High Prevalence of Influenza D Virus Infection in Swine, Northern Ireland

Figures

• 

  Figure 1. Molecular detection of influenza D virus (IDV) infection in swine, Northern Ireland. A) Percentage of nasal swab samples (n = 30) collected from 10- to 12-week-old growing pigs testing positive for IDV RNA by rRT-PCR. B) Plot of Ct values for IDV-positive rRT-PCR nasal swab samples per farm. Horizonal lines indicate mean Ct values. C) Locations and proximity of IDV-positive swine units. Ct, cycle threshold; rRT-PCR, real-time reverse transcription PCR.

• 

  Figure 2. Amino acid substitutions in swine-origin influenza D virus HEF protein relative to bovine-origin influenza D virus, Northern Ireland. Changes relative to the bovine-origin sequence are displayed. Amino acid numbering is according to Song et al. (6). Substitutions occurring at the receptor-binding site and esterase are highlighted with red text on a blue background. Sequence conservation at each position is indicated by logo generated at WebLogo (https://weblogo.berkeley.edu/logo.cgi) (bottom) on the basis of alignment of 169 influenza D virus sequences. HEF, hemagglutinin-esterase fusion; NI, Northern Ireland.

• 

  Figure 3. Locations of amino acid substitutions in swine-origin influenza D virus HEF protein structure, for high prevalence of influenza D virus infection in swine, Northern Ireland. A) Homology model of D/bovine/Northern_Ireland/24280/2017 hemagglutinin-esterase fusion protein generated with Swiss-Model (https://swissmodel.expasy.org) by using the structure of D/swine/Oklahoma/1334/2011 (https://doi.org/10.2210/pdb5e64/pdb) as a template. B) Close-up of receptor-binding site. C) Close-up of esterase. Homology model was annotated in ChimeraX version 1.8 (https://www.cgl.ucsf.edu/chimerax). Blue indicates receptor-binding site (F127, T171, A172, S173, W185, F229, Y231, T239, F240, V273, V275, F297) and esterase (S57, G85, N117, R326, D356, H359) residues. Pink indicates residues substituted in swine-origin isolates.