Dataset Information

Hepatitis C Virus NS5B Sequence-Based Genotyping Analysis of Patients From the Sharkia Governorate, Egypt.

ABSTRACT:

Background

Chronic hepatitis C virus infection and its sequela are major health problems facing the Egyptian community. The high prevalence and spread rates of the disease require serious actions to stop or decrease these rates. Determination of HCV genotypes and subgenotypes adds significant knowledge about the epidemiology of the disease, and provides an added value in the decision making process of what strategy to follow and what therapy response to expect. The molecular epidemiology and genetic variability of HCV variants circulating in Egypt still need further analysis.

Objectives

The study was held to evaluate the genotype and subgenotype of the hepatitis c virus circulating in Sharkia as one of the large governorates of Egypt, which was not included in any study for genotyping of the virus before.

Patients and methods

The HCV molecular epidemiology in Sharkia governorate was studied using direct sequencing and further phylogenetic analysis of a partial NS5B region of the HCV genome from 63 patients. HCV genotype and subtype were successfully determined in 62 out of 63 patients.

Results

The highest prevalent genotype was genotype 4a, which was found in 57 patients (92%) followed by 2 isolates (3%) with genotype 4o, 2 strains (3%) with genotype 1g and one isolate (2%) with genotype 4n.

Conclusions

This molecular epidemiology study revealed high prevalence of HCV genotype 4, subtype 4a among Egyptian patients residing in Sharkia governorate, Egypt.

SUBMITTER: Elsadek Fakhr A

PROVIDER: S-EPMC3867025 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Publications

Hepatitis C Virus NS5B Sequence-Based Genotyping Analysis of Patients From the Sharkia Governorate, Egypt.

Elsadek Fakhr Ahmed A Pourkarim Mahmoud Reza MR Maes Piet P Maes Piet P Atta Amal Hassan AH Marei Ayman A Azab Magda M Van Ranst Marc M

Hepatitis monthly 20131217 12

<h4>Background</h4>Chronic hepatitis C virus infection and its sequela are major health problems facing the Egyptian community. The high prevalence and spread rates of the disease require serious actions to stop or decrease these rates. Determination of HCV genotypes and subgenotypes adds significant knowledge about the epidemiology of the disease, and provides an added value in the decision making process of what strategy to follow and what therapy response to expect. The molecular epidemiology ...[more]

PMID: 24358038

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Project description:BACKGROUND:Current HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients. METHODS:All plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences. RESULTS:A total of 369 samples were received during the study period with high viral load values (median: 930,952?IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p?=?0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region. CONCLUSIONS:We found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1-4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.

Project description:The present study aimed to isolate Pasteurella multocida (P. multocida) from pulmonary cases in several avian species and then investigate the histopathological features, antimicrobial resistance determinants, virulence characteristics, and risk factors analysis of the isolates in each species in correlation with epidemiological mapping of pasteurellosis in Sharkia Governorate, Egypt. The obtained data revealed a total occurrence of 9.4% (30/317) of P. multocida among the examined birds (chickens, ducks, quails, and turkeys). The incidence rate was influenced by avian species, climate, breed, age, clinical signs, and sample type. Antimicrobial susceptibility testing revealed that all isolates were sensitive to florfenicol and enrofloxacin, while 86.6 and 73.3% of the isolates displayed resistance to amoxicillin-clavulanic acid and erythromycin, respectively. All of the P. multocida isolates showed a multiple-drug resistant pattern with an average index of 0.43. Molecular characterization revealed that the oma87, sodA, and ptfA virulence genes were detected in the all examined P. multocida isolates. The ermX (erythromycin), blaROB-1 (β-lactam), and mcr-1(colistin) resistance genes were present in 60, 46.6, and 40% of the isolates, respectively. Ducks and quails were the most virulent and harbored species of antimicrobial-resistant genes. These results were in parallel with postmortem and histopathological examinations which detected more severe interstitial pneumonia lesions in the trachea and lung, congestion, and cellular infiltration especially in ducks. Epidemiological mapping revealed that the Fakous district was the most susceptible to pasteurellosis infection. Thus, farmers are recommended to monitor their flocks for signs of respiratory disease, seek veterinary care promptly if any birds are sick, and avoid the random usage of antibiotics. In conclusion, this study presents a comprehensive picture of the risk factors in correlation to the pathognomonic characteristics of P. multocida infection in poultry sectors to help in developing more effective strategies for prevention and control.

Project description:BackgroundLumpy skin disease (LSD) is endemic in Egypt despite the Egyptian authorities' annual mass vaccination of cattle with sheeppox vaccine (Veterinary Serum and Vaccine Research Institute, Egypt), and the LSD virus (LSDV) continues to thrive practically every summer. The disease has a huge economic impact on the trade of the animal and its by-product.AimThis paper study the molecular characterization of LSDV strains that have been circulating in Sharkia Governorate, Egypt, for three successive years (2018, 2019, and 2020).MethodsA total of 61 specimens (26 skin nodules and 35 oculonasal swabs) were collected from a clinic in the hospital of veterinary medicine, Zagazig University, during the summer months (July, August, and September) of three outbreaks in 2018, 2019, and 2020. These were examined by polymerase chain reaction (PCR) based on the open reading frame 103 (ORF103) gene to confirm the suspected cases and determine the degree of homology between the three different outbreaks during three successive years between each other and between the derived sequences of GenBank.ResultsCattle is thought to be infected with LSDV due to the presence of scattered local or diffuse circumscribed skin nodules along with fever and lymph node enlargement and sometimes leg edema. The PCR approach proved rapid, sensitive, and specific for the detection of LSDV and confirmative diagnosis of the disease. Forty-six were detected to be positive by PCR (75.4%). The seven sequenced samples were translated to amino acid and registered in GenBank under accession number MW357655-MW357661. A single nucleotide mutation and amino acid variation were observed at positions 161 C (2020)/T (2018&2019) and consequently, a change in the amino acid at position 54 P (2020)/L (2018&2019) between the outbreak in 2020 and those in 2018 and 2019, respectively. The field LSDV isolates from Egypt cattle were more closely related to other LSDV sequences from Africa (Kenya), Asia, Europe, and the United States.These findings highlight the necessity of ongoing surveillance and characterization of circulating strains and the need to improve procedures for distinguishing vaccine strains from field viruses.

Project description:ObjectivesTo determine the prevalence and causes of blindness and vision impairment, and the coverage and quality of cataract surgical services, among population aged 50 years and older in Sohag governorate in Egypt.DesignA population-based cross-sectional survey using two-stage cluster random sampling following the rapid assessment of avoidable blindness methodology.SettingA community-based survey conducted by six teams of ophthalmologists, assistants and local guides. Enrolment and examination were door-to-door in selected clusters.ParticipantsUsing 2016 census data, 68 population units were randomly selected as clusters (of 60 people) with probability proportionate to population size. Anyone aged 50 years and older, residing in a non-institutional setting in a cluster for at least 6 months, was eligible to participate.Primary and secondary outcome measuresThe prevalence and causes of blindness and vision impairment. Secondary outcomes were CSC and effectiveness and participant-reported barriers to cataract surgery.ResultsOf 4078 participants enrolled, 4033 (98.9%) were examined. The age-adjusted and sex-adjusted prevalence of blindness, severe vision impairment and moderate vision impairment were 5.9% (95% CI 4.8% to 6.9%), 4.7% (95% CI 3.8% to 5.7%) and 18.9% (95% CI 16.8% to 21.0%), respectively. Cataract caused most of blindness (41.6%), followed by non-trachomatous corneal opacity (15.7%) and posterior segment diseases (14.5%). Cataract surgical coverage (CSC) for persons for visual acuity <3/60 was 86.8%, the proportion of cataract surgeries with poor visual outcome was 29.5% and effective CSC (eCSC) was 44.9%. eCSC was lower in women than men. The most frequently reported barrier to surgery was cost (51.5%).ConclusionsThe prevalence of blindness in Sohag governorate is higher than districts in other middle-income countries in the region. CSC was high; however, women suffer worse quality-corrected CSC than men. The quality of cataract surgery needs to be addressed, while health system strengthening across government and private settings could alleviate financial barriers.

Dataset Information

Hepatitis C Virus NS5B Sequence-Based Genotyping Analysis of Patients From the Sharkia Governorate, Egypt.

Background

Objectives

Patients and methods

Results

Conclusions

Publications

Hepatitis C Virus NS5B Sequence-Based Genotyping Analysis of Patients From the Sharkia Governorate, Egypt.

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