Rapid Molecular Detection of Genetically Diverted Foot and Mouth Disease Virus Serotype O During the Outbreak of 2012 in Egypt

Increasing the international trade of animals and their products and the continuous changing of Foot and Mouth Disease Virus (FMDV) lead to the rise of disease introductions and create an urgent need for laboratory methods facilitating a swift and sensitive confirmation of suspect outbreaks and fast characterization of new isolates. As FMDV is extremely contagious and affects all cloven-hoofed animals, it provides a continuous burden and risk to the livestock industries of the developing world, in particular due to mortality in young animals, weight and milk loss, lameness and the trade restrictions necessary to control the disease. The control of FMD in Egypt requires an accurate analysis of the newly introduced viral strains and an analysis of their relationship with the current circulating strains and the routinely used vaccines. This study evaluates a recently developed rapid Reverse-Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) for the identification of FMDV in samples from suspect cases. Samples were collected from gum, tongue epithelium, vesicular fluid, buccal and gum swabs, as well as saliva of infected cattle, buffalo and sheep and examined using two RT-qPCR of routine and high-speed formats using "IRES1" and "3D-OIE" primers. In addition, partial VP1 sequencing of some selected isolates was carried out for phylogenetic analysis. The high-speed RT-qPCR allowed a reliable diagnosis of FMDV in less than half an hour and can be used as a fast and valuable method for the monitoring and controlling of the foot and mouth disease. A new variant genotype (FMD-O/Eg/Mans/14) was circulating in Egypt during the outbreak of 2012 showing 98.5% identity to the isolated strain in Sudan (SUD_6_2008).