Sequence and phylogenetic analysis of FMD virus isolated from two outbreaks in Egypt

Despite intensive control efforts, Foot and mouth disease (FMD) outbreaks continue to occur regularly in Egypt and resulting in dramatic economic losses to the livestock industry. During 2018 and 2022, FMD was clinically suspected among previously vaccinated cattle in Beheira and Kafr El-Sheikh provinces, Egypt. FMDV RNA was detected in 18 (45%) out of 40 epithelial tissue samples using real-time RT-PCR based on a pan-FMDV primers set. The 2018 outbreak isolates (n = 8) included the FMDV serotypes A and SAT2, whereas all isolates (n = 10) from the 2022 outbreak belonged to the FMDV serotype A. Four selected isolates, designated FMDV/SAT2/EGY/Beheira/2018, FMDV/A/EGY/Kafr El-Sheikh/2018, FMDV/A/EGY/Kafr El-Sheikh/2022 and FMDV/A/EGY/Behiera/2022, were characterized on the basis of partial VP1 gene sequence analysis. The FMDV/SAT2/EGY/Beheira/2018 strain was clustered within the Lib-12 lineage of the topotype VII and shared 79.2–98.4% nucleotide identity with other Egyptian SAT2 strains available in Genbank database. On the other hand, the three FMDV serotype A sequences shared 74.4–99.1% nucleotide identity with each other. Also, they were phylogenetically classified within two distinct topotypes. The FMDV/A/Egy/Kafr El-Sheikh/2018 strain was grouped within the Asian topotype, meanwhile the FMDV/A/EGY/Kafr El-Sheikh/2022 and FMDV/A/EGY/Behiera/2022 strains were grouped together within the genotype IV of the African topotype. Interestingly, the deduced amino acid sequences of the four strains displayed numerous variations in comparison to the vaccine strains currently used in Egypt. In addition, most of these variations were present in prominent antigenic positions in the VP1 protein. These findings raise a crucial need to validate the protective potential of the vaccine strains against the newly emerging FMDV field strains and to update the vaccination strategy accordingly.