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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.

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.

Traditional live Infectious Bursal Disease virus (IBDV) vaccines were thought to have some degree of adverse effect on bursa of fabricous of chickens, which in turn may interfere with antibodies production against other poultry vaccines. In this study, 15 broiler flocks vaccinated against avian influenza (AI) virus were sampled for serum. The flocks have received IBDV vaccination either by the conventional live vaccines or with the new recombinant subunit vaccine. Haemagglutination inhibition (HI) test were carried on sera using different AI antigens. Sera measured by the variant A/chicken/Egypt/VRLCU67/2011(H5N1) isolate showed significant difference (P