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.

Amélie Chastagner,Edouard Hirchaud,Stéphane Quéguiner,Céline Deblanc,Séverine Hervé,Gaëlle Simon,Véronique Béven,Pierrick Lucas,Stéphane Gorin,Nicolas Barbier,Yannick Blanchard

doi:10.3390/v12111304

Amélie Chastagner, Edouard Hirchaud + Show 9 more

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https://doi.org/10.3390/v12111304

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Abstract

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.

Highlights

Influenza A viruses (IAVs) are members of the Orthomyxoviridae family and are composed of eight negative single-stranded RNA segments
M gene sequences obtained in this study formed a distinct cluster from M genes of avian IAV lineages as previously described [36], we focused the large-scale analysis on all sequences of M segments from swine influenza A viruses (swIAV) isolated in the Northern hemisphere, and human IAV isolated in Europe when associated with a known HA/NA subtype
The genetic evolution of swIAVs in France in the last two decades is characterized by geographical divergence in H1av Ny viruses and apparition of H1hu ∆146-147 strains, which entailed the adaptation of RT-PCR primers for HA subtyping

Summary

Introduction

Influenza A viruses (IAVs) are members of the Orthomyxoviridae family and are composed of eight negative single-stranded RNA segments. Inter-species transmissions play an important role in IAV evolution. They provide new sources of diversity, either following adaptation to a Viruses 2020, 12, 1304; doi:10.3390/v12111304 www.mdpi.com/journal/viruses. Amino acid mutations or segment exchanges can alter the virulence and pathogenicity, the antiviral resistance, escape to host immunity or vaccine protection, or further help to jump host [3]. When they occur in, or concern, the surface glycoproteins, i.e., the hemagglutinin (HA) and/or neuraminidase (NA) encoding genes, genetic modifications and reassortments can result in antigenic drift and shift, respectively [4]. Many new variants or reassortant viruses may be only sporadically detected, but some of them may expend in naïve immune populations

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