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Emergence of equine influenza virus H3Nx Florida clade 2 in Arabian racehorses in Egypt

Ahmed, Basem Mohamed; Bayoumi, Mahmoud Mohamed; Farrag, Mohamed Ali; Elgamal, Aly; Daly, Janet Mary; Amer, Haitham Mohamed


Basem Mohamed Ahmed

Mahmoud Mohamed Bayoumi

Mohamed Ali Farrag

Aly Elgamal

Professor of Viral Zoonoses

Haitham Mohamed Amer



Equine influenza is an important cause of respiratory disease in equids. The causative virus; EIV, is highly variable and can evolve by accumulation of mutations, particularly in the haemagglutinin (HA) gene. Currently, H3N8 is the sole subtype circulating worldwide with Florida clade 1 (FC1) is most prevalent in the Americas and FC2 in Asia and Europe. In Egypt, EIV was detected in two occasions: subtype H7N7 in 1989 and subtype H3N8 (FC1) in 2008. No data is available on the circulation pattern of EIV during the last decade despite frequent observation of suspected cases.


Twenty-two nasal swabs were collected from vaccinated and non-vaccinated horses showing respiratory signs suggestive of EIV infection in 2017–18. Three additional swabs were retrieved during a national race event in January 2018 from Arabian mares with high fever, gait stiffness and dry cough. Samples were screened by RT-qPCR and HA1 domain of the hemagglutinin gene was amplified and sequenced for sequence and phylogenetic analysis.


RT-qPCR screening revealed that only the 3 samples from the race were positive with cycle thresholds ranging from 16 to 21 indicating high viral load. Isolation attempts in hen’s eggs were unsuccessful. Sequence analysis of the HA1 domain gene has revealed two identical nucleotide sequences, while the third contained 3 synonymous mutations. Phylogenetic analysis clustered study sequences with recent FC2 sequences from Europe. Amino acid alignments revealed 14 and 13 amino acid differences in the study sequences compared to A/equine/Egypt/6066NANRU-VSVRI/08 (H3N8) and A/equine/Kentucky/1997 (H3N8), respectively, available as EIV vaccines in Egypt. Nine amino acids were different from A/equine/Richmond/1/2007 (H3N8), the recommended FC2 vaccine strain by the world organization of animal health expert surveillance panel (OIE-ESP), two of which were unique to the Egyptian sequences while the remaining 7 changes were shared with the FC2-144V subgroup detected in the United Kingdom from late 2015 to 2016.


The study represents the first reported detection of FC2-144V related EIV from Arabian mares in Egypt, and probably from the entire middle east region. The presented information about EIV epidemiology and spread may require reconsideration of the vaccine strains used in the national vaccination programs.


Ahmed, B. M., Bayoumi, M. M., Farrag, M. A., Elgamal, A., Daly, J. M., & Amer, H. M. (2022). Emergence of equine influenza virus H3Nx Florida clade 2 in Arabian racehorses in Egypt. Virology Journal, 19, Article 185.

Journal Article Type Article
Acceptance Date Oct 15, 2022
Online Publication Date Nov 12, 2022
Publication Date Nov 12, 2022
Deposit Date Oct 17, 2022
Publicly Available Date Nov 12, 2022
Journal Virology Journal
Electronic ISSN 1743-422X
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 19
Article Number 185
Public URL
Publisher URL


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