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Wang X, Ding P, Sun C, Wang D, Zhu J, Wu W, Wei Y, Xiang R, Ding X, Luo L, Li M, Zhang W, Jin X, Sun J, Liu H, Chen D. Comparative analysis of single cell lung atlas of bat, cat, tiger, and pangolin. Cell Biol Toxicol 2023; 39:2431-2435. [PMID: 36169743 PMCID: PMC9516514 DOI: 10.1007/s10565-022-09771-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
Abstract
Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as severe acute respiratory syndrome coronavirus (SARS-CoV). Bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the coronavirus disease 2019 (COVID-19) pandemic, multiple animal species were diseased by coronavirus infection, especially in the respiratory system. Herein, a comparative analysis with single nucleus transcriptomic data of the lungs across four species, including horseshoe bat, cat, tiger, and pangolin, were conducted. The distribution of entry factors for twenty-eight respiratory viruses was characterized for the four species. Our findings might increase our understanding of the immune background of horseshoe bats.
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Affiliation(s)
- Xiran Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Peiwen Ding
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengcheng Sun
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiacheng Zhu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wendi Wu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Yanan Wei
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | | | - Xiangning Ding
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lihua Luo
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Wensheng Zhang
- School of Basic Medical Sciences, Binzhou Medical University, No. 346, Guanhai Road, Laishan District, Yantai City, Shandong, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dongsheng Chen
- BGI-Shenzhen, Shenzhen, 518083, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Quarleri J, Galvan V, Delpino MV. Henipaviruses: an expanding global public health concern? GeroScience 2022; 44:2447-2459. [PMID: 36219280 PMCID: PMC9550596 DOI: 10.1007/s11357-022-00670-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/03/2022] [Indexed: 01/18/2023] Open
Abstract
Nipah virus (NiV) and Hendra virus (HeV) are highly pathogenic zoonotic viruses of the genus Henipavirus, family Paramyxoviridae that cause severe disease outbreaks in humans and also can infect and cause lethal disease across a broad range of mammalian species. Another related Henipavirus has been very recently identified in China in febrile patients with pneumonia, the Langya virus (LayV) of probable animal origin in shrews. NiV and HeV were first identified as the causative agents of severe respiratory and encephalitic disease in the 1990s across Australia and Southern Asia with mortality rates reaching up to 90%. They are responsible for rare and sporadic outbreaks with no approved treatment modalities. NiV and HeV have wide cellular tropism that contributes to their high pathogenicity. From their natural hosts bats, different scenarios propitiate their spillover to pigs, horses, and humans. Henipavirus-associated respiratory disease arises from vasculitis and respiratory epithelial cell infection while the neuropathogenesis of Henipavirus infection is still not completely understood but appears to arise from dual mechanisms of vascular disease and direct parenchymal brain infection. This brief review offers an overview of direct and indirect mechanisms of HeV and NiV pathogenicity and their interaction with the human immune system, as well as the main viral strategies to subvert such responses.
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Affiliation(s)
- Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires - Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Verónica Galvan
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Center for Geroscience and Healthy Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- US Department of Veterans Affairs, Oklahoma City VA Health Care System, Oklahoma City, OK, USA
| | - M Victoria Delpino
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires - Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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3
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Doan PTK, Low WY, Ren Y, Tearle R, Hemmatzadeh F. Newcastle disease virus genotype VII gene expression in experimentally infected birds. Sci Rep 2022; 12:5249. [PMID: 35347193 PMCID: PMC8960812 DOI: 10.1038/s41598-022-09257-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/07/2022] [Indexed: 11/23/2022] Open
Abstract
Newcastle disease virus genotype VII (NDV-GVII) is a highly contagious pathogen responsible for pandemics that have caused devastating economic losses in the poultry industry. Several features in the transcription of NDV mRNA, including differentially expressed genes across the viral genome, are shared with that for other single, non-segmented, negative-strand viruses. Previous studies measuring viral gene expression using northern blotting indicated that the NDV transcription produced non-equimolar levels of viral mRNAs. However, deep high-throughput sequencing of virus-infected tissues can provide a better insight into the patterns of viral transcription. In this report, the transcription pattern of virulent NDV-GVII was analysed using RNA-seq and qRT-PCR. This study revealed the transcriptional profiling of these highly pathogenic NDV-GVII genes: NP:P:M:F:HN:L, in which there was a slight attenuation at the NP:P and HN:L gene boundaries. Our result also provides a fully comprehensive qPCR protocol for measuring viral transcript abundance that may be more convenient for laboratories where accessing RNA-seq is not feasible.
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Affiliation(s)
- Phuong Thi Kim Doan
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia. .,Faculty of Animal and Veterinary Sciences, Tay Nguyen University, Dak Lak, Vietnam.
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Yan Ren
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
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4
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Reprogrammed Pteropus Bat Stem Cells as A Model to Study Host-Pathogen Interaction during Henipavirus Infection. Microorganisms 2021; 9:microorganisms9122567. [PMID: 34946167 PMCID: PMC8706405 DOI: 10.3390/microorganisms9122567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/04/2021] [Accepted: 12/08/2021] [Indexed: 01/13/2023] Open
Abstract
Bats are natural hosts for numerous zoonotic viruses, including henipaviruses, which are highly pathogenic for humans, livestock, and other mammals but do not induce clinical disease in bats. Pteropus bats are identified as a reservoir of henipaviruses and the source of transmission of the infection to humans over the past 20 years. A better understanding of the molecular and cellular mechanisms allowing bats to control viral infections requires the development of relevant, stable, and permissive cellular experimental models. By applying a somatic reprogramming protocol to Pteropus bat primary cells, using a combination of ESRRB (Estrogen Related Receptor Beta), CDX2 (Caudal type Homeobox 2), and c-MYC (MYC proto-oncogene) transcription factors, we generated bat reprogrammed cells. These cells exhibit stem cell-like characteristics and neural stem cell molecular signature. In contrast to primary fibroblastic cells, these reprogrammed stem cells are highly permissive to henipaviruses and exhibit specific transcriptomic profiles with the particular expression of certain susceptibility factors such as interferon-stimulated genes (ISG), which may be related to viral infection. These Pteropus bat reprogrammed stem cells should represent an important experimental tool to decipher interactions during henipaviruses infection in Pteropus bats, facilitate isolation and production of bat-borne viruses, and to better understand the bat biology.
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5
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Gamble A, Yeo YY, Butler AA, Tang H, Snedden CE, Mason CT, Buchholz DW, Bingham J, Aguilar HC, Lloyd-Smith JO. Drivers and Distribution of Henipavirus-Induced Syncytia: What Do We Know? Viruses 2021; 13:1755. [PMID: 34578336 PMCID: PMC8472861 DOI: 10.3390/v13091755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/21/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Syncytium formation, i.e., cell-cell fusion resulting in the formation of multinucleated cells, is a hallmark of infection by paramyxoviruses and other pathogenic viruses. This natural mechanism has historically been a diagnostic marker for paramyxovirus infection in vivo and is now widely used for the study of virus-induced membrane fusion in vitro. However, the role of syncytium formation in within-host dissemination and pathogenicity of viruses remains poorly understood. The diversity of henipaviruses and their wide host range and tissue tropism make them particularly appropriate models with which to characterize the drivers of syncytium formation and the implications for virus fitness and pathogenicity. Based on the henipavirus literature, we summarized current knowledge on the mechanisms driving syncytium formation, mostly acquired from in vitro studies, and on the in vivo distribution of syncytia. While these data suggest that syncytium formation widely occurs across henipaviruses, hosts, and tissues, we identified important data gaps that undermined our understanding of the role of syncytium formation in virus pathogenesis. Based on these observations, we propose solutions of varying complexity to fill these data gaps, from better practices in data archiving and publication for in vivo studies, to experimental approaches in vitro.
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Affiliation(s)
- Amandine Gamble
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.A.B.); (H.T.); (C.E.S.); (J.O.L.-S.)
| | - Yao Yu Yeo
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY 14850, USA; (Y.Y.Y.); (D.W.B.); (H.C.A.)
| | - Aubrey A. Butler
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.A.B.); (H.T.); (C.E.S.); (J.O.L.-S.)
| | - Hubert Tang
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.A.B.); (H.T.); (C.E.S.); (J.O.L.-S.)
| | - Celine E. Snedden
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.A.B.); (H.T.); (C.E.S.); (J.O.L.-S.)
| | - Christian T. Mason
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA;
| | - David W. Buchholz
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY 14850, USA; (Y.Y.Y.); (D.W.B.); (H.C.A.)
| | - John Bingham
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC 3220, Australia;
| | - Hector C. Aguilar
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY 14850, USA; (Y.Y.Y.); (D.W.B.); (H.C.A.)
| | - James O. Lloyd-Smith
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.A.B.); (H.T.); (C.E.S.); (J.O.L.-S.)
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6
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Davidson AD, Williamson MK, Lewis S, Shoemark D, Carroll MW, Heesom KJ, Zambon M, Ellis J, Lewis PA, Hiscox JA, Matthews DA. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein. Genome Med 2020; 12:68. [PMID: 32723359 PMCID: PMC7386171 DOI: 10.1186/s13073-020-00763-0] [Citation(s) in RCA: 283] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus's genomic and proteomic potential. METHODS We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells. RESULTS Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. CONCLUSIONS Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that the viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.
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Affiliation(s)
- Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Sebastian Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Deborah Shoemark
- School of Biochemistry, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Miles W Carroll
- Research and Development Institute, National Infection Service, Public Health, England, Porton Down, Wiltshire, UK
- National Institute Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Kate J Heesom
- Proteomics Facility Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Maria Zambon
- Virus Reference Department, Public Health England (Colindale), London, UK
| | - Joanna Ellis
- Virus Reference Department, Public Health England (Colindale), London, UK
| | - Philip A Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Julian A Hiscox
- National Institute Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Liverpool Health Partners, Liverpool, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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7
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Chen M, Tachedjian M, Marsh GA, Cui J, Wang LF. Distinct Cell Transcriptomic Landscapes Upon Henipavirus Infections. Front Microbiol 2020; 11:986. [PMID: 32508793 PMCID: PMC7248276 DOI: 10.3389/fmicb.2020.00986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/23/2020] [Indexed: 01/13/2023] Open
Abstract
Hendra virus (HeV) and Cedar virus (CedV) are henipaviruses, which fall into the Paramyxoviridae family of single-stranded, negative-sense RNA viruses. HeV is classified as a Biosafety Level-4 (BSL-4) agent, as it is highly pathogenic and is often fatal to humans. To date, no HeV prevention or treatment methods for human are available. In contrast, previous experimental infection studies have suggested that CedV is non-pathogenic. Flying foxes (pteropid bats) in Australia are the natural reservoirs of both viruses, but the cellular responses of bats to these viral infections remain unclear. Here, we infected bat and human cells with these viruses. We then examined the total transcriptomic landscapes of the cells at 6 or 24 h post infection. Unexpectedly, despite the close phylogenetic relationship between HeV and CedV, there was a dramatic difference in cellular gene expression patterns in response to the two different infections. It is likely that minor differences in the phosphoprotein (P) gene coding strategy between the two viruses cause the observed incongruence in host transcriptomic divergence and viral lethality. This study greatly expands our understanding of the pathogenic mechanisms of henipaviruses.
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Affiliation(s)
- Mingyue Chen
- Key Laboratory of Fermentation Engineering, National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Mary Tachedjian
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Glenn A Marsh
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Lin-Fa Wang
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, VIC, Australia.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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8
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Woon AP, Boyd V, Todd S, Smith I, Klein R, Woodhouse IB, Riddell S, Crameri G, Bingham J, Wang LF, Purcell AW, Middleton D, Baker ML. Acute experimental infection of bats and ferrets with Hendra virus: Insights into the early host response of the reservoir host and susceptible model species. PLoS Pathog 2020; 16:e1008412. [PMID: 32226041 PMCID: PMC7145190 DOI: 10.1371/journal.ppat.1008412] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/09/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022] Open
Abstract
Bats are the natural reservoir host for a number of zoonotic viruses, including Hendra virus (HeV) which causes severe clinical disease in humans and other susceptible hosts. Our understanding of the ability of bats to avoid clinical disease following infection with viruses such as HeV has come predominantly from in vitro studies focusing on innate immunity. Information on the early host response to infection in vivo is lacking and there is no comparative data on responses in bats compared with animals that succumb to disease. In this study, we examined the sites of HeV replication and the immune response of infected Australian black flying foxes and ferrets at 12, 36 and 60 hours post exposure (hpe). Viral antigen was detected at 60 hpe in bats and was confined to the lungs whereas in ferrets there was evidence of widespread viral RNA and antigen by 60 hpe. The mRNA expression of IFNs revealed antagonism of type I and III IFNs and a significant increase in the chemokine, CXCL10, in bat lung and spleen following infection. In ferrets, there was an increase in the transcription of IFN in the spleen following infection. Liquid chromatography tandem mass spectrometry (LC-MS/MS) on lung tissue from bats and ferrets was performed at 0 and 60 hpe to obtain a global overview of viral and host protein expression. Gene Ontology (GO) enrichment analysis of immune pathways revealed that six pathways, including a number involved in cell mediated immunity were more likely to be upregulated in bat lung compared to ferrets. GO analysis also revealed enrichment of the type I IFN signaling pathway in bats and ferrets. This study contributes important comparative data on differences in the dissemination of HeV and the first to provide comparative data on the activation of immune pathways in bats and ferrets in vivo following infection. Bats are natural reservoirs for a number of viruses, including HeV that cause severe disease in humans and other susceptible hosts. We examined acute HeV infection in pteropid bats, compared to ferrets, a species that develops fulminating disease following exposure to HeV, similar to humans. Analysis of HeV replication and transcription of innate immune genes was performed at 12, 36 and 60 hpe and global proteomics was performed on tissues at 60 hpe to obtain insight into the mechanisms responsible for innocuous (bats) compared to fatal (ferrets) HeV infection. We confirmed that both animal species had become infected on the basis of detection of viral RNA in bat lung (60 hpe) and ferret lung, lymph node, spleen, heart and intestine (36 and/or 60 hpe). Analysis of the transcription of IFNs and CXCL10, combined with global proteomics analysis revealed differences in the activation of the immune response between bats and ferrets, consistent with the difference in the control of viral replication and the development of pathology associated with disease between the two species. This study represents the first in vivo comparison between bats and a susceptible host and contributes important information on the kinetics and control of HeV in these two model species.
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Affiliation(s)
- Amanda P Woon
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Immunocore Ltd, Abingdon, Oxford, United Kingdom
| | - Victoria Boyd
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Shawn Todd
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Ina Smith
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Reuben Klein
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Isaac B Woodhouse
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.,Centre of Innate Immunity and Infectious Diseases, Hudson Institute of Medical Search, Clayton, Victoria, Australia
| | - Sarah Riddell
- CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Gary Crameri
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - John Bingham
- CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Deborah Middleton
- CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Michelle L Baker
- CSIRO Health and Biosecurity Business Unit, Australian Animal Health Laboratory, Geelong, Victoria, Australia
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9
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Reynolds DA, Yoo MJ, Dixson DL, Ross C. Exposure to the Florida red tide dinoflagellate, Karenia brevis, and its associated brevetoxins induces ecophysiological and proteomic alterations in Porites astreoides. PLoS One 2020; 15:e0228414. [PMID: 32032360 PMCID: PMC7006924 DOI: 10.1371/journal.pone.0228414] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/14/2020] [Indexed: 01/27/2023] Open
Abstract
As reef-building corals are increasingly being exposed to persistent threats that operate on both regional and global scales, there is a pressing need to better understand the complex processes that diminish coral populations. This study investigated the impacts of the Florida red tide dinoflagellate Karenia brevis and associated brevetoxins on selected facets of coral biology using Porites astreoides as a model system. When provided with choice assays, P. astreoides larvae were shown to actively avoid seawater containing red tide (5×105 cells L-1–7.6×106 cells L-1) or purified brevetoxins (0.018 μg mL-1 brevetoxin-2 and 0.0018 μg mL-1 brevetoxin-3). However, forced exposure to similar treatments induced time-dependent physiological and behavioral changes that were captured by PAM fluorometry and settlement and survival assays, respectively. Adult fragments of P. astreoides exposed to red tide or associated brevetoxins displayed signs of proteomic alterations that were characterized by the use of an iTRAQ-based quantitative proteomic analysis. The novel use of this technique with P. astreoides demonstrated that protein regulation was highly contingent upon biological versus chemical treatment (i.e. live K. brevis vs. solely brevetoxin exposure) and that several broad pathways associated with cell stress were affected including redox homeostasis, protein folding, energy metabolism and reactive oxygen species production. The results herein provide new insight into the ecology, behavior and sublethal stress of reef-building corals in response to K. brevis exposure and underscore the importance of recognizing the potential of red tide to act as a regional stressor to these important foundation species.
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Affiliation(s)
- David A. Reynolds
- Department of Biology, University of North Florida, Jacksonville, Florida, United States of America
| | - Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, United States of America
| | - Danielle L. Dixson
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, United States of America
| | - Cliff Ross
- Department of Biology, University of North Florida, Jacksonville, Florida, United States of America
- * E-mail:
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10
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Analysis of Paramyxovirus Transcription and Replication by High-Throughput Sequencing. J Virol 2019; 93:JVI.00571-19. [PMID: 31189700 PMCID: PMC6694822 DOI: 10.1128/jvi.00571-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/03/2019] [Indexed: 11/20/2022] Open
Abstract
High-throughput sequencing (HTS) of virus-infected cells can be used to study in great detail the patterns of virus transcription and replication. For paramyxoviruses, and by analogy for all other negative-strand RNA viruses, we show that directional sequencing must be used to distinguish between genomic RNA and mRNA/antigenomic RNA because significant amounts of genomic RNA copurify with poly(A)-selected mRNA. We found that the best method is directional sequencing of total cell RNA, after the physical removal of rRNA (and mitochondrial RNA), because quantitative information on the abundance of both genomic RNA and mRNA/antigenomes can be simultaneously derived. Using this approach, we revealed new details of the kinetics of virus transcription and replication for parainfluenza virus (PIV) type 2, PIV3, PIV5, and mumps virus, as well as on the relative abundance of the individual viral mRNAs. We have developed a high-throughput sequencing (HTS) workflow for investigating paramyxovirus transcription and replication. We show that sequencing of oligo(dT)-selected polyadenylated mRNAs, without considering the orientation of the RNAs from which they had been generated, cannot accurately be used to analyze the abundance of viral mRNAs because genomic RNA copurifies with the viral mRNAs. The best method is directional sequencing of infected cell RNA that has physically been depleted of ribosomal and mitochondrial RNA followed by bioinformatic steps to differentiate data originating from genomes from viral mRNAs and antigenomes. This approach has the advantage that the abundance of viral mRNA (and antigenomes) and genomes can be analyzed and quantified from the same data. We investigated the kinetics of viral transcription and replication during infection of A549 cells with parainfluenza virus type 2 (PIV2), PIV3, PIV5, or mumps virus and determined the abundances of individual viral mRNAs and readthrough mRNAs. We found that the mRNA abundance gradients differed significantly between all four viruses but that for each virus the pattern remained relatively stable throughout infection. We suggest that rapid degradation of non-poly(A) mRNAs may be primarily responsible for the shape of the mRNA abundance gradient in parainfluenza virus 3, whereas a combination of this factor and disengagement of RNA polymerase at intergenic sequences, particularly those at the NP:P and P:M gene boundaries, may be responsible in the other viruses. IMPORTANCE High-throughput sequencing (HTS) of virus-infected cells can be used to study in great detail the patterns of virus transcription and replication. For paramyxoviruses, and by analogy for all other negative-strand RNA viruses, we show that directional sequencing must be used to distinguish between genomic RNA and mRNA/antigenomic RNA because significant amounts of genomic RNA copurify with poly(A)-selected mRNA. We found that the best method is directional sequencing of total cell RNA, after the physical removal of rRNA (and mitochondrial RNA), because quantitative information on the abundance of both genomic RNA and mRNA/antigenomes can be simultaneously derived. Using this approach, we revealed new details of the kinetics of virus transcription and replication for parainfluenza virus (PIV) type 2, PIV3, PIV5, and mumps virus, as well as on the relative abundance of the individual viral mRNAs.
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11
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Hölzer M, Schoen A, Wulle J, Müller MA, Drosten C, Marz M, Weber F. Virus- and Interferon Alpha-Induced Transcriptomes of Cells from the Microbat Myotis daubentonii. iScience 2019; 19:647-661. [PMID: 31465999 PMCID: PMC6718828 DOI: 10.1016/j.isci.2019.08.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/10/2019] [Accepted: 08/07/2019] [Indexed: 12/25/2022] Open
Abstract
Antiviral interferons (IFN-alpha/beta) are possibly responsible for the high tolerance of bats to zoonotic viruses. Previous studies focused on the IFN system of megabats (suborder Yinpterochiroptera). We present statistically robust RNA sequencing (RNA-seq) data on transcriptomes of cells from the “microbat” Myotis daubentonii (suborder Yangochiroptera) responding at 6 and 24 h to either an IFN-inducing virus or treatment with IFN. Our data reveal genes triggered only by virus, either in both humans and Myotis (CCL4, IFNL3, CH25H), or exclusively in Myotis (STEAP4). Myotis cells also express a series of conserved IFN-stimulated genes (ISGs) and an unusually high paralog number of the antiviral ISG BST2 (tetherin) but lack several ISGs that were described for megabats (EMC2, FILIP1, IL17RC, OTOGL, SLC24A1). Also, in contrast to megabats, we detected neither different IFN-alpha subtypes nor an unusually high baseline expression of IFNs. Thus, Yangochiroptera microbats, represented by Myotis, may possess an IFN system with distinctive features. Virus- and IFN-responsive transcriptomes of the microbat Myotis daubentonii CCL4, IFNL3, CH25H, STEAP4 are IFNB-like genes triggered by virus only Microbats encode more paralogs of BST2 (tetherin) than any other mammal Clear differences between the IFN systems of microbats and megabats
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Affiliation(s)
- Martin Hölzer
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany; European Virus Bioinformatics Center, Jena, Germany
| | - Andreas Schoen
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany; Institute for Virology, Philipps University Marburg, Marburg, Germany; German Centre for Infection Research (DZIF), partner sites Marburg, Giessen, and Charité Berlin, Germany
| | - Julia Wulle
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany; Institute for Virology, Philipps University Marburg, Marburg, Germany; German Centre for Infection Research (DZIF), partner sites Marburg, Giessen, and Charité Berlin, Germany
| | - Marcel A Müller
- German Centre for Infection Research (DZIF), partner sites Marburg, Giessen, and Charité Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Christian Drosten
- German Centre for Infection Research (DZIF), partner sites Marburg, Giessen, and Charité Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany; European Virus Bioinformatics Center, Jena, Germany.
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany; Institute for Virology, Philipps University Marburg, Marburg, Germany; German Centre for Infection Research (DZIF), partner sites Marburg, Giessen, and Charité Berlin, Germany.
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12
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Saha S, Matthews DA, Bessant C. High throughput discovery of protein variants using proteomics informed by transcriptomics. Nucleic Acids Res 2019; 46:4893-4902. [PMID: 29718325 PMCID: PMC6007231 DOI: 10.1093/nar/gky295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/11/2018] [Indexed: 11/13/2022] Open
Abstract
Proteomics informed by transcriptomics (PIT), in which proteomic MS/MS spectra are searched against open reading frames derived from de novo assembled transcripts, can reveal previously unknown translated genomic elements (TGEs). However, determining which TGEs are truly novel, which are variants of known proteins, and which are simply artefacts of poor sequence assembly, is challenging. We have designed and implemented an automated solution that classifies putative TGEs by comparing to reference proteome sequences. This allows large-scale identification of sequence polymorphisms, splice isoforms and novel TGEs supported by presence or absence of variant-specific peptide evidence. Unlike previously reported methods, ours does not require a catalogue of known variants, making it more applicable to non-model organisms. The method was validated on human PIT data, then applied to Mus musculus, Pteropus alecto and Aedes aegypti. Novel discoveries included 60 human protein isoforms, 32 392 polymorphisms in P. alecto, and TGEs with non-methionine start sites including tyrosine.
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Affiliation(s)
- Shyamasree Saha
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End, London E1 4NS, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Conrad Bessant
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End, London E1 4NS, UK.,Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, Mile End, London E1 4NS, UK
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Chionh YT, Cui J, Koh J, Mendenhall IH, Ng JHJ, Low D, Itahana K, Irving AT, Wang LF. High basal heat-shock protein expression in bats confers resistance to cellular heat/oxidative stress. Cell Stress Chaperones 2019; 24:835-849. [PMID: 31230214 PMCID: PMC6629734 DOI: 10.1007/s12192-019-01013-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/29/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023] Open
Abstract
Bats, unique among mammals with powered flight, have many species with the longest size-proportionate lifespan of all mammals. Evolutionary adaptations would have been required to survive the elevated body temperatures during flight. Heat shock protein (HSP), highly conserved master regulators of cell stress, expression was examined across tissues and various cell lines in bats. Basal expression level of major HSPs (HSP70 and HSP90) is significantly higher in two different bat species compared to other mammals. This HSP expression could be a bat-unique, key factor to modulate cellular stress and death. Consequently, bat cells survive prolonged heat treatment, along with other stress stimuli, in a HSP-dependent manner, whereas other mammalian cells succumbed. This suggests HSP expression in bats could be an important adaption to intrinsic metabolic stresses like flight and therefore an important model to study stress resilience and longevity in general.
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Affiliation(s)
- Yok Teng Chionh
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Jie Cui
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Javier Koh
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Justin H J Ng
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Dolyce Low
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Koji Itahana
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Aaron T Irving
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Lin-Fa Wang
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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14
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Koh J, Itahana Y, Mendenhall IH, Low D, Soh EXY, Guo AK, Chionh YT, Wang LF, Itahana K. ABCB1 protects bat cells from DNA damage induced by genotoxic compounds. Nat Commun 2019; 10:2820. [PMID: 31249297 PMCID: PMC6597548 DOI: 10.1038/s41467-019-10495-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 05/14/2019] [Indexed: 01/02/2023] Open
Abstract
Bats are unusual mammals, with the ability to fly, and long lifespans. In addition, bats have a low incidence of cancer, but the mechanisms underlying this phenomenon remain elusive. Here we discovered that bat cells are more resistant than human and mouse cells to DNA damage induced by genotoxic drugs. We found that bat cells accumulate less chemical than human and mouse cells, and efficient drug efflux mediated by the ABC transporter ABCB1 underlies this improved response to genotoxic reagents. Inhibition of ABCB1 triggers an accumulation of doxorubicin, DNA damage, and cell death. ABCB1 is expressed at higher levels in several cell lines and tissues derived from bats compared to humans. Furthermore, increased drug efflux and high expression of ABCB1 are conserved across multiple bat species. Our findings suggest that enhanced efflux protects bat cells from DNA damage induced by genotoxic compounds, which may contribute to their low cancer incidence.
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Affiliation(s)
- Javier Koh
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Yoko Itahana
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Dolyce Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Eunice Xin Yi Soh
- School of Applied Science, Temasek Polytechnic, 21 Tampines Avenue 1, Singapore, 529757, Singapore
| | - Alvin Kunyao Guo
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Yok Teng Chionh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Koji Itahana
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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15
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Enhanced Autophagy Contributes to Reduced Viral Infection in Black Flying Fox Cells. Viruses 2019; 11:v11030260. [PMID: 30875748 PMCID: PMC6466025 DOI: 10.3390/v11030260] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/01/2019] [Accepted: 03/08/2019] [Indexed: 12/19/2022] Open
Abstract
Bats are increasingly implicated as hosts of highly pathogenic viruses. The underlying virus⁻host interactions and cellular mechanisms that promote co-existence remain ill-defined, but physiological traits such as flight and longevity are proposed to drive these adaptations. Autophagy is a cellular homeostatic process that regulates ageing, metabolism, and intrinsic immune defense. We quantified basal and stimulated autophagic responses in black flying fox cells, and demonstrated that although black flying fox cells are susceptible to Australian bat lyssavirus (ABLV) infection, viral replication is dampened in these bat cells. Black flying fox cells tolerated prolonged ABLV infection with less cell death relative to comparable human cells, suggesting post-entry mechanisms interference with virus replication. An elevated basal autophagic level was observed and autophagy was induced in response to high virus doses. Pharmacological stimulation of the autophagy pathway reduced virus replication, indicating autophagy acts as an anti-viral mechanism. Enhancement of basal and virus-induced autophagy in bat cells connects related reports that long-lived species possess homeostatic processes that dampen oxidative stress and macromolecule damage. Exemplifying the potential that evolved cellular homeostatic adaptations like autophagy may secondarily act as anti-viral mechanisms, enabling bats to serve as natural hosts to an assortment of pathogenic viruses. Furthermore, our data suggest autophagy-inducing drugs may provide a novel therapeutic strategy for combating lyssavirus infection.
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16
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Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host. Nat Microbiol 2019; 4:789-799. [PMID: 30804542 PMCID: PMC7096966 DOI: 10.1038/s41564-019-0371-3] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/16/2019] [Indexed: 01/22/2023]
Abstract
Bats are special in their ability to host emerging viruses. As the only flying mammal, bats endure high metabolic rates yet exhibit elongated lifespans. It is currently unclear whether these unique features are interlinked. The important inflammasome sensor, NLR family pyrin domain containing 3 (NLRP3), has been linked to both viral-induced and age-related inflammation. Here, we report significantly dampened activation of the NLRP3 inflammasome in bat primary immune cells compared to human or mouse counterparts. Lower induction of apoptosis-associated speck-like protein containing a CARD (ASC) speck formation and secretion of interleukin-1β in response to both 'sterile' stimuli and infection with multiple zoonotic viruses including influenza A virus (-single-stranded (ss) RNA), Melaka virus (PRV3M, double-stranded RNA) and Middle East respiratory syndrome coronavirus (+ssRNA) was observed. Importantly, this reduction of inflammation had no impact on the overall viral loads. We identified dampened transcriptional priming, a novel splice variant and an altered leucine-rich repeat domain of bat NLRP3 as the cause. Our results elucidate an important mechanism through which bats dampen inflammation with implications for longevity and unique viral reservoir status.
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17
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Viruses in bats and potential spillover to animals and humans. Curr Opin Virol 2019; 34:79-89. [PMID: 30665189 PMCID: PMC7102861 DOI: 10.1016/j.coviro.2018.12.007] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/17/2022]
Abstract
Bats are a very important source of emerging viruses. Bat coronavirus, filovirus, paramyxovirus and reovirus are known zoonotic viruses. Many of the emergent bat viruses are highly lethal in livestock and humans. Past incidents and viral genetic features predict bat coronaviruses as the highest risk.
In the last two decades, several high impact zoonotic disease outbreaks have been linked to bat-borne viruses. These include SARS coronavirus, Hendra virus and Nipah virus. In addition, it has been suspected that ebolaviruses and MERS coronavirus are also linked to bats. It is being increasingly accepted that bats are potential reservoirs of a large number of known and unknown viruses, many of which could spillover into animal and human populations. However, our knowledge into basic bat biology and immunology is very limited and we have little understanding of major factors contributing to the risk of bat virus spillover events. Here we provide a brief review of the latest findings in bat viruses and their potential risk of cross-species transmission.
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18
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Wynne JW, Todd S, Boyd V, Tachedjian M, Klein R, Shiell B, Dearnley M, McAuley AJ, Woon AP, Purcell AW, Marsh GA, Baker ML. Comparative Transcriptomics Highlights the Role of the Activator Protein 1 Transcription Factor in the Host Response to Ebolavirus. J Virol 2017; 91:e01174-17. [PMID: 28931675 PMCID: PMC5686711 DOI: 10.1128/jvi.01174-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/11/2017] [Indexed: 01/01/2023] Open
Abstract
Ebolavirus and Marburgvirus comprise two genera of negative-sense single-stranded RNA viruses that cause severe hemorrhagic fevers in humans. Despite considerable research efforts, the molecular events following Ebola virus (EBOV) infection are poorly understood. With the view of identifying host factors that underpin EBOV pathogenesis, we compared the transcriptomes of EBOV-infected human, pig, and bat kidney cells using a transcriptome sequencing (RNA-seq) approach. Despite a significant difference in viral transcription/replication between the cell lines, all cells responded to EBOV infection through a robust induction of extracellular growth factors. Furthermore, a significant upregulation of activator protein 1 (AP1) transcription factor complex members FOS and JUN was observed in permissive cell lines. Functional studies focusing on human cells showed that EBOV infection induces protein expression, phosphorylation, and nuclear accumulation of JUN and, to a lesser degree, FOS. Using a luciferase-based reporter, we show that EBOV infection induces AP1 transactivation activity within human cells at 48 and 72 h postinfection. Finally, we show that JUN knockdown decreases the expression of EBOV-induced host gene expression. Taken together, our study highlights the role of AP1 in promoting the host gene expression profile that defines EBOV pathogenesis.IMPORTANCE Many questions remain about the molecular events that underpin filovirus pathophysiology. The rational design of new intervention strategies, such as postexposure therapeutics, will be significantly enhanced through an in-depth understanding of these molecular events. We believe that new insights into the molecular pathogenesis of EBOV may be possible by examining the transcriptomic response of taxonomically diverse cell lines (derived from human, pig, and bat). We first identified the responsive pathways using an RNA-seq-based transcriptomics approach. Further functional and computational analysis focusing on human cells highlighted an important role for the AP1 transcription factor in mediating the transcriptional response to EBOV infection. Our study sheds new light on how host transcription factors respond to and promote the transcriptional landscape that follows viral infection.
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Affiliation(s)
- James W Wynne
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Shawn Todd
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Victoria Boyd
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Mary Tachedjian
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Reuben Klein
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Brian Shiell
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Megan Dearnley
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Alexander J McAuley
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Amanda P Woon
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Anthony W Purcell
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Glenn A Marsh
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Michelle L Baker
- CSIRO Health and Biosecurity/Australian Animal Health Laboratory, Geelong, Victoria, Australia
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De La Cruz-Rivera PC, Kanchwala M, Liang H, Kumar A, Wang LF, Xing C, Schoggins JW. The IFN Response in Bats Displays Distinctive IFN-Stimulated Gene Expression Kinetics with Atypical RNASEL Induction. THE JOURNAL OF IMMUNOLOGY 2017; 200:209-217. [PMID: 29180486 DOI: 10.4049/jimmunol.1701214] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/25/2017] [Indexed: 12/23/2022]
Abstract
Bats host a large number of zoonotic viruses, including several viruses that are highly pathogenic to other mammals. The mechanisms underlying this rich viral diversity are unknown, but they may be linked to unique immunological features that allow bats to act as asymptomatic viral reservoirs. Vertebrates respond to viral infection by inducing IFNs, which trigger antiviral defenses through IFN-stimulated gene (ISG) expression. Although the IFN system of several bats is characterized at the genomic level, less is known about bat IFN-mediated transcriptional responses. In this article, we show that IFN signaling in bat cells from the black flying fox (Pteropus alecto) consists of conserved and unique ISG expression profiles. In IFN-stimulated cells, bat ISGs comprise two unique temporal subclusters with similar early induction kinetics but distinct late-phase declines. In contrast, human ISGs lack this decline phase and remained elevated for longer periods. Notably, in unstimulated cells, bat ISGs were expressed more highly than their human counterparts. We also found that the antiviral effector 2-5A-dependent endoribonuclease, which is not an ISG in humans, is highly IFN inducible in black flying fox cells and contributes to cell-intrinsic control of viral infection. These studies reveal distinctive innate immune features that may underlie a unique virus-host relationship in bats.
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Affiliation(s)
| | - Mohammed Kanchwala
- McDermott Center Bioinformatics Core, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hanquan Liang
- McDermott Center Bioinformatics Core, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ashwani Kumar
- McDermott Center Bioinformatics Core, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Chao Xing
- McDermott Center Bioinformatics Core, University of Texas Southwestern Medical Center, Dallas, TX 75390.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390; and.,Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390;
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20
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Mok L, Wynne JW, Tachedjian M, Shiell B, Ford K, Matthews DA, Bacic A, Michalski WP. Proteomics informed by transcriptomics for characterising differential cellular susceptibility to Nelson Bay orthoreovirus infection. BMC Genomics 2017; 18:615. [PMID: 28806913 PMCID: PMC5556373 DOI: 10.1186/s12864-017-3994-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 08/01/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nelson Bay orthoreovirus (NBV) is a fusogenic bat borne virus with an unknown zoonotic potential. Previous studies have shown that NBV can infect and replicate in a wide variety of cell types derived from their natural host (bat), as well as from human, mouse and monkey. Within permissive cells, NBV induced significant cytopathic effects characterised by cell-cell fusion and syncytia formation. To understand the molecular events that underpin NBV infection we examined the host transcriptome and proteome response of two cell types, derived from bat (PaKiT03) and mouse (L929), to characterise differential cellular susceptibility to NBV. RESULTS Despite significant differences in NBV replication and cytopathic effects in the L929 and PaKiT03 cells, the host response was remarkably similar in these cells. At both the transcriptome and proteome level, the host response was dominated by IFN production and signalling pathways. The majority of proteins up-regulated in L929 and PaKiT03 cells were also up-regulated at the mRNA (gene) level, and included many important IFN stimulated genes. Further functional experimentation demonstrated that stimulating IFN signalling prior to infection, significantly reduced NBV replication in PaKiT03 cells. Moreover, inhibiting IFN signalling (through specific siRNAs) increased NBV replication in L929 cells. In line with the significant cytopathic effects seen in PaKiT03 cells, we also observed a down-regulation of genes involved in cell-cell junctions, which may be related to the fusogenic effects of NBV. CONCLUSIONS This study provides new multi-dimensional insights into the host response of mammalian cells to NBV infection. We show that IFN activity is capable of reducing NBV replication, although it is unlikely that this is solely responsible for the reduced replication of NBV in L929 cells. The molecular events that underpin the fusogenic cytopathic effects described here will prove valuable for identifying potential therapeutic targets against fusogenic orthoreovirus.
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Affiliation(s)
- Lawrence Mok
- CSIRO, Australian Animal Health Laboratory, East Geelong, VIC, Australia.,ARC Centre of Excellence in Plant Cell Walls School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - James W Wynne
- CSIRO, Australian Animal Health Laboratory, East Geelong, VIC, Australia.
| | - Mary Tachedjian
- CSIRO, Australian Animal Health Laboratory, East Geelong, VIC, Australia
| | - Brian Shiell
- CSIRO, Australian Animal Health Laboratory, East Geelong, VIC, Australia
| | - Kris Ford
- ARC Centre of Excellence in Plant Cell Walls School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - David A Matthews
- Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol, UK
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Wojtek P Michalski
- CSIRO, Australian Animal Health Laboratory, East Geelong, VIC, Australia
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21
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A comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus. Sci Rep 2017; 7:43144. [PMID: 28240256 PMCID: PMC5327407 DOI: 10.1038/srep43144] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/18/2017] [Indexed: 11/08/2022] Open
Abstract
The Ebola virus (EBOV) variant Makona (which emerged in 2013) was the causative agent of the largest outbreak of Ebola Virus Disease recorded. Differences in virus-host interactions between viral variants have potential consequences for transmission, disease severity and mortality. A detailed profile of the cellular changes induced by the Makona variant compared with other Ebola virus variants was lacking. In this study, A549 cells, a human cell line with a robust innate response, were infected with the Makona variant or with the Ecran variant originating from the 1976 outbreak in Central Africa. The abundance of viral and cellular mRNA transcripts was profiled using RNASeq and differential gene expression analysis performed. Differences in effects of each virus on the expression of interferon-stimulated genes were also investigated in A549 NPro cells where the type 1 interferon response had been attenuated. Cellular transcriptomic changes were compared with those induced by human respiratory syncytial virus (HRSV), a virus with a similar genome organisation and replication strategy to EBOV. Pathway and gene ontology analysis revealed differential expression of functionally important genes; including genes involved in the inflammatory response, cell proliferation, leukocyte extravasation and cholesterol biosynthesis. Whilst there was overlap with HRSV, there was unique commonality to the EBOV variants.
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Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A, Bessant C, Matthews DA, Davidson AD. Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti. BMC Genomics 2017; 18:101. [PMID: 28103802 PMCID: PMC5248466 DOI: 10.1186/s12864-016-3432-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/19/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs. Furthermore, as for many non-model organisms, incomplete genome annotation has hampered proteomic studies on Ae. aegypti. RESULTS We analysed the Ae. aegypti proteome using our new proteomics informed by transcriptomics (PIT) technique, which bypasses the need for genome annotation by identifying proteins through matched transcriptomic (rather than genomic) data. Our data vastly increase the number of experimentally confirmed Ae. aegypti proteins. The PIT analysis also identified hotspots of incomplete genome annotation, and showed that poor sequence and assembly quality do not explain all annotation gaps. Finally, in a proof-of-principle study, we developed criteria for the characterisation of proteomically active TEs. Protein expression did not correlate with a TE's genomic abundance at different levels of classification. Most notably, long terminal repeat (LTR) retrotransposons were markedly enriched compared to other elements. PIT was superior to 'conventional' proteomic approaches in both our transposon and genome annotation analyses. CONCLUSIONS We present the first proteomic characterisation of an organism's repertoire of mobile genetic elements, which will open new avenues of research into the function of transposon proteins in health and disease. Furthermore, our study provides a proof-of-concept that PIT can be used to evaluate a genome's annotation to guide annotation efforts which has the potential to improve the efficiency of annotation projects in non-model organisms. PIT therefore represents a valuable new tool to study the biology of the important vector species Ae. aegypti, including its role in transmitting emerging viruses of global public health concern.
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Affiliation(s)
- Kevin Maringer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA.
- Present address: Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Amjad Yousuf
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
- College of Applied Medical Sciences, Taibah University, Medina, Kingdom of Saudi Arabia
| | - Kate J Heesom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Jun Fan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - David Lee
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Conrad Bessant
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
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23
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Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A, Bessant C, Matthews DA, Davidson AD. Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti. BMC Genomics 2017. [PMID: 28103802 DOI: 10.1186/s12864-016-3432-5+10.1186/s12864-016-3432-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs. Furthermore, as for many non-model organisms, incomplete genome annotation has hampered proteomic studies on Ae. aegypti. RESULTS We analysed the Ae. aegypti proteome using our new proteomics informed by transcriptomics (PIT) technique, which bypasses the need for genome annotation by identifying proteins through matched transcriptomic (rather than genomic) data. Our data vastly increase the number of experimentally confirmed Ae. aegypti proteins. The PIT analysis also identified hotspots of incomplete genome annotation, and showed that poor sequence and assembly quality do not explain all annotation gaps. Finally, in a proof-of-principle study, we developed criteria for the characterisation of proteomically active TEs. Protein expression did not correlate with a TE's genomic abundance at different levels of classification. Most notably, long terminal repeat (LTR) retrotransposons were markedly enriched compared to other elements. PIT was superior to 'conventional' proteomic approaches in both our transposon and genome annotation analyses. CONCLUSIONS We present the first proteomic characterisation of an organism's repertoire of mobile genetic elements, which will open new avenues of research into the function of transposon proteins in health and disease. Furthermore, our study provides a proof-of-concept that PIT can be used to evaluate a genome's annotation to guide annotation efforts which has the potential to improve the efficiency of annotation projects in non-model organisms. PIT therefore represents a valuable new tool to study the biology of the important vector species Ae. aegypti, including its role in transmitting emerging viruses of global public health concern.
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Affiliation(s)
- Kevin Maringer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK. .,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA. .,Present address: Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Amjad Yousuf
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.,College of Applied Medical Sciences, Taibah University, Medina, Kingdom of Saudi Arabia
| | - Kate J Heesom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Jun Fan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - David Lee
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Conrad Bessant
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
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24
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Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A, Bessant C, Matthews DA, Davidson AD. Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti. BMC Genomics 2017. [PMID: 28103802 DOI: 10.1186/s12864-016-3432-5 10.1186/s12864-016-3432-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs. Furthermore, as for many non-model organisms, incomplete genome annotation has hampered proteomic studies on Ae. aegypti. RESULTS We analysed the Ae. aegypti proteome using our new proteomics informed by transcriptomics (PIT) technique, which bypasses the need for genome annotation by identifying proteins through matched transcriptomic (rather than genomic) data. Our data vastly increase the number of experimentally confirmed Ae. aegypti proteins. The PIT analysis also identified hotspots of incomplete genome annotation, and showed that poor sequence and assembly quality do not explain all annotation gaps. Finally, in a proof-of-principle study, we developed criteria for the characterisation of proteomically active TEs. Protein expression did not correlate with a TE's genomic abundance at different levels of classification. Most notably, long terminal repeat (LTR) retrotransposons were markedly enriched compared to other elements. PIT was superior to 'conventional' proteomic approaches in both our transposon and genome annotation analyses. CONCLUSIONS We present the first proteomic characterisation of an organism's repertoire of mobile genetic elements, which will open new avenues of research into the function of transposon proteins in health and disease. Furthermore, our study provides a proof-of-concept that PIT can be used to evaluate a genome's annotation to guide annotation efforts which has the potential to improve the efficiency of annotation projects in non-model organisms. PIT therefore represents a valuable new tool to study the biology of the important vector species Ae. aegypti, including its role in transmitting emerging viruses of global public health concern.
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Affiliation(s)
- Kevin Maringer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK. .,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA. .,Present address: Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Amjad Yousuf
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.,College of Applied Medical Sciences, Taibah University, Medina, Kingdom of Saudi Arabia
| | - Kate J Heesom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Jun Fan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - David Lee
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Conrad Bessant
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
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Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach. J Virol 2016; 90:4876-4888. [PMID: 26656699 PMCID: PMC4859727 DOI: 10.1128/jvi.02349-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/18/2015] [Indexed: 11/20/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of serious respiratory tract infection. Treatment options include administration of ribavirin, a purine analog, although the mechanism of its anti-HRSV activity is unknown. We used transcriptome sequencing (RNA-seq) to investigate the genome mutation frequency and viral mRNA accumulation in HRSV-infected cells that were left untreated or treated with ribavirin. In the absence of ribavirin, HRSV-specific transcripts accounted for up to one-third of total RNA reads from the infected-cell RNA population. Ribavirin treatment resulted in a >90% reduction in abundance of viral mRNA reads, while at the same time no such reduction was detected for the abundance of cellular transcripts. The presented data reveal that ribavirin significantly increases the frequency of HRSV-specific RNA mutations, suggesting a direct influence on the fidelity of the HRSV polymerase. The presented data show that transitions and transversions occur during HRSV replication and that these changes occur in hot spots along the HRSV genome. Examination of nucleotide substitution rates in the viral genome indicated an increase in the frequency of transition but not transversion mutations in the presence of ribavirin. In addition, our data indicate that in the continuous cell types used and at the time points analyzed, the abundances of some HRSV mRNAs do not reflect the order in which the mRNAs are transcribed. IMPORTANCE Human respiratory syncytial virus (HRSV) is a major pediatric pathogen. Ribavirin can be used in children who are extremely ill to reduce the amount of virus and to lower the burden of disease. Ribavirin is used as an experimental therapy with other viruses. The mechanism of action of ribavirin against HRSV is not well understood, although it is thought to increase the mutation rate of the viral polymerase during replication. To investigate this hypothesis, we used a high-resolution approach that allowed us to determine the genetic sequence of the virus to a great depth of coverage. We found that ribavirin did not cause a detectable change in the relative amounts of viral mRNA transcripts. However, we found that ribavirin treatment did indeed cause an increase in the number of mutations, which was associated with a decrease in virus production.
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26
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Contraction of the type I IFN locus and unusual constitutive expression of IFN-α in bats. Proc Natl Acad Sci U S A 2016; 113:2696-701. [PMID: 26903655 DOI: 10.1073/pnas.1518240113] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bats harbor many emerging and reemerging viruses, several of which are highly pathogenic in other mammals but cause no clinical signs of disease in bats. To determine the role of interferons (IFNs) in the ability of bats to coexist with viruses, we sequenced the type I IFN locus of the Australian black flying fox, Pteropus alecto, providing what is, to our knowledge, the first gene map of the IFN region of any bat species. Our results reveal a highly contracted type I IFN family consisting of only 10 IFNs, including three functional IFN-α loci. Furthermore, the three IFN-α genes are constitutively expressed in unstimulated bat tissues and cells and their expression is unaffected by viral infection. Constitutively expressed IFN-α results in the induction of a subset of IFN-stimulated genes associated with antiviral activity and resistance to DNA damage, providing evidence for a unique IFN system that may be linked to the ability of bats to coexist with viruses.
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27
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Mok L, Wynne JW, Ford K, Shiell B, Bacic A, Michalski WP. Proteomic analysis of Pteropus alecto kidney cells in response to the viral mimic, Poly I:C. Proteome Sci 2015; 13:25. [PMID: 26535029 PMCID: PMC4630911 DOI: 10.1186/s12953-015-0081-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/20/2015] [Indexed: 12/20/2022] Open
Abstract
Background Bats are recognised as an important reservoir for a number of highly pathogenic zoonotic viruses. While many of these viruses cause severe and often fatal disease in humans, bats are able to coexist with these viruses without clinical signs of disease. The mechanism conferring this antiviral response is not fully understood. Here, we investigated the differential protein expression of immortalised Pteropus alecto kidney cells (PaKiT03) following transfection with the viral mimic, Poly I:C. Two complementary proteomic approaches, difference gel electrophoresis (DIGE) and isobaric tagging for relative and absolute quantitation (iTRAQ) were used to quantify changes in protein expression following Poly I:C stimulation at 4, 8 and 20 hr post treatment (hpt). Results The expression of ISG54 gene, a known responder to virus infection and Poly I:C treatment, was significantly induced in transfected cells compared with mock-transfected cells. Through iTRAQ analysis we show that Poly I:C up-regulates key glycolytic enzymes at 4 hpt within PaKiT03 cells. In contrast, at 20 hpt PaKiT03 cells down-regulated ribosomal subunit proteins. The analysis with DIGE of Poly I:C transfected PaKiT03 cells showed over 215 individual spots differentially regulated, however only 25 spots could be unambiguously identified by LC-MS/MS. Immunoblotting confirmed the up-regulation of Eno1 and Tpi1 in PaKiT03 cells following Poly I:C transfection. A comparison with human cells (HEK293T and HeLa) and one additional bat cell line (PaLuT02), demonstrated that glycolytic pathways are also induced in these cell types, but at different intensities. Conclusion The two techniques, DIGE and iTRAQ identified largely overlapping sets of differentially expressed proteins, however DIGE unambiguously identified significantly less proteins than iTRAQ. Poly I:C induced a rapid metabolic shift towards glycolysis within the PaKiT03 cells at 4 hpt, presumably as a consequence of increased energy requirements. On the other hand ribosomal subunit proteins were seen as down-regulated by iTRAQ, these proteins may be the limiting factors in the translational machinery available for virus replication. This study provides new insight into the antiviral response of bat cells, highlighting the importance of energy metabolism. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0081-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lawrence Mok
- CSIRO, Australian Animal Health Laboratory, East Geelong, 3219 VIC Australia ; ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - James W Wynne
- CSIRO, Australian Animal Health Laboratory, East Geelong, 3219 VIC Australia
| | - Kris Ford
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Brian Shiell
- CSIRO, Australian Animal Health Laboratory, East Geelong, 3219 VIC Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC Australia ; Bio21 Institute for Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC Australia
| | - Wojtek P Michalski
- CSIRO, Australian Animal Health Laboratory, East Geelong, 3219 VIC Australia
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28
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Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, Hewson R, García-Dorival I, Bore JA, Koundouno R, Abdellati S, Afrough B, Aiyepada J, Akhilomen P, Asogun D, Atkinson B, Badusche M, Bah A, Bate S, Baumann J, Becker D, Becker-Ziaja B, Bocquin A, Borremans B, Bosworth A, Boettcher JP, Cannas A, Carletti F, Castilletti C, Clark S, Colavita F, Diederich S, Donatus A, Duraffour S, Ehichioya D, Ellerbrok H, Fernandez-Garcia MD, Fizet A, Fleischmann E, Gryseels S, Hermelink A, Hinzmann J, Hopf-Guevara U, Ighodalo Y, Jameson L, Kelterbaum A, Kis Z, Kloth S, Kohl C, Korva M, Kraus A, Kuisma E, Kurth A, Liedigk B, Logue CH, Lüdtke A, Maes P, McCowen J, Mély S, Mertens M, Meschi S, Meyer B, Michel J, Molkenthin P, Muñoz-Fontela C, Muth D, Newman ENC, Ngabo D, Oestereich L, Okosun J, Olokor T, Omiunu R, Omomoh E, Pallasch E, Pályi B, Portmann J, Pottage T, Pratt C, Priesnitz S, Quartu S, Rappe J, Repits J, Richter M, Rudolf M, Sachse A, Schmidt KM, Schudt G, Strecker T, Thom R, Thomas S, Tobin E, Tolley H, Trautner J, Vermoesen T, Vitoriano I, Wagner M, Wolff S, Yue C, Capobianchi MR, Kretschmer B, Hall Y, Kenny JG, Rickett NY, Dudas G, Coltart CEM, Kerber R, Steer D, Wright C, Senyah F, Keita S, Drury P, Diallo B, de Clerck H, Van Herp M, Sprecher A, Traore A, Diakite M, Konde MK, Koivogui L, Magassouba N, Avšič-Županc T, Nitsche A, Strasser M, Ippolito G, Becker S, Stoecker K, Gabriel M, Raoul H, Di Caro A, Wölfel R, Formenty P, Günther S. Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature 2015; 524:97-101. [PMID: 26083749 PMCID: PMC10601607 DOI: 10.1038/nature14594] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/01/2015] [Indexed: 01/17/2023]
Abstract
West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.
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Affiliation(s)
- Miles W. Carroll
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- University of Southampton, South General Hospital, Southampton, SO16 6YD UK
| | - David A. Matthews
- Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD UK
| | - Julian A. Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | | | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 2FL UK
- Fogarty International Center, National Institutes of Health, Bethesda, 20892 Maryland USA
- Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 2FL UK
| | - Roger Hewson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Isabel García-Dorival
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Joseph Akoi Bore
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Raymond Koundouno
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Saïd Abdellati
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Tropical Medicine, Antwerp, B-2000 Belgium
| | - Babak Afrough
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - John Aiyepada
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Patience Akhilomen
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Danny Asogun
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Barry Atkinson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Marlis Badusche
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Amadou Bah
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Swiss Tropical and Public Health Institute, University of Basel, Basel, CH-4002 Switzerland
| | - Simon Bate
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Jan Baumann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Dirk Becker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Beate Becker-Ziaja
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Anne Bocquin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Benny Borremans
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Department of Biology, University of Antwerp, Antwerp, B-2020 Belgium
| | - Andrew Bosworth
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Jan Peter Boettcher
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Angela Cannas
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Fabrizio Carletti
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Concetta Castilletti
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Simon Clark
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Francesca Colavita
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Sandra Diederich
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, 17493 Insel Riems Germany
| | - Adomeh Donatus
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Sophie Duraffour
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- KU Leuven Rega institute, Leuven, B-3000 Belgium
| | - Deborah Ehichioya
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Redeemer’s University, Osun State Nigeria
| | - Heinz Ellerbrok
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Maria Dolores Fernandez-Garcia
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, 28029 Spain
| | - Alexandra Fizet
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, 69365 France
| | - Erna Fleischmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Sophie Gryseels
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Department of Biology, University of Antwerp, Antwerp, B-2020 Belgium
| | - Antje Hermelink
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Julia Hinzmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Ute Hopf-Guevara
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Yemisi Ighodalo
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Lisa Jameson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Anne Kelterbaum
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Zoltan Kis
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Center for Epidemiology, National Biosafety Laboratory, Budapest, H-1097 Hungary
| | - Stefan Kloth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Claudia Kohl
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Miša Korva
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000 Slovenia
| | - Annette Kraus
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Public Health Agency of Sweden, Solna, 171 82 Sweden
| | - Eeva Kuisma
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Andreas Kurth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Britta Liedigk
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Christopher H. Logue
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Anja Lüdtke
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, 20251 Germany
| | - Piet Maes
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- KU Leuven Rega institute, Leuven, B-3000 Belgium
| | - James McCowen
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Stéphane Mély
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Marc Mertens
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, 17493 Insel Riems Germany
| | - Silvia Meschi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Benjamin Meyer
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, University of Bonn, Bonn, 53127 Germany
| | - Janine Michel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Peter Molkenthin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - César Muñoz-Fontela
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, 20251 Germany
| | - Doreen Muth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, University of Bonn, Bonn, 53127 Germany
| | - Edmund N. C. Newman
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Didier Ngabo
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Lisa Oestereich
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Jennifer Okosun
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Thomas Olokor
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Racheal Omiunu
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Emmanuel Omomoh
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Elisa Pallasch
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Bernadett Pályi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Center for Epidemiology, National Biosafety Laboratory, Budapest, H-1097 Hungary
| | - Jasmine Portmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Federal Office for Civil Protection, Spiez Laboratory, Spiez, CH-3700 Switzerland
| | - Thomas Pottage
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Catherine Pratt
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Simone Priesnitz
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bundeswehr Hospital, Hamburg, 22049 Germany
| | - Serena Quartu
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Julie Rappe
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Virology and Immunology, Mittelhäusern, CH-3147 Switzerland
| | - Johanna Repits
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Janssen-Cilag, Sollentuna, SE-192 07 Sweden
| | - Martin Richter
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Martin Rudolf
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Andreas Sachse
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Kristina Maria Schmidt
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Gordian Schudt
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Thomas Strecker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Ruth Thom
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Stephen Thomas
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Ekaete Tobin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Howard Tolley
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Jochen Trautner
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Thünen Institute, Hamburg, D-22767 Germany
| | - Tine Vermoesen
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Tropical Medicine, Antwerp, B-2000 Belgium
| | - Inês Vitoriano
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Matthias Wagner
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Svenja Wolff
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Constanze Yue
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Maria Rosaria Capobianchi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Birte Kretschmer
- Eurice - European Research and Project Office GmbH, Berlin, 10115 Germany
| | - Yper Hall
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
| | - John G. Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Natasha Y. Rickett
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 2FL UK
| | - Cordelia E. M. Coltart
- Department of Infection and Population Health, University College London, London, WC1E 6JB UK
| | - Romy Kerber
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Damien Steer
- Research IT, University of Bristol, Bristol, BS8 1HH UK
| | - Callum Wright
- Advanced Computing Research Centre, University of Bristol, Bristol, BS8 1HH UK
| | - Francis Senyah
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
| | | | - Patrick Drury
- World Health Organization, Geneva 27, 1211 Switzerland
| | | | | | | | | | - Alexis Traore
- Section Prévention et Lutte contre la Maladie à la Direction Préfectorale de la Santé de Guéckédou, Guéckédou, Guinea
| | - Mandiou Diakite
- Université Gamal Abdel Nasser de Conakry, CHU Donka, Conakry, Guinea
| | | | | | - N’Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Tatjana Avšič-Županc
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000 Slovenia
| | - Andreas Nitsche
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Marc Strasser
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Federal Office for Civil Protection, Spiez Laboratory, Spiez, CH-3700 Switzerland
| | - Giuseppe Ippolito
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Stephan Becker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Kilian Stoecker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Martin Gabriel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Hervé Raoul
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Antonino Di Caro
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Roman Wölfel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | | | - Stephan Günther
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
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Immunology of bats and their viruses: challenges and opportunities. Viruses 2015; 6:4880-901. [PMID: 25494448 PMCID: PMC4276934 DOI: 10.3390/v6124880] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/21/2014] [Accepted: 11/28/2014] [Indexed: 12/20/2022] Open
Abstract
Bats are reservoir hosts of several high-impact viruses that cause significant human diseases, including Nipah virus, Marburg virus and rabies virus. They also harbor many other viruses that are thought to have caused disease in humans after spillover into intermediate hosts, including SARS and MERS coronaviruses. As is usual with reservoir hosts, these viruses apparently cause little or no pathology in bats. Despite the importance of bats as reservoir hosts of zoonotic and potentially zoonotic agents, virtually nothing is known about the host/virus relationships; principally because few colonies of bats are available for experimental infections, a lack of reagents, methods and expertise for studying bat antiviral responses and immunology, and the difficulty of conducting meaningful field work. These challenges can be addressed, in part, with new technologies that are species-independent that can provide insight into the interactions of bats and viruses, which should clarify how the viruses persist in nature, and what risk factors might facilitate transmission to humans and livestock.
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Transcriptome Profiling of the Virus-Induced Innate Immune Response in Pteropus vampyrus and Its Attenuation by Nipah Virus Interferon Antagonist Functions. J Virol 2015; 89:7550-66. [PMID: 25972557 DOI: 10.1128/jvi.00302-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/02/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Bats are important reservoirs for several viruses, many of which cause lethal infections in humans but have reduced pathogenicity in bats. As the innate immune response is critical for controlling viruses, the nature of this response in bats and how it may differ from that in other mammals are of great interest. Using next-generation transcriptome sequencing (mRNA-seq), we profiled the transcriptional response of Pteropus vampyrus bat kidney (PVK) cells to Newcastle disease virus (NDV), an avian paramyxovirus known to elicit a strong innate immune response in mammalian cells. The Pteropus genus is a known reservoir of Nipah virus (NiV) and Hendra virus (HeV). Analysis of the 200 to 300 regulated genes showed that genes for interferon (IFN) and antiviral pathways are highly upregulated in NDV-infected PVK cells, including genes for beta IFN, RIG-I, MDA5, ISG15, and IRF1. NDV-infected cells also upregulated several genes not previously characterized to be antiviral, such as RND1, SERTAD1, CHAC1, and MORC3. In fact, we show that MORC3 is induced by both IFN and NDV infection in PVK cells but is not induced by either stimulus in human A549 cells. In contrast to NDV infection, HeV and NiV infection of PVK cells failed to induce these innate immune response genes. Likewise, an attenuated response was observed in PVK cells infected with recombinant NDVs expressing the NiV IFN antagonist proteins V and W. This study provides the first global profile of a robust virus-induced innate immune response in bats and indicates that henipavirus IFN antagonist mechanisms are likely active in bat cells. IMPORTANCE Bats are the reservoir host for many highly pathogenic human viruses, including henipaviruses, lyssaviruses, severe acute respiratory syndrome coronavirus, and filoviruses, and many other viruses have also been isolated from bats. Viral infections are reportedly asymptomatic or heavily attenuated in bat populations. Despite their ecological importance to viral maintenance, research into their immune system and mechanisms for viral control has only recently begun. Nipah virus and Hendra virus are two paramyxoviruses associated with high mortality rates in humans and whose reservoir is the Pteropus genus of bats. Greater knowledge of the innate immune response of P. vampyrus bats to viral infection may elucidate how bats serve as a reservoir for so many viruses.
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