Genetic analysis of human and swine influenza A viruses isolated in Northern Italy during 2010–2015

Chiapponi, Chiara; Ebranati, Erika; Pariani, Elena; Faccini, S.; Luppi, Andrea; Baioni, Laura; Manfredi, Roberta; Carta, Valentina; Merenda, M.; Affanni, Paola; Colucci, Maria Eugenia; Veronesi, Licia; Zehender, G.; Foni, Emanuela

doi:10.1111/zph.12378

Cited by 13 publications

(17 citation statements)

References 43 publications

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“…Full-length genomes of 18 isolates revealed the presence of previously reported genotypes 21 , 22 , 43 , with all except one virus containing the M gene from the H1pdm09 lineage. swIAV circulating in European pigs continue to exchange genes amongst each other resulting in second generation reassortants with different genotypes from their precursors.…”

Section: Discussionmentioning

confidence: 87%

Genetic and antigenic evolution of H1 swine influenza A viruses isolated in Belgium and the Netherlands from 2014 through 2019

Chepkwony

Parys

Vandoorn

et al. 2021

Sci Rep

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Surveillance of swine influenza A viruses (swIAV) allows timely detection and identification of new variants with potential zoonotic risks. In this study, we aimed to identify swIAV subtypes that circulated in pigs in Belgium and the Netherlands between 2014 and 2019, and characterize their genetic and antigenic evolution. We subtyped all isolates and analyzed hemagglutinin sequences and hemagglutination inhibition assay data for H1 swIAV, which were the dominant HA subtype. We also analyzed whole genome sequences (WGS) of selected isolates. Out of 200 samples, 89 tested positive for swIAV. swIAV of H1N1, H1N2 and H3N2 subtypes were detected. Analysis of WGS of 18 H1 swIAV isolates revealed three newly emerged genotypes. The European avian-like H1 swIAV (lineage 1C) were predominant and accounted for 47.2% of the total isolates. They were shown to evolve faster than the European human-like H1 (1B lineage) swIAV, which represented 27% of the isolates. The 2009 pandemic H1 swIAV (lineage 1A) accounted for only 5.6% of the isolates and showed divergence from their precursor virus. These results point to the increasing divergence of swIAV and stress the need for continuous surveillance of swIAV.

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Section: Discussionmentioning

confidence: 87%

Genetic and antigenic evolution of H1 swine influenza A viruses isolated in Belgium and the Netherlands from 2014 through 2019

Chepkwony

Parys

Vandoorn

et al. 2021

Sci Rep

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“…In contrast to other European countries in which swIAV diversity has been strongly impacted by the transmission of the H1N1 pandemic virus to pigs in 2009, the genotype diversity of French swIAVs has not changed greatly due to this new introduction between 2009 and 2018 [13,[15][16][17][18][19]. The H1 av and H1 hu viruses were widely established for years in northwestern France and might have hampered the H1N1pdm spread in French herds located in this high pig density area [22,25].…”

Section: Discussionmentioning

confidence: 93%

“…In Denmark, the H1N1pdm and the local H1 av N2 viruses were also more frequently detected than the H1 av N1 virus in recent years [13,15]. In Germany and Italy, the frequency of reassortant viruses harboring at least one H1N1pdm segment has increased continuously from 2009 [16][17][18][19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

Chastagner

Hervé

Quéguiner

et al. 2020

Viruses

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This study evaluated the genetic and antigenic evolution of swine influenza A viruses (swIAV) of the two main enzootic H1 lineages, i.e., HA-1C (H1av) and -1B (H1hu), circulating in France between 2000 and 2018. SwIAV RNAs extracted from 1220 swine nasal swabs were hemagglutinin/neuraminidase (HA/NA) subtyped by RT-qPCRs, and 293 virus isolates were sequenced. In addition, 146 H1avNy and 105 H1huNy strains were submitted to hemagglutination inhibition tests. H1avN1 (66.5%) and H1huN2 (25.4%) subtypes were predominant. Most H1 strains belonged to HA-1C.2.1 or -1B.1.2.3 clades, but HA-1C.2, -1C.2.2, -1C.2.3, -1B.1.1, and -1B.1.2.1 clades were also detected sporadically. Within HA-1B.1.2.3 clade, a group of strains named “Δ146-147” harbored several amino acid mutations and a double deletion in HA, that led to a marked antigenic drift. Phylogenetic analyses revealed that internal segments belonged mainly to the “Eurasian avian-like lineage”, with two distinct genogroups for the M segment. In total, 17 distinct genotypes were identified within the study period. Reassortments of H1av/H1hu strains with H1N1pdm virus were rarely evidenced until 2018. Analysis of amino acid sequences predicted a variability in length of PB1-F2 and PA-X proteins and identified the appearance of several mutations in PB1, PB1-F2, PA, NP and NS1 proteins that could be linked to virulence, while markers for antiviral resistance were identified in N1 and N2. Altogether, diversity and evolution of swIAV recall the importance of disrupting the spreading of swIAV within and between pig herds, as well as IAV inter-species transmissions.

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“…Euroasian avian-like swine H1N1 viruses are the predominant viruses in the pig population in Europe, but an increasing number of reassortments between the predominant enzootic swIAVs and the H1N1pdm have been observed [33][34][35][36][37]. The enzootic H1avN1av lineage is present in most European countries and usually circulates together with reassortant strains.…”

Section: Discussionmentioning

confidence: 99%

Improving Current Knowledge on Seroprevalence and Genetic Characterization of Swine Influenza Virus in Croatian Pig Farms: A Retrospective Study

et al. 2021

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In a total of 1536 blood serum samples analysed by ELISA, antibodies for IAV nucleoprotein (NP) were detected in 30.3%. Results from HI show that the most common subtype of swIAV in the Croatian pig population was H1N1 (44.6%), followed by H3N2 (42.7%) and H1N2 (26.3%). Antibodies to at least one subtype were detected in 62.19% of blood serum samples. Detection of swIAV antigen was performed by IHC and detected in 8 of 28 lung samples collected post-mortem. The matrix (M) gene was detected in nine of one hundred and forty-two lung tissue samples and in seven of twenty-nine nasopharyngeal swabs. Phylogenetic analysis of amplified HA and NA gene fragments in Croatian isolates suggests the presence of swIAV H1avN1av.

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Genetic analysis of human and swine influenza A viruses isolated in Northern Italy during 2010–2015

Abstract: Summary K E Y W O R D Shuman, influenza A virus, swine

Cited by 13 publications

References 43 publications

Genetic and antigenic evolution of H1 swine influenza A viruses isolated in Belgium and the Netherlands from 2014 through 2019

Genetic and antigenic evolution of H1 swine influenza A viruses isolated in Belgium and the Netherlands from 2014 through 2019

Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

Improving Current Knowledge on Seroprevalence and Genetic Characterization of Swine Influenza Virus in Croatian Pig Farms: A Retrospective Study

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