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Zhu P, Liu C, Liu GF, Liu H, Xie KM, Zhang HS, Xu X, Xiao J, Jiang JZ. Unveiling CRESS DNA Virus Diversity in Oysters by Virome. Viruses 2024; 16:228. [PMID: 38400004 PMCID: PMC10892194 DOI: 10.3390/v16020228] [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: 01/02/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.
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Affiliation(s)
- Peng Zhu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- Animal and Plant Inspection and Quarantine Technology Centre, Shenzhen Customs, Shenzhen 518000, China
| | - Chang Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Guang-Feng Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
| | - Hong Liu
- Animal and Plant Inspection and Quarantine Technology Centre, Shenzhen Customs, Shenzhen 518000, China
| | - Ke-Ming Xie
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- School of Life Science and Biopharmacy, Guangdong Pharmaceutical University, Guangzhou 510000, China
| | - Hong-Sai Zhang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
| | - Xin Xu
- Livestock, Aquaculture and Technology Promotion and Service Center of Conghua District, Guangzhou 510000, China
| | - Jian Xiao
- Livestock, Aquaculture and Technology Promotion and Service Center of Conghua District, Guangzhou 510000, China
| | - Jing-Zhe Jiang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- School of Life Science and Biopharmacy, Guangdong Pharmaceutical University, Guangzhou 510000, China
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2
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Gawra J, Valdivieso A, Roux F, Laporte M, de Lorgeril J, Gueguen Y, Saccas M, Escoubas JM, Montagnani C, Destoumieux-Garzόn D, Lagarde F, Leroy MA, Haffner P, Petton B, Cosseau C, Morga B, Dégremont L, Mitta G, Grunau C, Vidal-Dupiol J. Epigenetic variations are more substantial than genetic variations in rapid adaptation of oyster to Pacific oyster mortality syndrome. SCIENCE ADVANCES 2023; 9:eadh8990. [PMID: 37683000 PMCID: PMC10491289 DOI: 10.1126/sciadv.adh8990] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Disease emergence is accelerating with global changes. Understanding by which mechanisms host populations can rapidly adapt will be crucial for management practices. Pacific oyster mortality syndrome (POMS) imposes a substantial and recurrent selective pressure on oyster populations, and rapid adaptation may arise through genetics and epigenetics. In this study, we used (epi)genome-wide association mapping to show that oysters differentially exposed to POMS displayed genetic and epigenetic signatures of selection. Consistent with higher resistance to POMS, the genes targeted included many genes in several pathways related to immunity. By combining correlation, DNA methylation quantitative trait loci, and variance partitioning, we revealed that a third of phenotypic variation was explained by interactions between the genetic and epigenetic information, ~14% by the genome, and up to 25% by the epigenome alone. Similar to genetically based adaptation, epigenetic mechanisms notably governing immune responses can contribute substantially to the rapid adaptation of hosts to emerging infectious diseases.
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Affiliation(s)
- Janan Gawra
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, Perpignan, France
| | - Alejandro Valdivieso
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Fabrice Roux
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Martin Laporte
- Division de l'expertise sur la faune Aquatique, Ministère des Forêts, de la Faune et des Parcs (MFFP), 880 chemin Sainte-Foy, G1S 4X4 Québec, Québec, Canada
| | - Julien de Lorgeril
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, ENTROPIE, Nouméa, Nouvelle-Calédonie, France
| | - Yannick Gueguen
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Mathilde Saccas
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Caroline Montagnani
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | | | - Franck Lagarde
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Marc A. Leroy
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Philippe Haffner
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Bruno Petton
- Université de Brest, Ifremer, CNRS, IRD, LEMAR, F-29280 Plouzané, France
| | - Céline Cosseau
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, Perpignan, France
| | - Benjamin Morga
- Ifremer, ASIM, Adaptation Santé des Invertébrés Marins, La Tremblade, France
| | - Lionel Dégremont
- Ifremer, ASIM, Adaptation Santé des Invertébrés Marins, La Tremblade, France
| | - Guillaume Mitta
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, Perpignan, France
- Université de la Polynésie Française, ILM, IRD, Ifremer, F-98719 Tahiti, French Polynesia, France
| | - Christoph Grunau
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, Perpignan, France
| | - Jeremie Vidal-Dupiol
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
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Trancart S, Tweedie A, Liu O, Paul-Pont I, Hick P, Houssin M, Whittington RJ. Diversity and molecular epidemiology of Ostreid herpesvirus 1 in farmed Crassostrea gigas in Australia: Geographic clusters and implications for "microvariants" in global mortality events. Virus Res 2023; 323:198994. [PMID: 36332723 PMCID: PMC10194400 DOI: 10.1016/j.virusres.2022.198994] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/08/2022]
Abstract
Since 2010, mass mortality events known as Pacific oyster mortality syndrome (POMS) have occurred in Crassostrea gigas in Australia associated with Ostreid herpesvirus 1. The virus was thought to be an OsHV-1 µVar or "microvariant", i.e. one of the dominant variants associated with POMS in Europe, but there are few data to characterize the genotype in Australia. Consequently, the genetic identity and diversity of the virus was determined to understand the epidemiology of the disease in Australia. Samples were analysed from diseased C. gigas over five summer seasons between 2011 and 2016 in POMS-affected estuaries: Georges River in New South Wales (NSW), Hawkesbury River (NSW) and Pitt Water in Tasmania. Sequencing was attempted for six genomic regions. Numerous variants were identified among these regions (n = 100 isolates) while twelve variants were identified from concatenated nucleotide sequences (n = 61 isolates). Nucleotide diversity of the seven genotypes of C region among Australian isolates (Pi 0.99 × 10-3) was the lowest globally. All Australian isolates grouped in a cluster distinct from other OsHV-1 isolates worldwide. This is the first report that Australian outbreaks of POMS were associated with OsHV-1 distinct from OsHV-1 reference genotype, µVar and other microvariants from other countries. The findings illustrate that microvariants are not the only variants of OsHV-1 associated with mass mortality events in C. gigas. In addition, there was mutually exclusive spatial clustering of viral genomic and amino acid sequence variants between estuaries, and a possible association between genotype/amino acid sequence and the prevalence and severity of POMS, as this differed between these estuaries. The sequencing findings supported prior epidemiological evidence for environmental reservoirs of OsHV-1 for POMS outbreaks in Australia.
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Affiliation(s)
- Suzanne Trancart
- LABÉO Research Department, 1 Route de Rosel, Cedex 4, Caen 14053, France
| | - Alison Tweedie
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia; Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Olivia Liu
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia; Department of Agriculture, Water and the Environment, Canberra, ACT 2601, Australia
| | - Ika Paul-Pont
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia; LEMAR, Rue Dumont d'Urville, Plouzané 29280, France
| | - Paul Hick
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia; Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Maryline Houssin
- LABÉO Research Department, 1 Route de Rosel, Cedex 4, Caen 14053, France; UMR BOREA Université de Caen Normandie, MNHN, CNRS 8067, SU, IRD 207, UCN, UA, Esplanade de la Paix Caen Cedex 4 14032, France
| | - Richard J Whittington
- The University of Sydney, Sydney School of Veterinary Science, Faculty of Science, 425 Werombi Rd, Camden, NSW 2570, Australia.
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Dotto-Maurel A, Pelletier C, Morga B, Jacquot M, Faury N, Dégremont L, Bereszczynki M, Delmotte J, Escoubas JM, Chevignon G. Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly. Microb Genom 2022; 8:mgen000895. [PMID: 36355418 PMCID: PMC9836095 DOI: 10.1099/mgen.0.000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Whole-genome sequencing is widely used to better understand the transmission dynamics, the evolution and the emergence of new variants of viral pathogens. This can bring crucial information to stakeholders for disease management. Unfortunately, aquatic virus genomes are usually difficult to characterize because most of these viruses cannot be easily propagated in vitro. Developing methodologies for routine genome sequencing of aquatic viruses is timely given the ongoing threat of disease emergence. This is particularly true for pathogenic viruses infecting species of commercial interest that are widely exchanged between production basins or countries. For example, the ostreid herpesvirus type 1 (OsHV-1) is a Herpesvirus widely associated with mass mortality events of juvenile Pacific oyster Crassostrea gigas. Genomes of Herpesviruses are large and complex with long direct and inverted terminal repeats. In addition, OsHV-1 is unculturable. It therefore accumulates several features that make its genome sequencing and assembly challenging. To overcome these difficulties, we developed a tangential flow filtration (TFF) method to enrich OsHV-1 infective particles from infected host tissues. This virus purification allowed us to extract high molecular weight and high-quality viral DNA that was subjected to Illumina short-read and Nanopore long-read sequencing. Dedicated bioinformatic pipelines were developed to assemble complete OsHV-1 genomes with reads from both sequencing technologies. Nanopore sequencing allowed characterization of new structural variations and major viral isomers while having 99,98 % of nucleotide identity with the Illumina assembled genome. Our study shows that TFF-based purification method, coupled with Nanopore sequencing, is a promising approach to enable in field sequencing of unculturable aquatic DNA virus.
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Affiliation(s)
| | | | | | | | | | | | | | - Jean Delmotte
- IHPE, Univ. Montpellier, CNRS, Ifremer, UPVD, F-34095 Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, Univ. Montpellier, CNRS, Ifremer, UPVD, F-34095 Montpellier, France,*Correspondence: Jean-Michel Escoubas,
| | - Germain Chevignon
- Ifremer, ASIM, F-17390 La Tremblade, France,*Correspondence: Germain Chevignon,
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Scarpa F, Sanna D, Azzena I, Cossu P, Locci C, Angeletti S, Maruotti A, Ceccarelli G, Casu M, Fiori PL, Petrosillo N, Ciccozzi M. Genetic Variability of the Monkeypox Virus Clade IIb B.1. J Clin Med 2022; 11:6388. [PMID: 36362616 PMCID: PMC9695420 DOI: 10.3390/jcm11216388] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 08/27/2023] Open
Abstract
Monkeypox is caused by a sylvatic, double-stranded DNA zoonotic virus. Since 1 January 2022, monkeypox cases have been reported to WHO from 106 Member States across six WHO regions, and as of 2 October 2022, a total of 68,900 confirmed cases, including 25 deaths, occurred. Here, by using a whole genome approach, we perform a genetic and phylodynamic survey of the monkeypox virus Clade IIb B.1, which is the lineage causing the current multi-country outbreak. Results suggest that outbreaks seem to be isolated and localized in several epidemic clusters with geographic consistency. Currently, monkeypox appears to be a virus with a flattened genetic variability in terms of evolutionary path, with a very slow rate of growth in the population size. This scenario confirms that the monkeypox virus lacks the evolutionary advantage, given by the high level of mutation rate, which is very strong in RNA viruses. Of course, constant genome-based monitoring must be performed over time in order to detect the change in its genetic composition, if any.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Piero Cossu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Silvia Angeletti
- Department of Medicine and Surgery, Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Research Unit of Laboratory, University Hospital Campus Bio-Medico, 00128 Rome, Italy
| | | | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, 00161 Rome, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Nicola Petrosillo
- Infection Prevention and Control, University Hospital Campus Bio-Medico, 00128 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00100 Rome, Italy
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