Insights into the genetic evolution of duck hepatitis a virus in Egypt

Duck hepatitis virus (DHV) is one of the commercially important diseases of ducklings worldwide. It is an acute and highly infectious disease of ducklings caused by three different sero-types (1–3) of duck hepatitis A virus (DHAV), and serotype 1 is the most common in poultry. To date, little is known about the prevalence and genetic characterisation of DHAV-1 in Egypt. In the current study, isolation and complete genomic analyses of DHAVs circulating in commercial duck farms in different Egyptian governorates were conducted. A total of eighteen samples were collected from six Egyptian governorates of 3–11 days old ducklings (Pekin and Mullard) with a his-tory of nervous signs and high mortality rates. Five out of eighteen (5/18) samples were screened positive for the DHAV-1 based on the VP1 gene. These samples were individually used for virus isolation in embryonated duck embryos (EDE), followed by complete genome sequencing. Phylo-genomic analyses showed that DHAV serotype I; genotype I were diversified into four different groups (1, 2, 3 and 4). Most of the recent circulating Egyptian DHAV strains are clustered within group 4, while isolates characterised within this study were clustered within group 1. Recombination analyses revealed that the emergence of a new recombinant virus—DHAV-1 strain Egypt-10/2019—through recombination. Likewise, the selective pressure analyses showed the existence, inside or near areas of the viral attachment or related functions, of positive scores highlighting the importance of natural selection and viral evolution mechanism at different protein domains. The findings of this study provide updated information on the epidemiological and genetic features of DHAV-1 strains and underscore the importance of DHAV surveillance as well as re-evaluation for currently used vaccines

Comparative infectivity and transmissibility studies of wild-bird and chicken-origin highly pathogenic avian influenza viruses H5N8 in chickens

Despite the recent advances in avian influenza viruses surveillance and genomic data, fundamental questions concerning the ecology and evolution of these viruses remain elusive. In Egypt, H5N8 highly pathogenic avian influenza viruses (HPAIVs) are co-circulating simultaneously with HPAIVs of subtypes H5N1 and low-pathogenic avian influenza viruses (LPAIVs) of subtype H9N2 in both commercial and backyard poultry. In order to isolate AIVs from wild birds and to assess their potential in causing infection in commercial poultry, a total of thirty-four cloacal swab samples were collected from apparently healthy migratory wild birds (Anas acuta, Anas crecca, Rallus aquaticus, and Bubulcus ibis) from four Egyptian Governorates (Giza, Menoufia, Gharbia, and Dakahlia). Based on matrix (M) gene-targeting real-time reverse transcriptase PCR and subsequent genetic characterization, our results revealed two positive isolates (2/34) for H5N8 whereas no H5N1 and H9N2 subtypes were detected. Genetic characterization of the full-length haemagglutinin (HA) genes revealed the clustering of two reported isolates within genotype 5 of clade 2.3.4.4b. The potential of a wild bird-origin H5N8 virus isolated from a cattle egret for its transmission capability within and between chickens was investigated in compare to chicken origin H5N8 AIV. Chickens inoculated with cattle egret isolate showed varying clinical signs and detection of virus shedding. In contrast, the contact chickens showed less levels of virus secretion indicating efficient virus inter/intra-species transmission. These results demonstrated the possibility for spreading of wild bird origin H5N8 viruses between chicken. In conclusion, our study highlights the need for continuous and frequent monitoring of the genetic diversity of H5N8 AIVs in wild birds as well as commercial poultry sectors for better understanding and determining the genetic nature of these viruses, which is fundamental to predict any future threat through virus reassortment with the potential to threaten human and animal health. Likewise, an assessment of coverage and efficacy of different vaccines and or vaccination regimes in the field conditions should be reconsidered along with strict biosecurity measures

Transgenic chicks expressing interferon-inducible transmembrane protein 1 (Ifitm1) restrict highly pathogenic h5n1 influenza viruses

Mammalian cells utilize a wide spectrum of pathways to antagonize the viral replication. These pathways are typically regulated by antiviral proteins and can be constitutively expressed but also exacerbated by interferon induction. A myriad of interferon-stimulated genes (ISGs) have been identified in mounting broad-spectrum antiviral responses. Members of the interferon-induced transmembrane (IFITM) family of proteins are unique among these ISGs due to their ability to prevent virus entry through the lipid bilayer into the cell. In the current study, we generated transgenic chickens that constitutively and stably expressed chicken IFITM1 (chIFITM1) using the avian sarcomaleukosis virus (RCAS)-based gene transfer system. The challenged transgenic chicks with clinical dose 104 egg infective dose 50 (EID50 ) of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 (clade 2.2.1.2) showed 100% protection and significant infection tolerance. Although challenged transgenic chicks displayed 60% protection against challenge with the sub-lethal dose (EID50 105 ), the transgenic chicks showed delayed clinical symptoms, reduced virus shedding, and reduced histopathologic alterations compared to non-transgenic challenged control chickens. These finding indicate that the sterile defense against H5N1 HPAIV offered by the stable expression of chIFITM1 is inadequate; however, the clinical outcome can be substantially ameliorated. In conclusion, chIFITM proteins can inhibit influenza virus replication that can infect various host species and could be a crucial barrier against zoonotic infections. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

Biological characterization of wild-bird-origin avian avulavirus 1 and efficacy of currently applied vaccines against potential infection in commercial poultry

Newcastle disease virus (NDV), the type member of the species Avian avulavirus 1 (formerly known as avian paramyxovirus serotype 1), causes a highly contagious and economically important disease in a myriad of avian species around the globe. While extensive vaccination programs have been implemented in ND-endemic countries, the disease is continuously spreading in commercial, backyard, and wild captive poultry. In order to investigate the evolution of the virus and assess the efficiency of the vaccine regimens that are currently being applied in commercial poultry, four wild-bird-origin NDV strains were characterized biologically, based on mean death time and intracerebral pathogenicity index, and genetically, based on the cleavage motif (112RRQKRF117) in the fusion (F) protein. Based on these features, all of the isolates were characterized as velogenic strains of NDV. Phylogenetic analysis based on the complete genome sequence revealed clustering of these isolates within class II, genotype VII. This class of NDV remains the predominant genotype in the Egyptian poultry industry, as well as in those of many Asian and African countries. To investigate the potential of these wild-bird-origin NDV isolates to cause infection in domesticated poultry and to assess the efficacy of currently available vaccines for protection of commercial poultry, an extensive animal challenge experiment was performed. Cumulative clinicopathological and immunological investigations of virus-challenged chickens indicate that these isolates can potentially be transmitted between chicken and cause systemic infections, and the currently applied vaccines are unable to prevent clinical disease and virus shedding. Taken together, the data represent a comprehensive evaluation of the ability of Egyptian wild-bird-origin NDV strains to cause infection in commercial poultry and highlights the need for a continuous and large-scale surveillance as well as revised vaccine approaches. These integrated and multifaceted strategies would be crucial in any efforts to control and eradicate the disease globally

Quaternary structure independent folding of voltage-gated ion channel pore domain subunits

Every voltage-gated ion channel (VGIC) has a pore domain (PD) made from four subunits, each comprising an antiparallel transmembrane helix pair bridged by a loop. The extent to which PD subunit structure requires quaternary interactions is unclear. Here, we present crystal structures of a set of bacterial voltage-gated sodium channel (BacNaV) 'pore only' proteins that reveal a surprising collection of non-canonical quaternary arrangements in which the PD tertiary structure is maintained. This context-independent structural robustness, supported by molecular dynamics simulations, indicates that VGIC-PD tertiary structure is independent of quaternary interactions. This fold occurs throughout the VGIC superfamily and in diverse transmembrane and soluble proteins. Strikingly, characterization of PD subunit-binding Fabs indicates that non-canonical quaternary PD conformations can occur in full-length VGICs. Together, our data demonstrate that the VGIC-PD is an autonomously folded unit. This property has implications for VGIC biogenesis, understanding functional states, de novo channel design, and VGIC structural origins

Evolutionary Trajectories of Avian Avulaviruses and Vaccines Compatibilities in Poultry.

Newcastle disease virus (NDV) causes one of the highly infectious avian diseases in poultry leading to genuine financial misfortunes around the world. Recently, there has been an increasing trend in the number of ND-associated outbreaks in commercial Jordanian poultry flocks indicating a possible complex evolutionary dynamic of NDV infections in the country. To underpin the dynamics of circulating NDV strains and to assess the vaccine-escape potential, a total of 130 samples were collected from different poultry flocks in six Jordanian Governorates during 2019-2021. Twenty positive isolates, based on real-time reverse transcriptase PCR, were used for further genetic characterization and evolutionary analysis. Our results showed that there is a high evolutionary distance between the newly identified NDV strains (genotype VII.1.1) in this study and the commercially used vaccines (genotypes I and II), suggesting that circulating NDV field strains are under constant evolutionary pressure. These mutations may significantly affect flocks that have received vaccinations as well as flocks with insufficient immunity in terms of viral immunity and disease dynamics. To assess this further, we investigated the efficacy of the heterologous inactivated LaSota or homologous genotype VII.1.1 vaccine for their protection against virulent NDV in chicken. Vaccine-induced immunity was evaluated based on the serology, and protection efficacy was assessed based on clinical signs, survival rates, histopathology, and viral shedding. Chickens vaccinated with the inactivated genotype VII.1.1 based vaccine showed 100% protection with a significant reduction in virus shedding, and ameliorated histopathology lesions compared to LaSota vaccinated chicks that showed 60% protection. These results revealed that the usage of NDV inactivated vaccine from the circulating field strains can successfully ameliorate the clinical outcome and virus pathobiology in vaccinated chicks and will serve as an effective vaccine against the threat posed by commonly circulating NDV strains in the poultry industry

Antiviral Nanomedicine‑Based Approaches against Epstein‑Barr Virus Infection

Purpose of Review The Epstein-Barr virus (EBV) is a common virus around the globe with approximately 98% of adults testing positive against EBV. However, EBV infection typically begins early in the childhood. Owing to the ability to infect various body organ, EBV is linked to a broad spectrum of symptoms, diseases, and inflammatory conditions. Moreover, since EBV exists in both latent and replicating forms in most healthy individuals, any disruption in the balance between the virus and its host can lead to the development of different diseases, including autoimmune disorders and cancer. Given these circumstances, we draw attention to the crucial need for developing prophylactic measures and treatments for EBV and its associated diseases. Recent Findings We propose leveraging the advantages of nanomedicine, such as ferritin and iron oxide nanoparticles, for the creation of EBV vaccines. These advancements can also be applied to developing drugs to treat EBV-associated diseases, such as cancer, autoimmune disorders, and cytokine storm syndrome. Summary We emphasize the urgency of having accessible EBV vaccines, as well as effective treatments for EBV-related diseases, especially when early diagnosis is involved. This approach, which includes comprehensive cytokine profiling for patients, can significantly enhance the effectiveness of treatment programs

STRUCTURAL STUDIES OF UBIQUITIN-BINDING ZINC FINGER DOMAINS IN THE NUCLEAR FACTOR KAPPA B PATHWAY

Nuclear factor kappa B (NF-KB) is a key mediator of innate and adaptive immuneresponse. lncorrect regulation of NF-KB pathway has been linked to immune andinflammatory disease as well as cancers. TAX1-binding protein 1 (TAX1BP1) is anegative regulator of TNF-alpha- and IL-1β-induced NF-KB activation. TAX1BP1comprises two C-terminal zinc finger domains that bind to mono- and polyubiquitin,which are needed for TRAF6 (TNF-associated factor-6) or RIP1 (receptor interactingprotein-1) association followed by recruitment of A20 deubiquitinase (DUB), resulting inNF-KB inhibition. TAX1BP1 acts as an adaptor protein, facilitating the process of de-ubiquitination of target protein, resulting in the down regulation of the NF-KB pathway.ln order to acquire a better understanding of the molecular interaction between theubiquitin zinc finger binding (UBZ) domain and ubiquitin, TAX1BP1 UBZ domaininteraction with mono-ubiquitin and different polyubiquitin chains were investigated inthis study. TAX1BP1 UBZ domain showed remarkable difference in terms of bindingaffinities to monoubiquitin and polyubiquitin chains, as data reveals that there is asignificantly higher binding affinity to polyubiquitin (linear, lysine 63 and lysine 48linked diubiquitin) chains over monoubiquitin.The crystal structure of the C-terminal UBZ domains of TAX1BP1 in fusion with greenFluorescence Protein (GFP) was solved at 2.8 Å resolution. The crystal structure showstwo tandem zinc fingers of the classical type C2H2, owing to the zinc coordinatingatoms, both having a β-β-α fold. Other members of the same C2H2 UBZ family areproposed to bind ubiquitin exclusively through the α-helix in a manner similar to theinverted ubiquitin-interacting motif (IUIM). Superposition of the α-helix of the UBZdomain of TAX1BP1 to existing structural models indicates similar conformation of theubiquitin binding surface. However, through biochemical experiments, a model ofmonoubiquitin/diubiquitin UBZ domain complex is proposed, indicating a new mode ofinteraction between ubiquitin and UBZ domain of TAX1BP1, giving an insight to themechanism of ubiquitin recognition by TAX1BP1, and its function in the NF-KBpathway.Ubiquitin can be assembled in chains; the topology and signaling characteristics of these chains vary depending on the type of the linkage, adding an extra level of complexity in signaling. "Linear" polyubiquitin chain is a type of polyubiquitin assembly found recently, where ubiquitin moieties are threaded head to tail, and not like the classical lysine linked polyubiquitin chains. Linear polyubiquitin plays an indispensible role in the NF-KB pathway. The crystal structure of linear diubiquitin was solved at 1.9 Å resolution,giving a closer understanding of the mechanism of interactions. It is shown that linear diubiquitin can acquire more than one conformation in solution to meet the surface and chemical complementarities of the cognate domains, and also emphasizing the importance of the linker region, between the two ubiquitin moieties which plays a pivotal role in the process of specific recognition

Efficacy of composting poultry mortality and farms wastes with mixed respiratory infection viruses H9N2 and NDV in Egypt

Composting poultry mortality and farm wastes infected with mixed respiratory infection viruses one of major goals for control and combating this infection. To achieve fair level of biosecurity protocol in poultry farms infected with virus induced mortality, proper hygienic disposing is imperative from socioeconomic and health risk concept. Collected fresh dead birds, their litter and wastes from commercial flocks with high mortalities associated with mixed respiratory symptoms were subjected to composting process. Molecular characterization of avian influenza virus (H9N2) and Newcastle disease virus (H9N2 & NDV) were recorded from cecal tonsils and trachea respectively of morbid and dead chickens before subjecting to composting. Characterization was done by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) using specific primers targeting the matrix (M) gene, H9 gene of AIVs and fusion (F) gene of NDV were used. The (HA) hemagglutinin glycoprotein gene of H9N2 isolates were partially amplified by RT-PCR, directly sequenced. The nucleotide and amino acid sequence analysis of the hemagglutinin gene of the characterized Egyptian viruses showed the highest similarity with one group of recent Israeli circulating strains. The Phylogenetic analysis for HA gene of H9 AIV showed the placement of the Egyptian viruses within the same lineage of H9N2 viruses that circulated in the region from 2006 especially with recent Israeli strains of G1 lineage (group B). Failure of re-characterization of AIV (H9N2) and NDV in the current work on day 15th of composting treatment confirmed the efficacy of composting poultry farm mortalities and wastes. Composting in closed vessel (newly designed closed copmposter) achieved proper secure microbial activity that inactivated H9N2 AIV and NDV viruses via increased temperature and decreased moisture content of composting poultry mortality and farms wastes with no isolation and characterization of these viruses. The product suggested to be used for agronomic activities

Efficacy of composting poultry mortality and farms wastes with mixed respiratory infection viruses H5N1 and H9N2 in Egypt

Proper hygienic disposing of dead poultry with respiratory infection and their wastes is imperative from socioeconomic concept. Composting is one of disposing methods and represents a major goal for control and combating this infection. Collected fresh dead birds as well their litter and wastes from broiler farms with high mortalities associated mixed respiratory symptoms were subjected to composting process. The avian influenza viruses (H5N1 & H9N2) were isolated and characterized phenotypically and genotypically from trachea prior subjecting to composting. Compost mix was kept in environmentally controlled composter from 1-28 days (end experiment). Monitoring thermal profile of the composting process was recorded. Failure of re-isolation and characterization of AIV (H5N1 & H9N2) in current work on days 15th confirmed the efficacy of composting poultry farms mortality and wastes with special concern to the current isolated classical AIV H5N1 and H9N2. Secured Composting potentiated microclimatic determinants for both virus strains (heat and dryness) with failure of re- characterization from field dead birds and their wastes. Composting suggested being a reliable, environmentally safe way to dispose poultry mortality and wastes infected with mixed respiratory infection viruses H5N1 and H9N2