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Equine veterinary journal2026; doi: 10.1002/evj.70314

Phylogenetic and phylogeographic analysis of equine influenza in Colombia.

Abstract: In 2022, Colombia experienced an outbreak of equine influenza (EI) that primarily affected competition horses. Despite the epidemiological relevance of equine influenza virus (EIV) in the country, no previous phylogenetic or phylogeographic analyses based on complete genomes have been reported. Objective: To perform phylogenetic and phylogeographic analyses of complete EIV genomes obtained from horses with clinical signs in two Colombian regions between 2020 and 2023. Methods: Molecular epidemiological study based on whole-genome sequencing and evolutionary analyses. Methods: Nasopharyngeal samples were collected from horses presenting clinical signs compatible with EI. Infection was confirmed by quantitative PCR (qPCR). Two complete EIV genomes were generated using Oxford Nanopore sequencing technology. Phylogenetic relationships were inferred using reference sequences from global databases. Time-scaled phylogenetic analyses were conducted to estimate the time to the most recent common ancestor (tMRCA). Amino acid substitutions were analysed across all gene segments. Results: Two complete EIV genomes were obtained. Both sequences shared >90% nucleotide identity with contemporary strains circulating in the United States, including A/equine/Missouri/1/2022 (H3N8), A/equine/Florida/2/2022 (H3N8), and Ohio/OH21-6023/2021 (H3N8). A time-scaled analysis estimated a tMRCA in 2020 (95% highest posterior density interval: 2019-2021). A greater number of amino acid substitutions were identified in the HA and NA genes, followed by those in PB2, PA, and PB1, including novel substitutions in the Colombian sequences. Conclusions: The limited number of complete genomes restricts inference regarding nationwide viral diversity and transmission dynamics. Conclusions: Colombian EIV strains are closely related to recent North American lineages, supporting the role of international horse movement in viral introduction and dissemination. These findings underscore the importance of genomic surveillance for monitoring viral evolution and informing prevention strategies.
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Publication Date: 2026-08-26 PubMed ID: 42644280DOI: 10.1002/evj.70314Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • Researchers analyzed the genetic makeup and geographic spread of equine influenza virus (EIV) strains from horses in Colombia between 2020 and 2023.
  • The study identified that Colombian EIV strains are closely related to recent North American strains, suggesting international horse movement contributed to virus spread.

Background and Objective

  • Equine influenza (EI) is a significant respiratory disease affecting horses, with outbreaks causing notable economic and animal health impacts.
  • In 2022, Colombia experienced an EI outbreak mainly in competition horses.
  • Before this study, there were no comprehensive analyses of complete EIV genomes from Colombian cases to understand virus evolution and spread.
  • The objective was to perform phylogenetic (genetic relatedness) and phylogeographic (geographic distribution of genetic lineages) analyses of whole EIV genomes sampled from Colombian horses showing clinical signs of EI.

Methods

  • Clinical sampling: Nasopharyngeal swabs were collected from horses in two Colombian regions exhibiting symptoms consistent with EI.
  • Confirmation of infection was done using quantitative PCR (qPCR), a molecular technique to detect viral RNA.
  • Whole-genome sequencing of the virus was performed using Oxford Nanopore technology, an advanced sequencing method that reads long strands of viral genetic material.
  • Phylogenetic analysis involved comparing the obtained Colombian virus genomes to reference sequences from global public databases to infer genetic relationships.
  • Time-scaled phylogenetic analyses estimated the time to the most recent common ancestor (tMRCA), indicating when genetically related viruses last shared a common ancestor.
  • Amino acid substitution analysis checked for genetic changes across all gene segments, focusing on viral proteins integral to infection and immune recognition.

Key Results

  • Two complete EIV genomes were successfully obtained from sampled horses.
  • Genomic comparison showed over 90% nucleotide identity with strains circulating recently in the United States, specifically strains A/equine/Missouri/1/2022 (H3N8), A/equine/Florida/2/2022 (H3N8), and Ohio/OH21-6023/2021 (H3N8).
  • The estimated tMRCA of the sampled viruses was around 2020, with a confidence interval from 2019 to 2021, suggesting recent divergence from North American strains.
  • Notable amino acid changes were identified, particularly in the hemagglutinin (HA) and neuraminidase (NA) genes, which are critical surface proteins involved in viral entry and exit from host cells.
  • Other significant substitutions were observed in internal gene segments coding for polymerase proteins (PB2, PA, PB1).
  • Some amino acid changes were novel and unique to the Colombian sequences, hinting at local viral evolution after introduction.

Conclusions

  • The study revealed that Colombian EIV strains are genetically similar to recent North American strains, indicating the key role of international horse movement (such as transport of competition horses) in introducing and spreading EI in Colombia.
  • The limited number of complete genome sequences restricts comprehensive understanding of viral diversity and transmission dynamics across the entire country.
  • The identification of unique amino acid changes underscores the importance of ongoing genomic surveillance to detect viral evolution that could affect virulence or vaccine effectiveness.
  • This research supports the need for enhanced monitoring and prevention strategies in Colombia, especially given international horse movement, to better control equine influenza outbreaks.

Cite This Article

APA
Gonzalez-Obando J, Carrillo M, Diaz FJ, Garvey M, Usuga J, Moreno I, Hernandez-Ortiz JP, Forero JE, Diaz A, Rojas-Arbeláez C, Cullinane A, Ruiz-Saenz J. (2026). Phylogenetic and phylogeographic analysis of equine influenza in Colombia. Equine Vet J. https://doi.org/10.1002/evj.70314

Publication

Equine veterinary journal
ISSN: 2042-3306
NlmUniqueID: 0173320
Country: United States
Language: English

Researcher Affiliations

Gonzalez-Obando, Juliana
  • Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga, Colombia.
  • Grupo de Epidemiología, Universidad de Antioquia, Medellín, Colombia.
Carrillo, Marlen
  • Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga, Colombia.
Diaz, Francisco J
  • Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
Garvey, Marie
  • Virology Unit, The Irish Equine Centre, Johnstown, Ireland.
Usuga, Jaime
  • One Health Genomic Laboratory, National University of Colombia, Medellín, Colombia.
Moreno, Isabel
  • One Health Genomic Laboratory, National University of Colombia, Medellín, Colombia.
Hernandez-Ortiz, Juan Pablo
  • One Health Genomic Laboratory, National University of Colombia, Medellín, Colombia.
Forero, Jorge E
  • Grupo de Investigación en Microbiología Ambiental, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia.
Diaz, Andrés
  • Pig Improvement Company, Hendersonville, Tennessee, USA.
Rojas-Arbeláez, Carlos
  • Grupo de Epidemiología, Universidad de Antioquia, Medellín, Colombia.
Cullinane, Ann
  • Virology Unit, The Irish Equine Centre, Johnstown, Ireland.
Ruiz-Saenz, Julian
  • Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga, Colombia.

Grant Funding

  • INV2623 to J.R.-S. / CONADI-UCC

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