Avian coronaviruses (ACoVs) are continuously evolving and causing serious economic consequences in the poultry industry and around the globe. Owing to their extensive genetic diversity and high mutation rates, controlling ACoVs has become a challenge. In this context, the potential contribution of wild birds in the disease dynamics, especially in domesticated birds, remains largely unknown. In the present study, five hundred fifty-seven (n = 557) cloacal/fecal swabs were collected from four different wild bird species from eight Egyptian governorates during 2016 and a total of fourteen positive isolates were used for phylodynamics and evolutionary analysis. Genetic relatedness based on spike (S1) gene demonstrated the clustering of majority of these isolates where nine isolates grouped within Egy/variant 2 (IS/885 genotype) and five isolates clustered within Egy/variant 1 (IS/1494/06 genotype). Interestingly, these isolates showed noticeable genetic diversity and were clustered distal to the previously characterized Egy/variant 1 and Egy/variant 2 in Egyptian commercial poultry. The S1 gene based comparison of nucleotide identity percentages revealed that all fourteen isolates reported in this study were genetically related to the variant GI-23 lineage with 92–100% identity. Taken together, our results demonstrate that ACoVs are circulating in Egyptian wild birds and highlight their possible contributions in the disease dynamics. The study also proposes that regular monitoring of the ACoVs in wild birds is required to effectively assess the role of wild birds in disease spread, and the emergence of ACoVs strains in the country.

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Infectious laryngotracheitis (ILT) is a severe respiratory disease, which causes high morbidity and mortality in affected birds. In our study, ILT were reported in 42 farms from nine governates over two years (2018–2020) that showed clinical signs of ILT including dyspnea, blood expectoration of, excessive lacrimation, rattling, conjunctivitis. The disease affected different chicken breeds and age groups despite vaccination with licensed and commonly used vaccines. Samples of larynx, trachea, lungs and air sacs were examined and collected for histopathological, ultrastructural, immunohistochemical examination and molecular detection. Gross examination of laryngeal and tracheal lumen revealed different types of exudate varied from catarrhal to fibrinonecotric, also pneumonia and airsacculitis were detected. Histopathological examination showed different alternation in larynx, trachea, lung and air sac as characteristic syncytial cells containing intranuclear inclusion body hanged in fibrinoheterphilic exudate that precent in laryngeal, tracheal, bronchial and parabronchial lumen and air sacs. Tracheal lesion scoring system was used to categorize the severity of lesion in different governates. Tracheal lesion score showed that 6.02%, 26.5%, 43.3% of the birds exhibited mild, moderate, and severe changes, respectively, while 24.18% of the birds exhibited very severe changes. Furthermore, severe cases were related to the Qalyubia , Fayoum then Sharkia Governorate. Moreover, immunohistochemistry was used to detect viral particles in syncytial cells, inflammatory cells beside epithelium of trachea and lung. Transmission electron microscopy enabled the detection of virus particles and demonstrated that heterophils could be infected. PCR targeting a region in the thymidine kinase gene and glycoprotein gJ gene confirmed the presence of infectious laryngotracheitis ILT virus-specific DNA. In conclusion, anatomopathological, immunohistochemical, molecular and ultrastructural findings showed increased of ILTV severity in Egypt. Larynx, trachea, lungs and air sac should be collected and examined that aid in diagnosis. Importance of good biosecurity level to be considered.

<b><i>Introduction:</i></b> Gallid alphaherpesvirus 2 (GaHV-2) is a highly contagious oncogenic virus that causes Marek’s disease in chickens and occasionally in turkeys. Among 100 genes identified in GaHV-2 genome, the Meq gene appears to involve viral virulence, oncogenicity, and genetic diversity. Despite the use of Meq gene sequences in phylogenetic classification of GaHV-2 strains circulating in many countries worldwide, no integrated system exists yet. <b><i>Methods:</i></b> Turkeys from 2 commercial Egyptian farms were presented with signs of dullness, dehydration, and emaciation. Samples prepared from the internal organs were examined by histopathology and immunohistochemistry. Pools of the internal organs were analyzed by PCR for identification of GaHV-2, avian leucosis virus, and reticuloendotheliosis virus. The Meq gene of an Egyptian strain was sequenced and analyzed in comparison to 40 reference strains for generation of a universal system for phylogenetic classification of GaHV-2 strains. <b><i>Results:</i></b> Gross and histopathological examination revealed grayish-white soft masses in the internal organs characterized by diffuse infiltration of pleomorphic neoplastic cells. All lymphoma cells were identified as T-lymphocytes of CD3+ phenotype. Samples of both farms were only positive for GaHV-2 by PCR. Sequence analysis of the Meq gene has classified the current turkey strain as related to the Egyptian strains identified in chicken in 2012. A universal phylogenetic system for classification of GaHV-2 strains into 4 clusters was proposed. The vaccine strains were all grouped in cluster 2, and most of the classical American strains belonged to cluster 4. Cluster 1 was further divided into 3 subclusters (1.1–1.3). <b><i>Conclusion:</i></b> GaHV-2 was identified in turkeys for the first time in Africa and the Middle East. Sequence analysis of the Meq gene of the Egyptian strain along with a wide array of the global strains has enabled the construction of a novel phylogenetic classification system.

Infectious laryngotracheitis (ILT) is an economically crucial respiratory disease of poultry that affects the industry worldwide. Vaccination is the principal tool in the control of the disease outbreak. In an earlier study, we comprehensively characterized the circulating strains in Egypt and identified both CEO-like and recombinant strains are dominant. Herein, we investigated the pathogenicity of two virulent strains representing the CEO-like (Sharkia_2018) and recombinant strain (Qalubia_2018). Additionally, we evaluated the efficacy of different commercial vaccines (HVT-LT, CEO, and TCO) against the two isolates in terms of the histopathological lesion scores and the viral (gC) gene load. A total of 270 White Leghorn-specific pathogen-free male chicks were divided into nine groups of 30 birds, each housed in separate isolators. Birds were distributed as follows; one group was non-vaccinated, non-challenged, and served as a negative control. Two groups were non-vaccinated and infected with the two isolates of interest and served as a positive control to test the pathogenicity. Six groups were vaccinated and challenged; two groups were vaccinated with vector vaccine at one day old. The other four groups were vaccinated with either the CEO- or TCO- vaccine (two groups each) at four weeks of age. Three weeks after vaccination, birds were infected with the virulent ILTV isolates. The larynx, trachea, and harderian gland samples were taken at 1, 3, and 7 days post-infection for histopathological lesion score and molecular detection. Notably, The recombinant strain was more virulent and pathogenic than CEO-like ILTV strains. Moreover, the TCO vaccine was less immunogenic than the vector and CEO vaccines.