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Phumiphanjarphak W, Aiewsakun P. Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling. BMC Bioinformatics 2024; 25:222. [PMID: 38914932 PMCID: PMC11197340 DOI: 10.1186/s12859-024-05846-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Pan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic next-generation sequencing can offer a promising solution to this problem by providing an unbiased overview of the microbial community, enabling detection of any viruses without prior target selection. However, a major challenge in utilising metagenomic next-generation sequencing for virome investigation is that data analysis can be highly complex, involving numerous data processing steps. RESULTS Here, we present Entourage to address this challenge. Entourage enables short-read sequence assembly, viral sequence search with or without reference virus targets using contig-based approaches, and intrasample sequence variation quantification. Several workflows are implemented in Entourage to facilitate end-to-end virus sequence detection analysis through a single command line, from read cleaning, sequence assembly, to virus sequence searching. The results generated are comprehensive, allowing for thorough quality control, reliability assessment, and interpretation. We illustrate Entourage's utility as a streamlined workflow for virus detection by employing it to comprehensively search for target virus sequences and beyond in raw sequence read data generated from HeLa cell culture samples spiked with viruses. Furthermore, we showcase its flexibility and performance on a real-world dataset by analysing a preassembled Tara Oceans dataset. Overall, our results show that Entourage performs well even with low virus sequencing depth in single digits, and it can be used to discover novel viruses effectively. Additionally, by using sequence data generated from a patient with chronic SARS-CoV-2 infection, we demonstrate Entourage's capability to quantify virus intrasample genetic variations, and generate publication-quality figures illustrating the results. CONCLUSIONS Entourage is an all-in-one, versatile, and streamlined bioinformatics software for virome investigation, developed with a focus on ease of use. Entourage is available at https://codeberg.org/CENMIG/Entourage under the MIT license.
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Affiliation(s)
- Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Ratchathewi District, 272 Rama VI Road, Bangkok, 10400, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Ratchathewi District, 272 Rama VI Road, Bangkok, 10400, Thailand.
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.
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Chase EE, Monteil-Bouchard S, Gobet A, Andrianjakarivony FH, Desnues C, Blanc G. A High Rate Algal Pond Hosting a Dynamic Community of RNA Viruses. Viruses 2021; 13:2163. [PMID: 34834969 PMCID: PMC8619904 DOI: 10.3390/v13112163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022] Open
Abstract
Despite a surge of RNA virome sequencing in recent years, there are still many RNA viruses to uncover-as indicated by the relevance of viral dark matter to RNA virome studies (i.e., putative viruses that do not match to taxonomically identified viruses). This study explores a unique site, a high-rate algal pond (HRAP), for culturing industrially microalgae, to elucidate new RNA viruses. The importance of viral-host interactions in aquatic systems are well documented, and the ever-expanding microalgae industry is no exception. As the industry becomes a more important source of sustainable plastic manufacturing, a producer of cosmetic pigments and alternative protein sources, and a means of CO2 remediation in the face of climate change, studying microalgal viruses becomes a vital practice for proactive management of microalgae cultures at the industrial level. This study provides evidence of RNA microalgal viruses persisting in a CO2 remediation pilot project HRAP and uncovers the diversity of the RNA virosphere contained within it. Evidence shows that family Marnaviridae is cultured in the basin, alongside other potential microalgal infecting viruses (e.g., family Narnaviridae, family Totitiviridae, and family Yueviridae). Finally, we demonstrate that the RNA viral diversity of the HRAP is temporally dynamic across two successive culturing seasons.
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Affiliation(s)
- Emily E. Chase
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sonia Monteil-Bouchard
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
| | - Angélique Gobet
- MARBEC University Montpellier, CNRS, Ifremer, IRD, 34203 Sète, France;
| | - Felana H. Andrianjakarivony
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Christelle Desnues
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Guillaume Blanc
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
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3
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O’Brien CA, Pegg CL, Nouwens AS, Bielefeldt-Ohmann H, Huang B, Warrilow D, Harrison JJ, Haniotis J, Schulz BL, Paramitha D, Colmant AMG, Newton ND, Doggett SL, Watterson D, Hobson-Peters J, Hall RA. A Unique Relative of Rotifer Birnavirus Isolated from Australian Mosquitoes. Viruses 2020; 12:v12091056. [PMID: 32971986 PMCID: PMC7552023 DOI: 10.3390/v12091056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/13/2020] [Accepted: 09/17/2020] [Indexed: 01/24/2023] Open
Abstract
The family Birnaviridae are a group of non-enveloped double-stranded RNA viruses which infect poultry, aquatic animals and insects. This family includes agriculturally important pathogens of poultry and fish. Recently, next-generation sequencing technologies have identified closely related birnaviruses in Culex, Aedes and Anopheles mosquitoes. Using a broad-spectrum system based on detection of long double-stranded RNA, we have discovered and isolated a birnavirus from Aedes notoscriptus mosquitoes collected in northern New South Wales, Australia. Phylogenetic analysis of Aedes birnavirus (ABV) showed that it is related to Rotifer birnavirus, a pathogen of microscopic aquatic animals. In vitro cell infection assays revealed that while ABV can replicate in Aedes-derived cell lines, the virus does not replicate in vertebrate cells and displays only limited replication in Culex- and Anopheles-derived cells. A combination of SDS-PAGE and mass spectrometry analysis suggested that the ABV capsid precursor protein (pVP2) is larger than that of other birnaviruses and is partially resistant to trypsin digestion. Reactivity patterns of ABV-specific polyclonal and monoclonal antibodies indicate that the neutralizing epitopes of ABV are SDS sensitive. Our characterization shows that ABV displays a number of properties making it a unique member of the Birnaviridae and represents the first birnavirus to be isolated from Australian mosquitoes.
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Affiliation(s)
- Caitlin A. O’Brien
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Cassandra L. Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Amanda S. Nouwens
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Helle Bielefeldt-Ohmann
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Bixing Huang
- Public Health Virology, Queensland Health Forensic and Scientific Services, Brisbane, QLD 4108, Australia; (B.H.); (D.W.)
| | - David Warrilow
- Public Health Virology, Queensland Health Forensic and Scientific Services, Brisbane, QLD 4108, Australia; (B.H.); (D.W.)
| | - Jessica J. Harrison
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - John Haniotis
- New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (J.H.); (S.L.D.)
| | - Benjamin L. Schulz
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Devina Paramitha
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Agathe M. G. Colmant
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Natalee D. Newton
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Stephen L. Doggett
- New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (J.H.); (S.L.D.)
| | - Daniel Watterson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
| | - Roy A. Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.A.O.); (H.B.-O.); (J.J.H.); (B.L.S.); (D.P.); (A.M.G.C.); (N.D.N.); (D.W.); (J.H.-P.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4067, Australia; (C.L.P.); (A.S.N.)
- Correspondence:
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Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini FM, Kuhn JH. Global Organization and Proposed Megataxonomy of the Virus World. Microbiol Mol Biol Rev 2020; 84:e00061-19. [PMID: 32132243 PMCID: PMC7062200 DOI: 10.1128/mmbr.00061-19] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, Paris, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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Delmas B, Attoui H, Ghosh S, Malik YS, Mundt E, Vakharia VN, Ictv Report Consortium. ICTV virus taxonomy profile: Birnaviridae. J Gen Virol 2018; 100:5-6. [PMID: 30484762 DOI: 10.1099/jgv.0.001185] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Birnaviridae is a family of viruses with bi-segmented dsRNA genomes totalling about 6 kbp forming icosahedral, non-enveloped virions. The family includes four genera, members of three of which (Aquabirnavirus, Avibirnavirus and Blosnavirus) infect vertebrates (excluding mammals), whereas members of the fourth genus (Entomobirnavirus) infect insects. Each genus includes 1-3 species. Infectious pancreatic necrosis virus of salmonids and infectious bursal disease virus of poultry are two economically important birnaviruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Birnaviridae, which is available at www.ictv.global/report/birnaviridae.
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Affiliation(s)
- Bernard Delmas
- 1VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Houssam Attoui
- 2UMR1161 Virologie, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Souvik Ghosh
- 3Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts and Nevis
| | - Yashpal S Malik
- 4Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India
| | - Egbert Mundt
- 5Boehringer Ingelheim Veterinary Research Center, Bemeroder Str. 31 30559 Hannover, Germany
| | - Vikram N Vakharia
- 6Department of Marine Biotechnology, University of Maryland, Baltimore County, 701, East Pratt Street, Baltimore, MD 21202, USA
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6
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Caprari S, Metzler S, Lengauer T, Kalinina OV. Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses. Viruses 2015; 7:5388-409. [PMID: 26492264 PMCID: PMC4632390 DOI: 10.3390/v7102882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 12/20/2022] Open
Abstract
The origin and evolution of viruses is a subject of ongoing debate. In this study, we provide a full account of the evolutionary relationships between proteins of significant sequence and structural similarity found in viruses that belong to different classes according to the Baltimore classification. We show that such proteins can be found in viruses from all Baltimore classes. For protein families that include these proteins, we observe two patterns of the taxonomic spread. In the first pattern, they can be found in a large number of viruses from all implicated Baltimore classes. In the other pattern, the instances of the corresponding protein in species from each Baltimore class are restricted to a few compact clades. Proteins with the first pattern of distribution are products of so-called viral hallmark genes reported previously. Additionally, this pattern is displayed by the envelope glycoproteins from Flaviviridae and Bunyaviridae and helicases of superfamilies 1 and 2 that have homologs in cellular organisms. The second pattern can often be explained by horizontal gene transfer from the host or between viruses, an example being Orthomyxoviridae and Coronaviridae hemagglutinin esterases. Another facet of horizontal gene transfer comprises multiple independent introduction events of genes from cellular organisms into otherwise unrelated viruses.
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Affiliation(s)
- Silvia Caprari
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany.
| | - Saskia Metzler
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany.
- Saarbrücken Graduate School of Computer Science, University of Saarland, Campus E1 3, 66123 Saarbrücken, Germany.
| | - Thomas Lengauer
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany.
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany.
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7
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Dorobantu CM, Albulescu L, Harak C, Feng Q, van Kampen M, Strating JRPM, Gorbalenya AE, Lohmann V, van der Schaar HM, van Kuppeveld FJM. Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus. PLoS Pathog 2015; 11:e1005185. [PMID: 26406250 PMCID: PMC4583462 DOI: 10.1371/journal.ppat.1005185] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022] Open
Abstract
Cardioviruses, including encephalomyocarditis virus (EMCV) and the human Saffold virus, are small non-enveloped viruses belonging to the Picornaviridae, a large family of positive-sense RNA [(+)RNA] viruses. All (+)RNA viruses remodel intracellular membranes into unique structures for viral genome replication. Accumulating evidence suggests that picornaviruses from different genera use different strategies to generate viral replication organelles (ROs). For instance, enteroviruses (e.g. poliovirus, coxsackievirus, rhinovirus) rely on the Golgi-localized phosphatidylinositol 4-kinase III beta (PI4KB), while cardioviruses replicate independently of the kinase. By which mechanisms cardioviruses develop their ROs is currently unknown. Here we show that cardioviruses manipulate another PI4K, namely the ER-localized phosphatidylinositol 4-kinase III alpha (PI4KA), to generate PI4P-enriched ROs. By siRNA-mediated knockdown and pharmacological inhibition, we demonstrate that PI4KA is an essential host factor for EMCV genome replication. We reveal that the EMCV nonstructural protein 3A interacts with and is responsible for PI4KA recruitment to viral ROs. The ensuing phosphatidylinositol 4-phosphate (PI4P) proved important for the recruitment of oxysterol-binding protein (OSBP), which delivers cholesterol to EMCV ROs in a PI4P-dependent manner. PI4P lipids and cholesterol are shown to be required for the global organization of the ROs and for viral genome replication. Consistently, inhibition of OSBP expression or function efficiently blocked EMCV RNA replication. In conclusion, we describe for the first time a cellular pathway involved in the biogenesis of cardiovirus ROs. Remarkably, the same pathway was reported to promote formation of the replication sites of hepatitis C virus, a member of the Flaviviridae family, but not other picornaviruses or flaviviruses. Thus, our results highlight the convergent recruitment by distantly related (+)RNA viruses of a host lipid-modifying pathway underlying formation of viral replication sites. All positive-sense RNA viruses [(+)RNA viruses] replicate their viral genomes in tight association with reorganized membranous structures. Viruses generate these unique structures, often termed “replication organelles” (ROs), by efficiently manipulating the host lipid metabolism. While the molecular mechanisms underlying RO formation by enteroviruses (e.g. poliovirus) of the family Picornaviridae have been extensively investigated, little is known about other members belonging to this large family. This study provides the first detailed insight into the RO biogenesis of encephalomyocarditis virus (EMCV), a picornavirus from the genus Cardiovirus. We reveal that EMCV hijacks the lipid kinase phosphatidylinositol-4 kinase IIIα (PI4KA) to generate viral ROs enriched in phosphatidylinositol 4-phosphate (PI4P). In EMCV-infected cells, PI4P lipids play an essential role in virus replication by recruiting another cellular protein, oxysterol-binding protein (OSBP), to the ROs. OSBP further impacts the lipid composition of the RO membranes, by mediating the exchange of PI4P with cholesterol. This membrane-modification mechanism of EMCV is remarkably similar to that of the distantly related flavivirus hepatitis C virus (HCV), while distinct from that of the closely related enteroviruses, which recruit OSBP via another PI4K, namely PI4K IIIβ (PI4KB). Thus, EMCV and HCV represent a striking case of functional convergence in (+)RNA virus evolution.
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Affiliation(s)
- Cristina M. Dorobantu
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lucian Albulescu
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Christian Harak
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Qian Feng
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mirjam van Kampen
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jeroen R. P. M. Strating
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Hilde M. van der Schaar
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank J. M. van Kuppeveld
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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