Dataset Information

5' UTR and NS5B-based genotyping of hepatitis C virus in patients from Damietta governorate, Egypt.

ABSTRACT: Chronic hepatitis C virus (HCV) infection is a main health problem in Egypt causing high rates of mortalities. Egypt has the highest HCV prevalence in the world, with specific HCV subtypes epidemic and circulating extensively in the country. Different antiviral therapy protocols have been implemented for treating Egyptian HCV patients. Due to the limited data about HCV in Egypt, this study aimed to genotype HCV strains circulating in the Nile Delta Damietta governorate and to investigate the variation in the nonstructural 5B (NS5B) region targeted by the newly approved antiviral drugs. Thirty HCV samples from treatment-naïve patients were genotyped by restriction fragment length polymorphism. Some samples were genotyped by direct sequencing of their 5' untranslated region (UTR) and NS5B regions. Phylogenetic analysis was also performed on the sequences of their NS5B regions. Fourteen new sequences have been deposited in the GenBank database. Results showed that subtype 4a was prevalent in addition to subtype 1g. None of the previously reported NS5B substitutions were detected in the sequenced isolates from treatment-naïve patients, which may be a good predictor for efficient treatment of HCV Egyptian patients with Sofosbuvir. Further studies on Sofosbuvir treated-HCV Egyptian patients are required to investigate whether any NS5B substitutions can confer resistance to treatment.

SUBMITTER: El-Tahan RR

PROVIDER: S-EPMC6057237 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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5' UTR and NS5B-based genotyping of hepatitis C virus in patients from Damietta governorate, Egypt.

El-Tahan Radwa R RR Ghoneim Ahmed M AM Zaghloul Hosam H

Journal of advanced research 20180109

Chronic hepatitis C virus (HCV) infection is a main health problem in Egypt causing high rates of mortalities. Egypt has the highest HCV prevalence in the world, with specific HCV subtypes epidemic and circulating extensively in the country. Different antiviral therapy protocols have been implemented for treating Egyptian HCV patients. Due to the limited data about HCV in Egypt, this study aimed to genotype HCV strains circulating in the Nile Delta Damietta governorate and to investigate the var ...[more]

PMID: 30046475

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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: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

5' UTR and NS5B-based genotyping of hepatitis C virus in patients from Damietta governorate, Egypt.

Publications

5' UTR and NS5B-based genotyping of hepatitis C virus in patients from Damietta governorate, Egypt.

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