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Iridovirus infection has threatened the aquaculture industry worldwide. It has been associated with severe disease and economic losses in fish. In the present study, sixty-two fishes (Sea bream = 50; Sea bass = 3; Mullet = 9) were collected from Damietta and Sharkia Governorates, Egypt during May 2019-September 2020. The clinical signs, gross lesions and histopathological findings were recorded and later confirmed by molecular detection of Iridovirus in different fish species. Besides, isolation of molecularly identified Iridovirus from fish tissues in Vero cell cultures was done. Clinically, the affected fishes become lethargic, exhibit severe anemia, petechiae in the skin and gills. Unilateral hemorrhages in eye and cloudy eye were recorded only in Sea bream fish. Necropsy of the infected fishes revealed congestion of the internal organs, petechial hemorrhages on spleen, liver, kidneys and heart. Necrotic foci on liver were also observed. Histopathological examination revealed congestion of portal veins, cytoplasmic vacuolation with presence of intranuclear eosinophilic inclusion bodies within degenerated hepatocytes. Multifocal necrosis and various degree of inflammation in different fish tissues were observed. Molecularly, the obtained 1000 bp amplicon by PCR confirmed the presence of Iridovirus major capsid protein (MCP) gene with a percentage of 12.1%. It was detected in both fry and market size fish as well as in clinically infected and apparently healthy fish. The molecularly identified virus was able to replicate in Vero cells at 28oC, but not at 37 oC. To our knowledge, this is the first report of Iridovirus isolation in Vero cells and detection in fish within Damietta and Sharkia Governorates, Egypt. Further studies are recommended to investigate its presence on a broader scale with genomic sequence analysis.

The present study aimed to diagnose infectious myonecrosis virus (IMNV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) among cultured penaeid shrimp (Penaeus semisulcatus, n = 120) collected from private farms in 2 Egyptian provinces (Damietta and North Sinai) along the Mediterranean coast. The collected shrimp were subjected to clinical examination, histopathology, molecular characterization, and phylogenetic analysis. Most of the shrimp infected with IMNV showed a distinctive appearance resembling cooked shrimp and white necrosis on distal abdominal segments and tail fans. Simultaneously, IHHNV-infected cases displayed opaque abdominal muscles, white milky to buff mottling on the shell, and a pathognomonic runt-deformity syndrome. Histopathological examination of infected specimens revealed muscular edema, hemocyte infiltration, deformities, Zenker’s necrosis, and eosinophilic intra-nuclear inclusion bodies (Cowdry type A). PCR results gave predictable amplicon sizes of 139 and 81 bp and confirmed the presence of IMNV and IHHNV with a total prevalence of 37.5 and 25%, respectively. A homology search by BLAST analysis showed that the retrieved isolates putatively belonged to IMNV and IHHNV based on 96.3 to 97% nucleotide identity to the corresponding open reading frame gene of each virus. The phylogenetic analysis clearly showed genetic similarity and cross-lineage between our isolates and other isolates from Egypt, the USA, Brazil, Indonesia, China, Korea, Taiwan, and Ecuador. In conclusion, gross inspection and histopathology may aid in the diagnosis of viral diseases; however, molecular tools are indispensable for confirming a possible infection. The current study recommends strict regulations during live shrimp transportation and implementing health control certificates over all imports and exports, especially in developing countries, including Egypt.

Bovine astrovirus (BAstV) is a small single-stranded RNA virus, which belongs taxonomically to genus Mamastrovirus under the family Astroviridae. The BAstV is strongly linked to neonatal diarrhea of calves. A few studies are available on BAstV, mainly from Asia, and to a lesser extent from Europe, South America, and Africa. There is only one report from Egypt, in which BAstV was found in diarrheic calves, either in single- or co-infections, based on reverse transcription polymerase chain reaction (RT-PCR) and BAstV-polymerase enzyme targeting primers. One of the samples was further subjected to genomic characterization using Illumina platform for next generation sequencing (NGS). After being processed, the returned BAstV complete genome was subjected to sequence and phylogenetic analysis in comparison to reference strains. The BAstV open reading frames (ORF1a, ORF1b, and ORF2) followed a nearly similar genetic topology, as they belonged to the same unclassified lineage, which was earlier proposed as BAstV-lineage 1, and is known to be disseminated worldwide. This close phylogenetic relationship between the study strain and other members of this lineage was further confirmed by high nucleotide and amino acid (aa) identities. Additionally, a total of 24 unique aa residues were found through the entire BAstV genome. As being the first report in Egypt, indeed Africa, we believe that this record shall be useful in either taxonomic classification or epidemiological tracking of BAstV. The status of BAstV in Egypt should be carefully investigated with possible to-be-implemented precautions for the protection of animal-raising industries. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13337-021-00668-5.

Avian orthoavulavirus 1, formerly known as avian paramyxovirus type-1 (APMV-1), infects more than 250 different species of birds. It causes a broad range of clinical diseases and results in devastating economic impact due to high morbidity and mortality in addition to trade restrictions. The ease of spread has allowed the virus to disseminate worldwide with subjective virulence, which depends on the virus strain and host species. The emergence of new virulent genotypes among global epizootics, including those from Egypt, illustrates the time-to-time genomic alterations that lead to simultaneous evolution of distinct APMV-1 genotypes at different geographic locations across the world. In Egypt, the Newcastle disease was firstly reported in 1947 and continued to occur, despite rigorous prophylactic vaccination, and remained a potential threat to commercial and backyard poultry production. Since 2005, many researchers have investigated the nature of APMV-1 in different outbreaks, as they found several APMV-1 genotypes circulating among various species. The unique intermingling of migratory, free-living, and domesticated birds besides the availability of frequently mobile wild birds in Egypt may facilitate the evolution power of APMV-1 in Egypt. Pigeons and waterfowls are of interest due to their inclusion in Egyptian poultry industry and their ability to spread the infection to other birds either by presence of different genotypes (as in pigeons) or by harboring a clinically silent disease (as in waterfowl). This review details (i) the genetic and pathobiologic features of APMV-1 infections in Egypt, (ii) the epidemiologic and evolutionary events in different avian species, and (iii) the vaccine applications and challenges in Egypt.

White spot syndrome virus (WSSV) is poorly understood as no available information regarding its possible spread among shrimp cultured in Egypt. Therefore, this work aimed to diagnose WSSV in cultured shrimp by pathological examination and molecular based methods (PCR). A total of 20 shrimp samples were collected from shrimp farms in Egypt. Diseased shrimps exhibited sudden mass mortalities and showed loose cuticle with numerous scattered melanised visible white spots on external surface. Histopathological examination revealed nuclear hypertrophy with eosinophilic (Cowdry A inclusion) to basophilic inclusions in the internal organs (connective tissues). Spheroids were observed in the lymphoid tissues. Cell encapsulation was accompanied by pyknosis and karyorrhexis. PCR results with primers specific for WSSV gave a predicted amplified product at 414 bp fragments using agarose gel electrophoresis. The present findings request more investigations for White spot syndrome virus disease among shrimp in Egyptian farms and recommend the establishment of preventive measures against this virus in Egypt.

Hypertrophied nodules or papilloma like lesions were detected in the skin and fin of Sea bream farms (at Mothalath El Deba and Bardaweil Lake) in Egypt with morbidity rate reached to 70% and mortality rate up to 40%. A total of 20 affected cultured sea bream samples were collected for laboratory examinations. Histopathological examination revealed intracytoplasmic basophilic inclusion bodies in the skin and fins lesions. In addition, a thick hyaline capsule surrounding the hypertrophied fibroblast and contain heavily enlarged cells (lymphocystis) with necrosis and inflammatory response. PCR results with primers specific for the gene encoding major capsid protein (MCP) gave a predicted amplified product at 405 bp fragment by agarose gel electrophoresis. The current results encourage further investigations for this virus in Egyptian farms and recommend the development of prevention strategies against LCDV in Egypt.

Avian orthoavulavirus 1, formerly known as avian paramyxovirus type-1 (APMV-1), infects more than 250 different species of birds. It causes a broad range of clinical diseases and results in devastating economic impact due to high morbidity and mortality in addition to trade restrictions. The ease of spread has allowed the virus to disseminate worldwide with subjective virulence, which depends on the virus strain and host species. The emergence of new virulent genotypes among global epizootics, including those from Egypt, illustrates the time-to-time genomic alterations that lead to simultaneous evolution of distinct APMV-1 genotypes at different geographic locations across the world. In Egypt, the Newcastle disease was firstly reported in 1947 and continued to occur, despite rigorous prophylactic vaccination, and remained a potential threat to commercial and backyard poultry production. Since 2005, many researchers have investigated the nature of APMV-1 in different outbreaks, as they found several APMV-1 genotypes circulating among various species. The unique intermingling of migratory, free-living, and domesticated birds besides the availability of frequently mobile wild birds in Egypt may facilitate the evolution power of APMV-1 in Egypt. Pigeons and waterfowls are of interest due to their inclusion in Egyptian poultry industry and their ability to spread the infection to other birds either by presence of different genotypes (as in pigeons) or by harboring a clinically silent disease (as in waterfowl). This review details (i) the genetic and pathobiologic features of APMV-1 infections in Egypt, (ii) the epidemiologic and evolutionary events in different avian species, and (iii) the vaccine applications and challenges in Egypt.

Highly pathogenic avian influenza (HPAI) H5N1 virus poses a major challenge to the poultry industry and human health in Egypt. Twenty one households and eight duck farms in Sharkia Province, Egypt were investigated for the presence of avian influenza virus (AIV) and/or duck hepatitis virus 1 (DHV-1). Mortality rates among the investigated farms and yards were, 18.9% (69/365) of native ducks, 60.9% (25/41) of Pekin ducks, 60.2% (6306/10473) of Muscovy ducks and 44.9% (1353/3015) of Mallard ducks. The RT-PCR revealed the circulation of HPAI-H5N1 virus (81/104) among the examined birds with a high percentage in Muscovy (83.7%) and Pekin (83.4%) ducks. Interestingly, co-infection of HPAI and DHV-1 viruses in three ducklings with age of 4–19 days was detected. Severe neurological signs with high mortality were observed in ducklings as early as 4 days of age. Influenza virus antigen was detected in the neurons and glial cells of the brain, hepatocytes, and the intestinal submucosal plexus. Although, genetic characterization of H5N1 isolates revealed HPAIV of clade 2.2.1.2, such increased mortalities and neurological signs regardless of the duck age might imply the natural selection of HPAI in ducks. Crucial monitoring of the disease situation in ducks is essential for the implementation of an effective prevention and control program. Keywords: Egypt, Ducklings, Immunohistochemistry, Mortality, Nervous signs, Phylogeny

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. Electronic supplementary material The online version of this article (10.1007/s00705-018-3758-1) contains supplementary material, which is available to authorized users.

In January-April 2016, cattle and buffalo farm owners and veterinarians reported clinical signs suggestive of foot and mouth disease virus (FMDV) outbreaks among non-vaccinated cattle and buffalo herds in Egypt. The clinical disease observed was either mild (small oral lesions and speedy recovery) or severe (extensive oral lesions and/or mortalities), and the form of the disease (either mild or severe) segregated by farm. This study aimed to confirm the presence of FMDV and to characterize the circulating strains associated with the outbreaks. Vesicular epithelia were collected from 41 animals representing 15 affected cattle and buffalo farms in five governorates (Behira, Cairo, Daqahlia, Giza and Ismailia), and tested by real time (rt) RT-PCR. Consequently, 92% (38/41) of examined samples were positive. Furthermore, the VP1 coding region of 60% (23/38) of positive specimens were amplified by RT-PCR and sequenced. The phylogenetic analysis identified two distinct strains characterized as serotype O topotype EA-3 and serotype A (African topotype) of genotype IV in the severe and mild disease forms, respectively. The newly identified strains clustered in distinct clades in the phylogenetic trees, indicating the likelihood of new incursions into Egypt. Those strains were most closely related to previously described Sudanese strains.

Foot-and-mouth disease (FMD) is endemic in Egypt and in most parts of Africa causing huge economic losses. Control of FMD using vaccination requires information on the occurrence of various FMDV serotypes. This study aimed to determine the prevalence of FMDV serotypes in Sharkia Governorate, Egypt. A total number of 643 different samples, within ten different localities, were collected from both cattle and buffaloes (n = 283) of different, age, sex, immune status against FMD, and health status. Field samples (n = 360) have been screened for FMDV by RT-PCR using universal primers and were further subtyped using serotype-specific primers. Additionally, serum samples (n = 283) have been analyzed by applying FMDV serotype-specific antibody ELISA. The RT-PCR screening revealed that a total number of 39/283 (13.8%), 61/283 (21.6%) and 17/38 (44.7%) animals were positive for FMDV serotype O, A and SAT2, respectively. While, by ELISA, neutralizing antibodies directed against FMDV serotype O, A, and SAT2, were found in 177/283 (62.5%), 171/283 (60.4%) and 27/38 (71.1%) serum samples, respectively. These results indicated the endemic status of the FMDV serotypes O, A and SAT2 in Sharkia Governorate despite routine FMD vaccination programs. Although many variations of disease prevalence were recorded between animals of different, age, sex and immune and health status but it was obvious that FMD was more prominent and prevalent in buffaloes (47.1%) than in cattle (34.1%). Therefore, control efforts should focus on reducing the circulation of FMDV among susceptible livestock with special attention towards water buffaloes. Continuous surveillance, at molecular and immunological levels, of FMDV serotypes is needed for the effectiveness of any adopted control strategy targeting FMD including vaccination.

In recent years, avian influenza virus (AIV) and Newcastle disease virus (NDV) have caused large-scale outbreaks in many countries, including Egypt. The culling and vaccination strategies have failed to control both viruses in Egypt. In this study, we investigated the outbreaks of nervous manifestations and deaths in pigeons between 2013 and 2015. The H5N1 subtype of the highly pathogenic avian influenza virus and pigeon paramyxovirus-1, an antigenic variant of NDV, were found to be the cause; AIV and pigeon paramyxovirus-1 were isolated from 61.3% (19/31) and 67.8% (21/31) of tested pigeons, respectively. Co-infection with both viruses was detected in 51.6% of pigeons (16/31). The AIV sequences showed PQGEKRRKKR/GLF motif at the haemagglutinin gene cleavage site, which is typical of the highly pathogenic H5N1 subtype. The phylogenetic tree showed that the highly pathogenic avian influenza belonged to clade 2.2.1.2. The NDV sequences carried one of the three motifs, 112GKQGRL117, 112KRQKRF117 or 112RRQKRF117, at the fusion protein cleavage site and were classified as genotypes I, VI and II in NDV-class II, respectively. This indicated that different genotypes of NDV can circulate simultaneously among pigeons. Further analysis revealed the clustering of some sequences in sub-genotypes Ia and VIb.2. To the best of our knowledge, these sub-genotypes have not been previously reported from pigeons in Egypt. Our results should serve as a base for future studies on both viruses in Egypt.

Bovine viral diarrhea virus (BVDV) exists in two main biotypes: cytopathic (cp) and noncytopathic (ncp). Although some studies were done on the effect of interferon alpha (IFN-α) on BVDV, the effect of exogenous IFN against BVDV biotypes remains unclear. In the present study, we evaluated the comparative effect of exogenous human IFN-α (HuIFN-α) on different BVDV biotypes and genotypes. The results showed that exogenous HuIFN-α greatly inhibited the growth of different BVDV biotypes and genotypes. However, HuINF-α has a significant inhibitory effect on cp biotype compared to ncp one without significant variation between different genotypes. The effect of HuIFN-α on BVDV reached the maximum level at early stages of infection (0-20 h post infection) and increased in a dose-dependent manner (10-500 U/ml). Quantitative real-time RT-PCR was used to evaluate the effect of exogenous HuIFN-α on RNA synthesis of both BVDV biotypes. HuIFN-α reduced RNA production of cp by 4 logs compared to only 2 logs for ncp strains. Additionally, the antiviral effect of IFN-α against both BVDV biotypes seems to be independent of the RNA-dependent protein kinase (PKR) activation as assayed by direct analysis of in vivo phosphorylation of eIF2-α and by 2-aminopurine (2-AP) treatment. Collectively, these results indicated that the exogenous HuIFN-α treatment has an inhibitory effect not only on cp BVDV biotype but also on the ncp BVDV. The antiviral effect of exogenous HuIFN-α was biotype, time, dose but not genotype dependent. PKR has no role in the inhibitory effect suggesting that other IFN-antiviral pathways were involved. Keywords: BVDV biotypes; HuIFN-α; RNA synthesis; PKR-independent.

Bovine viral diarrhea virus (BVDV) infection causes immune dysfunction. The current study investigated the effect of cytopathic (cp) or noncytopathic (ncp) strains of BVDV on immunomodulation by the levels of total serum immunoglobulin G (IgG), the IgG1, IgG2, BVDV neutralizing antibodies and total white blood cell (WBC) count. Twenty (20) BVDV seronegative dairy calves (5–6 months old) were divided in two groups of ten. The animals were infected with either a cp or ncp virus isolated from the same animal (ncp BVDV1b-TGAN or cp BVDV1b-TGAC). One group of 10 was infected with ncp TGAN while the other group of 10 was infected with cp TGAC. Calves infected with cp BVDV had a significant decrease in total IgG as well as IgG1 concentration at 7 days post infection (DPI) that recovered by 21 DPI (total IgG) and 35 DPI (IgG1), respectively. There was no effect of ncp BVDV infection on total IgG concentration in the first 7 days of infection (DOI); however, IgG1 concentration was significantly reduced and IgG2 concentration was significantly increased at 7 DOI. At 35 DPI, ncp TGAN-infected calves had significantly higher total IgG, IgG1 as well as IgG2 compared to cp TGAC-infected calves. Ncp BVDV induced higher BVDV homologous and heterologous neutralizing antibodies compared to the cp BVDV strain. Calves infected with ncp BVDV had significantly reduced WBC counts at 7 DPI that recovered by 14 DPI. Overall, these findings indicate that humoral immunosuppression occurs early following BVDV infection with the largest effect on IgG1 levels.

Infectious bursal disease (IBD) virus (IBDV) is the causative agent of a highly contagious and immunosuppressive disease of chickens with huge economic losses to the poultry industry despite extensive vaccination. Analysis of isolated IBDV field strains from vaccinated birds would greatly improve the current immunization regimens and support the development of vaccines that offer better immunity. The study investigated the genetic characteristics and pathologic features of IBDVs in commercial broiler chicken farms, as well as the effect of IBDV infection on the efficacy of vaccination against avian influenza virus (AIV) and Newcastle disease virus (NDV) under field conditions. A preliminary diagnosis of IBD was made on the basis of the flock history and the characteristic gross pathologic findings. Microscopically, lymphoid depletion in bursal follicles with infiltration of lymphomononuclear cells along with cystic cavitations reflected the IBDV infection. The molecular analysis confirmed the IBDV infection in (57.1%) of tested flocks. Upon phylogenetic analysis of the VP2 hypervariable region of 14 Egyptian IBDVs, most viruses (Virus de la enfermedad de la bolsa infecciosa: perspectivas epidemiológicas moleculares e impacto sobre la eficacia de la vacunación contra los virus de influenza aviar y de la enfermedad de Newcastle. El virus de la enfermedad de la bolsa infecciosa (IBD) es el agente causante de una enfermedad altamente contagiosa e inmunosupresora de los pollos con grandes pérdidas económicas para la industria avícola a pesar de la vacunación extensiva. El análisis de cepas de campo del virus de Gumboro aisladas de aves vacunadas mejoraría en gran medida los regímenes de inmunización actuales y respaldaría el desarrollo de vacunas que ofrezcan una mejor inmunidad. Este estudio investigó las características genéticas y patológicas de los virus de la enfermedad infecciosa de la bolsa en granjas comerciales de pollos de engorde, así como el efecto de la infección por el virus de Gumboro en la eficacia de la vacunación contra el virus de la influenza aviar (AIV) y el virus de la enfermedad de Newcastle (NDV) bajo condiciones de campo. Se realizó un diagnóstico preliminar de la enfermedad infecciosa de la bolsa con base en la historia de la parvada y de los hallazgos patológicos macroscópicos característicos. Microscópicamente, la despoblación linfoide en los folículos bursales con infiltración de células linfomononucleares junto con formaciones quísticas reflejó la infección por el virus de Gumboro. El análisis molecular confirmó la infección por este virus en 57.1% de las parvadas analizadas. Después del análisis filogenético de la región hipervariable del gene VP2 de 14 virus egipcios, la mayoría de los virus (

Neonatal calf diarrhea (NCD) is a major cause of morbidity, mortality and economic losses in the beef and dairy industries. This study was conducted to investigate the existence of enteric viruses in two Egyptian farms with a history of recurrent diarrhea. Fecal samples were collected from 25 diarrheic calves. RNA was extracted and tested by reverse transcription polymerase chain reaction (RT-PCR) for the presence of rotavirus, norovirus, astrovirus, torovirus, coronavirus and bovine viral diarrhea virus. Overall, 76 % (19/25) of samples tested positive for one or more viruses. Rota-, noro- and astroviruses were detected in 48 %, 24 % and 32 % of tested samples, respectively. About 37 % (7/19) of positive samples had two different viruses. One-month-old calves were the group most vulnerable to infections. Based on phylogenetic analysis, bovine rotaviruses were of genotypes G6 and G10, bovine noroviruses were in GIII.2, and bovine astroviruses were in the BAstV lineage 1. Astrovirus sequences showed a high level nucleotide sequence similarity with the Brazilian BAstV sequences available in GenBank. We believe this is the first report of bovine norovirus and bovine astrovirus circulating among calves in Egypt. Further epidemiological studies are recommended to investigate their presence on a wider scale, to predict their association with NCD, and to design appropriate diagnostic and control methods. Electronic supplementary material The online version of this article (doi:10.1007/s00705-016-3088-0) contains supplementary material, which is available to authorized users.

Epidemic outbreaks of avian influenza (AI) virus H5N1 have been frequently reported in Egypt during the last nine years. Here we investigate the involvement of AI H5N1 in outbreaks of acute respiratory disease that occurred in several commercial chicken farms in Egypt in 2011, and we describe to the pathology caused by the virus in the course of the outbreak.Twenty-one chicken farms with history of acute respiratory symptoms and high mortalities were screened for AI H5N1. Virus identification was based on hemagglutination inhibition test, and PCR detection and sequencing of the hemagglutinin and neuraminidase genes. Virus distribution was determined by immunohistochemical staining of AI antigens in organs of infected birds. Standard H&E staining was performed for histological examination of affected organs.Eighty-one % of the examined birds, representing 100% of the screened farms, were positive for AI H5N1 virus. Phylogenetic analysis of the hemagglutinin and neuraminidase genes of the isolated virus reveals its affiliation to clade 2.2.1. Viral antigens were localized in the endothelial cells of the heart, liver, lungs and skin, where pathological lesions including congestion, hemorrhages, multifocal inflammation and necrosis were concurrently observed. According to the pattern of the viral antigen and lesion distribution in the visceral organs, we suggest cardiovascular and circulatory failures as the probable cause of death during these outbreaks. In conclusion, the present study further confirms the epidemic status of AI H5N1 virus in Egypt and reveals the highly pathogenic nature of the local isolates.

Purpose Two distinguishable subclades of H5N1 (classic and variant strains) are cocirculating among the poultry populations in Egypt despite the intensive vaccination programs. A study to investigate the genetic relationship between avian influenza virus (AIV) isolates from backyard chickens in Sharkia (2009–2011), subclades, and commercially available vaccines was carried out. Methods Forty-eight suspected AIV infected birds were clinically examined and used for virus isolation followed by reverse transcription-polymerase chain reaction. Four H5N1 virus isolates were sequenced and analyzed. The intravenous pathogenicity index (IVPI) of three AIV isolates was determined. Results Thirty-four hemagglutinating viral agents (30 AIV subtype H5N1 and 4 Newcastle disease virus) were detected. Both the nucleotide and amino acid sequence identities of four H5N1 virus isolates (SHZA-0412/2009, SHZA-0801/2010, SHMK-1903/2010, and SHAH-1403/2011) were high—98.4–99.7% and 100%, respectively—indicative of their genetic homogeneity. The hemagglutinin cleavage site characterization revealed the presence of multiple basic amino acids (–PQRERRRKKR/GL–) of the highly pathogenic phenotype. These results were supported by IVPI in chickens of 2.69–2.90. The similarity of our isolates with H5N1 AIV vaccine strains (93.9–95.1%) was higher than that with H5N2 strains (77.8–91.9%). The divergence of four sequences with classic and variant lineages is 2–2.7% and 2.3–3%, respectively, with two amino acid substitutions (A249P and N251Y). Conclusion Genetic characterization and IVPI data of backyard H5N1 isolates are indicative of a highly pathogenic avian influenza virus with hemagglutinin cleavage site constancy and two amino acids substitutions with Egyptian classic and variant lineages, suggesting a beginning of antigenic drift.

The highly pathogenic avian influenza virus (HPAIV) subtype H5N1 threatens animal and human health worldwide. Susceptibility of pigeons to HPAIV (H5N1) and their role in avian influenza virus transmission to domestic birds and humans remain questionable. In this study, an outbreak in domestic pigeons (1 to 18 months old) with 50% mortality was investigated. Pigeons exhibited nervous manifestations and greenish diarrhoea. Necropsy of the naturally infected pigeons revealed congestion of the internal organs, particularly the lungs and brain. The HPAIV subtype H5N1 designated A/Pigeon/Egypt/SHAH-5803/2011 was isolated from a 40-day-old pigeon. Sequencing of the haemagglutinin gene showed it to be closely related to viruses in group 2.2.1/C. Intravenous inoculation of the isolate in chickens induced 100% mortality within 2 days post inoculation and the intravenous pathogenicity index was 2.7. Virus pathogenicity and transmissibility was determined experimentally in 6-week-old domestic pigeons. Thirty per cent of pigeons inoculated oronasally with 10(6) median embryo infective dose showed congested beak, conjunctivitis, depression, and greenish diarrhoea. A mortality rate of 10% was recorded preceded by severe neurologic signs consisting of torticollis, incoordination, tremors, and wing paralysis. Pathological examination revealed a friable brain tissue and congested meningeal blood vessels. The lungs appeared oedematous and severely haemorrhagic. Subepicardial and petechial haemorrhages on the coronary fat were observed. Both infected and contact pigeons shed virus via the oropharynx and cloaca. To our knowledge, this is the first description and characterization of HPAIV in naturally infected pigeons in Egypt. Our findings reveal that pigeons can indeed be susceptible to H5N1 HPAIVs and could be a source of infection to other birds and humans.

The purified Immunoglobulin G (IgG) is effectively used in passive immunization. There are various methods to isolate the IgG from serum, with its own advantages and disadvantages. In the current study, a comparative efficacy of the affinity chromatography...

During 2015, duck farms (n = 27) in Sharkia Province, Egypt, experienced several disease outbreaks leading to mortality and nervous manifestations. Upon necropsy, the affected ducklings showed liver lesions, such as hemorrhage or necrosis, suggestive of duck virus hepatitis (DVH). Reverse transcription-PCR (RT-PCR), on the basis of the 3D gene, found duck livers from 21 farms to be positive for duck hepatitis A virus serotype 1 (DHAV-1). All duck breeds (Pekin, Mallard, and Muscovy) were infected. The virus was isolated in embryonated chicken eggs, which showed embryonic mortality (40%-80%) within 5-7 days, stunting or dwarfing (69.6%), and necrotic liver foci (60.9%). The VP1 gene of 11 DHAV-1 strains was characterized by RT-PCR and Sanger sequencing. All study strains were clustered in a monophyletic branch within subclade B2 of Group 4 and were separated from the Egyptian vaccine strain. Several amino acid (aa) residues, such as V129, S142 (only in four strains), L181, G184, and K217, were related to virus attenuation. However, two aa residues (N193 and E205), found in virulent DHAV-1 strains, were also observed in our strains. This study confirms the circulation of DHAV-1 (subclade B2) in Lower Egypt and elucidates the phylogenetic characters of the VP1 genes, which will be useful in following the local trends of DHAV-1 infections. Further studies are indicated to determine the correlation between these mutations and the virulence of the Egyptian DHAV-1 isolates.

Loop-mediated isothermal amplification (LAMP) is a simple, powerful state-of-the-art gene amplification technique used for the rapid diagnosis and early detection of microbial diseases. Many LAMP assays have been developed and validated for important epizootic diseases of livestock. We review the LAMP assays that have been developed for the detection of 18 viruses deemed notifiable of ruminants, swine and poultry by the World Organization for Animal Health (OIE). LAMP provides a fast (the assay often takes less than an hour), low cost, highly sensitive, highly specific and less laborious alternative to detect infectious disease agents. The LAMP procedure can be completed under isothermal conditions so thermocyclers are not needed. The ease of use of the LAMP assay allows adaptability to field conditions and works well in developing countries with resource-limited laboratories. However, this technology is still underutilized in the field of veterinary diagnostics despite its huge capabilities.

Highly pathogenic avian influenza virus (HPAIV) H5N1 has been endemic in Egypt since 2006, and there is increasing concern for its potential to become highly transmissible among humans. Infection by HPAIV H5N1 has been described in experimentally challenged birds. However, the pathogenicity of the H5N1 isolated in Egypt has never been reported in naturally infected chickens and ducks. Here we report a 2013 outbreak of HPAIV H5N1 in commercial poultry farms and backyards in Sharkia Province, Egypt. The main symptoms were ecchymosis on the shanks and feet, cyanosis of the comb and wattles, subcutaneous edema of the head and neck for chickens, and nervous signs (torticollis) for ducks. Within 48-72 hrs of the onset of illness, the average mortality rates were 22.8-30% and 28.5-40% in vaccinated chickens and non-vaccinated ducks, respectively. Tissue samples of chickens and ducks were collected for analyses with cross-section immunohistochemistry and real-time RT-PCR for specific viral RNA transcripts. While viral RNA was detected in nearly all tissues and sera collected, viral nucleoprotein was detected almost ubiquitously in all tissues, including testis. Interestingly, viral antigen was also observed in endothelial cells of most organs in chickens, and clearly detected in the trachea and brain in particular. Viral nucleoprotein was also detected in mononuclear cells of various organs, especially pulmonary tissue. We performed phylogenetic analyses and compared the genomic sequences of the hemagglutinin (HA) and nonstructural proteins (NS) among the isolated viruses, the HPAIV circulated in Egypt in the past and currently, and some available vaccine strains. Further analysis of deduced amino acids of both HA and NS1 revealed that our isolates carried molecular determinants of HPAIV, including the multibasic amino acids (PQGERRRK/KR*GLF) in the cleavage site in HA and glutamate at position 92 (D92E) in NS1. This is the first report of the pathogenicity of the HPAIVH5N1 strain currently circulating in naturally infected poultry in Egypt, which may provide unique insights into the viral pathogenesis in HPAIV-infected chickens and ducks.