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Gaudino M, Salem E, Ducatez MF, Meyer G. Identification of Astrovirus in the virome of the upper and lower respiratory tracts of calves with acute signs of bronchopneumonia. Microbiol Spectr 2023; 11:e0302623. [PMID: 37982636 PMCID: PMC10714732 DOI: 10.1128/spectrum.03026-23] [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: 08/03/2023] [Accepted: 10/22/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Astroviruses (AstV) are known suspects of enteric disease in humans and livestock. Recently, AstV have been linked to encephalitis in immunocompromised patients and other animals, such as cattle, minks, and swine. In our study, we also identified AstV in the respiratory samples of calves with signs of bronchopneumonia, suggesting that their tropism could be even broader. We obtained one bovine AstV (BAstV) complete genome sequence by next-generation sequencing and showed that respiratory and enteric AstV from different species formed a divergent genetic cluster with AstV isolated from encephalitis cases, indicating that tropism might be strain-specific. These data provide further insight into understanding the biology of these understudied pathogens and suggest BAstV as a potential new candidate for bovine respiratory disease.
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Affiliation(s)
- Maria Gaudino
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Elias Salem
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Gilles Meyer
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
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Marques S, Gomes-Neves E, Baptista CS, Pereira FR, Alves-Pereira A, Osório P, Müller A. A Survey on Vaccination and Disease Occurrence in Municipal and Non-Profit Animal Shelters in Portugal. Animals (Basel) 2023; 13:2723. [PMID: 37684987 PMCID: PMC10486493 DOI: 10.3390/ani13172723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Few studies are available describing animal shelters in Portugal. The aim was to characterize prophylactic measures and disease occurrence in shelters with a questionnaire. The response rates of 67 shelters (42 municipal shelters, 25 associations) were compared by the Fisher's exact test. More veterinarians answered for municipal shelters (98%) than for associations (40%; p < 0.001). Over 80% of the respondents indicated using individual medical records and routine prophylaxis. Excessive length of stay for dogs was reported by 54% of associations and 33% of municipal shelters. Management tools should be promoted to improve the situation. Puppy vaccinations were similar and a final vaccination at 16 weeks was indicated by >33% of shelters. Annual revaccination of dogs was reported more frequently by associations (88%) than municipal shelters (55%; p = 0.02). The three most reported diseases were parvovirus and mange in dogs, upper respiratory disease and panleukopenia in cats, and dermatophytosis in both species. Similar response rates for diagnostic options were obtained by both shelter types, except for distemper. Testing for feline retroviruses was indicated by most shelters (>69%), but only a few (<24%) confirmed positive test results. Clinical diagnoses should be complemented by testing. Additional information on disease occurrence should be obtained by objective monitoring.
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Affiliation(s)
- Sara Marques
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; (E.G.-N.); (C.S.B.); (F.R.P.)
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Laboratório Associado em Biodiversidade e Biologia Evolutiva (InBIO), University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas No. 7, 4485-661 Vila do Conde, Portugal
| | - Eduarda Gomes-Neves
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; (E.G.-N.); (C.S.B.); (F.R.P.)
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente (ICETA), Laboratório Associado AL4AnimalS, University of Porto, 4050-313 Porto, Portugal
| | - Cláudia S. Baptista
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; (E.G.-N.); (C.S.B.); (F.R.P.)
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente (ICETA), Laboratório Associado AL4AnimalS, University of Porto, 4050-313 Porto, Portugal
| | - Francisca R. Pereira
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; (E.G.-N.); (C.S.B.); (F.R.P.)
| | | | - Pedro Osório
- Shelter Veterinarian, 4050-313 Porto, Portugal; (A.A.-P.); (P.O.)
| | - Alexandra Müller
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; (E.G.-N.); (C.S.B.); (F.R.P.)
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente (ICETA), Laboratório Associado AL4AnimalS, University of Porto, 4050-313 Porto, Portugal
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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Van Brussel K, Wang X, Shi M, Carrai M, Feng S, Li J, Holmes EC, Beatty JA, Barrs VR. The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats. Transbound Emerg Dis 2022; 69:e2952-e2966. [PMID: 35765950 PMCID: PMC9796298 DOI: 10.1111/tbed.14646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/29/2022] [Accepted: 06/18/2022] [Indexed: 01/01/2023]
Abstract
Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline panleukopenia virus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used meta-transcriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV-cases) and 36 age-matched healthy shelter cats (healthy controls). Sequencing reads from mammalian infecting viral families largely belonged to the Coronaviridae, Parvoviridae and Astroviridae. The most abundant viruses among the healthy control cats were feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (feline bocavirus), with frequent coinfections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6 out of 36, 16.7%). Among the FPV-cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, feline coronavirus and C. bocaparvovirus 4 (feline bocaparvovirus 2). The latter and feline bocaparvovirus 3 were detected significantly more frequently in FPV-cases than in healthy controls. Feline calicivirus was present in a higher proportion of FPV-cases (11 out of 23, 47.8%) compared to healthy controls (5 out of 36, 13.9%, p = 0.0067). Feline kobuvirus infections were also common among FPV-cases (9 out of 23, 39.1%) and were not detected in any healthy controls (p < .0001). While abundant in both groups, astroviruses were more frequently present in FPV-cases (19 out of 23, 82.6%) than in healthy controls (18 out of 36, p = .0142). The differences in eukaryotic virome composition revealed here indicate that further investigations are warranted to determine associations between enteric viral co-infections on clinical disease severity in cats with FPL.
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Affiliation(s)
- Kate Van Brussel
- School of Veterinary ScienceFaculty of ScienceUniversity of SydneySydneyNew South WalesAustralia,Sydney Institute for Infectious DiseasesSchool of Life and Environmental Sciences and School of Medical SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Xiuwan Wang
- Jockey Club College of Veterinary Medicine & Life SciencesCentre for Animal Health and WelfareCity University of Hong KongKowloon TongHong KongChina
| | - Mang Shi
- Sydney Institute for Infectious DiseasesSchool of Life and Environmental Sciences and School of Medical SciencesUniversity of SydneySydneyNew South WalesAustralia,School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Maura Carrai
- Jockey Club College of Veterinary Medicine & Life SciencesCentre for Animal Health and WelfareCity University of Hong KongKowloon TongHong KongChina
| | - Shuo Feng
- Jockey Club College of Veterinary Medicine & Life SciencesCentre for Animal Health and WelfareCity University of Hong KongKowloon TongHong KongChina
| | - Jun Li
- Jockey Club College of Veterinary Medicine & Life SciencesCentre for Animal Health and WelfareCity University of Hong KongKowloon TongHong KongChina,School of Data ScienceCity University of Hong KongHong KongChina
| | - Edward C. Holmes
- Sydney Institute for Infectious DiseasesSchool of Life and Environmental Sciences and School of Medical SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Julia A. Beatty
- School of Veterinary ScienceFaculty of ScienceUniversity of SydneySydneyNew South WalesAustralia,Jockey Club College of Veterinary Medicine & Life SciencesCentre for Animal Health and WelfareCity University of Hong KongKowloon TongHong KongChina,Centre for Animal Health and WelfareCity University of Hong KongHong KongChina
| | - Vanessa R. Barrs
- School of Veterinary ScienceFaculty of ScienceUniversity of SydneySydneyNew South WalesAustralia,Jockey Club College of Veterinary Medicine & Life SciencesCentre for Animal Health and WelfareCity University of Hong KongKowloon TongHong KongChina,Centre for Animal Health and WelfareCity University of Hong KongHong KongChina
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Roach SN, Langlois RA. Intra- and Cross-Species Transmission of Astroviruses. Viruses 2021; 13:v13061127. [PMID: 34208242 PMCID: PMC8230745 DOI: 10.3390/v13061127] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Astroviruses are non-enveloped, single-stranded RNA viruses that infect mammalian and avian species. In humans, astrovirus infections are one of the most common causes of gastroenteritis in children. Infection has also been linked to serious neurological complications, especially in immunocompromised individuals. More extensive disease has also been characterized in non-human mammalian and avian species. To date, astroviruses have been detected in over 80 different avian and mammalian hosts. As the number of hosts continues to rise, the need to understand how astroviruses transmit within a given species as well as to new host species becomes increasingly important. Here, we review the current understanding of astrovirus transmission, the factors that influence viral spread, and the potential for cross-species transmission. Additionally, we highlight the current gaps in knowledge and areas of future research that will be key to understanding astrovirus transmission and zoonotic potential.
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Affiliation(s)
- Shanley N. Roach
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence:
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