Abstract
Influenza D virus (IDV) was first described in 2011 and has been found to mainly circulate among cattle and swine populations worldwide. Nasal swab samples were collected from 100 Danish calf herds (83 dairy and 17 veal herds) from 2018–2020. Influenza D virus was detected in 12 of the herds. Samples with the lowest cycle quantification value were selected for full genome sequencing. A hemagglutinin-esterase fusion (HEF) gene sequence from a Danish IDV collected in 2015 was also included in this study. Phylogenetic analysis showed that viruses from seven of the IDV-positive herds belonged to the D/OK lineage and clustered together in the HEF tree with the IDV collected in 2015. Viruses from the four other herds belonged to the D/660 lineage, where three of the viruses clustered closely together, while the fourth virus was more phylogenetically distant in all gene segments. The high level of genetic similarity between viruses from two different herds involved in calf trading suggests that transmission occurred through the movement of calves. This study is, to our knowledge, the first to describe the characterization of IDV in calves in Denmark.
Highlights
Influenza D virus (IDV) is a segmented negative-sense single-stranded RNA virus that belongs to the family Orthomyxoviridae, which contain the species influenza A virus (IAV), B virus (IBV), and C virus (ICV)
Some IDV-positive calves were co-infected with other bovine respiratory pathogens (Supplementary Materials, Table S1)
IDV has mainly been detected in ruminants, with cattle being considered the primary reservoir
Summary
Influenza D virus (IDV) is a segmented negative-sense single-stranded RNA virus that belongs to the family Orthomyxoviridae, which contain the species influenza A virus (IAV), B virus (IBV), and C virus (ICV). IDV is genetically most closely related to ICV, but they share only around 50% amino acid identity for HEF and 70% for polymerase basic protein 1 (PB1), which is the most conserved segment. IDV was isolated for the first time in 2011 from pigs exhibiting an influenza-like illness in Oklahoma in the USA [2]. Horses, sheep, goats, camelids, and feral swine have been found to be IDV-seropositive, which suggests a broad host-range of the virus [5,6,7,8]. Despite the broad host-range, it is believed that bovines are the natural reservoir of IDVs, due to the frequent isolation of these viruses from cattle and the finding of high seroprevalences in bovine herds [5,9]. The first European report of IDV in cattle was in 2012 in France [14]
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