Co-circulation of GI.1 and GI.2 genotypes of rabbit hemorrhagic disease virus in Egypt

Recently, Egypt has experienced an increased incidence of rabbit hemorrhagic disease virus (RHDV) infection even among vaccinated rabbits. The present study estimates the emergence of RHDV in vaccinated (n = 10) and unvaccinated (n = 8) domestic rabbitries in Beheira and Kafr El-Sheikh provinces, Egypt, during the period 2018-2020. A total of 8 out of 18 (44.4%) liver extracts were able to agglutinate human type O RBCs with HA titers ranged from 8 to 12 log2, and then subsequently confirmed for the presence of RHDV RNA using a reverse transcriptase-polymerase chain reaction (RT-PCR). The VP60 gene sequences of three selected isolates, designated Beh-1, Beh-9 and kaf-14, were submitted to the GenBank database and the accession numbers MZ782083 to MZ782085 were assigned, respectively. Phylogenetic analysis revealed that the Kaf-14 isolate was placed into the GI.1 genotype, while the Beh-1 and Beh-9 isolates were grouped into the GI.2 genotype. Overall, the three isolates shared 78.6-98.7%.nucleotide identity with previously published Egyptian sequences. In comparison with the GI.1a Giza2006 vaccine strain, the three isolates exhibited divergence ranging from 4.5 to 17.4% at the amino acid level. Approximately 55.5-87.5% of the amino acid substitutions were located in the P2 subdomain of the VP60 capsid protein which contains the main determinants of antigenicity and cellular recognition. In conclusion, our results provide crucial evidence for the co-circulation of RHDV GI.1 and GI.2 genotypes in Egypt and highlight the antigenic diversity among vaccine and field strains. Therefore, new effective vaccines are urgently required to counter the spread of GI.1 and GI.2 genotypes in Egypt.

Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation

Infectious bronchitis virus (IBV), a gamma-coronavirus, causes infectious bronchitis (IB), a major respiratory disease of chicken. Its high mutation rate in conjunction with recombination of the RNA genome constantly creates IBV variants that are difficult to control by currently available vaccines. In this study, we addressed the question whether small-scale holdings might harbor IBV variants that serve as a reservoir for newly emerging variants. Egyptian IBV isolate EGY/NR725/2016 (NR725/16) from a small-scale broiler farm was assigned to genotype I, clade 23 (S1:GI-23), based on partial S1 gene sequences and corroborated by full genome sequencing. Analysis of the S1 gene established three subclades for historical IBV strains (S1:GI-23.1, S1:GI-23.2.1 and S1:GI-23.2.2) and confirmed NR725/16 as being part of a separate fourth subclade (S1:GI-23.3). Samples from the years 2018 and 2019 revealed that the new subclade prevails in Egypt, carrying fixed mutations within the hypervariable regions (HVR) 1-3 of the S1 protein that affect two neutralization sensitive epitopes at sites 294F, 297S and 306Y (48.2) and 329R (62.1). In addition, recombination was recognized in isolate NR 725/16, with intra-subtype mixing for the entire genes 3ab and E and inter-subtype mixing for the entire gene 6b with a close match to QX like viruses of genotype GI-19. Further analysis of gene 3ab detected the homologous gene pool to NR725/16 in samples from 2013 (3ab:C) and closely related 3ab genotypes in IBV Egyptian isolates from 2016, 2018 and 2019. These data prove a flourishing exchange between poultry holdings with a common gene pool. The continued circulation of viruses harboring genes S1:GI-23.3 and 3ab:C indicates an evolutionary advantage of this combination possibly by combining antigenic escape with modulated pathogenicity to facilitate IBV spread in the vaccinated poultry population in Egypt.