Phylogenetic and phylogeographic analysis of equine influenza in Colombia

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.

To perform phylogenetic and phylogeographic analyses of complete EIV genomes obtained from horses with clinical signs in two Colombian regions between 2020 and 2023.

Molecular epidemiological study based on whole-genome sequencing and evolutionary analyses.

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.

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.

The limited number of complete genomes restricts inference regarding nationwide viral diversity and transmission dynamics.

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.