Genome sequences of equine influenza A subtype H3N8 viruses by long read sequencing and functional characterization of the PB1-F2 virulence factor of A/equine/Paris/1/2018

Lena Kleij (1) , Elise Bruder (1) , Dorothée Raoux-Barbot (2) , Nathalie Lejal (1) , Quentin Nevers (1) , Charlotte Deloizy (1) , Bruno Da Costa (1) , Loïc Legrand (3, 4) , Eric Barrey (5) , Alexandre Chenal (1) , Stéphane Pronost (3, 6, 4) , Bernard Delmas (1) , Sophie Dhorne-Pollet (5)

1 VIM (UR 0892) - Virologie et Immunologie Moléculaires
2 UPCité - Université Paris Cité
3 BIOTARGEN - Biologie, génétique et thérapies ostéoarticulaires et respiratoires
4 LABÉO - LABÉO, Pôle d’analyses et de recherche de Normandie
5 AgroParisTech
6 ImpedanCELL

Abstract Equine influenza virus (EIV) remains a persistent threat to equines, despite the availability of vaccines. Currently, strategies to monitor the virus and prevent any potential vaccine failure revolve around serological assays, RT‒qPCR amplification, and sequencing the viral hemagglutinin (HA) and neuraminidase (NA) genes. These approaches overlook the contribution of other viral proteins in driving virulence. This study assesses the potential of long-read nanopore sequencing for swift and precise sequencing of circulating equine influenza viruses. To this end, two French Florida Clade 1 strains, including the one circulating in winter 2018-2019 exhibiting more pronounced pathogenicity than usual, as well as the two currently used OIE-recommended vaccine strains, were sequenced. Our results demonstrated the reliability of this sequencing method in generating accurate sequences. Sequence analysis of HA revealed a subtle antigenic drift in the French EIV strains, with specific substitutions, such as T163I in A/equine/Paris/1/2018 and the N188T mutation in post-2015 strains; both substitutions were located in antigenic site B. Antigenic site E exhibited modifications in post-2018 strains, with the N63D substitution. Segment 2 sequencing also revealed that the A/equine/Paris/1/2018 strain encodes a longer variant of the PB1-F2 protein when compared to other Florida clade 1 strains (90 amino acids long versus 81 amino acids long). Further biological and biochemistry assays demonstrated that this PB1-F2 variant has enhanced abilities to abolish the mitochondrial membrane potential ΔΨm and permeabilize synthetic membranes. Altogether, our results highlight the interest in rapidly characterizing the complete genome of circulating strains with next-generation sequencing technologies to adapt vaccines and identify specific virulence markers of EIV.

Mots clés: serous nasal discharge dyspnea muscle; serous nasal discharge; dyspnea; muscle

Domaines: Santé

Lena Kleij, Elise Bruder, Dorothée Raoux-Barbot, Nathalie Lejal, Quentin Nevers, et al.. Genome sequences of equine influenza A subtype H3N8 viruses by long read sequencing and functional characterization of the PB1-F2 virulence factor of A/equine/Paris/1/2018. 2024. ⟨hal-04494595⟩