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Since the detection of antigenically atypical very virulent Infectious bursal disease viruses (vvIBDV) in Egypt in 1999, the country has been experiencing recurrent outbreaks with high mortality rates and typical gross lesions associated with typical vvIBDV. However, a significant change occurred in 2023, marked by a notable increase in reported subclinical IBDV cases. To evaluate the field situation, samples from 21 farms in 2023 and 18 farms from 2021 and 2022, all of which had experienced IBD outbreaks based on clinical diagnosis, were collected, and subjected to VP2-HVR sequencing. Phylogenetic analysis revealed that all samples collected in 2021 and 2022 clustered with classical virulent strains and vvIBDV. In 2023, one sample clustered with the Egyptian vvIBDV, another with classical virulent IBDV, and the rest with the novel variant IBDV (nVarIBDV) circulating in China. The alignment of deduced amino acid sequences for VP2 showed that all Egyptian classic virulent strains were identical to the Winterfield or Lukert strains, while vvIBDV strains exhibited two out of the three typical residues found in Egyptian vvIBDV, namely Y220F and G254S, but not A321T. Meanwhile, all Egyptian variant strains exhibited typical residues found in nVarIBDV. However, all Egyptian variants showed a mutation at position 321 (321V), which represents the most exposed part of the capsid and is known to have a massive impact on IBDV antigenicity, except for one sample that had 318G instead. This report highlights the emergence of a new variant IBDV in Egypt, clustered with the Chinese new variants, spreading subclinically in broiler farms across a wide geographic area. RESEARCH HIGHLIGHTS New variant IBDV which emerged in Egypt clustered with Chinese nVarIBDV. nVarIBDV spread subclinically across a wide geographic area. Mutation at 321 represents capsid's most exposed part, a defining feature. Antigenically modified vvIBDV still circulating in Egypt with typical lesions. [ABSTRACT FROM AUTHOR]

The very virulent infectious bursal disease virus (vvIBDV) induces an acute, highly contagious and immunosuppressive disease in younger chicken causing massive economic losses globally. A major challenge in the field's clinical diagnosis is distinguishing gross lesions caused by vvIBDV from those induced by classic IBDV (cIBDV), commonly used as live attenuated vaccines. This study introduces a one-step multiplex real-time PCR assay designed to distinguish between vvIBDV and non-vvIBDV viruses. Via simultaneously targeting the VP2 sequence for vvIBDV detection and the VP1 sequence for non-vvIBDV identification, including classic, American variant and the recently emerged novel variant IBDV (nvarIBDV), the assay's specificity was validated against common avian viral diseases and nonspecific IBDV strains without any observed cross-reactions. It effectively differentiated between vvIBDV and non-vvIBDV field samples, including nvarIBDV, as confirmed by genotyping based on VP2 sequencing. The assay demonstrated a limit of detection ranging from 1.9Ã--1010 to 10³ DNA copies for vvIBDV-VP2, 9.2Ã--1010 to 10³ DNA copies for classic strains, and 1.2Ã--1011 to 104 DNA copies for nvarIBDV in VP1 detection of non-vvIBDV. In conclusion, this study presents a specific, sensitive, and straight forward multiplex real-time PCR assay. [ABSTRACT FROM AUTHOR]

A variety of illnesses, including arthritis, tenosynovitis, stunted growth, and malabsorption syndrome, are caused by Avian Reoviruses (ARVs), which have become more prevalent in Egypt during recent years and resulted in significant economic losses. This study investigated 27 suspected samples collected from 14 broiler breeders and 13 broilers suffering from immunosuppression, decreased body weight, and diarrhea. Fourteen samples tested positive based on RT-PCR, and the virus could be isolated from ten samples in Specific Pathogen Free (SPF) embryonated chicken eggs. Ten isolates were subjected to molecular and genetic analysis of the S1 gene (sigma C) and S2 gene (sigma A). The amino acid identity of the S1 gene revealed that these viruses are closely related to the viruses that were identified in Israel during 2020 (91.8%-97.2% identity) and belonged to the genetic cluster 5 (genotype 5), which also includes some viruses that are circulating in the United States and Canada. They also showed weak similarity (48.9%-50.2%) with the available vaccine strains in the Egyptian field that belong to cluster 1, genotype 1. The S2 gene showed amino acid homology of 91.7%-98.2% with the current vaccine used in Egypt. However, the Egy-Reo-7-2021 virus had the lowest similarity (84.2%-87.6%) to the available vaccine. It is hypothesized that the difference between field and vaccine strains may have contributed to the failure of current vaccinations to produce protective immunity against current ARV strains circulated in Egypt, which made the disease a problem to the poultry industry. Developing homologous vaccines and evaluating their potency and efficacy are required in Egypt. [ABSTRACT FROM AUTHOR]

Background and Aim: Biosecurity implementation is fundamental to combating diseases and antibiotic resistance. Therefore, this study aimed to examine the correlation between the implementation of biosecurity measures in small-scale duck farms and the incidence of infectious diseases that threaten the duck industry. Materials and Methods: Twenty small-scale duck farms of different breeds and production stages were collected as representative samples, focused on two districts in the Qalyoubia governorate, which possesses high-density small-scale farms. A 30-point structured questionnaire was designed to assess the level of biosecurity measures implemented in the sampled farms. These farms were examined for bacterial infection by cultivation, typing, and antibiotic sensitivity tests, in addition to molecular techniques for detecting suspected viral diseases. Results: The results showed that the farms had high or low levels of biosecurity; only 25% possessed high-level biosecurity. Bacteria, including Salmonella, Escherichia coli, Staphylococcus, and Pasteurella, were isolated from all sampled farms. High rates of antimicrobial resistance-reaching up to 100% were observed against some drugs. However, viral causative agents, including HPAI-H5N8, duck viral hepatitis, and goose parvovirus, were isolated from only five farms. Conclusion: The lack of commitment to biosecurity implementation, particularly personal hygiene, was observed in most sampled farms. Increasing the level of biosecurity reduced the incidence of mixed infections. [ABSTRACT FROM AUTHOR]

Bacillus cereus is one of the opportunistic foodborne bacteria producing food poisoning producing severe economic loss and representing a high risk to the human. The contamination of poultry feed with Bacillus cereus produces gastric damage and facilitates other bacterial infections. For these reasons, fresh fecal matters were collected from poultry farms located in 3 Egyptian Governorates (Giza, Gharbia, and Dakahlia) to isolate and identify Bacillus cereus, determine their susceptibility to different antimicrobial agents, and examine their virulence and resistance factors. Eleven B. Cereus out of 50 examined samples was isolated with a percentage of (11/50, 22%) and subjected to confirmation using the VITEK2 instrument. Disc diffusion tests showed that all isolates were resistant to trimethoprim-sulfamethoxazole, imipenem, cefotaxime, ampicillin, amoxicillin/clavulanic acid, and penicillin G and sensitive to chloramphenicol, gentamicin, and ciprofloxacin. The molecular characterizations of virulence and resistance factors revealed the detection of targeting the groEL gene in all isolates (100%). The toxin gene profiling showed the existence of the nhe gene (90.9%) and the hbl genes (18.18%). The ces and cytk genes were not detected in the examined isolates. Two antimicrobial resistance genes were detected in the examined isolates with (33.33%) for the tetA gene and (45.45%) for bla gene. Therefore, it was concluded that the isolation of B. cereus carrying genes responsible for antimicrobial resistance and toxins production in broiler farms, represents major threats for human health and poultry industry. So that control programs of biosecurity should be implemented in poultry farms to mitigate the losses of B. cereus infection. [ABSTRACT FROM AUTHOR]

The highly pathogenic avian influenza (HPAI) H5N8 virus was first detected in Egypt in late 2016. Since then, the virus has spread rapidly among different poultry sectors, becoming the dominant HPAI H5 subtype reported in Egypt. Different genotypes of the HPAI H5N8 virus were reported in Egypt; however, the geographic patterns and molecular evolution of the Egyptian HPAI H5N8 viruses are still unclear. Here, extensive epidemiological surveillance was conducted, including more than half a million samples collected from different poultry sectors (farms/backyards/live bird markets) from all governorates in Egypt during 2019–2021. In addition, genetic characterization and evolutionary analyses were performed using 47 selected positive H5N8 isolates obtained during the same period. The result of the conducted surveillance showed that HPAI H5N8 viruses of clade 2.3.4.4b continue to circulate in different locations in Egypt, with an obvious seasonal pattern, and no further detection of the HPAI H5N1 virus of clade 2.2.1.2 was observed in the poultry population during 2019–2021. In addition, phylogenetic and Bayesian analyses revealed that two major genotypes (G5 and G6) of HPAI H5N8 viruses were continually expanding among the poultry sectors in Egypt. Notably, molecular dating analysis suggested that the Egyptian HPAI H5N8 virus is the potential ancestral viruses of the European H5N8 viruses of 2020–2021. In summary, the data of this study highlight the current epidemiology, diversity, and evolution of HPAI H5N8 viruses in Egypt and call for continuous monitoring of the genetic features of the avian influenza viruses in Egypt. [ABSTRACT FROM AUTHOR]

Poultry health problems of chickens are usually accompanied by bacterial systemic infections causing severe losses in flocks, sick birds were systemically could be infected by several bacteria regardless of the clinical signs. 16s RNA sequence is a modern approach for the diagnosis of bacterial infection, especially of multiple causative agents. Ten field cases suffering from systemic infections have been examined for bacterial causes, using conventional isolation and 16S rRNA sequencing, The ten sequenced samples were compatible with the results of isolation; six samples were similar to E.coli species with identity% = 97-99%, while it had similarity% < 96% with Salmonella enterica. While the other samples showed variable identity ranging from 94-99% with Salmonella enterica, E. coli, Enterobacter spp and Klebsiella spp In conclusion, although conventional isolation is the golden standard method for bacterial diagnosis, however, the 16s RNA sequencing has elaborated excellence in diagnosis and identification of bacterial infection, concerning the time consuming, detection of multicaused infections and sensitivity. [ABSTRACT FROM AUTHOR]

In this work the changes in the refractive optical properties of nylon 66 fibres occurring due to heating in water and detergent solutions of different concentrations have been studied with the aid of interferometric techniques. Multiple-beam Fizeau fringes for the two alternative input light polarisations have been used in order to determine the refractive indices of the core and skin, their mean value, and the corresponding birefringences. [ABSTRACT FROM AUTHOR]

Mathematical expression for multiple-beam Fizeau fringes crossing quasi-D-shaped optical fiber is derived. The numerical simulations for the derived equations at different fiber rotations angles have been presented. Experimental validation for the derived equations is verified. Microinterferograms for Fizeau fringes crossing the fiber in transmission is also presented. [ABSTRACT FROM AUTHOR]

Low pathogenic avian influenza (LPAI) virus of subtype H9N2 is the most frequently detected subtype among domestic poultry and is a public health concern because of its zoonotic potential. Due to the multiple and complex routes of LPAIV H9N2 between geographic regions, little is known about the spatial diffusion of H9N2 virus to, within, and from Egypt, where it is endemic among poultry since 2011. Using close to 800 publicly available hemagglutinin (HA) segment nucleotide sequences, associated location and temporal data, we conducted a Bayesian discrete phylogeographic analysis. Here, we reconstructed and traced the origin, spread and principal transmission routes of H9N2 across large geographical regions, in addition to the transmission between Egypt and the rest of the world and between different Egyptian governorates. Our analysis suggests that during the last few decades, H9N2 has been introduced back and forth continuously between the countries where it is endemic. Amongst these regions, Saudi Arabia, United Arab Emirates and Iraq act as main distribution hubs and drive the viral migration worldwide, with bi-directional and long-distance diffusions. It is noteworthy that H9N2 was introduced once to Egypt via Israel in mid 2009, and that the descendants of the Egyptian LAIVs H9N2 were back-transmitted to Israel in 2015. Additionally, governorates in middle Egypt (Giza, Fayoum and Bani Souwaif) are major hubs in the LPAIV H9N2 transmission network in Egypt. This knowledge highlights that H9N2 is both a global and a national concern and can aid in updating the surveillance program and vaccine strain selection., (Copyright © 2020 Li, Adel, Bohlin, Lundkvist, Olsen, Pettersson and Naguib.)

Since the introduction of H9N2 low pathogenic avian influenza virus in Egypt, it became an endemic disease causing considerable economic losses in different poultry sectors especially in the presence of other secondary bacterial and viral infections. The H9N2 viruses in Egypt are in continuous evolution that needs deep analysis for their evolution pattern based on the genetic constitutions of the pathogenic determinant genes (HA, PB2, PB1, PA, and NS). In this work, samples were collected from the backyard chickens from 3 Egyptian governorates. Five selected viruses were sequenced and analyzed for the hemagglutinin gene which showed genetic relatedness to the Asian G1 lineage group B, similar to the circulating H9N2 viruses in Egypt since 2013. The sequence for PB2, PB1, PA, HA and NS genes of the selected five viruses indicate a natural re-assortment event with recent Eurasian subtypes and similar to Egyptian H9N2 virus isolated from pigeon in Egypt during 2014. The Egyptian viruses of our study possess amino acids signatures including S42, V127, L550, L672 and V504 in the internal genes NS1, PA, and PB2, of respectively of an impact on virus transmission and replication. This work indicates that the H9N2 is in continuous evolution with alarming to the reassortment occurrence., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)