of restrictions to lentivirus replication in cells identifies critical steps in the viral life cycle and potential therapeutic targets. We previously reported that a human immunodeficiency virus type 2 (HIV-2) isolate was restricted to infection in some human cells, which led us to identify a step in the life cycle of HIV-2 detected after reverse transcription but prior to nuclear entry. The block is bypassed with a vesicular stomatitis virus glycoprotein G (VSV-G) envelope (A. McKnight et al., J. Virol. 75:6914-6922, 2001). We hypothesized that, although the restriction is apparent at a post-reverse transcription step, the lack of progress results from a failure of the virus to reach a cellular compartment with access to the nucleus. Here we analyzed molecular clones of the restricted virus, MCR, and an unrestricted virus, MCN. Using sequence analysis and gene swapping, we mapped the viral determinants to gag and env. Site-directed mutagenesis identified a single amino acid at position 207 in CA to be responsible for the gag restriction. Pseudotype experiments indicate that this step is also important for the infection of cells by HIV-1. The HIV-1 NL4.3 core is restricted if supplied with a restricted MCR envelope but not with VSV-G. Also the NL4.3 envelope rescues the restricted core of HIV-2 MCR. Abrogation experiments with MLV demonstrate that the restriction is distinct from Fv1/Ref1/Lv1. We propose that this represents a new lentiviral restriction, Lv2. Thus, the envelope and capsid of HIV act to ensure that the virus is delivered into an appropriate cellular compartment that allows postentry events in viral replication to proceed efficiently.
Collapse
Affiliation(s)
- Christian Schmitz
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, UCL, London W1T 4JF, United Kingdom
| | | | | | | | | | | | | |
Collapse
|