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BMC veterinary research2026; doi: 10.1186/s12917-025-05279-6

Molecular characterization and phylogeography of equine influenza virus H3N8 detected in donkeys in Nigeria 2022-2023.

Abstract: Equine influenza virus (EIV) H3N8 is a highly contagious respiratory pathogen that poses significant health and economic risks to equids globally. In southeastern Nigeria where equids are sold and slaughtered, limited data exist on EIV epidemiology and circulating lineages. Methods: To address this gap, an active surveillance was conducted between January 2022 and October 2023. A total of 400 nasal swabs were collected from horses and donkeys at slaughterhouses and animal markets. The swabs were screened for equine influenza virus (EIV) using quantitative Reverse-Transcription Polymerase Chain Reaction (RT-qPCR), and positive samples underwent whole-genome sequencing. A spatiotemporal Bayesian phylogeographic analysis was performed. Amino acid comparisons were carried out against the World Organization for Animal Health (WOAH) recommended Florida clade-1 (Fc-1) vaccine strains (accession numbers GU447312, DQ124192) and mutations were mapped onto 3D H3 hemagglutinin structure with protein data bank 4UO0 using PyMOL. Results: Two samples (0.5%) from non clinical signs and deceased donkeys tested positive for the H3N8 virus. A spatiotemporal Bayesian phylogeographic analysis, which included sequences from outbreaks in Africa between 2018 and 2023, revealed multiple introductions of the virus into Africa. The introductions of Fc-1 lineage into Africa may have originated from Argentina (2018/2019) and the UK (2021), while Florida clade-2 seems to have originated from Ireland (2019). The 2022 H3N8 strains identified in this study may be a result of persistence from the 2018/2019 epizootic in northern Nigeria. Additionally, we discovered previously unreported hemagglutinin substitutions compared to the WOAH recommended Fc-1 vaccine strain, along with novel changes adjacent to antigenic sites and four distinct glycosylation profiles in the virus, which underscores their potential epidemiological significance. Conclusions: Our findings revealed multiple introductions of EIV probably from South America and Western Europe, rapid virus evolution, and significant transboundary spread facilitated by livestock trade, particularly involving donkeys and subclinical infections in the transmission of the virus. These results underscore the persistence and evolution of EIV H3N8 (Fc-1) in Nigeria and emphasize the need for improved genomic surveillance, control measures, and vaccination strategies against EIV in Africa. Additionally, regulating transboundary livestock trade is essential to mitigate the risk of future outbreaks.
© 2026. The Author(s).
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Publication Date: 2026-02-03 PubMed ID: 41629904DOI: 10.1186/s12917-025-05279-6Google Scholar: Lookup
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  • Journal Article

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

  • This study investigated the molecular characteristics and geographic spread of the equine influenza virus (EIV) H3N8 in donkeys in southeastern Nigeria during 2022-2023.
  • It identified the virus’s introduction sources, genetic mutations, and emphasized the importance of enhanced surveillance and control measures to manage EIV in Africa.

Background and Objectives

  • Equine influenza virus H3N8 is a highly contagious virus affecting horses and donkeys worldwide, causing respiratory illness with significant economic impact.
  • In southeastern Nigeria, where equids are commonly traded and slaughtered, there has been limited information on the prevalence, genetic diversity, and spread of EIV.
  • The study aimed to fill this knowledge gap by conducting active surveillance of EIV in horses and donkeys from January 2022 to October 2023, analyzing the virus at a molecular level, and investigating its geographic origins and evolutionary history.

Methods

  • Sample Collection: 400 nasal swabs were collected from horses and donkeys in slaughterhouses and animal markets.
  • Detection: Reverse-transcription quantitative PCR (RT-qPCR) was used to detect EIV presence in samples.
  • Sequencing: Positive samples underwent whole-genome sequencing to analyze the virus’s genetic makeup.
  • Phylogeographic Analysis: A Bayesian spatiotemporal approach was employed to trace the geographic origins and pathways of virus introductions into Africa.
  • Protein Analysis: Amino acid sequences were compared against the World Organization for Animal Health (WOAH) recommended Florida clade-1 (Fc-1) vaccine strains.
  • Structural Mapping: Detected mutations were visualized on the 3D structure of the H3 hemagglutinin protein using PyMOL to understand their potential functional impact.

Key Results

  • Prevalence: Only 2 out of 400 (0.5%) samples tested positive for EIV H3N8, both from donkeys with no apparent clinical symptoms or that were deceased.
  • Virus Origins:
    • Phylogeographic analysis revealed multiple introductions of the virus into Africa from different regions.
    • Florida clade-1 lineage likely entered Africa from Argentina (2018/2019) and the United Kingdom (2021).
    • Florida clade-2 lineage appeared to originate from Ireland (2019).
    • The 2022 Nigerian strains may represent local persistence of the virus from the 2018/2019 outbreaks in northern Nigeria.
  • Genetic Mutations:
    • Novel hemagglutinin protein mutations were identified that were not previously reported compared to WOAH Fc-1 vaccine strains.
    • Some mutations were near antigenic sites, potentially affecting immune recognition and vaccine efficacy.
    • Four unique glycosylation patterns were found in the virus, which could influence virus infectivity and immune escape mechanisms.

Conclusions and Implications

  • The study revealed that EIV H3N8 is introduced into Africa from multiple international sources, particularly South America and Western Europe, facilitated by the global livestock trade.
  • The virus evolves rapidly, with ongoing genetic changes implying challenges for current vaccination strategies and disease control.
  • Donkeys can carry the virus subclinically, acting as hidden reservoirs that support virus transmission and complicate outbreak detection.
  • Results underscore the importance of:
    • Enhanced genomic surveillance across equid populations in Nigeria and Africa to monitor virus evolution and spread.
    • Implementing effective control measures, including updated vaccinations considering the genetic variability of circulating strains.
    • Better regulation of transboundary livestock trade to prevent virus introduction and spread.
  • This study provides critical insights necessary for protecting equid health, improving economic outcomes in affected communities, and reducing the risk of future EIV outbreaks.

Cite This Article

APA
Mkpuma N, Meseko C, Shittu I, Chukwu C, Afiukwa FN, Iroha IR, Muhammad M, Ogbu O. (2026). Molecular characterization and phylogeography of equine influenza virus H3N8 detected in donkeys in Nigeria 2022-2023. BMC Vet Res. https://doi.org/10.1186/s12917-025-05279-6

Publication

BMC veterinary research
ISSN: 1746-6148
NlmUniqueID: 101249759
Country: England
Language: English

Researcher Affiliations

Mkpuma, Nicodemus
  • Regional Laboratory for Animal Influenza and Other Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria. nicodemusmkpuma@gmail.com.
  • Department of Applied Microbiology, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria. nicodemusmkpuma@gmail.com.
Meseko, Clement
  • Regional Laboratory for Animal Influenza and Other Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria.
Shittu, Ismaila
  • Regional Laboratory for Animal Influenza and Other Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria.
Chukwu, Chukwu
  • Molecular Biology Department, Federal College of Veterinary and Medical Laboratory Technology, Vom, Nigeria.
Afiukwa, Felicitas Ngozi
  • Department of Applied Microbiology, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria.
Iroha, Ifeanyichukwu Romanus
  • Department of Applied Microbiology, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria.
Muhammad, Maryam
  • National Veterinary Research Institute, Vom, Nigeria.
Ogbu, Ogbonnaya
  • Department of Applied Microbiology, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria.

Conflict of Interest Statement

Declarations. Ethics approval and consent to participate: Ethical approval for this study was granted by the Animal Care and Use Committee of the National Veterinary Research Institute, Vom (AEC/02/101/21). Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

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