A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing.
Authors: Pellegrini Francesco, Buonavoglia Alessio, Omar Ahmed H, Diakoudi Georgia, Lucente Maria S, Odigie Amienwanlen E, Sposato Alessio, Augelli Raffaella, Camero Michele, Decaro Nicola, Elia Gabriella, Bányai Krisztián, Martella Vito, Lanave Gianvito
Journal: Animals : an open access journal from MDPI
Summary
# Editorial Summary: A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing Researchers in Italy used Oxford Nanopore sequencing technology to investigate the genomic origins of an H3N8 equine influenza virus isolated during a 2005 outbreak in Apulia, whose epidemiological source had remained unexplained for nearly two decades. By sequencing the complete eight-segment genome of the isolate (strain ITA/2005/horse/Bari), they demonstrated >99% nucleotide-level identity across all segments to viruses circulating in Poland between 2005–2008, providing compelling evidence that the Italian outbreak resulted from virus introduction via international horse trading for meat production. Phylogenetic analysis revealed the strain's reassortant nature: whilst the haemagglutinin (HA) and matrix (M) genes clustered with the Florida 2 sub-lineage, the remaining six segments grouped with the Eurasian lineage, indicating a complex genetic history involving multiple ancestral sources. This work exemplifies how long-read sequencing platforms can retrospectively solve disease investigations using archival samples, offering valuable epidemiological insights decades after outbreaks occur. For equine professionals involved in disease surveillance, trade regulation, and outbreak response, these findings underscore the critical importance of biosecurity protocols around international horse movements and the utility of genomic investigations in tracing virus sources to prevent future incursions.
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Practical Takeaways
- •Nanopore sequencing can be used to investigate epidemiological origins of equine influenza outbreaks even from old samples, helping trace disease sources and trading routes
- •H3N8 equine influenza in Europe may result from reassortant viruses with mixed genetic origins, important for understanding disease dynamics and prevention strategies
- •Documentation of viral genetics from past outbreaks provides critical baseline data for recognizing future strain introductions and implementing targeted biosecurity measures around horse trading
Key Findings
- •Nanopore sequencing successfully determined the complete genome of an H3N8 equine influenza virus from a 2005 archival sample from Italy
- •The virus showed >99% nucleotide identity to strains identified in Poland (2005-2008), indicating introduction via horse trading for meat industry
- •Phylogenetic analysis revealed a multi-reassortant nature with HA and M genes clustering with Florida 2 sub-lineage while other segments clustered with Eurasian lineage strains