Fatal multiple outbreaks of equine influenza H3N8 in Nigeria, 2019: The first introduction of Florida clade 1 to West Africa.

This research discusses the multiple fatal outbreaks of equine influenza subtype H3N8 in Nigeria during 2019, caused by a strain of the virus hitherto unknown in West Africa. It details the need for extensive disease surveillance in the region to control the outbreak and protect horses and donkeys.

About the Outbreak

In December 2018, suspected outbreaks of equine influenza, a highly contagious disease that affects horses, were noticed in donkeys in Sokoto State, in Nigeria’s extreme northwest, near the Republic of Niger.
The responsible virus, an equine influenza virus subtype H3N8, was identified in real-time through RT-qPCR and sequencing of both the haemagglutinin (HA) gene and the complete genome.

• This particular strain of H3N8 spread to 7 of the 19 northern states of Nigeria, affecting both donkeys and horses.
• This was the first reported outbreak of equine influenza caused by an Fc-1 virus in Nigeria and West Africa.

Findings from Phylogenetic Analysis

The researchers performed a phylogenetic analysis, a method used to research the evolutionary relationships between different organisms, of the partial and complete HA gene.

• The results showed a very high nucleotide similarity (99.7%) with EIVs from the Florida clade 1 (Fc-1) of the American lineage, which were isolated in 2018 from Argentina and Chile.
• This is significant because these kinds of amino acid substitutions could potentially affect the virus’s antigenicity, its ability to elicit an immune response.

Notable Differences

When comparing the H3N8 virus with the OIE-recommended Fc-1 vaccine strains, 80 amino acid substitutions were noticed in the viral proteins.

• Among these, the HA and neuraminidase proteins, significant in viral entry into host cells and release of newly formed virus particles, had respectively 13 and 16 amino acid substitutions.

Implications and Recommendations

This research implies that a new strain of H3N8 virus, markedly different from current vaccine strains, is responsible for the equine influenza outbreaks in Nigeria.

• It is the first reported outbreak of equine influenza caused by the Fc-1 virus in Nigeria and West Africa.
• The researchers recommend extensive disease surveillance in equids to establish the circulating lineages and devise an effective control strategy to protect horses and donkeys.
• This strategy would help to contain the disease spread and mitigate the potential devastating effects on the considerable population of horses and donkeys in Nigeria and broader West Africa.