Molecular detection, phylogenetic analysis and genetic diversity of recently isolated foot- and-mouth disease virus serotype A in Egypt

Foot-and-mouth Disease (FMD) is a serious contagious viral disease principally affecting all hoof cloven animals. Serotypes A, O and SAT 2 of foot-and-mouth disease virus (FMDV) are circulating in Egypt vaccination. The present study aimed to detect and molecularly characterize FMDV strains circulating in the Northern Egypt during the last 2022 epidemic. RNA was extracted from the epithelial specimens, vesicular fluid and heparinized blood samples from affected animals. Samples were screened using real time reverse-transcription polymerase chain reaction (RT-PCR) that targets RNA-dependent RNA polymerase (RdRp) gene. Positive samples were subjected to individual serotype specific amplification using different set of primers for VP1 of O, A, C and SAT 2 serotypes. Direct sequencing of the positive samples was conducted on positive samples. Biochemical parameters were also screened at time of sampling and at 4, 15 and 30 days. Real time RT-PCR showed positive samples from epithelia and vesicular fluid samples but not the blood of infected animals. Seven out of 16 samples were found positive to FMDV serotype A. Six out of the seven positive samples were classified as serotype A-African topotype-G-IV. Decreases in urea and blood urea nitrogen were detected in infected animals. It was concluded that continuous monitoring of the evolution of circulating the FMDV strains is needed to evaluate and help in vaccine strains selection for controlling FMDV in Egypt.