Influenza D Virus in Cattle, Ireland

Flynn, Orla; Gallagher, Clare; Mooney, Jean; Irvine, Claire; Ducatez, Mariette; Hause, Ben M.; McGrath, Guy; Ryan, Eoin

doi:10.3201/eid2402.170759

Cited by 71 publications

(70 citation statements)

References 9 publications

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“…To our knowledge, this is the first report of identification of IDV in western Canada. IDV was initially identified in swine in the United States, and then was found to be prevalent in cattle of the United States, Luxembourg, Ireland, France, Japan and China (Flynn et al, ; Mekata et al, ; Snoeck et al, ; Su, Fu, Li, Kerlin, & Veit, ). IDV may be an emerging pathogen in Canadian cattle; or, on the other hand, the lack of Canadian reports before may be due to the unavailability of a diagnostic assay.…”

Section: Discussionmentioning

confidence: 99%

Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease

Zhang

Hill

Fernando

et al. 2019

Transbound Emerg Dis

116

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Bovine respiratory disease (BRD) causes considerable economic losses in North America. The pathogenesis involves interactions between bacteria, viruses, environment and management factors. Primary viral infection can increase the risk of secondary fatal bacterial infection. The objective of this study was to use metagenomic sequencing to characterize the respiratory viromes of paired nasal swabs and tracheal washes from western Canadian feedlot cattle, with or without BRD. A total of 116 cattle (116 nasal swabs and 116 tracheal washes) were analysed. The presence of influenza D virus (IDV), bovine rhinitis A virus (BRAV), bovine rhinitis B virus (BRBV), bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) was associated with BRD. Agreement between identification of viruses in nasal swabs and tracheal washes was generally weak, indicating that sampling location may affect detection of infection. This study reported several viruses for the first time in Canada and provides a basis for further studies investigating candidate viruses important to the prevention of BRD.

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Section: Discussionmentioning

confidence: 99%

Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease

Zhang

Hill

Fernando

et al. 2019

Transbound Emerg Dis

116

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“…It is however unclear why/how BCoV, BRSV, or BVDV would spread differently than other bovine RNA viruses. Influenza D viruses (IDV), which primarily infects bovine hosts, seem for example to have emerged recently but genetically and anti-genetically similar viruses circulate in Europe and North America [29,[83][84][85][86]. One may therefore hypothesize that different routes of transmission may be used for the different pathogens.…”

Section: Little Exchanges Of Bcov Between Europe and The Other Continmentioning

confidence: 99%

Global Transmission, Spatial Segregation, and Recombination Determine the Long-Term Evolution and Epidemiology of Bovine Coronaviruses

Salem

Vijaykrishna

Cassard

et al. 2020

Viruses

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Bovine coronavirus (BCoV) is widespread in cattle and wild ruminant populations throughout the world. The virus causes neonatal calf diarrhea and winter dysentery in adult cattle, as well as upper and lower respiratory tract infection in young cattle. We isolated and deep sequenced whole genomes of BCoV from calves with respiratory distress in the south-west of France and conducted a comparative genome analysis using globally collected BCoV sequences to provide insights into the genomic characteristics, evolutionary origins, and global diversity of BCoV. Molecular clock analyses allowed us to estimate that the BCoV ancestor emerged in the 1940s, and that two geographically distinct lineages diverged from the 1960s-1970s. A recombination event in the spike gene (breakpoint at nt 1100) may be at the origin of the genetic divergence sixty years ago. Little evidence of genetic mixing between the spatially segregated lineages was found, suggesting that BCoV genetic diversity is a result of a global transmission pathway that occurred during the last century. However, we found variation in evolution rates between the European and non-European lineages indicating differences in virus ecology.Viruses 2020, 12, 534 2 of 16 epithelium damage, [7] and altering commensal microbiota and local biofilm [8][9][10], thus leading to complex secondary bacterial infections [8,10,11].BCoV is a pneumoenteric virus frequently isolated from the fecal samples of diarrheic calves [12-15] and from upper and lower respiratory tract samples during BRD episodes worldwide [16][17][18][19]. While both forms of BCoV infection are widespread with high prevalence among cattle [12,13,15,20,21] and wild ruminants [22], the putative differences between strains isolated from enteric and respiratory tracts are still not clear, and it is unknown whether these differences are related to tissue tropism or simply to distinct times and locations of isolation. Some reports indeed suggest that all the BCoV are similar at genomic and antigenic levels [18,23], while others suggest that enteric and respiratory strains are genetically and antigenically different [24,25]. Zhang et al. highlighted molecular differences within a single host, with intra-host quasispecies and enteric strains more prone to genetic changes than their respiratory counterparts [26]. The global genetic and antigenic diversity of BCoV is also poorly understood. Using a short variable region of the BCoV genome and with sporadically collected samples from a few countries in Europe, Asia, and North America, it has been suggested that BCoV are segregated into European and American BCoV lineages [17,[27][28][29], with periodic introductions of North American BCoV observed in Asian countries (for example in Japan during the 1990s [30]) highlighting global movement of BCoV likely through cattle trade. Coronaviruses are enveloped particles with a large non-segmented, linear, polyadenylated, single-stranded positive sense RNA genome [31]. They belong to the family Coronaviridae in the order Nidoviral...

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“…IDV is an emerging pathogen and it has been found to be associated with BRD in metagenomic studies [6][7][8] but its pathogenic role is unclear. Cattle experimentally infected by IDV by itself showed mild to moderate respiratory disease [4,9] and IDV-positive samples are reported from both cattle manifesting clinical signs associated with BRD and from healthy animals [10,11].…”

Section: Introductionmentioning

confidence: 99%

“…In Europe, IDV viruses have been detected and sequenced in France, Italy [14][15][16], Republic of Ireland and Northern Ireland (UK) [14][15][16]. D/OK is the most reported lineage circulating in Europe, even though two strains clustering separately have been reported in France and Ireland (D/bovine/France/2986/2012 and D/bovine/Ireland/07780/2014) [10,17]. In particular, since 2014, we have detected in Italy the circulation of a single genetic group within the D/OK lineage in swine and cattle population [15,16].…”

Section: Introductionmentioning

confidence: 99%

Detection of a New Genetic Cluster of Influenza D Virus in Italian Cattle

Chiapponi

Faccini

Fusaro

et al. 2019

Viruses

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Influenza D virus (IDV) has been increasingly reported all over the world. Cattle are considered the major viral reservoir. Based on the hemagglutinin-esterase (HEF) gene, three main genetic and antigenic clusters have been identified: D/OK distributed worldwide, D/660 detected only in the USA and D/Japan in Japan. Up to 2017, all the Italian IDV isolates belonged to the D/OK genetic cluster. From January 2018 to May 2019, we performed virological surveillance for IDV from respiratory outbreaks in 725 bovine farms in Northern Italy by RT-PCR. Seventy-four farms were positive for IDV. A full or partial genome sequence was obtained from 29 samples. Unexpectedly, a phylogenetic analysis of the HEF gene showed the presence of 12 strains belonging to the D/660 cluster, previously unreported in Europe. The earliest D/660 strain was collected in March 2018 from cattle imported from France. Moreover, we detected one viral strain with a reassortant genetic pattern (PB2, PB1, P42, HEF and NP segments in the D/660 cluster, whilst P3 and NS segments in the D/OK cluster). These results confirm the circulation of IDV in the Italian cattle population and highlight the need to monitor the development of the spreading of this influenza virus in order to get more information about the epidemiology and the ecology of IDV viruses.

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Influenza D Virus in Cattle, Ireland

Cited by 71 publications

References 9 publications

Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease

Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease

Global Transmission, Spatial Segregation, and Recombination Determine the Long-Term Evolution and Epidemiology of Bovine Coronaviruses

Detection of a New Genetic Cluster of Influenza D Virus in Italian Cattle

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