Infectious bronchitis virus (IBV) continues to circulate worldwide, with a significant impact on the poultry industry and affecting both vaccinated and unvaccinated flocks. Several studies have focused on the hypervariable regions (HVRs) of the spike gene (S1); however, genetic and bioinformatics studies of the whole S1 gene are limited. In this study, the whole S1 gene of five Egyptian IBVs was genetically analyzed. Phylogenetic analysis revealed that the Egyptian IBVs are clustered within two distinct groups: the classic group resembling the GI-1 genotype (vaccine strains) and the variant group (field strains) of the GI-23 genotype. The variant genotype was divided into two distinct subgroups (Egy/var I and Egy/var II) resembling the Israeli variants IS/1494 and IS885 strain, respectively. Significant amino acid sequence differences between the two subgroups, especially in the epitope sites, were identified. A deletion at position 63 and an I69A/S substitution mutation associated with virus tropism were detected in the receptor-binding sites. The deduced amino acid sequence of HVRs of the variant subgroups indicated different genetic features in comparison to the classic vaccine group (H120 lineage). The Egyptian variant IBVs also contained additional N-glycosylation sites compared to the classical viruses. Recombination analysis gave evidence for distinct patterns of origin by recombination throughout the S1 gene, suggesting that the recent virus IBV-EG/1586CV-2015 emerged as a recombinant of two viruses from the variant groups Egy/var I and Egy/var II, providing another example of intra-genotypic recombination among IBVs and the first example of recombination within the GI-23 genotype. Our data suggest that both mutation and recombination may be contributing to the emergence of IBV variants. Moreover, we found that the commercially used vaccines are genotypically distant from the circulating field strains. Hence, continuous follow-up of the current vaccine strategy is highly recommended for better control and prevention of infectious bronchitis virus in the poultry sector in Egypt.

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Wild migratory birds have the capability to spread avian influenza virus (AIV) over long distances as well as transmit the virus to domestic birds. In this study, swab and tissue samples were obtained from 190 migratory birds during close surveillance in Egypt in response to the recent outbreaks of the highly pathogenic avian influenza (HPAI) H5N1 virus. The collected samples were tested for a variety of AIV subtypes (H5N1, H9N2, H5N8, and H6N2) as well as other pathogens such as NDV, IBV, ILT, IBDV, and WNV. Among all of the tested samples, the HPAI H5N1 virus was found in six samples; the other samples were found to be negative for all of the tested pathogens. The Egyptian HPAI H5N1 strains shared genetic traits with the HPAI H5N1 strains that are currently being reported in Europe, North America, Asia, and Africa in 2021–2022. Whole genome sequencing revealed markers associated with mammalian adaption and virulence traits among different gene segments, similar to those found in HPAI H5N1 strains detected in Europe and Africa. The detection of the HPAI H5N1 strain of clade 2.3.4.4b in wild birds in Egypt underlines the risk of the introduction of this strain into the local poultry population. Hence, there is reason to be vigilant and continue epidemiological and molecular monitoring of the AIV in close proximity to the domestic–wild bird interface.

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