Egyptian Virus Research Articles

High Prevalence of Hepatitis C Virus among B-Cell Non Hodgkin Lymphoma Patients in Mansoura Region (Egypt), ANRS 12263 Study.

BackgroundThe prevalence of Hepatitis C virus in Egypt reaches 15%, which is considered the highest in the world. Genotype 4 represents 93 % of Egyptian HCV infections. Non-Hodgkin lymphoma (NHL) is the 5th most common cancer in Egypt. The association between HCV infection and occurrence of B-cell NHL is well known while data are scarce in Eastern countries.ObjectivesWe aimed to evaluate the prevalence of HCV infection among patients with B-cell NHL and the clinical characteristics of HCV associated B-cell NHL in the Delta region (Mansoura-Egypt).MethodsBetween March 2012 and March 2013, 110 adult patients newly diagnosed with B-cell NHL were enrolled in the current study. This study was carried out at Oncology Center, Mansoura University. Study subjects provided serum for HCV testing.ResultsThe prevalence of HCV infection among these patients was 61% (67/110 patients). Among them, 80% (32/40 tested patients) presented with viremia. In contrast with the histological distribution previously described in Northern regions, the majority of HCV associated lymphomas were DLBCLs (72%) followed by SLL/CLL (13%), follicular lymphomas (7.5%) and marginal zone lymphomas (7.5%).ConclusionsB-cell lymphomas are highly associated with HCV infection in Egypt. Further developments are needed to give access to antiviral treatment for these patients.

Occurrence of Avian Influenza H5N1 among Chicken, Duck Farms and Human in Egypt

Avian influenza (AI) H5N1 virus consider a potential threat to the poultry industry with sever zoonotic effect associated with a high risk on human being associated with the poultry production. The disease become endemic in Egypt and cause more than 359 confirmed human infection cases in the last few years. Samples (serum and tissues) collected from 160 poultry farms that suspected to be infected with H5N1. Samples were collected from 75 broiler chicken farms, 55 broiler duck farms and 30 layer duck farms. As well as 115 human samples (serum and throat swabs) collected from persons suffering from respiratory manifestations and have a history of contact with infected birds. Samples were examined using Haemagglutination inhibition (HI) test and Reverse Transcription Real Time PCR (RT- qPCR) for detection of avian influenza H5N1 virus. HI test detect H5N1 antibodies in 71 poultry samples out of 160 (44.4%). While, RT- qPCR detect H5N1 in 13 out of 160 samples (8.1%). On the other hand, HI test detect H5N1 antibodies in six human sample out of 115 human cases (5.2%) while, RT- qPCR detect H5N1 in two human samples out of 115 human cases (1.7%). There was an increase in rate of highly pathogenic avian influenza transmission from poultry-to-human. Adaption of AI virus was increased to duck flocks with higher percentage of vaccinal escape. Thus, there is a need to give more attention to the vaccination programs and increasing the usage of the vaccines prepared from Egyptian H5N1 virus or update the current vaccines with the isolates representing the circulating virus in the Egyptian market. All these measures will increase the protection level in poultry farms and intern decrease the risk of human infection rates.

Pathology and Molecular Diagnosis of White Spot Syndrome Virus (WSSV) among Vannamei Shrimp 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.

Minor groove binder probe real-time RT-PCR for detection of foot-and mouth disease virus in Egypt

Shorter, more specific minor groove binders (MGBs) probes are dsDNA-binding agents attached to the 3' end of TaqMan probes that could be designed strictly to invariant region. Application and assessing of a new trend for viral detection in Egypt depending on MGB probe real-time RT-PCR (rRT-PCR) was applied on local FMDV serotypes O, A, and SAT2. Moreover, FMDV O were detected using two serotype specific primer sets by SYBR Green real-time RT-PCR assaying rapid formats. The limit of detection of diluted RNAs using MGB probe rRT-PCR assay reached to ≤ 6 fg/ul. Besides, high specificity of the former assay was clear. In contrary, the employing of FMDV O specific primer pairs in SYBR Green real-time RT-PCR showed a relative less sensitivity and specificity, particularly one of them displayed a very poor performance. Lastly, the local financial cost of MGB probe is considered the obvious hinder.

Molecular and pathological characterization of duck enteritis virus in Egypt.

In winter 2016, a fatal disease outbreak suspected to be duck virus enteritis (DVE) stroke over a million ducklings in 10 white Pekin and Muscovy ducks flocks in Dakahlia and Gharbia Governorates, Egypt, causing heavy economic losses. The disease quickly killed 20%-60% of affected farms. The clinical signs were inappetence, ataxia, crowding in corners, partially closed eye lids and blue beaks. Post mortem examination revealed white necrotic foci in liver, mottled spleen and sometimes cecal core. A total of 10 intestines, livers and spleens samples were collected from diseased flocks. Each sample was pooled randomly from eight to ten ducklings. Polymerase chain reaction (PCR) and histopathological examination were utilized for DEV identification in collected samples. Nucleotides sequences of the amplified DNA polymerase gene were compared with the other DEVs available on GeneBank. Also, existence of co-infection with Salmonella spp. was verified via PCR. DEV nucleic acid was detected by PCR in 8 of 10 collected samples (80%) with positive amplification of polymerase gene. Histopathological examination revealed eosinophilic and basophilic intranuclear inclusion bodies in enterocytes. In some infected enterocytes, intranuclear and intracytoplasmic inclusions were observed in the same cell. Respectively, eosinophilic intranuclear inclusion bodies found in hepatocytes and reticular cells of liver and spleen of diseased ducklings. Four of the 10 collected samples showed positive results for Salmonella spp. infection that may be involved in enhancing infection with DEV. The identified DEVs revealed close genetic relationship with DEVs detected previously in India and China indicating potential transmission of the virus from there that crucially needs further work for better understanding of virus origin. In conclusion, our study revealed infection of duckling farms with DEV and Salmonella that necessitate the implementation of restricted early preventive and control measures for both diseases to decrease the expected economic losses.

Efficacy, Safety and Relapse of Sofosbuvir in Combination with Daclatasvir, Ledipasvir and Simeprevir for Treatment of Hepatitis C Virus in Egypt

AbstractBackground: Hepatitis C Virus infects about 185 million people equating 2.8% of worldwide population and about 500,000 people die annually from hepatitis C related liver diseases. The most common clinical presentation of the disease is the chronic hepatitis and its complications such as: Com-pensated cirrhosis, portal hypertension, decompensated cir-rhosis and Hepatocellular Carcinoma (HCC). Therapeutic management of chronic HCV patients traditionally depended on combination of peg-interferon (IFN) with ribavirin but this regimen showed many serious side effects beside its non-satisfactory efficacy. In 2013, a second generation of Direct Acting Antiviral Agents (DAAs) gave a promising efficacy and safety. Although many IFN free regimens were approved, further evaluations are needed for these regimens.Aim: To compare sofosbuvir in combination with Da-clatasvir, Ledipasvir and Simeprevir in patients with chronic hepatitis C infection according to safety, efficacy, relapse and patient outcomes.Patients and Methods: This is a prospective study con-ducted on 150 patients of chronic HCV who were admitted to the Viral Hepatitis Center in Al-Ahrar Educational Hospital in Zagazig {National Committee for the Control of Viral Hepatitis (NCCVH) during the first 9 months of 2017 and were selected according to the inclusion and exclusion criteria set by the (NCCVH). 58% of overall participants had cirrhosis and 2.7% were treatment-experienced. Patients were assigned into three groups: 50 patients received Sofosbuvir + Daclatasvir ± Ribavirin (SOF/DCV ± RBV) therapy, 50 patients received Sofosbuvir + Ledipasvir ± Ribavirin (SOF/LDV ± RBV) therapy and 50 patients received Sofosbuvir + Simeprevir ± Ribavirin (SOF/SIM±RBV) therapy. Three regimens were given for 12 weeks. Primary end point was the rate of achieving SVR12 by HCV RNA PCR, while secondary end point was the occurrence of virologic relapse.Results: The SVR rate of three groups was 98%, 100% and 100% for SOF/DCV, SOF/LDV and SOF/SIM groups respectively. Only one patient had a virological failure and he was in SOF/DCV group but these results showed no statistical significance. Virological relapse occurred in only 1 patients (.67%) of the 149 patients. The patient who showed virological failure wasn't included, while the only one patient relapsed (2%) was in SOF/SIM therapy group. Results of virological relapse were statistically not significant. RVR showed a predictive value in SVR achievement and relapse occurrence was also confirmed in our study, in SVR (p=>.05) and in relapse (p=.9). Adverse events occurred in (22%) of SOF/DCV group, (26%) of SOF/LDV group and (40%) of SOF/SIM group (p=.153), thus SOF/SIM therapy showed a higher incidence of adverse events occurrence.Conclusions: Sofosbuvir based antiviral combination therapy with (DCV, LDV and SIM) showed a highly safety, tolerability and efficacy for treatment of chronic Hepatitis C Virus.

Biodiversity and full genome sequence of potato viruses Alfalfa mosaic virus and potato leaf roll virus in Egypt.

Solanum tuberosum (potato) is the second most important vegetable crop in Egypt. It is locally consumed, manufactured or supplied for export to Europe and other Arab countries. Potato is subject to infection by a number of plant viruses, which affect its yield and quality. Potato virus Y (PVY), potato leaf roll virus (PLRV), and Alfalfa mosaic virus (AMV) were detected in major potato-growing areas surveyed. Multiplex-RT-PCR assay was used for the detection of these three viruses in one reaction using three specific primer pairs designed to amplify genomic parts of each virus (1594 bp for PLRV, 795 bp for AMV, 801 bp for PVY). All three viruses were detected in a single reaction mixture in naturally infected field-grown potatoes. Multiplex RT-PCR improved sensitivity necessary for the early detection of infection. Incidence of single, double, or triple infection has been recorded in some locations. Full-length sequencing has been performed for an Egyptian FER isolate of PLRV. Through phylogenetic analysis, it was shown to occupy the same clade with isolate JokerMV10 from Germany. Complete nucleotide sequence of an Egyptian FER isolate of AMV and phylogenetic analysis was also performed; we propose that it is a new distinct strain of AMV belonging to a new subgroup IIC. This is the first complete nucleotide sequence of an Egyptian isolate of AMV. Genetic biodiversity of devastating potato viruses necessitates continuous monitoring of new genetic variants of such viruses.

Efficacy of commercial vaccines against newly emerging avian influenza H5N8 virus in Egypt

The newly emerging, highly pathogenic avian influenza (HPAI) H5N8 virus of clade 2.3.4.4 was recently detected in wild birds and domestic poultry in Egypt in the 2016/2017 winter season. Vaccination based on commercial H5 vaccines is used as an essential control strategy in Egyptian poultry. Here, we studied the efficacy of the eight most common commercial H5 poultry vaccines in the Egyptian market and compared them with an experimental vaccine based on the Egyptian LPAI H5N8 virus that was prepared by using reverse genetics. The experimental vaccine and Re-5 commercial vaccine were able to completely protect chickens and significantly reduce virus shedding. Our results indicate that most of the commercial poultry H5 vaccines used in the present study were ineffective because the seed viruses in these vaccines are genetically distinct from the H5N8 viruses currently circulating in Egypt. Although some of the commercial vaccines protected chickens from mortality, they failed to prevent chickens from shedding the virus. Accordingly, we recommend updating and reinforcing the H5N8 prevention and control strategies in Egypt. The vaccination strategy should be reconsidered based on currently circulating viruses.

Comparison of 2 different antibody assay methods, Elecsys Anti-HCVII (Roche) and Vidas Anti-HCV (Biomerieux), for the detection of antibody to hepatitis C virus in Egypt

The measurement of antibodies against hepatitis C virus (HCV) is important to screen HCV infection. The aim of this study is to investigate the reliability of 2 commercially available anti-HCV antibody kits used in routine laboratory testing in Egypt. One thousand nine hundred and thirty-one serum samples were analyzed using 2 anti-HCV test systems: Cobas e 411® Elecsys Anti-HCVII and Vidas® Anti-HCV Biomerieux. Discrepant samples were tested using the recombinant immunoblot assay Innogenetics® INNO-LIA HCV Score. Overall agreement of the 2 tests was 94%. Following discrepant sample testing by LIA, sensitivity and specificity using Vidas were 94% and 99%, respectively, while those for Cobas were 97% and 96%, respectively. This study demonstrates superior specificity by Vidas and higher sensitivity by Cobas. Both methods are suitable for laboratory and/or blood screening programs. The concomitant use of a supplementary or confirmatory assay is necessary to compare the accuracy of HCV serological assays.

Epidemiology and diagnosis of feline panleukopenia virus in Egypt: Clinical and molecular diagnosis in cats.

Aim:This work aimed to study epidemiology and diagnosis of feline panleukopenia virus (FPV) using clinical examination, direct ELISA, RNA viral isolation and identification, and knowing phylogenetic tree of our isolate.Materials and Methods:One hundred and sixty-five cats of different ages and sex were examined. Each cat was examined clinically to detect the clinical manifestations of the disease showing symptoms suggestive of feline panleukopenia (FP) as well as ELISA, and polymerase chain reaction (PCR) amplification analyses were conducted.Results:Our finding includes (a) clinical signs detected in 165 of 165 cats were in the form of lethargy, fever, anorexia, thirst, vomiting, diarrhea, dehydration, and leukopenia. (b) ELISA results revealed that 66 of all examined cats were positive for FPV. (c) The amplification products from all positive samples were confirmed as FPV (VP1) gene by nucleotide sequences analysis, in which 75 samples were positive using PCR amplification for the FPV. (d) Statistical evaluation of ELISA results in comparison to PCR findings. ELISA showed 88%, 100%, and 94.5% for sensitivity, specificity, and accuracy, respectively, while the prevalence of FP among the examined population was 45%. No effect of sex, breed, and age on ELISA results as recorded using Chi-square analysis.Conclusion:The results of the sequence analysis indicated that PCR products of the FPV cDNA exhibited very low variation in their nucleotide sequence of all isolates compared with the published FPV genome, which could be suggested that FPV appears to be genomically stasis compared with other Parvoviruses. The genome sequence of FPLV strain in this study has been deposited in GenBank under the accession number KY466003. Our isolate closely related 100% to isolates from Portugal, which might be the origin of infection to Egypt through importation of cats.

Potential Biological and Climatic Factors That Influence the Incidence and Persistence of Highly Pathogenic H5N1 Avian Influenza Virus in Egypt.

Highly pathogenic H5N1 avian influenza virus (A/H5N1) of clade 2.2.1 is endemic in poultry in Egypt where the highest number of human infections worldwide was reported. During the last 12 years the Egyptian A/H5N1 evolved into several genotypes. In 2007-2014 vaccinated poultry suffered from antigenic drift variants of clade 2.2.1.1 and in 2014/2015 an unprecedented upsurge of A/H5N1 clade 2.2.1.2 occurred in poultry and humans. Factors contributing to the endemicity or re-emergence of A/H5N1 in poultry in Egypt remain unclear. Here, three potential factors were studied: climatic factors (temperature, relative humidity, and wind speed), biological fitness in vitro, and pathogenicity in domestic Pekin and Muscovy ducks. Statistical analyses using negative binomial regression models indicated that ambient temperature in winter months influenced the spread of A/H5N1 in different geographic areas analyzed in this study. In vitro, at 4 and 56°C 2.2.1.1 and recent 2.2.1.2 viruses were more stable than other viruses used in this study. Further, Pekin ducks were more resistant than Muscovy ducks and the viruses were excreted for up to 2 weeks post-infection assuming a strong role as a reservoir. Taken together, ambient temperature in winter months potentially contributes to increasing outbreaks in some regions in Egypt. Heat stability of clade 2.2.1.1 and recent 2.2.1.2 viruses probably favors their persistence at elevated temperatures. Importantly, asymptomatically infected Pekin ducks may play an important role in the spread of avian and human-like A/H5N1 in Egypt. Therefore, control measures including targeted surveillance and culling of silently infected Pekin ducks should be considered.

Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt.

Highly pathogenic avian influenza (HPAI) H5N1 viruses are currently endemic in poultry in Egypt. Eradication of the viruses has been unsuccessful due to improper application of vaccine-based control strategies among other preventive measures. The viruses have evolved rapidly with increased bird-to-human transmission efficacy, thus affecting both animal and public health. Subsequent spread of potentially zoonotic low pathogenic avian influenza (LPAI) H9N2 in poultry has also hindered efficient control of avian influenza. The H5N1 viruses acquired enhanced bird-to-human transmissibility by (1) altering amino acids in hemagglutinin (HA) that enable binding affinity to human-type receptors, (2) loss of the glycosylation site and 130 loop in the HA protein and (3) mutation of E627K in the PB2 protein to enhance viral replication in mammalian hosts. The receptor binding site of HA of Egyptian H9N2 viruses has been shown to contain the Q234L substitution along with a H191 mutation, which can increase human-like receptor specificity. Therefore, co-circulation of H5N1 and H9N2 viruses in poultry farming and live bird markets has increased the risk of human exposure, resulting in complication of the epidemiological situation and raising a concern for potential emergence of a new influenza A virus pandemic. For efficient control of infection and transmission, the efficacy of vaccine and vaccination needs to be improved with a comprehensive control strategy, including enhanced biosecurity, education, surveillance, rapid diagnosis and culling of infected poultry.

Five BoLA-DRB3 genotypes detected in Egyptian buffalo infected with Foot and Mouth disease virus serotype O.

Foot and Mouth disease (FMD) is a contagious disease leads to economically loss in livestock production all over the world. This serious disease is caused due to the infection of the animal with a single-stranded RNA virus (FMDV). This study aimed to investigate the genetic polymorphism of BoLA-DRB3 gene in Egyptian buffalo as a candidate genetic marker included in multi-factorial process of FMD resistance/susceptibility. Also this work aimed to genetically characterization and serotyping of circulating FMD virus in Egypt during 2016.For serotyping of FMDV, RT-PCR was used for FMDV-positive samples and the results declared the presence of serotype O in all tested animals. The sequence analysis of FMDV samples revealed five different patterns for the detected serotype O which were submitted to GenBank under the accession Nos.: MG017361–MG017365.The 302-bp amplified fragments from BoLA-DRB3 exon 2 were digested with HaeIII endonuclease and the results showed that the presence of five BoLA-DRB3 genotypes, among them the genotype AA might be associated with FMD-resistance (P < 0.01). On the other hand, genotype AC could be correlated with susceptibility (P < 0.01) to FMD in Egyptian buffaloes where it was absent in resistant group. The five detected genotypes of BoLA-DRB3 exon 2 were submitted to GenBank with the accession Nos.: MF977316–MF977320. In conclusion, our findings suggested that the detection of different BoLA-DRB3 genotypes may be has a promising role for raising the resistance of Egyptian buffalo against FMDV especially serotype O which is prevalent in Egypt with preferring genotype AA.

In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus.

The polymerase complex proteins (PB2, PB1, and PA) are responsible primarily for the replication of avian influenza virus and play an important role in virus virulence, mammalian adaptation, and interspecies transmission. In this study; eight Egyptian LPAI-H9N2 viruses isolated from apparent healthy chickens and quails from 2014 to 2016. Characterization of complete nucleotide sequences, phylogenetic and mutation analysis were carried out. The measurement of thermodynamic stability of the H9N2 polymerase protein in comparison to human H3N2 and H1N1 proteins was carried out using in silico method. Phylogenetic analysis of these viruses revealed a close relationship to viruses isolated from neighboring Middle Eastern countries with an average of 96–99% homology. They are sharing the common ancestor A/quail/Hong Kong/G1/1997 (G1-Like) without any evidence for genetic reassortment. In addition, eight markers related to virulence were identified, including the combination of 627V and 391E in the PB2 gene with full-length PB1-F2 and PA-X proteins were observed in all viruses and the substitution N66S in PB1-F2 which suggest increasing virus virulence. Moreover, six markers that may affect the virus replication and transmission in mammalian hosts were identified. Five mutations related to mammalian adaptation show a structural stabilizing effect on LPAI-H9N2 polymerase complex protein according to the free-energy change (ΔΔG). Three out of those six adaptive mutations shown to increase polymerase complex protein stability were found in Egyptian LPAI-H9N2 viruses similar to Human H3N2 and H1N1 (661 in PB2, 225 and 409 in PA genes). Our results suggested that the stabilizing mutations in the polymerase complex protein have likely affected the protein structure and induced favorable conditions for avian virus replication and transmission in mammalian hosts. Indeed, the study reports the mutational analysis of the circulating LPAI-H9N2 strains in Egypt.

Multiple introductions of reassorted highly pathogenic avian influenza viruses (H5N8) clade 2.3.4.4b causing outbreaks in wild birds and poultry in Egypt

Recently, an increased incidence of outbreaks of highly pathogenic avian influenza (HPAI) H5N8 in poultry linked to infected migratory birds has been reported from different European, Asian and African countries.In Egypt, incursion of HPAI H5N8 virus of clade 2.3.4.4b has been recently registered. Full genomic characterization of 3 virus isolates from wild birds and poultry (backyard and commercial farm sectors) showed high nucleotide similarity among the HA, NA, M, and NS gene segments of the three Egyptian HPAI H5N8 viruses, indicating that they are descendants of a common ancestral virus. However, the analyzed Egyptian H5N8 viruses revealed distinct genotypes involving different origins of the PB2, PB1, PA and/or NP segments. In genotype-1 represented by strain A/common-coot/Egypt/CA285/2016 the PB2 and NP segments showed closest relationship to H5N6 and H6N2 viruses, recently detected in Italy. The second is replacement of PB1 and NP genes A novel reassortant, represented by strain A/duck/Egypt/SS19/2017, showed an exchange of PB1 and NP genes which might have originated from H6N8 or H1N1 and H6N2 viruses. Finally, replacement of PA and NP genes characterized strain A/duck/Egypt/F446/2017. Bayesian phylogeographic analyses revealed that Egyptian H5N8 viruses are highly likely derived from Russian 2016 HPAI H5N8 virus (A/great_crested_grebe/Uvs-Nuur_Lake/341/2016 (H5N8)) and the reassortment likely occurred before incursion to Egypt.

Convenience of rapid detection tests in suspecting prevalence of FMD virus in Egypt between 2016-2017

Convenience of rapid detection tests in suspecting prevalence of FMD virus in Egypt between 2016-2017

Phylogenetic assessment reveals continuous evolution and circulation of pigeon-derived virulent avian avulaviruses 1 in Eastern Europe, Asia, and Africa

BackgroundThe remarkable diversity and mobility of Newcastle disease viruses (NDV) includes virulent viruses of genotype VI. These viruses are often referred to as pigeon paramyxoviruses 1 because they are normally isolated and cause clinical disease in birds from the Columbidae family. Genotype VI viruses occasionally infect, and may also cause clinical disease in poultry. Thus, the evolution, current spread and detection of these viruses are relevant to avian health.ResultsHere, we describe the isolation and genomic characterization of six Egyptian (2015), four Pakistani (2015), and two Ukrainian (2007, 2013) recent pigeon-derived NDV isolates of sub-genotype VIg. These viruses are closely related to isolates from Kazakhstan, Nigeria and Russia. In addition, eight genetically related NDV isolates from Pakistan (2014–2016) that define a new sub-genotype (VIm) are described. All of these viruses, and the ancestral Bulgarian (n = 2) and South Korean (n = 2) viruses described here, have predicted virulent cleavage sites of the fusion protein, and those selected for further characterization have intracerebral pathogenicity index assay values characteristic of NDV of genotype VI (1.31 to 1.48). A validated matrix gene real-time RT-PCR (rRT-PCR) NDV test detect all tested isolates. However, the validated rRT-PCR test that is normally used to identify the virulent fusion gene fails to detect the Egyptian and Ukrainian viruses due to mismatches in primers and probe. A new rapid rRT-PCR test to determine the presence of virulent cleavage sites for viruses from sub-genotypes VIg was developed and evaluated on these and other viruses.ConclusionsWe describe the almost simultaneous circulation and continuous evolution of genotype VI Newcastle disease viruses in distant locations, suggesting epidemiological connections among three continents. As pigeons are not migratory, this study suggests the need to understand the possible role of human activity in the dispersal of these viruses. Complete genomic characterization identified previously unrecognized genetic diversity that contributes to diagnostic failure and will facilitate future evolutionary studies. These results highlight the importance of conducting active surveillance on pigeons worldwide and the need to update existent rapid diagnostic protocols to detect emerging viral variants and help manage the disease in affected regions.

Insights into genetic diversity and biological propensities of potentially zoonotic avian influenza H9N2 viruses circulating in Egypt

Low pathogenic avian influenza (LPAI) H9N2 viruses have established endemic status in Egyptian poultry populations since 2012. Recently, four cases of human H9N2 virus infections in Egypt demonstrated the zoonotic potential of these viruses. Egyptian H9N2 viruses obtained from 2011 to 2014 phylogenetically grouped into three clusters (1−3) within subclade B of the G1 lineage. Antigenically, a close clustering of the Egyptian H9N2 viruses with other recent G1-B like H9N2 strains and a significant antigenic distance from viruses outside the G1-B lineage was evident. Recent Egyptian LPAIV H9N2 showed a tendency to increased binding with erythrocytes expressing α 2,6-linked sialic acid which correlated with the Q226L amino acid substitution at the receptor binding unit of the hemagglutinin (Q234L, H9 numbering). Sequence analyses of the N2 neuraminidase (NA) revealed substitutions in the NA hemadsorption site similar to the N2 of prepandemic H3N2/1968, but no distinct antigenic or functional characteristics of the H9N2 NA associated with increased zoonotic potential could be identified.

Isolation and characterization of basil mosaic virus in Egypt

Different viral infection symptoms were observed on leaves of basil plants (Ocimum basilicum L.), growing at El-Monofia Governorate, Egypt, during 2015–2016. The majority of these symptoms were mosaic and leaf malformation. The pathogenic agent of this disease is known as basil mosaic virus (BsMV). The sensitive hosts to BsMV are Chenopodium amaranticolor and Phaseolus vulgaris cv. (brown beans). The biological properties of BsMV were found to be 10−4, 6 days and 66 °C for dilution end point, longevity in vitro and thermal inactivation point, respectively. The electron micrograph of the isolated virus indicated this virus was found to be isometric particles of approximately, 50 nm in diameter and could be classified as tentative member of the Fabavirus. Real-time PCR detection by the Fab primer pairs was confirmed at Ct value = 25.44 for the total cDNA isolated from infected Basil plants and 27.94 for the cDNA of purified virus particles, while CMV primer pairs showed no amplification for both samples. According to the available reports this seems to be the first record for basil mosaic virus in Egypt.

Cost-Effectiveness Analysis of New HCV Treatments in Egyptian Cirrhotic and Non-Cirrhotic Patients: A Societal Perspective

ObjectivesTo evaluate the cost-effectiveness of sofosbuvir (SOF) + ribavirin (RBV), SOF + daclatasvir (DCV), and SOF + ledipasvir (LDV) + RBV compared with SOF + pegylated interferon alfa (pegIFN) + RBV in the treatment of patients infected with hepatitis C virus in Egypt. MethodsTwo Markov models were developed on the basis of the Egyptian clinical data and practice and were derived from published sources. The clinical parameters were derived from two sources: the Egypt multicenter national treatment program and previously published randomized clinical trials. The utility of the health states was derived using the available published data. Direct medical costs were obtained from the National Liver Institute database. ResultsIn noncirrhotic patients, incremental cost-effectiveness ratios of US $2330 per quality-adjusted life-year (QALY) gained for the SOF + LDV + RBV, −US $9043/QALY for the SOF + DCV, and −US $1332/QALY for the SOF + RBV regimens were yielded. In cirrhotic patients, incremental cost-effectiveness ratios of −US $4170/QALY gained for the SOF + LDV + RBV, −US $9515/QALY for the SOF + DCV, and –US $2289/QALY for the SOF + RBV regimens were yielded. The SOF + DCV regimen was the most cost-saving option for cirrhotic and noncirrhotic patients. Deterministic sensitivity analyses remain robust. ConclusionsThe present study concludes that the SOF + DCV regimen among other currently available regimens is the most cost-saving option that yields the most favorable future health economic outcomes compared with the SOF + pegIFN + RBV regimen across a broad spectrum of patients, including those with cirrhosis.