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Home / Equine Research Bank / Animals (Basel) / A Cold Case of Equine Influenza Disentangled with Nanopore S...
Animals : an open access journal from MDPI2023; 13(7); 1153; doi: 10.3390/ani13071153

A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing.

Abstract: Massive sequencing techniques have allowed us to develop straightforward approaches for the whole genome sequencing of viruses, including influenza viruses, generating information that is useful for improving the levels and dimensions of data analysis, even for archival samples. Using the Nanopore platform, we determined the whole genome sequence of an H3N8 equine influenza virus, identified from a 2005 outbreak in Apulia, Italy, whose origin had remained epidemiologically unexplained. The virus was tightly related (>99% at the nucleotide level) in all the genome segments to viruses identified in Poland in 2005-2008 and it was seemingly introduced locally with horse trading for the meat industry. In the phylogenetic analysis based on the eight genome segments, strain ITA/2005/horse/Bari was found to cluster with sub-lineage Florida 2 in the HA and M genes, whilst in the other genes it clustered with strains of the Eurasian lineage, revealing a multi-reassortant nature.
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Publication Date: 2023-03-24 PubMed ID: 37048408PubMed Central: PMC10093709DOI: 10.3390/ani13071153Google Scholar: Lookup
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Summary

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The research article discusses the use of advanced sequencing techniques to determine the whole genome sequence of an H3N8 equine influenza virus from a 2005 outbreak in Italy, finding it to be closely related to viruses from Poland and revealing its multi-reassortant nature.

Advanced Sequencing Techniques and Whole Genome Sequencing

  • The paper starts by highlighting the impact of advanced sequencing techniques in building straightforward methods for whole genome sequencing of viruses, including influenza viruses.
  • Information generated from these techniques can enhance levels and dimensions of data analysis even for archived samples. This allows for a comprehensive understanding of the genetic makeup of the virus, revealing crucial insights into its behavior, origin, and evolution.

Use of the Nanopore Platform

  • The researchers used the Nanopore platform, a revolutionary sequencing technology, that provides real-time data analysis.
  • Nanopore sequencing provided the ability to identify the complete genome sequence of the H3N8 equine influenza virus from the 2005 Italy outbreak.

Phylogenetic Analysis and Results

  • Phylogenetic analysis, a technique used to study the evolutionary relationships among various biological species based on their genetic characteristics, was performed based on the eight genome segments of the virus.
  • The identified virus was found to be closely related (>99% at the nucleotide level) in all genome segments to viruses identified in Poland during 2005-2008. This suggests that the virus could have been introduced locally, perhaps through horse trading for the meat industry.
  • The strain was found to belong to the sub-lineage Florida 2 in the HA and M genes, indicating that it was possibly part of a larger, widespread outbreak in the equine population.
  • In the remaining genes, the strain clustered with strains of the Eurasian lineage, implying that the virus was multi-reassortant, or a ‘mix’ of genes from different sources. This further expands our knowledge of equine influenza virus’s genetical versatility and adaptability.

Cite This Article

APA
Pellegrini F, Buonavoglia A, Omar AH, Diakoudi G, Lucente MS, Odigie AE, Sposato A, Augelli R, Camero M, Decaro N, Elia G, Bányai K, Martella V, Lanave G. (2023). A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing. Animals (Basel), 13(7), 1153. https://doi.org/10.3390/ani13071153

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 13
Issue: 7
PII: 1153

Researcher Affiliations

Pellegrini, Francesco
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Buonavoglia, Alessio
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Omar, Ahmed H
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Diakoudi, Georgia
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Lucente, Maria S
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Odigie, Amienwanlen E
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Sposato, Alessio
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Augelli, Raffaella
  • Office UVAC, Ministry of Health, 70122 Bari, Italy.
Camero, Michele
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Decaro, Nicola
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Elia, Gabriella
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Bányai, Krisztián
  • Veterinary Medical Research Institute, 1143 Budapest, Hungary.
  • Department of Pharmacology and Toxicology, University of Veterinary Medicine, 1400 Budapest, Hungary.
Martella, Vito
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.
Lanave, Gianvito
  • Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy.

Grant Funding

  • Project no. PE00000007, INF-ACT / EU, MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

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