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.

PMID35062251 DOI10.3390/v14010047 Year2021 Journal Viruses Languageeng Statusepublish

Abstract

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.

Supporting text Virus Host Location

antigenic characterization 2 genetic characterization 5 influenza A virus 227 subtyping 1 swine 267 Data Analysis 1 Genetic Variation 127 Animals 1948 Antigenic Variation 14 Evolution, Molecular 176 Farms 30 Genotype 137 Hemagglutinin Glycoproteins, Influenza Virus 180 Humans 1440 Influenza A virus 186 Influenza A Virus, H1N1 Subtype 74 Influenza A Virus, H1N2 Subtype 4 Influenza A Virus, H3N2 Subtype 48 Italy 20 Orthomyxoviridae Infections 228 Swine 258 Swine Diseases 153

Evidence records

5 total

Zoonotic Surveillance

1 records · 1 evidence types

Evidence type Viral Detection

1 records

OVE5562 Viral Detection

Key finding

Influenza A viruses were detected in pigs from farms in Northern Italy between 2017 and 2020 using RT-PCR during passive surveillance.

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
Sample type: samples from pig farms
Geographic raw: Northern Italy
Country inferred: ITA

Functional Mechanism

1 records · 1 evidence types

Evidence type Molecular Adaptation

1 records

OVE5565 Molecular Adaptation

Key finding

Amino acid deletions in the HA-1C receptor binding site of swine influenza A viruses were associated with antigenic drift, indicating adaptive molecular changes affecting receptor binding and antigenicity.

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: HA | HA-1C
Mutations: amino acid deletions in receptor binding site
Mechanism types: receptor binding | immune escape

Genomic Evolution

3 records · 2 evidence types

Evidence type Recombination or Reassortment

1 records

OVE5566 Recombination or Reassortment

Key finding

The Italian HA-1B.1.2.2 swine influenza lineage carried a 1990s human-derived NA gene, indicating reassortment between swine and human influenza lineages.

Virus

Host

Location

Supporting text

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.

Event type: reassortment
Genes or segments: NA gene

Evidence type Phylogenetic Evolution

2 records

OVE5564 Phylogenetic Evolution

Key finding

H1Nx swine influenza A viruses were classified into HA-1A, HA-1B, and HA-1C hemagglutinin lineages, with diversification of HA-1C into multiple sublineages.

Virus

Host

Location

Supporting text

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.

Genes or proteins: hemagglutinin
Analysis methods: phylogenetic lineage analysis | sequence analysis

OVE5563 Phylogenetic Evolution

Key finding

H1N1 and H1N2 swine influenza A virus strains showed high genotypic diversity, whereas H3N2 strains showed a stable genetic pattern.

Virus

Host

Location

Supporting text

High genotypic diversity was detected among the H1N1 and H1N2 strains, while the H3N2 strains showed a stable genetic pattern.

Analysis methods: genotypic analysis | full genome sequencing

References

37 references

Reference network

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38 nodes · 37 links

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Evidence overview

Evidence 5

Categories 3

Types 4

Virus 6

Host 1

Country 1

Host context

Natural host 3

Evidence categories

Linked entities

Viruses

Hosts

pig Sus scrofa

Locations

Publication metadata

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