Molecular differentiation and phylogenetic analysis of the Egyptian foot-and-mouth disease virus SAT2

Abstract

In February 2012, a massive new foot-and-mouth disease (FMD) outbreak struck Egypt. In this work, one-step RT-PCR assays were used for in-house detection and differentiation of foot-and-mouth disease virus (FMDV) in Egypt in this year using pan-serotypic and serotype-targeting sequence primers. FMDV SAT2 was the dominant virus in the examined isolates from the epidemic. The complete VP1 coding regions of two isolates were sequenced. The two isolates had 99.2 % sequence identity to most contemporary Egyptian SAT2 reference viruses, whereas they had 89.7-90.1 % identity to the SAT2/EGY/2/2012 isolate, which was collected from Alexandria, Egypt, and previously sequenced by WRLFMD. Phylogenetic analysis showed that Egypt had one topotype and two lineage of FMDV SAT2 in 2012. The Egyptian and the Palestinian 2012 strains were associated mainly with topotype VII, lineage SAT2/VII/Ghb-12, while the virus isolated from Alexandria Governorate belonged to the SAT2/VII/Alx-12 lineage. Topotype VII also comprised lineages that included strains isolated from Libya in 2012 and 2003. Furthermore, within the same topotype, the Egyptian SAT2/2012 isolates were related to strains from Saudi Arabia, Sudan, Eritrea, Cameroon and Nigeria. Nevertheless, more epidemiological work with neighboring countries is needed to prevent cross-border spread of disease and to reach a precise conclusion about the origin of the 2012 FMDV SAT2 emergency in the Middle East.

Molecular Epidemiology of Foot and Mouth Disease Virus during 2014 with References to Biochemical Changes in Egyptian Buffaloes

“…The results of real time RT-qPCR assays indicated that the serotype responsible for the endemic is SAT2 and confirmed by 716 bp amplified product using RT-PCR. This result agreement with the newly introduced SAT-2 serotype, which has been emerged during February to April 2012 in Upper Egypt (Salem et al, 2012) Delta Governorates (Ahmed et al, 2012 andValdazo Gonzales et al, 2012), Gharbia (Elhaig and Elsheery 2014) and Alexandria (El-Shehawy et al, 2014). Moreover, the failure in detection of serotypes A and O not prevent their implications in field cases (Salem et al, 2012).…”

A Comparative Study on the Hemato-Biochemical and Immunological Effects of the Hexavalent FMD Vaccine Alone or in Combination with Trivalent FMD Vaccine in Cattle

“…Egypt has been considered to be endemic by A and O FMD strains until 2012 [9] [10] [21]. During 2012/2013, a new extensive FMD outbreak struck Egypt and killed more than 4600 animals and laboratory investigations supported the cause to be the serotype SAT2 [7] [21] [22]. From that time and till now, SAT2 clinically has manifested itself by causing severe clinical disease in cattle and buffalo and no other serotypes were detected [23].…”

Genomics and outbreaks: foot and mouth disease

“…The combination of Sanger-based sequencing and phylogenetic analysis has been instrumental in identifying the source of outbreaks from the distribution of diversity within viral populations (23) since the methodology was first employed to investigate diversity in A and O strains in Europe (24) (Table I). In addition to characterising FMD outbreaks in endemic regions of the world (14,56,57), genomic data have been used recently to characterise FMD viruses recovered from exotic incursions, including the spread of FMD due to serotype SAT 2 into Egypt (58,59), to monitor the spread of lineages into new geographical regions (15,42,60), in the discovery of novel lineages (13,61) and to retrospectively analyse the diversity in previous outbreaks (53,62). Such surveillance highlights the transboundary movements of FMDV, providing critical support for both regional and country-level control programmes.…”