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Sarry M, Bernelin-Cottet C, Michaud C, Relmy A, Romey A, Salomez AL, Renson P, Contrant M, Berthaud M, Huet H, Jouvion G, Hägglund S, Valarcher JF, Bakkali Kassimi L, Blaise-Boisseau S. Development of a primary cell model derived from porcine dorsal soft palate for foot-and-mouth disease virus research and diagnosis. Front Microbiol 2023; 14:1215347. [PMID: 37840704 PMCID: PMC10570842 DOI: 10.3389/fmicb.2023.1215347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hoofed animals that has a significant socio-economic impact. One concern associated with this disease is the ability of its etiological agent, the FMD virus (FMDV), to persist in its hosts through underlying mechanisms that remain to be elucidated. While persistence has been described in cattle and small ruminants, it is unlikely to occur in pigs. One of the factors limiting the progress in understanding FMDV persistence and, in particular, differential persistence is the lack of suitable in vitro models. A primary bovine cell model derived from the dorsal soft palate, which is the primary site of replication and persistence of FMDV in cattle, has been developed, and it seemed relevant to develop a similar porcine model. Cells from two sites of FMDV replication in pigs, namely, the dorsal soft palate and the oropharyngeal tonsils, were isolated and cultured. The epithelial character of the cells from the dorsal soft palate was then assessed by immunofluorescence. The FMDV-sensitivity of these cells was assessed after monolayer infection with FMDV O/FRA/1/2001 Clone 2.2. These cells were also grown in multilayers at the air-liquid interface to mimic a stratified epithelium susceptible to FMDV infection. Consistent with what has been shown in vivo in pigs, our study showed no evidence of persistence of FMDV in either the monolayer or multilayer model, with no infectious virus detected 28 days after infection. The development of such a model opens up new possibilities for the study and diagnosis of FMDV in porcine cells.
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Affiliation(s)
- Morgan Sarry
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
- AgroParistech, Paris, France
| | - Cindy Bernelin-Cottet
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
| | - Caroline Michaud
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
| | - Anthony Relmy
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
| | - Aurore Romey
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
| | - Anne-Laure Salomez
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
| | - Patricia Renson
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Maud Contrant
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Maxime Berthaud
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Hélène Huet
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
| | - Grégory Jouvion
- Dynamyc Research Team, Université Paris-Est Créteil, Ecole Nationale Vétérinaire d’Alfort, ANSES, Créteil, France
- Unité d’Histologie et d’Anatomie Pathologique, Ecole Nationale Vétérinaire d’Alfort, Maisons-Alfort, France
| | - Sara Hägglund
- Host Pathogen Interaction Group, Section of Ruminant Medicine, Department of Clinical Science, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Jean-François Valarcher
- Host Pathogen Interaction Group, Section of Ruminant Medicine, Department of Clinical Science, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Labib Bakkali Kassimi
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
| | - Sandra Blaise-Boisseau
- UMR VIROLOGIE, INRAe, EnvA, ANSES Laboratoire de Santé Animale, Université Paris-Est, Maisons-Alfort, France
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Contrant M, Bigault L, Andraud M, Desdouits M, Rocq S, Le Guyader FS, Blanchard Y. Porcine Epidemic Diarrhea Virus, Surrogate for Coronavirus Decay Measurement in French Coastal Waters and Contribution to Coronavirus Risk Evaluation. Microbiol Spectr 2023; 11:e0184423. [PMID: 37395665 PMCID: PMC10433961 DOI: 10.1128/spectrum.01844-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 07/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infected patients mainly displays pulmonary and oronasal tropism; however, the presence of the virus has also been demonstrated in the stools of patients and consequently in wastewater treatment plant effluents, raising the question of the potential risk of environmental contamination (such as seawater contamination) through inadequately treated wastewater spillover into surface or coastal waters even if the environmental detection of viral RNA alone does not substantiate risk of infection. Therefore, here, we decided to experimentally evaluate the persistence of the porcine epidemic diarrhea virus (PEDv), considered as a coronavirus representative model, in the coastal environment of France. Coastal seawater was collected, sterile-filtered, and inoculated with PEDv before incubation for 0 to 4 weeks at four temperatures representative of those measured along the French coasts throughout the year (4, 8, 15, and 24°C). The decay rate of PEDv was determined using mathematical modeling and was used to determine the half-life of the virus along the French coast in accordance with temperatures from 2000 to 2021. We experimentally observed an inverse correlation between seawater temperature and the persistence of infectious viruses in seawater and confirm that the risk of transmission of infectious viruses from contaminated stool in wastewater to seawater during recreational practices is very limited. The present work represents a good model to assess the persistence of coronaviruses in coastal environments and contributes to risk evaluation, not only for SARS-CoV-2 persistence, but also for other coronaviruses, specifically enteric coronaviruses from livestock. IMPORTANCE The present work addresses the question of the persistence of coronavirus in marine environments because SARS-CoV-2 is regularly detected in wastewater treatment plants, and the coastal environment, subjected to increasing anthropogenic pressure and the final receiver of surface waters and sometimes insufficiently depurated wastewater, is particularly at risk. The problem also arises in the possibility of soil contamination by CoV from animals, especially livestock, during manure application, where, by soil impregnation and runoff, these viruses can end up in seawater. Our findings are of interest to researchers and authorities seeking to monitor coronaviruses in the environment, either in tourist areas or in regions of the world where centralized systems for wastewater treatment are not implemented, and more broadly, to the scientific community involved in "One Health" approaches.
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Affiliation(s)
- Maud Contrant
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Health Safety (ANSES), Ploufragan, France
| | - Lionel Bigault
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Health Safety (ANSES), Ploufragan, France
| | - Mathieu Andraud
- Epidemiology, Animal Health and Welfare Unit (EPISABE), French Agency for Food, Environmental and Occupational Health Safety (ANSES), Ploufragan, France
| | - Marion Desdouits
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, Nantes, France
| | - Sophie Rocq
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, Nantes, France
| | | | - Yannick Blanchard
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Health Safety (ANSES), Ploufragan, France
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Vilimova M, Contrant M, Randrianjafy R, Dumas P, Elbasani E, Ojala PM, Pfeffer S, Fender A. Correction to 'Cis regulation within a cluster of viral microRNAs'. Nucleic Acids Res 2021; 49:10804-10805. [PMID: 34520556 PMCID: PMC8501946 DOI: 10.1093/nar/gkab806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Monika Vilimova
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Maud Contrant
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Ramy Randrianjafy
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Philippe Dumas
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Department of Integrated Structural Biology, 1 rue Laurent Fries, BP10142, 67404 Illkirch-Graffenstaden, France
| | - Endrit Elbasani
- Translational Cancer Medicine Research Program, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland
| | - Päivi M Ojala
- Translational Cancer Medicine Research Program, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland
| | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Aurélie Fender
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
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Vilimova M, Contrant M, Randrianjafy R, Dumas P, Elbasani E, Ojala PM, Pfeffer S, Fender A. Cis regulation within a cluster of viral microRNAs. Nucleic Acids Res 2021; 49:10018-10033. [PMID: 34417603 PMCID: PMC8464075 DOI: 10.1093/nar/gkab731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs involved in virtually all biological processes. Although many of them are co-expressed from clusters, little is known regarding the impact of this organization on the regulation of their accumulation. In this study, we set to decipher a regulatory mechanism controlling the expression of the ten clustered pre-miRNAs from Kaposi's sarcoma associated herpesvirus (KSHV). We measured in vitro the efficiency of cleavage of each individual pre-miRNA by the Microprocessor and found that pre-miR-K1 and -K3 were the most efficiently cleaved pre-miRNAs. A mutational analysis showed that, in addition to producing mature miRNAs, they are also important for the optimal expression of the whole set of miRNAs. We showed that this feature depends on the presence of a canonical pre-miRNA at this location since we could functionally replace pre-miR-K1 by a heterologous pre-miRNA. Further in vitro processing analysis suggests that the two stem-loops act in cis and that the cluster is cleaved in a sequential manner. Finally, we exploited this characteristic of the cluster to inhibit the expression of the whole set of miRNAs by targeting the pre-miR-K1 with LNA-based antisense oligonucleotides in cells either expressing a synthetic construct or latently infected with KSHV.
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Affiliation(s)
- Monika Vilimova
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Maud Contrant
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Ramy Randrianjafy
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Philippe Dumas
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Department of Integrated structural Biology, 1 rue Laurent Fries, BP10142, 67404 Illkirch-Graffenstaden, France
| | - Endrit Elbasani
- Translational Cancer Medicine Research Program, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland
| | - Päivi M Ojala
- Translational Cancer Medicine Research Program, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland
| | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Aurélie Fender
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 allée Konrad Roentgen, 67084 Strasbourg, France
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Courtillon C, Briand FX, Allée C, Contrant M, Beven V, Lucas P, Blanchard Y, Mouchel S, Eterradossi N, Delforterie Y, Grasland B, Brown P. Description of the first isolates of guinea fowl corona and picornaviruses obtained from a case of guinea fowl fulminating enteritis. Avian Pathol 2021; 50:507-521. [PMID: 34545751 DOI: 10.1080/03079457.2021.1976725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Guinea fowl fulminating enteritis has been reported in France since the 1970s. In 2014, a coronavirus was identified and appeared as a possible viral pathogen involved in the disease. In the present study, intestinal content from a guinea fowl involved in a new case of the disease in 2017 was analysed by deep sequencing, revealing the presence of a guinea fowl coronavirus (GfCoV) and a picornavirus (GfPic). Serial passage assays into the intra-amniotic cavity of 13-day-old specific pathogen-free chicken eggs and 20-day-old conventional guinea fowl eggs were attempted. In chicken eggs, isolation assays failed, but in guinea fowl eggs, both viruses were successfully obtained. Furthermore, two GfCoV and two GfPic isolates were obtained from the same bird but from different sections of its intestines. This shows that using eggs of the same species, in which the virus has been detected, can be the key for successful isolation. The consensus sequence of the full-length genomes of both GfCoV isolates was highly similar, and correlated to those previously described in terms of genome organization, ORF length and phylogenetic clustering. According to full-length genome analysis and the structure of the Internal Ribosome Entry Site, both GfPic isolates belong to the Anativirus genus and specifically the species Anativirus B. The availability of the first isolates of GfCoV and GfPic will now provide a means of assessing their pathogenicity in guinea fowl in controlled experimental conditions and to assess whether they are primary viral pathogens of the disease "guinea fowl fulminating enteritis".RESEARCH HIGHLIGHTSFirst isolation of guinea fowl coronaviruses and picornaviruses.Eggs homologous to the infected species are key for isolation.Isolates available to precisely evaluate the virus roles in fulminating enteritis.First full-length genome sequences of guinea fowl picornaviruses.
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Affiliation(s)
- Céline Courtillon
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - François-Xavier Briand
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Chantal Allée
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Maud Contrant
- GVB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Véronique Beven
- GVB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Pierrick Lucas
- GVB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Yannick Blanchard
- GVB Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | | | - Nicolas Eterradossi
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | | | - Béatrice Grasland
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
| | - Paul Brown
- VIPAC Unit, Agence Nationale de Sécurité Sanitaire (Anses), Laboratoire de Ploufragan-Plouzané-Niort Ploufragan, France
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Desdouits M, Piquet JC, Wacrenier C, Le Mennec C, Parnaudeau S, Jousse S, Rocq S, Bigault L, Contrant M, Garry P, Chavanon F, Gabellec R, Lamort L, Lebrun L, Le Gall P, Meteigner C, Schmitt A, Seugnet JL, Serais O, Peltier C, Bressolette-Bodin C, Blanchard Y, Le Guyader FS. Can shellfish be used to monitor SARS-CoV-2 in the coastal environment? Sci Total Environ 2021; 778:146270. [PMID: 33714825 PMCID: PMC7938784 DOI: 10.1016/j.scitotenv.2021.146270] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/26/2021] [Accepted: 02/28/2021] [Indexed: 05/21/2023]
Abstract
The emergence and worldwide spread of SARS-CoV-2 raises new concerns and challenges regarding possible environmental contamination by this virus through spillover of human sewage, where it has been detected. The coastal environment, under increasing anthropogenic pressure, is subjected to contamination by a large number of human viruses from sewage, most of them being non-enveloped viruses like norovirus. When reaching coastal waters, they can be bio-accumulated by filter-feeding shellfish species such as oysters. Methods to detect this viral contamination were set up for the detection of non-enveloped enteric viruses, and may need optimization to accommodate enveloped viruses like coronaviruses (CoV). Here, we aimed at assessing methods for the detection of CoV, including SARS-CoV-2, in the coastal environment and testing the possibility that SARS-CoV-2 can contaminate oysters, to monitor the contamination of French shores by SARS-CoV-2 using both seawater and shellfish. Using the porcine epidemic diarrhea virus (PEDV), a CoV, as surrogate for SARS-CoV-2, and Tulane virus, as surrogate for non-enveloped viruses such as norovirus, we assessed and selected methods to detect CoV in seawater and shellfish. Seawater-based methods showed variable and low yields for PEDV. In shellfish, the current norm for norovirus detection was applicable to CoV detection. Both PEDV and heat-inactivated SARS-CoV-2 could contaminate oysters in laboratory settings, with a lower efficiency than a calicivirus used as control. Finally, we applied our methods to seawater and shellfish samples collected from April to August 2020 in France, where we could detect the presence of human norovirus, a marker of human fecal contamination, but not SARS-CoV-2. Together, our results validate methods for the detection of CoV in the coastal environment, including the use of shellfish as sentinels of the microbial quality of their environment, and suggest that SARS-CoV-2 did not contaminate the French shores during the summer season.
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Affiliation(s)
- Marion Desdouits
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Jean-Côme Piquet
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Candice Wacrenier
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Cécile Le Mennec
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Sylvain Parnaudeau
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Sarah Jousse
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Sophie Rocq
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Lionel Bigault
- ANSES, Génétique Virale et Biosécurité, Ploufragan, France
| | - Maud Contrant
- ANSES, Génétique Virale et Biosécurité, Ploufragan, France
| | - Pascal Garry
- Ifremer, laboratoire de Microbiologie, SG2M/LSEM, BP 21105, 44311 Nantes, France
| | - Fabienne Chavanon
- Ifremer, Laboratoire Environnement Ressource Provence-Azur-Corse, la Seyne sur Mer, France
| | - Raoul Gabellec
- Ifremer, Laboratoire Environnement Ressource Morbihan Pays de la Loire, Lorient, France
| | - Laure Lamort
- Ifremer, Laboratoire Environnement Ressource Normandie, Port en Bessin, France
| | - Luc Lebrun
- Ifremer, Laboratoire Environnement Ressource Bretagne Occidentale, Concarneau, France
| | - Patrik Le Gall
- Ifremer, Laboratoire Environnement Ressource Bretagne Nord, Dinard, France
| | - Claire Meteigner
- Ifremer, Laboratoire Environnement Ressource Arcachon, Arcachon, France
| | - Anne Schmitt
- Ifremer, Laboratoire Environnement Ressource Morbihan Pays de la Loire, Lorient, France
| | - Jean Luc Seugnet
- Ifremer, Laboratoire Environnement Ressource Pertuis-Charentais, la Tremblade, France
| | - Ophélie Serais
- Ifremer, Laboratoire Environnement Ressource Languedoc Roussillon, Sète, France
| | - Cécile Peltier
- Nantes Université, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Céline Bressolette-Bodin
- Nantes Université, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
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7
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Cubas-Gaona LL, Flageul A, Courtillon C, Briand FX, Contrant M, Bougeard S, Lucas P, Quenault H, Leroux A, Keita A, Amelot M, Grasland B, Blanchard Y, Eterradossi N, Brown PA, Soubies SM. Genome Evolution of Two Genetically Homogeneous Infectious Bursal Disease Virus Strains During Passages in vitro and ex vivo in the Presence of a Mutagenic Nucleoside Analog. Front Microbiol 2021; 12:678563. [PMID: 34177862 PMCID: PMC8226269 DOI: 10.3389/fmicb.2021.678563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
The avibirnavirus infectious bursal disease virus (IBDV) is responsible for a highly contagious and sometimes lethal disease of chickens (Gallus gallus). IBDV genetic variation is well-described for both field and live-attenuated vaccine strains, however, the dynamics and selection pressures behind this genetic evolution remain poorly documented. Here, genetically homogeneous virus stocks were generated using reverse genetics for a very virulent strain, rvv, and a vaccine-related strain, rCu-1. These viruses were serially passaged at controlled multiplicities of infection in several biological systems, including primary chickens B cells, the main cell type targeted by IBDV in vivo. Passages were also performed in the absence or presence of a strong selective pressure using the antiviral nucleoside analog 7-deaza-2'-C-methyladenosine (7DMA). Next Generation Sequencing (NGS) of viral genomes after the last passage in each biological system revealed that (i) a higher viral diversity was generated in segment A than in segment B, regardless 7DMA treatment and viral strain, (ii) diversity in segment B was increased by 7DMA treatment in both viruses, (iii) passaging of IBDV in primary chicken B cells, regardless of 7DMA treatment, did not select cell-culture adapted variants of rvv, preserving its capsid protein (VP2) properties, (iv) mutations in coding and non-coding regions of rCu-1 segment A could potentially associate to higher viral fitness, and (v) a specific selection, upon 7DMA addition, of a Thr329Ala substitution occurred in the viral polymerase VP1. The latter change, together with Ala270Thr change in VP2, proved to be associated with viral attenuation in vivo. These results identify genome sequences that are important for IBDV evolution in response to selection pressures. Such information will help tailor better strategies for controlling IBDV infection in chickens.
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Affiliation(s)
- Liliana L Cubas-Gaona
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Alexandre Flageul
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Céline Courtillon
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Francois-Xavier Briand
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Maud Contrant
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Stephanie Bougeard
- Epidemiology, Animal Health and Welfare Unit (EPISABE), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Pierrick Lucas
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Hélène Quenault
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Aurélie Leroux
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Alassane Keita
- Experimental Poultry Unit (SELEAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Michel Amelot
- Experimental Poultry Unit (SELEAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Béatrice Grasland
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Yannick Blanchard
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Nicolas Eterradossi
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Paul Alun Brown
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Sébastien Mathieu Soubies
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
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Ferhadian D, Contrant M, Printz-Schweigert A, Smyth RP, Paillart JC, Marquet R. Structural and Functional Motifs in Influenza Virus RNAs. Front Microbiol 2018; 9:559. [PMID: 29651275 PMCID: PMC5884886 DOI: 10.3389/fmicb.2018.00559] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/12/2018] [Indexed: 12/22/2022] Open
Abstract
Influenza A viruses (IAV) are responsible for recurrent influenza epidemics and occasional devastating pandemics in humans and animals. They belong to the Orthomyxoviridae family and their genome consists of eight (-) sense viral RNA (vRNA) segments of different lengths coding for at least 11 viral proteins. A heterotrimeric polymerase complex is bound to the promoter consisting of the 13 5′-terminal and 12 3′-terminal nucleotides of each vRNA, while internal parts of the vRNAs are associated with multiple copies of the viral nucleoprotein (NP), thus forming ribonucleoproteins (vRNP). Transcription and replication of vRNAs result in viral mRNAs (vmRNAs) and complementary RNAs (cRNAs), respectively. Complementary RNAs are the exact positive copies of vRNAs; they also form ribonucleoproteins (cRNPs) and are intermediate templates in the vRNA amplification process. On the contrary, vmRNAs have a 5′ cap snatched from cellular mRNAs and a 3′ polyA tail, both gained by the viral polymerase complex. Hence, unlike vRNAs and cRNAs, vmRNAs do not have a terminal promoter able to recruit the viral polymerase. Furthermore, synthesis of at least two viral proteins requires vmRNA splicing. Except for extensive analysis of the viral promoter structure and function and a few, mostly bioinformatics, studies addressing the vRNA and vmRNA structure, structural studies of the influenza A vRNAs, cRNAs, and vmRNAs are still in their infancy. The recent crystal structures of the influenza polymerase heterotrimeric complex drastically improved our understanding of the replication and transcription processes. The vRNA structure has been mainly studied in vitro using RNA probing, but its structure has been very recently studied within native vRNPs using crosslinking and RNA probing coupled to next generation RNA sequencing. Concerning vmRNAs, most studies focused on the segment M and NS splice sites and several structures initially predicted by bioinformatics analysis have now been validated experimentally and their role in the viral life cycle demonstrated. This review aims to compile the structural motifs found in the different RNA classes (vRNA, cRNA, and vmRNA) of influenza viruses and their function in the viral replication cycle.
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Affiliation(s)
- Damien Ferhadian
- CNRS - UPR 9002, Architecture et Réactivité de l'ARN, IBMC, Université de Strasbourg, Strasbourg, France
| | - Maud Contrant
- CNRS - UPR 9002, Architecture et Réactivité de l'ARN, IBMC, Université de Strasbourg, Strasbourg, France
| | - Anne Printz-Schweigert
- CNRS - UPR 9002, Architecture et Réactivité de l'ARN, IBMC, Université de Strasbourg, Strasbourg, France
| | - Redmond P Smyth
- CNRS - UPR 9002, Architecture et Réactivité de l'ARN, IBMC, Université de Strasbourg, Strasbourg, France
| | - Jean-Christophe Paillart
- CNRS - UPR 9002, Architecture et Réactivité de l'ARN, IBMC, Université de Strasbourg, Strasbourg, France
| | - Roland Marquet
- CNRS - UPR 9002, Architecture et Réactivité de l'ARN, IBMC, Université de Strasbourg, Strasbourg, France
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Haar J, Contrant M, Bernhardt K, Feederle R, Diederichs S, Pfeffer S, Delecluse HJ. The expression of a viral microRNA is regulated by clustering to allow optimal B cell transformation. Nucleic Acids Res 2015; 44:1326-41. [PMID: 26635399 PMCID: PMC4756819 DOI: 10.1093/nar/gkv1330] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 11/13/2015] [Indexed: 02/02/2023] Open
Abstract
The Epstein-Barr virus (EBV) transforms B cells by expressing latent proteins and the BHRF1 microRNA cluster. MiR-BHRF1–3, its most transforming member, belongs to the recently identified group of weakly expressed microRNAs. We show here that miR-BHRF1–3 displays an unusually low propensity to form a stem–loop structure, an effect potentiated by miR-BHRF1–3's proximity to the BHRF1 polyA site. Cloning miR-BHRF1–2 or a cellular microRNA, but not a ribozyme, 5′ of miR-BHRF1–3 markedly enhanced its expression. However, a virus carrying mutated miR-BHRF1–2 seed regions expressed miR-BHRF1–3 at normal levels and was fully transforming. Therefore, miR-BHRF1–2's role during transformation is independent of its seed regions, revealing a new microRNA function. Increasing the distance between miR-BHRF1–2 and miR-BHRF1–3 in EBV enhanced miR-BHRF1–3's expression but decreased its transforming potential. Thus, the expression of some microRNAs must be restricted to a narrow range, as achieved by placing miR-BHRF1–3 under the control of miR-BHRF1–2.
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Affiliation(s)
- Janina Haar
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany Inserm unit U1074, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
| | - Maud Contrant
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Katharina Bernhardt
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany Inserm unit U1074, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
| | - Regina Feederle
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany Inserm unit U1074, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Clinic for Thoracic Surgery, University Hospital Freiburg, Breisacher Str. 86b, 79110 Freiburg, Germany Division of RNA Biology & Cancer, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany & Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Henri-Jacques Delecluse
- Pathogenesis of Virus Associated Tumors, German Cancer Research Center, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany Inserm unit U1074, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
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Contrant M, Fender A, Chane-Woon-Ming B, Randrianjafy R, Vivet-Boudou V, Richer D, Pfeffer S. Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs. Nucleic Acids Res 2014; 42:7981-96. [PMID: 24831544 PMCID: PMC4081064 DOI: 10.1093/nar/gku424] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNAs themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNA accumulation. To this end, we used the Kaposi's sarcoma herpesvirus, which encodes a cluster of 12 pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNAs could be as high as 60-fold. Using high-throughput selective 2′-hydroxyl acylation analyzed by primer extension, we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops or by targeted mutagenesis of selected miRNAs, which resulted in a perturbed accumulation of the mature miRNA.
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Affiliation(s)
- Maud Contrant
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Aurélie Fender
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Béatrice Chane-Woon-Ming
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Ramy Randrianjafy
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Valérie Vivet-Boudou
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Delphine Richer
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
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Suffert G, Malterer G, Hausser J, Viiliäinen J, Fender A, Contrant M, Ivacevic T, Benes V, Gros F, Voinnet O, Zavolan M, Ojala PM, Haas JG, Pfeffer S. Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis. PLoS Pathog 2011; 7:e1002405. [PMID: 22174674 PMCID: PMC3234232 DOI: 10.1371/journal.ppat.1002405] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
Kaposi's sarcoma herpesvirus (KSHV) encodes a cluster of twelve micro (mi)RNAs, which are abundantly expressed during both latent and lytic infection. Previous studies reported that KSHV is able to inhibit apoptosis during latent infection; we thus tested the involvement of viral miRNAs in this process. We found that both HEK293 epithelial cells and DG75 cells stably expressing KSHV miRNAs were protected from apoptosis. Potential cellular targets that were significantly down-regulated upon KSHV miRNAs expression were identified by microarray profiling. Among them, we validated by luciferase reporter assays, quantitative PCR and western blotting caspase 3 (Casp3), a critical factor for the control of apoptosis. Using site-directed mutagenesis, we found that three KSHV miRNAs, miR-K12-1, 3 and 4-3p, were responsible for the targeting of Casp3. Specific inhibition of these miRNAs in KSHV-infected cells resulted in increased expression levels of endogenous Casp3 and enhanced apoptosis. Altogether, our results suggest that KSHV miRNAs directly participate in the previously reported inhibition of apoptosis by the virus, and are thus likely to play a role in KSHV-induced oncogenesis.
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Affiliation(s)
- Guillaume Suffert
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Georg Malterer
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Jean Hausser
- Biozentrum der Universität Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Johanna Viiliäinen
- Genome-Scale Biology Program, Biomedicum Helsinki and Institute of Biomedicine, University of Helsinki, Helsinki, Finland
| | - Aurélie Fender
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Maud Contrant
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Tomi Ivacevic
- GeneCore (Genomics Core Facility), EMBL, Heidelberg, Germany
| | - Vladimir Benes
- GeneCore (Genomics Core Facility), EMBL, Heidelberg, Germany
| | - Frédéric Gros
- Immunologie et Chimie Thérapeutiques UPR 9021, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Olivier Voinnet
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
| | - Mihaela Zavolan
- Biozentrum der Universität Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Päivi M. Ojala
- Genome-Scale Biology Program, Biomedicum Helsinki and Institute of Biomedicine, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
- * E-mail: (PMO); (JGH); (SP)
| | - Juergen G. Haas
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Munich, Germany
- Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, United Kingdom
- * E-mail: (PMO); (JGH); (SP)
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
- * E-mail: (PMO); (JGH); (SP)
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