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A proper vaccination against avian influenza viruses in chicken can significantly reduce the risk of human infection. Egypt has the highest number of recorded humans highly pathogenic avian influenza (HPAI)-H5N1 infections worldwide despite the widespread use of homologous vaccines in poultry. Enhancing H5N1 vaccine efficacy is ultimately required to better control HPAI-H5N1. The aim of this study is to boost chicken immunity by combined with inactivated HPAI-H5N1 with selenium nanoparticles (SeNPs). The chickens groups 1-3 were fed diets supplemented with SeNPs concentrations (0.25, 0.5, and 1 mg/kg) for 3 weeks and then vaccinated (inactivated HPAI-H5N1). while groups 4,5 and 6 were fed with SeNPs free diets and administered with 0.5ml of the vaccine combined with 0.02, 0.06, and 0.1mg/dose of SeNPs and then all groups were challenged with homologous virus 3 weeks post-vaccination (WPV). Group 7, 8 were used as control positive and negative respectively. At 4, 5, and 6 WPV, antibody titer was considerably higher in the group fed a meal supplemented with 1 mg SeNPs/kg. In contrast, both methods of SeNPs supplementation significantly increased the Interleukin 2 (IL2), Interleukin 6 (IL6), and Interferon γ (IFNγ) expressions in the blood cells in a dose-dependent manner, with a higher expression observed in the group that was vaccinated with 0.1 mg/dose. After the challenge, all groups that received SeNPs via diet or vaccines dose showed significant reduction in viral shedding and milder inflammation in lung, trachea, spleen, and liver in addition to higher expression of IL2, IL6, and IFNγ, with the highest expression observed in the group that was vaccinated with 0.1mg/dose compared the plain vaccinated group. The groups of 1mg SeNPs/kg and combined vaccinated with 0.1mg/dose showed the best vaccine efficacy. However, the group vaccinated with 0.1mg/dose showed the earliest reduction in viral shedding. Overall, SeNPs supplementation in the diet and the administration of the vaccine formula with SeNPs could enhance vaccine efficacy and provide better protection against HPAI-H5N1 in chickens by enhancing cellular immunity and reducing inflammation. We recommend using SeNPs as a vaccine combination or feeding with diet to increase the immunity and vaccine efficacy against H5N1.

Background and Aim: The Marek's disease virus (MDV) is a neoplastic disease causing serious economic losses in poultry production. This study aimed to investigate MDV occurrence in poultry flocks in the Lower Egypt during the 2020 breakout and genetically characterized Meq, gL, and ICP4 genes in field strains of MDV. Materials and Methods: Forty samples were collected from different breeds from eight Egyptian governorates in 2020. All flocks had received a bivalent vaccine (herpesvirus of turkey FC-126 + Rispens CVI988). However, weight loss, emaciation, reduced egg production, paralysis, and rough/raised feather follicles occurred. Samples were collected from feather follicles, liver, spleen, and nerve tissue for diagnosis by polymerase chain reaction. MDV genetic characterization was then performed by sequencing the Meq, gL, and ICP4 genes of five positive samples representing different governorates and breeds. Results: A total of 28 samples were positive for MDV field strains, while two were related to MDV vaccinal strains. All samples tested negative for ALV (A, B, C, D, and J) and REV. Phylogenetic analysis of the Meq gene of sequenced samples revealed that all MDVs were related to the highly virulent European viruses (Gallid herpesvirus 2 ATE and PC12/30) with high amino acid (A.A.) identity 99.2-100%. Alternatively, there was low A.A. identity with the vaccine strains CVI988 and 3004 (up to 82.5%). These results indicate that further investigation of the efficacy of current Egyptian vaccines is required. The Egyptian strains also harbor a specific mutation, allowing clustering into two subgroups (A and B). By mutation analysis of the Meq gene, the Egyptian viruses in our study had R101K, P217A, and E263D mutations present in all Egyptian viruses. Furthermore, R176A and T180A mutations specific to our strains contributed to the high virulence of highly virulent strains. There were no mutations of the gL or ICP4 genes. Conclusion: Further studies should evaluate the protection contributed by current vaccines used in Egypt.

Fowl adenoviruses (FAdVs) are a large group of viruses of different serotypes. They are responsible for inclusion body hepatitis, adenoviral gizzard erosion, and hepatitis hydropericardium syndrome. The present study presents a comprehensive overview of FAdVs in Egypt, with a focus on the epidemiological features of virus serotypes across the country. We conducted molecular investigation of multiple FAdV species based on the genetic signature of hypervariable regions 1–4 in the loop1 (L1) region of the hexon gene. Epidemiologically, the Nile Delta governorates showed high positivity of FAdVs, which were more commonly found in broilers than in layers. Genetically, species D and serotype 8a/E dominated, and the findings also revealed the emergence of new FAdV serotypes 1, 3, and 8b. The comparative analysis of hypervariable regions in the L1 region of the hexon gene revealed variables specific to each virus serotype. In silico predictions of L1 region revealed variations in the molecular structure and predicted the antigenic epitopes which may affect the cross-antigenicity between the different FAdV species and serotypes., Fowl adenovirus, Loop1, HVRs, Egypt.

Background and Aim: Respiratory bacterial agents represent one of the most harmful factors that ordinarily threaten the poultry industry and usually lead to great economic losses. Meanwhile, there is a global demand to avoid the highly emerging antibiotic resistance and antibiotic residues in edible meat. Whereas, the use of alternatives became of great priority, especially for those substances extracted from natural plant origin. The study aimed to evaluate the antibacterial effect of cinnamon oil as a herbal extract on different respiratory bacterial agents. Materials and Methods: One hundred and fifty biological samples were collected through targeted surveillance for respiratory diseased poultry farms representing three governorates, from which bacterial isolation and identification, DNA sequencing of representative strains were performed. Furtherly, phenotypic and genotypic evaluation of the antibacterial effect of cinnamon oil was performed by minimum inhibitory concentration, agar disk diffusion, and virulence genes expression real-time polymerase chain reaction. Results: Cinnamon oil gave rise to acceptable degrees of virulence genes downregulation of 0.15, 0.19, 0.37, 0.41, 0.77, and 0.85 for Staphylococcus aureus sed gene, Escherichia coli stx1 gene, Avibacterium paragallinarum HPG-2 gene, Pasteurella multocida ptfA gene, Mycoplasma gallisepticum Mgc2 gene, and Ornithobacterium rhinotracheale adk gene, respectively. Phenotypically, using agar disk diffusion assay and broth microdilution susceptibility, cinnamon oil showed also tolerable results as it stopped the growth of S. aureus, E. coli, P. multocida, and A. paragallinarum with varying zones of inhibition. Conclusion: The encountered results declared the successful in vitro effect of cinnamon oil that recommends its application for living birds for future use as a safe antibacterial in the poultry industry.

AIMS: This study was designed to investigate, in an in vivo setting, the effects of single and combined infections with either Mycoplasma gallisepticum (MG) and/or Escherichia coli on the chicken immune response induced by Newcastle disease virus (NDV) vaccine. METHODS AND RESULTS: Humoral immunity was measured through detection of NDV antibody and anti‐NDV IgG titres using haemagglutination‐inhibition test and enzyme‐linked immunosorbent assay, respectively. In addition, the expression levels of pro‐inflammatory cytokines' genes (interleukin (IL) 6, IL4 and interferon (IFN) γ) were analysed using quantitative reverse transcription PCR. Significant (P

The emergence of extensive drug-resistant (XDR) Salmonella in livestock animals especially in poultry represents a serious public health and therapeutic challenge. Despite the wealth of information available on Salmonella resistance to various antimicrobials, there have been limited data on the genetic determinants of XDR Salmonella exhibiting co-resistance to ciprofloxacin (CIP) and tigecycline (TIG). This study aimed to determine the prevalence and serotype diversity of XDR Salmonella in poultry flocks and contact workers and to elucidate the genetic determinants involved in the co-resistance to CIP and TIG. Herein, 115 Salmonella enterica isolates of 35 serotypes were identified from sampled poultry (100/1210, 8.26%) and humans (15/375, 4.00%), with the most frequent serotype being Salmonella Typhimurium (26.96%). Twenty-nine (25.22%) Salmonella enterica isolates exhibited XDR patterns; 25 out of them (86.21%) showed CIP/TIG co-resistance. Exposure of CIP- and TIG-resistant isolates to the carbonyl cyanide 3-chlorophenylhydrazone (CCCP) efflux pump inhibitor resulted in an obvious reduction in their minimum inhibitory concentrations (MICs) values and restored the susceptibility to CIP and TIG in 17.24% (5/29) and 92% (23/25) of the isolates, respectively. Molecular analysis revealed that 89.66% of the isolates contained two to six plasmid-mediated quinolone resistance genes with the predominance of qepA gene (89.66%). Mutations in the gyrA gene were detected at codon S83 (34.62%) or D87 (30.77%) or both (34.62%) in 89.66% of XDR Salmonella. The tet(A) and tet(X4) genes were detected in 100% and 3.45% of the XDR isolates, respectively. Twelve TIG-resistant XDR Salmonella had point mutations at codons 120, 121, and 181 in the tet(A) interdomain loop region. All CIP and TIG co-resistant XDR Salmonella overexpressed ramA gene; 17 (68%) out of them harbored 4-bp deletion in the ramR binding region (T-288/A-285). However, four CIP/TIG co-resistant isolates overexpressed the oqxB gene. In conclusion, the emergence of XDR S. enterica exhibiting CIP/TIG co-resistance in poultry and humans with no previous exposure to TIG warrants an urgent need to reduce the unnecessary antimicrobial use in poultry farms in Egypt.

Newcastle disease (ND), caused by avian orthoavulavirus type‐1 (NDV), is endemic in poultry in many regions of the world and causes continuing outbreaks in poultry populations. In the Middle East, genotype XXI, , used to be present in poultry in Egypt but has been replaced by genotype VII. We investigated whether virus evolution contributed to superseding and focused on the antigenic sites within the Hemagglutinin‐Neuraminidase (HN) spike protein. Full length sequences of an NDV genotype VII isolate currently circulating in Egypt was compared to a genotype XXI isolate that was present as co‐infection with vaccine type viruses (II) in a historical virus isolated in 2011. Amino acid differences in the HN glycoprotein for both XXI and VII viruses amounted to 11.7% and 11.9 %, respectively, compared to the La Sota vaccine type. However, mutations within the globular head (aa 126‐570), bearing relevant antigenic sites, were underrepresented (aa divergence of 8.8% and 8.1 % compared to 22.4% and 25.6% within the protein domains encompassing cytoplasmic tail, transmembrane part and stalk regions (aa 1‐125) for genotypes XXI and VII, respectively). Nevertheless, reaction patterns of HN‐specific monoclonal antibodies inhibiting receptor binding revealed differences between vaccine type viruses and genotype XXI and VII viruses for epitopes located in the head domain. Accordingly, compared to Egyptian vaccine type isolates and the La Sota vaccine reference strain, single aa substitutions in 6 of 10 described neutralizing epitopes of HN were found. However, the same alterations in neutralization sensitive epitopes were present in old genotype XXI as well as in newly emerged genotype VII isolates. In addition, isolates were indistinguishable by polyclonal chicken sera raised against different genotypes including vaccine viruses. These findings suggest that factors other than antigenic differences within the HN protein account for facilitating the spread of genotype VII versus genotype XXI viruses in Egypt.

In late 2016, Egypt was subjected to multiple introductions of reassorted highly pathogenic avian influenza viruses (HPAI) subtype H5N8. In a previous study, we reported three distinct genotypes during the first wave of infection represented by CAO285, SS19, and F446 viruses that were isolated from wild birds, backyard, and a commercial farm, respectively. F466 has subsequently become the predominant genotype currently circulating in Egypt and has been implicated in the emerging of the H5N2 virus. In the present study, we investigated the difference in the pathogenicity and transmissibility of the three genotypes. The intravenous pathogenicity index (IVPI) ranged from 2.68 to 2.9. With the natural route of infection, all these strains took longer to cause mortality in comparison to S75 (HPAI-H5N1). When compared the H5N8 viruses to each other showed that F446 had high mortality rate after inoculation from original concentration of 106 and 104 EID50 of virus. Chickens inoculated with F446 showed the highest viral titer with significant differnt in all tested samples (H5N8 and H5N1 viruses) in experimental and sentinel contact chicken with more efficient transmission to sentinel contact birds and spread from contact to other birds. Histopathological findings revealed the H5N1 and H5N8 viruses affect all organs examined (lung, trachea, brain, spleen) with relatively different affect the S75 cauterized by early marked respiratory adverse effect and F446 & SS19 were characterized by early systematic pathological alteration with mild respiratory pathological changes. The efficient viral replication and transmissibility in the main bird species, like chicken in case of Egypt, represent a key element for the spread and maintains of certain influenza genotypes of H5N8 virus and decrease the incidence of H5N1.

Newcastle disease (ND), caused by avian orthoavulavirus type-1 (NDV), is endemic in poultry in the Middle East causing continuing outbreaks in poultry populations despite efforts to vaccinate. In the past, genotype 2.XXI (former 2.VI) was present in poultry in Egypt but has been replaced by genotype 2.VII. We investigated whether virus evolution contributed to superseding, and focused on the antigenic sites within the Heamagglutinin-Neuramindase (HN) spike protein. Full length sequences of a NDV genotype 2.VII isolate currently circulating in Egypt was compared to a genotype 2.XXI isolate that was present as co-infection with vaccine type viruses (2.II) in an historical isolate of the year 2011. Amino acid differences in the HN glycoprotein for both 2.XXI and 2.VII viruses amounted to 11,7% and 11,9 % compared to LaSota vaccine type. However, mutations within the globular head (aa 126-570), bearing relevant antigenic sites, were underrepresented (aa divergence of 8,8% and 8,1 % compared to 22,4% and 25,6% within the fragment encompassing cytoplasmic tail, transmembrane part and stalk regions (aa 1-125) for genotypes 2.XXI and 2.VII, respectively. Nevertheless, reaction patterns of HN-specific monoclonal antibodies revealed differences between vaccine type viruses and genotype 2.XXI and 2.VII viruses for specific epitopes. Accordingly, compared to Egyptian vaccine type isolates and the LaSota vaccine reference strain, single aa substitutions in 6 of 10 described neutralizing epitopes were found within the attachment protein. However, the same alterations in neutralization sensitive epitopes were present in old genotype 2.XXI as well as in newly emerged genotype 2.VII isolates. In addition, isolates were indistinguishable by polyclonal chicken sera raised against different genotypes including vaccine viruses. These findings suggest, that factors other than antigenic differences within the HN-protein account for facilitating spread of genotype 2.VII while displacing genotype 2.XXI viruses in Egypt.

Derzsy&rsquo, s disease causes disastrous losses in domestic waterfowl farms. A genetically variant strain of Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV) was named novel goose parvovirus (NGPV), which causes characteristic syndrome in young ducklings. The syndrome was clinically characterized by deformity in beaks and retarded growth, called short beaks and dwarfism syndrome (SBDS). Ten mule and pekin duck farms were investigated for parvovirus in three Egyptian provinces. Despite low recorded mortality rate (20%), morbidity rate was high (70%), but the economic losses were remarkable as a result of retarded growth and low performance. Isolation of NGPV was successful on primary cell culture of embryonated duck liver cells with a clear cytopathic effect. Partial gene sequence of the VP1 gene showed high amino acids identity among isolated strains and close identity with Chinese strains of NGPV, and low identity with classic GPV and MDPV strains. To the best of our knowledge, this can be considered the first record of NGPV infections in Egypt.

Immunosuppressive viral diseases have a great economic importance in the poultry industry due to the increased susceptibility to secondary infections. Chicken anaemia virus (CAV) is one of the major immunosuppressive diseases in chickens. In addition, low pathogenic avian influenza (LPAI) of subtype H9N2 and infectious bronchitis (IB) viruses are among the most frequently reported respiratory viral diseases in poultry worldwide. In the present study, specific pathogen free chickens were used to understand the impact of CAV on secondary infection with LPAI-H9N2 or IB viruses. Clinical outcomes, viral shedding dynamics, and cytokine levels wereassessed. The results exhibit that chickens previously infected with CAV produceconsiderablyhigher titresof LPAI-H9N2 or IB viruses in the oropharyngeal swabs (P

Duck hepatitis A virus (DHAV) causes acute hepatitis and mortality, resulting in high economic losses in the duck farm industry. The current study describes the outbreak of DHAV in vaccinated duck farms in North Egypt during 2019 and molecular characterization of the 3′ untranslated region (UTR) and viral protein VP1 genes. The 30 samples were collected from 7- to 28-day-old commercial Pekin ducks that showed a history of nervous signs and sudden deaths and were on farms in 6 governorates. DHAV was typed by reverse transcription–polymerase chain reaction (RT-PCR) for 3′ UTR and VP1 genes and revealed 20 positive farms, with the first detection of DHAV genotype 3 (DHAV-3) in 18 samples and the classic DHAV-1 in 2 samples. The phylogenetic analysis of VP1 and 3′ UTR genes of the nine selected strains representative of six governorates revealed that seven strains were clustered with DHAV-3 Chinese and Korean-Vietnamese strains within different subgroups with 92.4%–93.7% amino acid identity; such strains were distinguishable from the vaccine strain of DHAV-1 used in Egypt with 74.4% amino acid identity. The other strains were closely related to the DHAV-1 Asian strain and the vaccine strain used in Egypt with 98.7%–99.6% amino acid identity for the VP1 gene with different clustering than that of recently isolated DHAV-1 Egyptian strains. The VP1 gene of DHAV-3 had 1 hypervariable region (HVR) with 10 amino acid mutations compared with DHAV3/DN2/Vietnam/2011, but DHAV-1 had 3 HVRs with 1 amino acid mutation in HVRII compared with the DHAV-1 vaccine strain. In conclusion, a new introduction of DHAV-3 with the classical DHAV-1 was recorded in Pekin duck farms in North Egypt that is genetically distant from the vaccinal strain.

Avian influenza H9N2 (AIV-H9N2) and Infectious bronchitis (IB) viruses are the most commonly isolated viruses from poultry flocks suffering from respiratory signs with mortalities. The outcome of co-infection with both viruses hasn’t been yet well understood. In this study, eighty 1-day-old specific pathogen free chicks were divided into four distinct groups. Group 1 remained uninfected as negative control group; groups 2, 3 and 4 were inoculated with either AIV-H9N2 or IBV or co infected with AIV-H9N2 followed by IBV three days post inoculation respectively. Chicks were monitored for clinical and pathological changes, virus shedding and both Interleukin-6 (IL6) and Interferon gamma (IFNγ) cytokines immune responses. Clinical signs varied from mild to moderate respiratory signs in all challenged groups but were more severe in group 4 with mortalities in groups 3 and 4. Tracheal shedding of both viruses washigher in group 4 than group 2 and 3. Mean AIV-H9 virus titer in lung and kidney was higher in group 4 than group 2 in all time points. IFNγ mRNA gene expression in lung was significantly lower in groups3 and 4. In conclusion, this study reports that co-infection of chicks with both viruses enhances the pathogenicity, increases both viruses shedding and extend AIV-H9 replication with impairment of IFNγ stimulation in lung.

Wild migratory birds are often implicated in the introduction, maintenance, and global dissemination of different pathogens, such as influenza A viruses (IAV) and antimicrobial-resistant (AMR) bacteria. Trapping of migratory birds during their resting periods at the northern coast of Egypt is a common and ancient practice performed mainly for selling in live bird markets (LBM). In the present study, samples were collected from 148 wild birds, representing 14 species, which were being offered for sale in LBM. All birds were tested for the presence of AIV and enterobacteriaceae. Ten samples collected from Northern Shoveler birds (Spatula clypeata) were positive for IAV and PCR sub-typing and pan HA/NA sequencing assays detected H5N8, H9N2, and H6N2 viruses in four, four, and one birds, respectively. Sequencing of the full haemagglutinin (HA) gene revealed a high similarity with currently circulating IAV in Egypt. From all the birds, E.coli was recovered from 37.2% and Salmonella from 20.2%, with 66%&ndash, 96% and 23%&ndash, 43% isolates being resistant to at least one of seven selected critically important antimicrobials (CIA), respectively. The presence of enzootic IAV and the wide prevalence of AMR enterobacteriaceae in wild birds highlight the potential role of LBM in the spread of different pathogens from and to wild birds. Continued surveillance of both AIV and antimicrobial-resistant enterobacteriaceae in wild birds&rsquo, habitats is urgently needed.

BackgroundAvian influenza viruses (AIVs) have been identified from more than 100 different species of wild birds around the globe. Wild migratory birds can act as potential spreaders for AIVs to domestic birds between different countries. Egypt is situated on important migratory flyways for wild birds between different continents. While much is known about circulation of zoonotic potential H5N1 and H9N2 AIVs in domestic poultry in Egypt, little is known about the pivotal role of migratory birds in the maintenance and transmission of the viruses in Egypt.MethodsTargeted AIV surveillance has been conducted in 2017 in different wetlands areas in Northern and Eastern Egypt.ResultsAIV of subtype H5 was detected in two bird species. In addition, a novel reassortant strain of the H6N2 subtype was identified which reveals the continuous risk of new influenza virus(es) introduction into Egypt. This novel virus possesses a reassortant pattern originating from different AIV gene pools.ConclusionsIntervention control strategies should be performed to minimize the possible contact of domestic birds with wild birds to lower the risk of virus transmission at this interface. In addition, constant monitoring of AIVs in migratory birds is essential in the early detection of influenza virus introduction into Egypt.

The infectious bursal disease virus (IBDV) is a continuing serious problem facing poultry industry in Egypt. In this study, 24 bursae samples collected from different broiler flocks (from Giza, Dakahleya, Ismailia, Damietta and Alexanderia) experiencing high mortality rate and bursal lesions during 2012 to 2014 were examined. Clear differences in pathotyping between very virulent Infectious bursal disease (vvIBD) and classical IBD were observed in pathological examination. Reverse transcriptase polymerase chain reaction (RT-PCR) was applied for IBD targeting hyper variable region (HVR) of VP2 gene. Genetic analysis revealed that 15 viruses belonged to vvIBD that had amino acids A222, I256, I294 and S299 which are highly conserved among vvIBD starins, while 9 viruses belonged to classical IBDV (similar to vaccine strains). The genotyping of Egyptian vvIBDV indicate progressive evolution compared with previously isolated strains which indicates persistence of vvIBDV in Egyptian poultry environment.

Rabbit farming is a growing industry to satisfy the great demand for food, particularly in developing countries. In this study, out of 450 samples collected from 150 rabbit cases suffering from wry neck, 100 from clinically diseased rabbits and 50 freshly dead ones with a history of wry neck. All cases were subjected to clinical examination, bacterial culture and polymerase chain reaction. 30 samples out of 450 samples were positive for M. haemolytica with an incidence of 6.6% mixed with E.coli (serotypes O78, O26 and O2) and Staph aureus with incidence of 3.3% and 2.2% respectively were concomitantly isolated. In-vitro antimicrobial susceptibility testing showed a wide range of multidrug resistance against penicillins and fluoroquinolones whereas colistin sulphate was the most effective antibiotic followed by chloramphenicol, neomycin and oxytetracycline. The findings of this study revealed that multidrug resistant bacteria constitute a serious problem in commercial rabbiteries in Egypt. PCR technique was done on original samples and it appeared that conventional PCR technique more sensitive than the conventional microbiological technique (CMT). Effective control measures are required to mitigate the economic impact on the rabbit industry and to prevent possible public hazards.

Duck hepatitis virus (DHV) is an acute highly contagious disease of ducklings caused by three distinct serotypes of duck hepatitis A virus (DHAV), a member of the RNA family Picornaviridae, where serotype 1 is the most widespread serotype worldwide. To date, little if any is known about the prevalence and genetic characterisation of DHAV outside Asia. The current study describes surveillance on DHV in 46 commercial duck farms in Egypt with a history of high mortality in young ducklings from 3 to 15 day-old from 2012 to 2014. Clinical samples were examined by generic RT-PCR assays followed by partial sequence analysis of the 5’UTR, VP1 and 3D genes of the vaccine strain and 15 field viruses. The overall positive rate was 37% (n = 17/46). All duck breeds (Pekin, Muscovy, Mallard and Green Winged) were susceptible to the disease with mortality ranged from 15% to 96.7%. Sequence and phylogenetic analyses indicated that the Egyptian strains cluster in the DHAV serotype 1 with Asian viruses and distinguishable from the vaccine strains. So far, this is the first report on the genetic characterisation of DHAV in Egypt. This study may be useful to better understand the epidemiology and evolution of DHAV.

Differentiation between field and vaccinal strains of Mycoplasma gallisepticumis important for the epidemiology of the disease. Real time PCR assay was applied to detect MG and further tested by mgc2 rt-PCR for F, 6/85 and TS-11 strains. Twenty four farms were positive for MG Out of the 50 farms, from which 12 were positive for F strain and 5 were positive for 6/85 strain, while 7 farms were MG positive but negative for live vaccine rt-PCR. DNA nucleotide sequencing for 20 positive cases for mgc2 gene confirmed the rt-PCR results, some point mutations were found in the isolated strains and grouped the sequenced samples into 4 groups (F, 6/85 and two field strain groups named field group A and B).

Chicken anemia virus (CAV) is one of the commercially important diseases of poultry worldwide. In Egypt, CAV has been reported to be a potential threat to the commercial poultry sectors. Hence, this study was aimed at isolation and full genomic analysis of CAVs circulating in chicken populations in different geographical location in Egypt. A total of 42 samples were collected from broiler chicken flocks in 9 governorates in Egypt from 12 to 42 days of age. The mortality rate observed among chickens was ranging from 3% to 22%. Nineteen out of 42 farms were found positive for the CAV genome by polymerase chain reaction (PCR). Full genome sequencing was conducted for 18 positive samples. Genetic analysis revealed a high similarity of >99% in 11 viruses with the vaccine strain Del-Ros; while the other seven samples shared close similarity to CAV field strains isolated from China, Taiwan, and Brazil. The data also indicated Q139 and Q144 amino acids substitutions among the VP1 of Egyptian field strains, which are known to be important in virus replication and spread. Phylogenetic analysis of the sequenced viruses (n = 18) based on either the full gene nucleotide sequence or VP1 coding sequence, suggested the circulation of four distinct genotypes in Egypt designated as group A, B, C and D. Moreover, evidence of recombination was detected among four Egyptian CAVs located within group A. The findings of this study succeeded to elucidate the epidemiological and genetic features of CAVs circulating in Egypt, and underscores the important of CAVs surveillance.

We isolated highly pathogenic avian influenza virus (H5N8) of clade 2.3.4.4 from the common coot (Fulica atra) in Egypt, documenting its introduction into Africa through migratory birds. This virus has a close genetic relationship with subtype H5N8 viruses circulating in Europe. Enhanced surveillance to detect newly emerging viruses is warranted.

It is almost a decade since the highly pathogenic H5N1 avian influenza virus (A/H5N1) of clade 2.2.1 was introduced to Egypt in 2005, most likely, via wild birds; marking the longest endemic status of influenza viruses in poultry outside Asia. The endemic A/H5N1 in Egypt still compromises the poultry industry, poses serious hazards to public health and threatens to become potentially pandemic. The control strategies adopted for A/H5N1 in Egyptian poultry using diverse vaccines in commercialized poultry neither eliminated the virus nor did they decrease its evolutionary rate. Several virus clades have evolved, a few of them disappeared and others prevailed. Disparate evolutionary traits in both birds and humans were manifested by accumulation of clade-specific mutations across viral genomes driven by a variety of selection pressures. Viruses in vaccinated poultry populations displayed higher mutation rates at the immunogenic epitopes, promoting viral escape and reducing vaccine efficiency. On the other hand, viruses isolated from humans displayed changes in the receptor binding domain, which increased the viral affinity to bind to human-type glycan receptors. Moreover, viral pathogenicity exhibited several patterns in different hosts. This review aims to provide an overview of the viral evolution, pathogenicity and vaccine efficacy of A/H5N1 in Egypt during the last ten years.