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. 2022 Feb 18;14(2):423.
doi: 10.3390/v14020423.

Characterization of Influenza D Virus in Danish Calves

Nicole B Goecke  1 , Yuan Liang  1 , Nina D Otten  1 , Charlotte K Hjulsager  2 , Lars E Larsen  1
Affiliations

Characterization of Influenza D Virus in Danish Calves

Nicole B Goecke et al. Viruses. .

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.

Keywords: Denmark; PCR; bovine; calves; influenza D virus; phylogeny; sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The maximum-likelihood phylogenetic tree of the IDV HEF gene. The highlighted areas denote which lineage the viruses belong to. The sequence of the virus detected in Denmark in 2015 is shown in green text, depicted in red are the IDV viruses found in 2019, and those from 2020 are in blue. All bootstrap values < 70% have been removed. The scale bar indicates nucleotide substitutions per site per year.
Figure 2
Figure 2
The maximum-likelihood phylogenetic trees of the IDV PB2, PB1, P3, NP, P42, and NS genes. The sequences of IDVs detected in Denmark in 2019 are depicted in red, and depicted in blue are sequences from viruses found in 2020. All bootstrap values < 70% have been removed. The scale bar indicates nucleotide substitutions per site per year.
See this image and copyright information in PMC

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