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Infectious bronchitis virus (IBV) affects both vaccinated and unvaccinated flocks worldwide, with a significant impact on the poultry industry. The aim of the present study is to characterize an emerging variant pathogenic IBV originating from field outbreaks in vaccinated Egyptian layer flock. Samples were collected from disease-suspected flock with a history of administration of live and inactivated IBV vaccines (Ma5 type). Virus propagation in embryonated chicken eggs (ECEs), after three successive passages, revealed typical IBV lesions such as curling and dwarfism. The reported isolate was identified by a real-time reverse transcriptase PCR assay targeting nucleocapsid (N) gene and, further characterized by full-length spike (S1) gene sequencing. Phylogenetic analysis revealed clustering of the isolated virus within 4/91 genotype of GI-13 lineage. Deduced amino acid sequences identity revealed 75–76% and 88–90% similarity with the currently used classic (H120, Ma5, and M41) and variant vaccine strains (4/91 and CR88) in Egypt, respectively. Recombination analysis gave an evidence for distinct patterns of origin for the studied isolate providing another example of intra-genotypic recombination among IBVs and the first example of recombination within the GI-13 lineage in the Egyptian field. The studied isolate (IBV/CK/EG/Fadllah-10/2019) emerged as a result of recombination between the variant group (Egy/var I genotype, GI-23 lineage) as a major parent and the CR88 variant vaccine strain (4/91 genotype, GI-13 lineage) as minor parent. Our data suggest that both mutation and recombination may be contributing to the emergence of IBV variants which ascertain the importance of disease monitoring in vaccinated flocks as well as re-appropriation for the current vaccine strategies. Electronic supplementary material The online version of this article (10.1007/s11262-019-01693-9) contains supplementary material, which is available to authorized users.

This study aimed to replace liquid foot pan in the poultry farm, with a novel model that is used more effectively in biosecurity program convenient with the workers in Egyptian farms that avoid foot pan. This novel model dry foot pan, semiliquid (wet) foot pan and floor mat that enabled the disinfectants to be worked for a longer time. In the present study authors are looking for a durable footbath, stable, fast, easily applied and log acting in the reduction of salmonellae. The efficacy of powder disinfectant (calcium hypochlorite powder, Halamid, Staldren, Virkon S and paraformaldehyde) were tested against salmonellae in a novel form of foot pan dry, semi-liquid and floor mat models. The disinfectants were diluted by calcium carbonate or sodium chloride powder in the dry form, surfactant in the semiliquid form and use of the sponge as a mat in the third form. Daily measurement of the active principle of the tested disinfectants and the log reduction of the Salmonellae were done. The dry form and semi liquid form of the Calcium hypochlorite was successfully effective for 10 days in dry form and 9 days in semiliquid form. However, Halamid and Staldren were successfully effective in dry form for 14 days and 17 days respectively, semiliquid form was worked for 21 day and 3 days and floor mat was effective for 21 days and 3 days respectively. Paraformaldehyde powder was also effective for 6 days in the dry form, but in the semiliquid form was effective for 10 days, floor mat was effective for 12 days. 5% Virkon S could be effective for 3 days in the dry form and semi-liquid form but only 2 days in the floor mat form.

Large-scale surveillance is crucial for understanding the evolution and the emergence of avian influenza viruses (AIVs) in endemic areas. Circulation of highly pathogenic avian influenza (HPAI) subtype H5N1 is continuously causing significant economic losses to the Egyptian poultry industry and is a threat to public health. In this report, a HPAI H5N1 strain (A/chicken/Egypt/Fadllah-7/2014) was detected from a vaccinated flock showing clinical signs of infection. Genetic characterization of the isolate indicated a high level of nucleotide identity (95-98%) with variant and classical groups of H5N1. Moreover, multiple-nucleotide and amino acid alignments revealed several prominent and characteristic substitutions in the surface glycoprotein, which may have biological relevance to the pathobiology of the virus. Phylogenetic analysis demonstrated that the reported isolate closely relates to H5N1 AIVs subclade 2.2.1.1 in spite of no reports of this subclade since 2011 from AI reported cases in Egyptian avian species. In conclusion, our results highlight the re-emergence of a novel H5N1 AIV variant subclade 2.2.1.1 that could escape immunity induced by vaccines. This discovery illustrates the importance of continuous monitoring of poultry in this country for controlling AIV including identifying sources of vaccine seed viruses.

Two HPAI H5N1 viruses were isolated from vaccinated layer and broiler commercial poultry farms in Egypt at years 2011 and 2013; respectively. By phylogenetic analysis, the viruses fall into two genetically diverse clades: (i) A/chicken/Egypt/VRLCU67/2011 classified as a variant virus, clade 2.2.1.1; and (ii) A/chicken/Egypt/13VIR3729-4/2013 classified as a classic virus, clade 2.2.1. Cross HI-test confirmed that the reaction between the two viruses is weak; furthermore, it showed the antigenic diversity between viruses belong to different clades and antigenic groups. Antigenic relatedness was calculated between six AI antigens and their antisera representing the different clades and antigenic groups circulated in Egyptian field; including the A/chicken/Egypt/VRLCU67/2011 strain which showed very low R-values with the other viruses’ groups; ranging from 17 % to zero. Results demonstrated the genetic and antigenic diversity of the variant viruses and how can the vaccine seed be a weak point in the vaccination program that could be broken by the drifted viruses antigenically distant from the vaccine strain.

Necrotic enteritis and the subclinical form of Clostridium perfringens infection in poultry are caused by C. perfringens type A, producing the alpha toxin, and to a lesser extent type C, producing both alpha toxin and beta toxin C and have become serious threats to poultry health.This study was undertaken to determine the activity of 4 commonly available disinfectants against C. perfringens spores after 5,7.5,10,15,30 and 60 minutes of contact under dirty conditions, Of the 4 products tested, calcium hypochlorite 1% and Germicidan KOK 4% achieved the required reduction in microbial viability (≥103-fold) for relatively long contact times of 30 min, under dirty (3% yeast) conditions, One product (Biosentury 904, 2% conc) achieved the required reduction in microbial viability (≥103-fold) for contact times of 10 minutes, while Prophyl 75,1% concentration. achieved the required reduction in microbial viability (≥103-fold) for contact times of 5minutes.Upon addition of formic acid 2% and urea 1% the required reduction improved for (Biosentury 904, 2% conc) and Prophyl 75,1% concentration and achieved after 5 minutes and after 7.5 minutes for Germicidan KOK 4% while calcium hypochlorite was not improved by addition of formic acid 2% or urea 1%. Application of surface test using the four disinfectants was used alone and in combination with formic acid 2% or urea 1% showed nearly the same results obtained in the suspension test.