Molecular characterization and phylogeography of equine influenza virus H3N8 detected in donkeys in Nigeria 2022-2023.
Authors: Mkpuma Nicodemus, Meseko Clement, Shittu Ismaila, Chukwu Chukwu, Afiukwa Felicitas Ngozi, Iroha Ifeanyichukwu Romanus, Muhammad Maryam, Ogbu Ogbonnaya
Journal: BMC veterinary research
Summary
# Editorial Summary: EIV H3N8 in Nigerian Donkeys—Implications for African Equine Health Equine influenza virus H3N8 represents a persistent threat across Africa, yet genomic surveillance data remain sparse outside major horse-trading nations. Between January 2022 and October 2023, researchers conducted active surveillance at Nigerian slaughterhouses and animal markets, screening 400 nasal swabs from equids using RT-qPCR and sequencing positive samples for whole-genome analysis alongside spatiotemporal Bayesian phylogeography. Although only two samples (0.5%) tested positive—both from donkeys with absent or fatal clinical signs—genomic analysis revealed critical epidemiological patterns: multiple virus introductions into Africa traceable to Argentina (2018/2019), the UK (2021), and Ireland (2019), with the Nigerian 2022 strains likely persisting from a 2018/2019 northern Nigerian epizootic. The identified strains exhibited previously unreported hemagglutinin substitutions relative to the World Organisation for Animal Health–recommended Florida clade-1 vaccine strain, including novel changes flanking antigenic sites and four distinct glycosylation profiles, suggesting ongoing viral evolution that may compromise vaccine effectiveness. For equine professionals across Africa, these findings underline a critical gap: subclinical donkey infections and transboundary livestock trade facilitate silent virus circulation despite low detection rates, whilst antigenic drift in circulating strains may reduce the protective value of current vaccination protocols. Enhanced genomic surveillance, stricter livestock trade controls, and reassessment of vaccination strategies tailored to locally circulating lineages are now essential to prevent future outbreaks and protect both working equids and broader herd health in resource-limited settings.
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Practical Takeaways
- •Donkeys can harbour EIV H3N8 asymptomatically and pose a transmission risk at markets and slaughterhouses—screening and biosecurity measures should include all equids, not just horses
- •Current WOAH-recommended Florida clade-1 vaccines may have reduced efficacy against circulating Nigerian strains due to novel mutations; vaccination protocols may need updating based on local surveillance data
- •Transboundary livestock trade and unregulated animal markets are key drivers of EIV spread in Africa; implementing trade regulations and market biosecurity will reduce outbreak risk
Key Findings
- •Two donkeys (0.5% of 400 nasal swabs) tested positive for H3N8 virus, including asymptomatic animals and deceased animals
- •Multiple introductions of EIV H3N8 into Africa detected, likely originating from Argentina (2018/2019), UK (2021), and Ireland (2019)
- •Novel hemagglutinin substitutions and four distinct glycosylation profiles identified in the 2022 Nigerian strains, indicating significant viral evolution and potential vaccine mismatch
- •Evidence suggests EIV persistence from 2018/2019 epizootic in northern Nigeria with transboundary spread through livestock trade, particularly involving donkeys