Newcastle disease virus (NDV) infections are one of the most devastating causes of economic losses in the poultry industry and despite extensive vaccination, outbreaks are being reported around the globe especially from developing and tropical countries. Analysis of NDV field strains from vaccinated flocks would highlight essential areas of consideration not only to design effective immunization strategies but also to devise vaccines that provide sterile immunity. For this purpose, 91 NDV suspected outbreaks were investigated and screened for NDV genetic material. A total of 16 NDV-positive isolates were examined using biological, genetics and bioinformatics analysis to assess the epidemiological association and to identify motifs that are under vaccine-induced immune pressures. In line with the clinical outcomes, all isolates showed the RRQKR|F cleavage motif and phylogenetic analysis revealed grouping of isolates into the genotype VII, and specifically sub-genotype VIId. Further analysis of the putative fusion protein sequence showed a number of substitutions (n=10) in functionally important domains and based on these differences, the studied isolates could be categorized into four distinct groups (A-D). Importantly, two residues (N and K) were conserved in the commercial live vaccine and Egyptian field strains that are present in class II, genotype II. Collectively, these data enhance our knowledge of the evolution of genotype VIId NDV under the vaccine-induced immune pressures. In addition, our findings suggest that the use of genotype II-type vaccines in Egypt may be implicated in the emergence of new variants rather than providing benefits against NDV infections.

During hepatitis B virus (HBV) infections, subviral particles (SVP) consisting only of viral envelope proteins and lipids are secreted. Heterologous expression of the small envelope protein S in mammalian cells is sufficient for SVP generation. S is synthesized as a transmembrane protein with N-terminal (TM1), central (TM2), and hydrophobic C-terminal (HCR) transmembrane domains. The loops between TM1 and TM2 (the cytosolic loop [CL]) and between TM2 and the HCR (the luminal loop [LL]) are located in the cytosol and the endoplasmic reticulum (ER) lumen, respectively. To define the domains of S mediating oligomerization during SVP morphogenesis, S mutants were characterized by expression in transiently transfected cells. Mutation of 12 out of 15 amino acids of TM1 to alanines, as well as the deletion of HCR, still allowed SVP formation, demonstrating that these two domains are not essential for contacts between S proteins. Furthermore, the oligomerization of S was measured with a fluorescence-activated cell sorter (FACS)-based Förster resonance energy transfer (FRET) assay. This approach demonstrated that the CL, TM2, and the LL independently contributed to S oligomerization, while TM1 and the HCR played minor roles. Apparently, intermolecular homo-oligomerization of the CL, TM2, and the LL drives S protein aggregation. Detailed analyses revealed that the point mutation C65S in the CL, the mutation of 13 out of 19 amino acids of TM2 to alanine residues, and the simultaneous replacement of all 8 cysteine residues in the LL by serine residues blocked the abilities of these domains to support S protein interactions. Altogether, specific domains and residues in the HBV S protein that are required for oligomerization and SVP generation were defined. The small hepatitis B virus envelope protein S has the intrinsic ability to direct the morphogenesis of spherical 20-nm subviral lipoprotein particles. Such particles expressed in yeast or mammalian cells represent the antigenic component of current hepatitis B vaccines. Our knowledge about the steps leading from the initial, monomeric, transmembrane translation product of S to SVP is very limited, as is our information on the structure of the complex main epitope of SVP that induces the formation of protective antibodies after vaccination. This study contributes to our understanding of the oligomerization process of S chains during SVP formation and shows that the cytoplasmic loop, one membrane-embedded domain, and the luminal loop of S independently drive S-S oligomerization.

Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean  strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa.

The hepatitis B virus (HBV Hepatitis B virus (HBV) has infected more than 40% of the living human population and causes 240 million persistent infections (1). The treatment of chronic infections is limited to date to use of inhibitors of the viral reverse transcriptase and stimulation of the immune system by interferon. Alternative antiviral strategies are desirable.During HBV replication, an RNA molecule (pregenome) is packaged together with the reverse transcriptase by 180 or 240 copies of the viral core protein. The assembled particle is an icosahedron with T ϭ 3 or T ϭ 4 symmetry and has a diameter of approximately 30 nm. The pregenome serves as a template for the synthesis of the viral DNA genome by reverse transcription occurring in the lumen of the capsid (2). This particle can then be enveloped by the three viral transmembrane surface proteins S, M, and L at an intracellular membrane, and the resulting virion is subsequently secreted from the host cell (3). Interestingly, the immature capsid containing the pregenome is not enveloped, in contrast to the case for the mature, DNA-containing capsid (4). Apparently, a structural change of the capsid surface is coupled to the synthesis of the viral DNA genome (5).Heterologous expression of the core protein in eukaryotic cells and even in bacteria leads to capsids almost indistinguishable from authentic capsids with respect to their antigenicity and appearance by electron microscopy. The C-terminal 30-amino-acid (aa)-long region of the core protein is very rich in arginine residues and has nucleic acid binding properties. Deletion of this domain is compatible with capsid formation (6).The budding of mature capsids is supported by cellular factors involved in multivesicular body formation (7). In addition, budding is dependent on a linear, 22-aa-long domain (matrix domain [MD]) of the surface protein L exposed at the cytoplasmic side of the cellular membrane and on a region on the capsid surface (matrix binding domain [MBD]) comprised of a ring-like groove around the base of the spike protruding from the capsid and a small area close to the pores of the capsid shell (8). Numerous single point mutations in either of the two domains block nucleocapsid envelopment (9, 10). It seems conceivable that the two