Diversity of influenza A viruses retrieved from respiratory disease outbreaks and subclinically infected herds in Spain (2017-2019).
epidemiology
influenza A
lineages
pig
sequencing
Journal
Transboundary and emerging diseases
ISSN: 1865-1682
Titre abrégé: Transbound Emerg Dis
Pays: Germany
ID NLM: 101319538
Informations de publication
Date de publication:
Mar 2021
Mar 2021
Historique:
revised:
23
06
2020
received:
07
02
2020
accepted:
23
06
2020
pubmed:
4
7
2020
medline:
3
6
2021
entrez:
4
7
2020
Statut:
ppublish
Résumé
The present study was aimed to assess the diversity of influenza A viruses (IAV) circulating in pig farms in the Iberian Peninsula. The study included two different situations: farms suffering respiratory disease outbreaks compatible with IAV (n = 211) and randomly selected farms without overt respiratory disease (n = 19). Initially, the presence of IAV and lineage determination was assessed by qRT-PCR using nasal swabs. IAV was confirmed in 145 outbreaks (68.7%), mostly in nurseries (53/145; 36.5%). Subtyping by RT-qPCR was possible in 94 of those cases being H1avN2hu (33.6%), H1avN1av (24.3%) and H1huN2hu (18.7%), the most common lineages. H3huN2hu and H1pdmN1pdm represented 7.5% and 6.5% of the cases, respectively. As for the randomly selected farms, 15/19 (78.9%) were positive for IAV. Again, the virus was mostly found in nurseries and H1avN2hu was the predominant lineage. Virus isolation in MDCK cells was attempted from positive cases. Sixty of the isolates were fully sequenced with Illumina MiSeq®. Within those 60 isolates, the most frequent genotypes had internal genes of avian origin, and these were D (19/60; 31.7%) and A (11/60; 18.3%), H1avN2hu and H1avN1av, respectively. In addition, seven previously unreported genotypes were identified. In two samples, more than one H or N were found and it was not possible to precisely establish their genotypes. A great diversity was observed in the phylogenetic analysis. Notably, four H3 sequences clustered with human isolates from 2004-05 (Malaysia and Denmark) that were considered uncommon in pigs. Overall, this study indicates that IAV is a very common agent in respiratory disease outbreaks in Spanish pig farms. The genetic diversity of this virus is continuously expanding with clear changes in the predominant subtypes and lineages in relatively short periods of time. The current genotyping scheme has to be enlarged to include the new genotypes that could be found in the future.
Identifiants
pubmed: 32619306
doi: 10.1111/tbed.13709
pmc: PMC8246522
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
519-530Informations de copyright
© 2020 The Authors. Transboundary and Emerging Diseases published by Blackwell Verlag GmbH.
Références
J Virol. 2013 Oct;87(19):10460-76
pubmed: 23824819
Vet Microbiol. 2014 Jun 4;170(3-4):266-77
pubmed: 24685238
Transbound Emerg Dis. 2021 Jan;68(1):62-75
pubmed: 32187882
Vet Res. 2012 Mar 27;43:24
pubmed: 22452923
Vet Res. 2019 May 22;50(1):36
pubmed: 31113477
Vet Res. 2010 Sep-Oct;41(5):74
pubmed: 20663475
Influenza Other Respir Viruses. 2016 Nov;10(6):504-517
pubmed: 27397600
Vet Microbiol. 2016 Nov 15;195:25-29
pubmed: 27771067
PLoS One. 2014 Dec 26;9(12):e115815
pubmed: 25542013
Vet Res. 2017 Oct 10;48(1):63
pubmed: 29017603
J Virol. 2015 Oct;89(19):9920-31
pubmed: 26202246
Vet Microbiol. 2013 Mar 23;162(2-4):543-550
pubmed: 23201246
Vet Microbiol. 2013 Dec 27;167(3-4):345-56
pubmed: 24139631
Vet Microbiol. 2011 Apr 21;149(1-2):56-63
pubmed: 21112702
Emerg Infect Dis. 2010 Jan;16(1):96-9
pubmed: 20031049
Viral Immunol. 2006 Summer;19(3):373-82
pubmed: 16987057
Influenza Other Respir Viruses. 2017 May;11(3):298-303
pubmed: 28245096
Zoonoses Public Health. 2011 Mar;58(2):93-101
pubmed: 20042068
Vet Res. 2013 Sep 04;44:72
pubmed: 24007505
Vet Microbiol. 2009 Sep 18;138(3-4):361-7
pubmed: 19398171
Vet Microbiol. 2011 May 5;149(3-4):472-7
pubmed: 21208754
Emerg Infect Dis. 2011 Jun;17(6):1049-52
pubmed: 21749767
Transbound Emerg Dis. 2021 Mar;68(2):519-530
pubmed: 32619306
Vet Rec. 2009 Jul 18;165(3):74-7
pubmed: 19617611
Influenza Other Respir Viruses. 2019 Jan;13(1):71-82
pubmed: 30264926
Influenza Other Respir Viruses. 2008 May;2(3):99-105
pubmed: 19453469