Genetic characterization and phylogenetic analysis of foot and mouth disease virus vaccine strains and recent field isolate

Foot and Mouth Disease (FMD) control is a national and regional responsibility. FMD outbreaks were detected in three farms in Port-Said Governorate in 2020, although animals in these farms were vaccinated with the local polyvalent inactivated vaccine. Samples from tongue epithelium and vesicular fluid were collected from these farms, where FMDV isolation was performed on BHK-21 cell culture. Viral RNA was extracted from the virus isolates, and vaccine strains were then screened for FMDV using conventional Reverse transcriptase polymerase chain reaction. The substitution rates and phylogenetic relationship between the field isolate and the vaccine strains were determined using DNA sequence and bioinformatics analyses. The results illustrate that the sequence analysis for the 1D region of FMDV field isolate was serotype A‑Africa topotype, Genotype IV, and closely related to isolated A‑Africa topotype Genotype IV by Animal Health Research Institute, 2020 with nucleotide similarity ranging from 97.1% to 99.74%, and revealing genetic variation of 5.63-7.88% from previously Egyptian isolated A‑Africa topotype, Genotype IV in 2016 and 2018. High genetic variations were determined from the locally used vaccine strain serotype A of the Asia topotype, lineage Iran‑05, in the major antigenic sites of the VP1 region with a nucleotide difference of 26.34%. Depending on these findings, the Veterinary Serum and Vaccine Research Institute produced an emergency inactivated monovalent vaccine using the newly isolated strain, and we recommended adding it to the subsequent prepared vaccine batches.