Foot-and-mouth disease virus (FMDV) SAT2 serotype is endemic
in Egypt since 2012. The objectives of the present study were to
investigate strain identification of FMDV infecting water buffaloes
(Bubalus bubalis) in April, 2014, Qalyubia, Egypt. Therefore partial
sequences were generated after detection by real time RT-PCR and
subsequent gel purification of RT-PCR amplified products of VP1 gene
of FMDV- SAT2. Partial sequencing of purified virus revealed that SAT2
serotype of FMD was circulating in this region. Sequences were further
examined by sequence analysis and subsequent phylogeny to compare
these sequences from known strains of FMDV-SAT2 circulating globally
and retrieved from GenBank. Nucleotide substitution generates
polymorphism at position 13 nucleotide, where a Cytosine replaced a
Thymine and at the levels of 22 nucleotide where Guanine substituted
Adenosine. A partial sequence of SAT2 showed the highest level of
homology 99.4% similarity with sequences from Egypt 2012 with
diversion 0.6 but it is variable from its neighbor countries isolates.
Phylogenetic analysis showed a robust tree clustering all samples with
sequences belonging to the FMDV-SAT2 variant with strong bootstrap
values at relevant nodes and the evolutionary distance between groups is
very short. There is a substitution in the sequences of amino acids at the
position of 8, where an Alanine is changed to a Threonine