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Molecular characterization and epidemic history of hepatitis C virus using core sequences of isolates from Central Province, Saudi Arabia.

ABSTRACT: The source of HCV transmission in Saudi Arabia is unknown. This study aimed to determine HCV genotypes in a representative sample of chronically infected patients in Saudi Arabia. All HCV isolates were genotyped and subtyped by sequencing of the HCV core region and 54 new HCV isolates were identified. Three sets of primers targeting the core region were used for both amplification and sequencing of all isolates resulting in a 326 bp fragment. Most HCV isolates were genotype 4 (85%), whereas only a few isolates were recognized as genotype 1 (15%). With the assistance of Genbank database and BLAST, subtyping results showed that most of genotype 4 isolates were 4d whereas most of genotype 1 isolates were 1b. Nucleotide conservation and variation rates of HCV core sequences showed that 4a and 1b have the highest levels of variation. Phylogenetic analysis of sequences by Maximum Likelihood and Bayesian Coalescent methods was used to explore the source of HCV transmission by investigating the relationship between Saudi Arabia and other countries in the Middle East and Africa. Coalescent analysis showed that transmissions of HCV from Egypt to Saudi Arabia are estimated to have occurred in three major clusters: 4d was introduced into the country before 1900, the major 4a clade's MRCA was introduced between 1900 and 1920, and the remaining lineages were introduced between 1940 and 1960 from Egypt and Middle Africa. Results showed that no lineages seem to have crossed from Egypt to Saudi Arabia in the last 15 years. Finally, sequencing and characterization of new HCV isolates from Saudi Arabia will enrich the HCV database and help further studies related to treatment and management of the virus.

SUBMITTER: Shier MK

PROVIDER: S-EPMC5580995 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Molecular characterization and epidemic history of hepatitis C virus using core sequences of isolates from Central Province, Saudi Arabia.

Shier Medhat K MK Iles James C JC El-Wetidy Mohammad S MS Ali Hebatallah H HH Al Qattan Mohammad M MM

PloS one 20170901 9

The source of HCV transmission in Saudi Arabia is unknown. This study aimed to determine HCV genotypes in a representative sample of chronically infected patients in Saudi Arabia. All HCV isolates were genotyped and subtyped by sequencing of the HCV core region and 54 new HCV isolates were identified. Three sets of primers targeting the core region were used for both amplification and sequencing of all isolates resulting in a 326 bp fragment. Most HCV isolates were genotype 4 (85%), whereas only ...[more]

PMID: 28863156

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Project description:BackgroundThere is paucity in the literature regarding gallbladder cancer in Saudi Arabia, possibly because it is not among the top 10 cancers diagnosed nationwide according to the Saudi Cancer Registry. Moreover, national or regional data on gallbladder cancer in Saudi Arabia have not been analyzed. The purpose of this study was to describe the presentation, disease stage, histology, and survival rates for gallbladder cancer in Saudi patients at a single institution between January 1, 2010 and December 31, 2017.Materials and methodsThis was a retrospective study of 76 patients who presented to our hospital between January 1, 2010 and December 31, 2017, with established diagnosis of gallbladder carcinoma. The diagnosis was made either histopathologically following simple laparoscopic cholecystectomy or biopsy from metastatic liver lesion in patients with gallbladder mass, or the high suspicion of gallbladder carcinoma based on incidental radiological findings. Presentation, disease stage, histology, and treatment modalities were analyzed using descriptive statistics and frequency distributions. Survival rates were analyzed and presented using Kaplan-Meier curves.ResultsBased on initial analyses the disease was more frequent among women (62.0%) than men (39.0%). Surgical resection was attempted in 40.8% patients. The average age at presentation and diagnosis of gallbladder carcinoma was 62.4 years. The disease had two peaks, one at 51.0 years and the other between 66.0 and 70.0 years. The median survival time for the overall at-risk patients was only 1.0 year, while for stage IVB patients was 7.2 months. Adenocarcinoma not otherwise specified (NOS) was the most common histopathology type (75.0%), with most patients presenting with stage IVB disease (75.0%). Gallbladder carcinoma was incidentally detected in 42.1%, including three cases (3.9%) diagnosed at our hospital.ConclusionsGallbladder cancer is a rare type of cancer in Saudi Arabia, and most patients are treated surgically, despite being mostly diagnosed at the advanced stage of the disease.

Project description:BackgroundEastern province of Saudi Arabia is an industrial zone with large immigrant population and high level of tuberculosis case notification among immigrants. The impact of immigration and current trends of tuberculosis transmission among immigrants and autochthonous population in the region had not been investigated so far using molecular tools.MethodologyDuring 2009- 2011, a total of 524 Mycobacterium tuberculosis isolates were collected from the central tuberculosis reference laboratory, representing an estimated 79.2% of the culture-positive tuberculosis cases over the study period in the province. These isolates were genotyped by using 24 locus-based MIRU-VNTR typing and spoligotyping followed by first line drug susceptibility testing. The molecular clustering profiles and phylogenetic diversity of isolates were determined and compared to the geographical origins of the patients.Principle findingsGenotyping showed an overall predominance of Delhi/CAS (29.4%), EAI (23.8%) and Ghana (13.3%) lineages, with slightly higher proportions of Delhi/CAS among autochthonous population (33.3 %) and EAI (30.9%) among immigrants. Rate of any drug resistance was 20.2% with 2.5% of multi-drug resistance. Strain cluster analysis indicated 42 clusters comprising 210 isolates, resulting in a calculated recent transmission index of 32.1%. Overall shared cluster ratio was 78.6% while 75.8% were shared between autochthonous population and immigrant population with a predominance of immigrants from South east Asia (40.7%). In contrast, cross national transmission within the immigrant population was limited (24.2%). Younger age (15-30- p value-0.043, 16-45, p value 0.030), Saudi nationality (p value-0.004) and South East Asian origin (p value-0.011) were identified as significant predisposing factors for molecular strain clustering.ConclusionsThe high proportion of molecular clusters shared among the autochthonous and immigrant populations suggests a high permeability of tuberculosis transmission between both populations in the province. These results prompt for the need to strengthen the current tuberculosis control strategies and surveillance programs.

Dataset Information

Molecular characterization and epidemic history of hepatitis C virus using core sequences of isolates from Central Province, Saudi Arabia.

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Molecular characterization and epidemic history of hepatitis C virus using core sequences of isolates from Central Province, Saudi Arabia.

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