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Waller SJ, Egan E, Crow S, Charsley A, Lokman PM, Williams EK, Holmes EC, Geoghegan JL. Host and geography impact virus diversity in New Zealand's longfin and shortfin eels. Arch Virol 2024; 169:85. [PMID: 38546898 PMCID: PMC10978610 DOI: 10.1007/s00705-024-06019-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024]
Abstract
The fishing and aquaculture industry is vital for global food security, yet viral diseases can result in mass fish die-off events. Determining the viromes of traditionally understudied species, such as fish, enhances our understanding of the global virosphere and the factors that influence virome composition and disease emergence. Very little is known about the viruses present in New Zealand's native fish species, including the shortfin eel (Anguilla australis) and the longfin eel (Anguilla dieffenbachii), both of which are fished culturally by Māori (the indigenous population of New Zealand) and commercially. Through a total RNA metatranscriptomic analysis of longfin and shortfin eels across three different geographic locations in the South Island of New Zealand, we aimed to determine whether viruses had jumped between the two eel species and whether eel virome composition was impacted by life stage, species, and geographic location. We identified nine viral species spanning eight different families, thereby enhancing our understanding of eel virus diversity in New Zealand and the host range of these viral families. Viruses of the family Flaviviridae (genus Hepacivirus) were widespread and found in both longfin and shortfin eels, indicative of cross-species transmission or virus-host co-divergence. Notably, both host specificity and geographic location appeared to influence eel virome composition, highlighting the complex interaction between viruses, hosts, and their ecosystems. This study broadens our understanding of viromes in aquatic hosts and highlights the importance of gaining baseline knowledge of fish viral abundance and diversity, particularly in aquatic species that are facing population declines.
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Affiliation(s)
- Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Eimear Egan
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Shannan Crow
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Anthony Charsley
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - P Mark Lokman
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Erica K Williams
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand.
- Institute of Environmental Science and Research, Wellington, New Zealand.
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Zhu J, Qi M, Jiang C, Peng Y, Peng Q, Chen Y, Hu C, Chen J, Chen X, Chen H, Guo A. Prevalence of bovine astroviruses and their genotypes in sampled Chinese calves with and without diarrhoea. J Gen Virol 2021; 102. [PMID: 34424158 PMCID: PMC8513638 DOI: 10.1099/jgv.0.001640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bovine astrovirus (BoAstV) belongs to genus Mamastravirus (MAstV). It can be detected in the faeces of both diarrhoeal and healthy calves. However, its prevalence, genetic diversity, and association with cattle diarrhoea are poorly understood. In this study, faecal samples of 87 diarrhoeal and 77 asymptomatic calves from 20 farms in 12 provinces were collected, and BoAstV was detected with reverse transcription-polymerase chain reaction (RT-PCR). The overall prevalence rate of this virus in diarrhoeal and asymptomatic calves was 55.17 % (95 % CI: 44.13, 65.85 %) and 36.36 % (95 % CI: 25.70, 48.12 %), respectively, indicating a correlation between BoAstV infection and calf diarrhoea (OR=2.15, P=0.024). BoAstV existed mainly in the form of co-infection (85.53 %) with one to five of nine viruses, and there was a strong positive correlation between BoAstV co-infection and calf diarrhoea (OR=2.83, P=0.004). Binary logistic regression analysis confirmed this correlation between BoAstV co-infection and calf diarrhoea (OR=2.41, P=0.038). The co-infection of BoAstV and bovine rotavirus (BRV) with or without other viruses accounted for 70.77 % of all the co-infection cases. The diarrhoea risk for the calves co-infected with BoAstV and BRV was 8.14-fold higher than that for the calves co-infected with BoAstV and other viruses (OR=8.14, P=0.001). Further, the co-infection of BoAstV/BRV/bovine kobuvirus (BKoV) might increase the risk of calf diarrhoea by 14.82-fold, compared with that of BoAstV and other viruses (OR=14.82, P <0.001). Then, nearly complete genomic sequences of nine BoAstV strains were assembled by using next-generation sequencing (NGS) method. Sequence alignment against known astrovirus (AstV) strains at the levels of both amino acids and nucleotides showed a high genetic diversity. Four genotypes were identified, including two known genotypes MAstV-28 (n=3) and MAstV-33 (n=2) and two novel genotypes designated tentatively as MAstV-34 (n=1) and MAstV-35 (n=3). In addition, seven out of nine BoAstV strains showed possible inter-genotype recombination and cross-species recombination. Therefore, our results increase the knowledge about the prevalence and the genetic evolution of BoAstV and provide evidence for the association between BoAstV infection and calf diarrhoea.
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Affiliation(s)
- Jie Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Chuanwen Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Yongchong Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Qingjie Peng
- Wuhan Keqian Biology Co.Ltd, Wuhan, 430070, PR China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Ruminant Bio-products of Ministry of Agriculture and and Rural Affairs, Huazhong Agriculture University, Wuhan 430070, PR China
| | - Changmin Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jianguo Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xi Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Wuhan Keqian Biology Co.Ltd, Wuhan, 430070, PR China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Ruminant Bio-products of Ministry of Agriculture and and Rural Affairs, Huazhong Agriculture University, Wuhan 430070, PR China
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