Regardless mass vaccination programs in Egypt with inactivated polyvalent vaccines of FMD
virus. FMD virus is still persistent with major economic burden. Serotypes of FMD namely,
A, O, and South African Territories (SAT2) are endemic with repeated outbreaks of new
lineage. So, selection of appropriate vaccine is very difficult. In this study; Phylogenetic
analysis of VP1 genome for the existing serotype (A, O and SAT2) between 2016 to 2019
approved circulation of serotype O of East Africa 3 (EA-3) topotype, AIran05 lineage and A
Africa G-IV lineage of serotype A and topotype VII of serotype SAT2 including Alx-12 and
Lib-12 lineages. Significant amino acid changes in critical antigenic sites between field isolates
and vaccine strains were observed. The present findings indicate the importance of an active
routine surveillance system incorporating antigenic and genetic analysis designated to
continually update information about field isolates of FMDV. Such protocols may influence
FMD control strategy in Egypt and surrounding country(s).