Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle
Increased evidence suggests that cattle are the primary host of Influenza D virus (IDV) and may contribute to respiratory disease in this species. The aim of this study was to detect and characterise IDV in the Swedish cattle population using archived respiratory samples. This retrospective study co...
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2024-12-01
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| author | Ignacio Alvarez Fereshteh Banihashem Annie Persson Emma Hurri Hyeyoung Kim Mariette Ducatez Erika Geijer Jean-Francois Valarcher Sara Hägglund Siamak Zohari |
| author_facet | Ignacio Alvarez Fereshteh Banihashem Annie Persson Emma Hurri Hyeyoung Kim Mariette Ducatez Erika Geijer Jean-Francois Valarcher Sara Hägglund Siamak Zohari |
| author_sort | Ignacio Alvarez |
| collection | DOAJ |
| description | Increased evidence suggests that cattle are the primary host of Influenza D virus (IDV) and may contribute to respiratory disease in this species. The aim of this study was to detect and characterise IDV in the Swedish cattle population using archived respiratory samples. This retrospective study comprised a collection of a total 1763 samples collected between 1 January 2021 and 30 June 2024. The samples were screened for IDV and other respiratory pathogens using real-time reverse transcription quantitative PCR (rRT-qPCR). Fifty-one IDV-positive samples were identified, with a mean cycle threshold (Ct) value of 27 (range: 15–37). Individual samples with a Ct value of <30 for IDV RNA were further analysed by deep sequencing. Phylogenetic analysis was performed by the maximum likelihood estimation method on the whole IDV genome sequence from 16 samples. The IDV strains collected in 2021 (n = 7) belonged to the D/OK clade, whereas samples from 2023 (n = 4) and 2024 (n = 5) consisted of reassortants between the D/OK and D/660 clades, for the PB2 gene. This study reports the first detection of IDV in Swedish cattle and the circulation of D/OK and reassortant D/OK-D/660 in this population. |
| format | Article |
| id | doaj-art-da6b39c5af254937b6c6e7d5f53ceb99 |
| institution | Kabale University |
| issn | 1999-4915 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Viruses |
| spelling | doaj-art-da6b39c5af254937b6c6e7d5f53ceb992025-01-24T13:52:16ZengMDPI AGViruses1999-49152024-12-011711710.3390/v17010017Detection and Phylogenetic Characterization of Influenza D in Swedish CattleIgnacio Alvarez0Fereshteh Banihashem1Annie Persson2Emma Hurri3Hyeyoung Kim4Mariette Ducatez5Erika Geijer6Jean-Francois Valarcher7Sara Hägglund8Siamak Zohari9Division of Ruminant Medicine, Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 756 51 Uppsala, SwedenDepartment of Microbiology, Swedish Veterinary Agency, Ulls väg 2B, 751 89 Uppsala, SwedenDepartment of Microbiology, Swedish Veterinary Agency, Ulls väg 2B, 751 89 Uppsala, SwedenDepartment of Clinical Sciences, Swedish University of Agricultural Sciences, 756 51 Uppsala, SwedenDepartment of Epidemiology, Surveillance and Risk Assessment, Swedish Veterinary Agency, Ulls väg 2B, 751 89 Uppsala, SwedenInteractions Hôtes-Agents-Pathogènes, Ecole Vétérinaire de Toulouse (ENVT), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31300 Toulouse, FranceGård & Djurhälsan, Kungsängens Gård, 753 23 Uppsala, SwedenDivision of Ruminant Medicine, Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 756 51 Uppsala, SwedenDivision of Ruminant Medicine, Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 756 51 Uppsala, SwedenDepartment of Microbiology, Swedish Veterinary Agency, Ulls väg 2B, 751 89 Uppsala, SwedenIncreased evidence suggests that cattle are the primary host of Influenza D virus (IDV) and may contribute to respiratory disease in this species. The aim of this study was to detect and characterise IDV in the Swedish cattle population using archived respiratory samples. This retrospective study comprised a collection of a total 1763 samples collected between 1 January 2021 and 30 June 2024. The samples were screened for IDV and other respiratory pathogens using real-time reverse transcription quantitative PCR (rRT-qPCR). Fifty-one IDV-positive samples were identified, with a mean cycle threshold (Ct) value of 27 (range: 15–37). Individual samples with a Ct value of <30 for IDV RNA were further analysed by deep sequencing. Phylogenetic analysis was performed by the maximum likelihood estimation method on the whole IDV genome sequence from 16 samples. The IDV strains collected in 2021 (n = 7) belonged to the D/OK clade, whereas samples from 2023 (n = 4) and 2024 (n = 5) consisted of reassortants between the D/OK and D/660 clades, for the PB2 gene. This study reports the first detection of IDV in Swedish cattle and the circulation of D/OK and reassortant D/OK-D/660 in this population.https://www.mdpi.com/1999-4915/17/1/17influenza D viruscattlebovinePCRSwedenco-infection |
| spellingShingle | Ignacio Alvarez Fereshteh Banihashem Annie Persson Emma Hurri Hyeyoung Kim Mariette Ducatez Erika Geijer Jean-Francois Valarcher Sara Hägglund Siamak Zohari Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle Viruses influenza D virus cattle bovine PCR Sweden co-infection |
| title | Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle |
| title_full | Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle |
| title_fullStr | Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle |
| title_full_unstemmed | Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle |
| title_short | Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle |
| title_sort | detection and phylogenetic characterization of influenza d in swedish cattle |
| topic | influenza D virus cattle bovine PCR Sweden co-infection |
| url | https://www.mdpi.com/1999-4915/17/1/17 |
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