Fifty three of Middle East avian influenza virus H5N1 strains
were retrieved from GenBank Database. Other 23 H5N1 representative strains
from Asian, Europe, Africa, and North America were also used in this study.
Phylogenetic analysis and pairwise comparison of nucleotide and amino acid
sequences of.hemagglutinin (HA) gene region of these strains revealed that
the H5N1 viruses circulating in Middle East displayed high similarity. The
HA protein of the virus contained multiple basic amino acid residues
(QGERRRKKR) or (QGEGRRKKR) adjacent to the cleavage site between
the HA1 and HA2 domains, showing the highly pathogenic characteristics.
Further analyses of these H5N1 strains showed that all of them carried (Gln)
238Q and (Gly) 240G at the receptor binding pocket which indicates
preferential binding to alpha-2,3-NeuAcGal receptors. Phylogenetic analysis
also confirmed that these H5N1 viruses belonged to the Qinghai lineage or
Astrakhan lineage of highly pathogenic avian influenza (HPAI) viruses H5N1
(subclade 2.2 or EMA). As a result, 2 closely related but distinguishable
H5N1 sub-subclades are defined and called (2.2.1 (EMA-1) and 2.2.3
(EMA3).