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Article

Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses

1
National Veterinary Institute, Technical University of Denmark, Kemitorvet Building 204, DK-2800 Kongens Lyngby, Denmark
2
Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark
3
Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kemitorvet Building 208, DK-2800 Kongens Lyngby, Denmark
4
SEGES, Danish Pig Research Centre, Agro Food Park 15, DK-8200 Aarhus, Denmark
5
Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
6
Ceva Santé Animale 10 Avenue de la Ballastière, 33500 Libourne, France
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(2), 248; https://doi.org/10.3390/v12020248
Received: 28 January 2020 / Revised: 18 February 2020 / Accepted: 20 February 2020 / Published: 23 February 2020
(This article belongs to the Section Animal Viruses)
The degree of antigenic drift in swine influenza A viruses (swIAV) has historically been regarded as minimal compared to that of human influenza A virus strains. However, as surveillance activities on swIAV have increased, more isolates have been characterized, revealing a high level of genetic and antigenic differences even within the same swIAV lineage. The objective of this study was to investigate the level of genetic drift in one enzootically infected swine herd over one year. Nasal swabs were collected monthly from sows (n = 4) and piglets (n = 40) in the farrowing unit, and from weaners (n = 20) in the nursery. Virus from 1–4 animals were sequenced per month. Analyses of the sequences revealed that the hemagglutinin (HA) gene was the main target for genetic drift with a substitution rate of 7.6 × 10−3 substitutions/site/year and evidence of positive selection. The majority of the mutations occurred in the globular head of the HA protein and in antigenic sites. The phylogenetic tree of the HA sequences displayed a pectinate typology, where only a single lineage persists and forms the ancestor for subsequent lineages. This was most likely caused by repeated selection of a single immune-escape variant, which subsequently became the founder of the next wave of infections. View Full-Text
Keywords: swine influenza A virus; genetic drift; antigenic drift; molecular clock; immune escape variants; selection; enzootic infections; substitution rate; hemagglutinin; sows swine influenza A virus; genetic drift; antigenic drift; molecular clock; immune escape variants; selection; enzootic infections; substitution rate; hemagglutinin; sows
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MDPI and ACS Style

Ryt-Hansen, P.; Pedersen, A.G.; Larsen, I.; Kristensen, C.S.; Krog, J.S.; Wacheck, S.; Larsen, L.E. Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses. Viruses 2020, 12, 248. https://doi.org/10.3390/v12020248

AMA Style

Ryt-Hansen P, Pedersen AG, Larsen I, Kristensen CS, Krog JS, Wacheck S, Larsen LE. Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses. Viruses. 2020; 12(2):248. https://doi.org/10.3390/v12020248

Chicago/Turabian Style

Ryt-Hansen, Pia, Anders G. Pedersen, Inge Larsen, Charlotte S. Kristensen, Jesper S. Krog, Silke Wacheck, and Lars E. Larsen 2020. "Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses" Viruses 12, no. 2: 248. https://doi.org/10.3390/v12020248

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