Genetic Characterization of Foot and Mouth Disease Virus (FMD) Serotypes in Egypt (2016-2017) and Identification of a New Lineage of Serotype O Topotype EA-3

many farmers and veterinarians complained about FMD outbreaks in various Egyptian governorates. Therefore; the present study aimed to characterize the circulating FMD viruses during this period. Clinical data and vaccination histories were collected from nine affected farms and 27 individual cases owned by small farmers in 10 Egyptian governorates. A total of 59 vesicular epithelia were gathered and tested by real-time (rt) RT-PCR to detect and quantify the virus. Furthermore, the positive samples with sufficient genomic loads were analyzed by the less sensitive conventional RT-PCR to amplify the full length of the VP1 region; amplicons were sequenced and phylogenetic trees were constructed. Of 59 samples analyzed, 49 (83.1%) were positive by rt RT-PCR, but only 22/39 produced amplicons by conventional RT-PCR. About 19 amplicons were suitable for sequencing and showed serotypes O, A, and SAT2 in 15, 1 and 3 samples, respectively. Phylogenetic analyses clustered the characterized strains in serotypes O, topotypes EA-3; serotype A, African topotype of genotype IV; and serotype SAT2, topotype VII, respectively. Interestingly, two lineages of serotype O topotype EA-3 strains were distinguished and referred to as Ism-16 and Alx-17. Ism-16 lineage clustered with the previously characterized viruses in Egypt in 2016, but the Alx-17 lineage clustered in a separate clade and is hereby reported for the first time. Further studies are required to evaluate the cross-protection between the vaccine and heterologous circulating strains in Egypt, especially for serotype O.