Influenza D virus in respiratory disease in Canadian, province of Québec, cattle: Relative importance and evidence of new reassortment between different clades

Abstract

Background: Influenza D virus (IDV), a segmented single stranded negative sense ribonucleic acid (RNA) virus belongs to the new Delta influenza virus genus of the Orthomyxoviridae family.Cattle was proposed as the natural reservoir of IDV in which infection was associated with mild to moderate respiratory clinical signs (i.e. cough, nasal discharge, and dyspnoea). Methods and principal findings: In order to investigate the role of IDV in bovine respiratory disease, during the period 2017-2020, 883 nasal or naso-pharyngeal swabs from Canadian cattle with respiratory signs (cough and/or dyspnoea) were tested by (RT-)qPCR for IDV and other major bovine viral (bovine herpesvirus 1, bovine viral diarrhoea virus, bovine respiratory syncytial virus, bovine parainfluenza virus 3, and bovine coronavirus) and bacterial (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis) respiratory pathogens. In addition, whole genome sequencing and phylogenetic analyses were carried out on five IDV positive samples. The prevalence of IDV RT-qPCR (with cut-off: Cq < 38) at animal level was estimated at 5.32% (95% confidence interval: 3.94-7.02). Positive result of IDV was significantly associated with (RT-)qPCR positive results for bovine respiratory syncytial virus and Mycoplasma bovis. While phylogenetic analyses indicate that most segments belonged to clade D/660, reassortment between clades D/660 and D/OK were evidenced in four samples collected in 2018-2020. Conclusions and significance: Relative importance of influenza D virus and associated pathogens in bovine respiratory disease of Canadian dairy cattle was established. Whole genome sequencing demonstrated evidence of reassortment between clades D/660 and D/OK. Both these new pieces of information claim for more surveillance of IDV in cattle production worldwide.

The Prevalence, Coexistence, and Correlations between Seven Pathogens Detected by a PCR Method from South-Western Poland Dairy Cattle Suffering from Bovine Respiratory Disease

“…The prevalence of P. multocida varies widely ranging from a few percent to over eighty [ 5 , 8 , 14 , 15 , 16 , 17 , 19 , 20 , 28 , 32 , 35 , 36 , 37 , 38 ]. Similar to our results, Paller et al noted that the highest prevalence occurred for P. multocida (58.64%) [ 32 ].…”

“…Pathogens noted in the course of BRD include: Pasteurella multocida ( P. multocida ), Mannheimia haemolytica ( M. haemolytica ), Mycoplasma bovis ( M. bovis ), Histophilus somni (H. somni), bovine parainfluenza virus type 3 (BPIV-3), bovine respiratory syncytial virus (BRSV), bovine coronavirus (BcoV), bovine viral diarrhea virus (BVDV), bovine herpes virus type 1 (BHV-1), bovine adenovirus (BadV), and influenza D virus (IDV). Stress or viral infections create a basis for opportunistic bacteria to multiply, which contributes to clinical symptoms [ 2 , 5 , 7 , 8 , 9 , 10 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ].…”

Enhanced Pathogenesis Caused by Influenza D Virus and Mycoplasma bovis Coinfection in Calves: a Disease Severity Linked with Overexpression of IFN-γ as a Key Player of the Enhanced Innate Immune Response in Lungs

“…We recently identified frequent codetection of IDV and M. bovis in cattle with clinical respiratory signs on French veal farms (M. Gaudino, M.F. Ducattez, G. Meyer, personal communication) and Canadian dairy farms ( 23 ). Our field surveillance indicates that both IDV and M. bovis infections occurred at the same time, just after calves’ allocation, suggesting that M. bovis and IDV may act together as primary disease pathogens (Gaudino et al, personal communication).…”

Pathophysiology of Influenza D Virus Infection in Specific-Pathogen-Free Lambs with or without Prior Mycoplasma ovipneumoniae Exposure

“…We posit that on their own, both M. ovipneumoniae and IDV are minimally immunostimulatory in sheep, but that M. ovipneumoniae infection may prime the lamb immune system to respond more robustly to secondary infection by IDV. In the context of two subclinical infections, this may not lead to overt respiratory symptoms, but virulence varies widely between M. ovipneumoniae strains [ 66 , 81 , 86 ], and IDV is not genetically stable [ 74 , 87 ], it readily reassorts [ 88 ], and its tissue tropism and host range can vary by strain [ 74 , 89 ]. Changes in any of these parameters could dramatically alter outcomes to coinfection of both of these pathogens in sheep.…”