In spite of annual mass vaccination programs with polyvalent inactivated vaccines, the incidence and economic impact of foot-and-mouth disease (FMD) in Egypt is high. Viruses of the A, O and SAT 2 serotypes are endemic and repeated incursions of new lineages from other countries lead to an unstable situation that makes the selection of appropriate vaccine antigens very difficult. In this study, whole genome sequencing of a 2016 serotype A isolate from Egypt revealed a recombination event with an African serotype O virus. Based on available vaccine matching data, none of the vaccines currently used in Egypt are expected to sufficiently protect against this virus or other viruses of this lineage (A/AFRICA/G-IV) circulating there since 2012. In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucleic acid fragments, the composition of a local inactivated vaccine was analyzed in depth. The serotype O strain identified in the vaccine was genetically identical to viruses found in recent FMD outbreaks in Egypt.

Sheeppox virus (SPPV) together with goatpox virus and lumpy skin disease virus form the genus Capripoxvirus of the Poxviridae family. Due to their great economic importance and major impact on livelihood of small-scale farmers, OIE guidelines classify capripox viruses as notifiable diseases. In the present study, we examined pathogenesis of an Indian SPPV isolate and an Egyptian SPPV isolate in sheep. Three different infection routes were tested: (i) intravenous infection, (ii) intranasal infection and (iii) contact transmission between infected and naïve sheep. Clinical course, viremia and viral shedding as well as seroconversion were analyzed in order to establish a challenge model for SPPV infections that can be used in future vaccine studies. Next to in vivo characterization, both SPPV strains underwent next- and third-generation sequencing to obtain high quality full-length genomes for genetic characterization and comparison to already published SPPV sequences.

Ovine gammaherpesvirus-2 (OvHV-2) causes a lethal disease in cattle and some wild ruminants called malignant catarrhal fever (MCF), which affects the epithelial and lymphoid tissues of the respiratory and digestive tracts and has an important impact on the livestock industry. In this study, MCF was diagnosed in 18 of 427 cattle from different sites in Egypt by its typical clinical signs, found in all 18 animals: corneal opacity, fever, erosions in the buccal cavity, lymphadenitis, and purulent nasal discharge. All affected cattle had been reared in contact with clinically inconspicuous sheep. Of the 18 clinically ill cattle, 13 succumbed to the disease, resulting in estimated morbidity and case fatality rates of 4.2% and 72.2%, respectively. Five samples collected from the affected cattle were positive for OvHV-2 by real-time PCR and were used for sequencing of an 832-bp fragment of the ORF27/gp48 gene. The ORF27 nucleotide sequence of all Egyptian samples was identical, but distinct from viruses found in other parts of Africa and the Mediterranean.

| Newcastle disease (ND) as a devastating disease is a challenge of poultry industry not only in developing countries, but also all over the world. The pathogenesis of ND in quails is still poorly understood. The present study aimed to investigate the natural occurrence and pathological changes of ND in quails in Egypt. The diseased quails were collected from eleven flocks in Egypt exhibited respiratory, nervous signs and whitish green diarrhea in addition to egg abnormalities and lower production with mortalities. No characteristic gross lesions were observed except heamorrhages in brain, congested liver, spleen, brain and muscles besides greenish content of the gizzard. The histopathological examination of lung, brain, liver, and trachea of these diseased quails revealed non-suppurative encephalitis, perivascular cuffing, congestion of hepatic sinusoids, degenerative changes in the hepatic cells and interstitial lymphocytic aggregations in the liver and focal pneumonic areas in the lung. Pooled samples from the investigated quails were inoculated in specific pathogen free embryonated chicken eggs (SPF-ECEs). The dead embryos showed hemorrhages, congestion and dwarfism. The collected allantoic fluids were examined later by haemagglutination (HA) and haemagglutination inhibition (HAI) test. The allantoic fluids of 5 pooled samples expressed positive using specific Newcastle disease virus (NDV) antiserum. The NDV field isolates were confirmed by reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing targeting F gene of amplicon size (362) bp containing the region 112RRQKRF117 motif, which is the determinant part of virus virulence. The sequenced isolate was grouped in class II genotype VII.1.1 with small distance from NDV strains in chickens and turkeys which is alarming for the potential transmission of NDVs from quails to other poultry species.