Literature detail

Genetic Variability among Swine Influenza Viruses in Italy: Data Analysis of the Period 2017-2020.

Chiara Chiapponi^1,2 Alice Prosperi¹ Ana Moreno¹ Laura Baioni¹ Silvia Faccini¹ Roberta Manfredi¹ Irene Zanni¹ Valentina Gabbi¹ Irene Calanchi¹ Alice Fusaro³ Maria Serena Beato³ Lara Cavicchio³ Camilla Torreggiani¹ Giovanni Loris Alborali¹ Andrea Luppi¹

Affiliations 3 institutions

OIE Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), 25124 Brescia, Italy.
Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, 43124 Parma, Italy.
Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy.

PMID 35062251 2021 Viruses eng epublish

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Article

Publication summary

Swine play an important role in the ecology of influenza A viruses (IAVs), acting as mixing vessels. Swine (sw) IAVs of H1N1 (including H1N1pdm09), H3N2, and H1N2 subtypes are enzootic in pigs globally, with different geographic distributions. This study investigated the genetic diversity of swIAVs detected during passive surveillance of pig farms in Northern Italy between 2017 and 2020. A total of 672 samples, IAV-positive according to RT-PCR, were subtyped by multiplex RT-PCR. A selection of strains was fully sequenced. High genotypic diversity was detected among the H1N1 and H1N2 strains, while the H3N2 strains showed a stable genetic pattern. The hemagglutinin of the H1Nx swIAVs belonged to HA-1A, HA-1B, and HA-1C lineages. Increasing variability was found in HA-1C strains with the circulation of HA-1C.2, HA-1C.2.1 and HA-1C.2.2 sublineages. Amino acid deletions in the HA-1C receptor binding site were observed and antigenic drift was confirmed. HA-1B strains were mostly represented by the Δ146-147 Italian lineage HA-1B.1.2.2, in combination with the 1990s human-derived NA gene. One antigenic variant cluster in HA-1A strains was identified in 2020. SwIAV circulation in pigs must be monitored continuously since the IAVs' evolution could generate strains with zoonotic potential.

antigenic characterization genetic characterization influenza A virus subtyping swine Data Analysis Genetic Variation Animals Antigenic Variation Evolution, Molecular Farms Genotype Hemagglutinin Glycoproteins, Influenza Virus Humans Influenza A virus Influenza A Virus, H1N1 Subtype Influenza A Virus, H1N2 Subtype Influenza A Virus, H3N2 Subtype

Structured evidence records

Evidence records

5 total

Genomic Evolution 2 records

Genomic Evolution Extraction confidence 0.90

Key finding

Whole-genome sequencing and lineage analysis of swine influenza A viruses revealed high genotypic diversity and distinct hemagglutinin lineage patterns in H1N1 and H1N2 viruses from pigs in Italy.

Virus

Host

Location

Supporting text

A selection of strains was fully sequenced. High genotypic diversity was detected among the H1N1 and H1N2 strains, while the H3N2 strains showed a stable genetic pattern. The hemagglutinin of the H1Nx swIAVs belonged to HA-1A, HA-1B, and HA-1C lineages.

Genes or proteins: hemagglutinin; neuraminidase
Analysis methods: whole genome sequencing; lineage analysis

Genomic Evolution Extraction confidence 0.90

Key finding

HA-1C hemagglutinin sublineages of swine influenza A viruses showed amino acid deletions in the receptor binding site, indicating ongoing molecular evolution and antigenic drift.

Virus

Host

Location

Supporting text

Increasing variability was found in HA-1C strains with the circulation of HA-1C.2, HA-1C.2.1 and HA-1C.2.2 sublineages. Amino acid deletions in the HA-1C receptor binding site were observed and antigenic drift was confirmed.

Genes or proteins: hemagglutinin
Analysis methods: sequence analysis; phylogenetic sublineage characterization

Molecular Adaptation 1 records

Molecular Adaptation Extraction confidence 0.80

Key finding

HA-1C swine influenza viruses showed amino acid deletions in the hemagglutinin receptor binding site, confirming antigenic drift as a mechanism of molecular adaptation.

Virus

Host

Location

Supporting text

Amino acid deletions in the HA-1C receptor binding site were observed and antigenic drift was confirmed.

Genes or proteins: hemagglutinin
Mechanism types: receptor_binding; immune_escape

Receptor Usage 1 records

Receptor Usage Extraction confidence 0.70

Key finding

HA-1C lineage swine influenza A viruses showed amino acid deletions in the receptor binding site of hemagglutinin, suggesting modification of receptor-binding properties.

Virus

Host

Location

Supporting text

Amino acid deletions in the HA-1C receptor binding site were observed and antigenic drift was confirmed.

Method: genetic sequencing
Receptors: hemagglutinin receptor binding site

Zoonotic Surveillance 1 records

Zoonotic Surveillance Extraction confidence 0.95

Key finding

Passive surveillance of pigs in Northern Italy revealed diverse swine influenza A virus subtypes (H1N1, H3N2, H1N2), indicating ongoing viral evolution with potential zoonotic significance.

Virus

Host

Location

Supporting text

This study investigated the genetic diversity of swIAVs detected during passive surveillance of pig farms in Northern Italy between 2017 and 2020. A total of 672 samples, IAV-positive according to RT-PCR, were subtyped by multiplex RT-PCR.

Method: RT-PCR; multiplex RT-PCR; genomic sequencing
Geographic raw: Northern Italy
Country inferred: Italy

Citation context

References

37 references

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Evidence overview

Evidence 5

Types 4

Virus 2

Host 1

Evidence types

Genomic Evolution 2 Molecular Adaptation 1 Receptor Usage 1 Zoonotic Surveillance 1

Linked entities

Viruses

Hosts

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Publication metadata

Journal: Viruses
Volume / Issue / Pages: 14 / 1 / -
ISSN: 1999-4915
Journal country: Switzerland
DOI: 10.3390/v14010047