scholarly journals Genetic Subtypes and Natural Resistance Mutations in HCV Genotype 4 Infected Saudi Arabian Patients

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1832
Author(s):  
Mariantonietta Di Stefano ◽  
Mona H. Ismail ◽  
Thomas Leitner ◽  
Giuseppina Faleo ◽  
Saada A. Elmnan Adem ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Direct Sequencing ◽  
Phylogenetic Analyses ◽  
Natural Resistance ◽  
Resistance Mutations ◽  
Hepatitis C Infection ◽  
Genotype 4 ◽  
Genetic Subtypes ◽  
Small Cohort ◽  
Lost To Follow Up

This study aimed to characterize the HCV genetic subtypes variability and the presence of natural occurring resistance-associated substitutions (RASs) in Saudi Arabia patients. A total of 17 GT patients were analyzed. Sequence analysis of NS3, NS5A, and NS5B regions was performed by direct sequencing, and phylogenetic analyses were used to determine genetic subtypes, RAS, and polymorphisms. Nine patients were infected by GT 4a, two with GT 4o and three with GT 4d. Two patients were infected with apparent recombinant virus (4a/4o/4a in NS3/NS5A/NS5B), and one patient was infected with a previously unknown, unclassifiable, virus of GT 4. Natural RASs were found in six patients (35%), including three infected by GT 4a, two by GT 4a/GT 4o/GT 4a, and one patient infected by an unknown, unclassifiable, virus of GT 4. In particular, NS3-RAS V170I was demonstrated in three patients, while NS5A-RASs (L28M, L30R, L28M + M31L) were detected in the remaining three patients. All patients were treated with sofosbuvir plus daclatasvir; three patients were lost to follow-up, whereas 14 patients completed the treatment. A sustained virological response (SVR) was obtained in all but one patient carrying NS3-RAS V170I who later relapsed. GT 4a is the most common subtype in this small cohort of Saudi Arabia patients infected with hepatitis C infection. Natural RASs were observed in about one-third of patients, but only one of them showed a treatment failure.

scholarly journals Genetic Subtypes and Natural Resistance Mutations in HCV Genotype 4 Infected Saudi Arabian Patients

2021 ◽  
Author(s):  
Mariantonietta Di Stefano ◽  
Mona Ismail ◽  
Giuseppina Faleo ◽  
Saada Elmnan Adem ◽  
Mohamed Elamin ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Direct Sequencing ◽  
Natural Resistance ◽  
Resistance Mutations ◽  
Hepatitis C Infection ◽  
Genotype 4 ◽  
Genetic Subtypes ◽  
Small Cohort ◽  
Lost To Follow Up

This study aimed to characterize the genetic subtypes of HCV-GT4 and identify the presence of natural occurring resistance-associated substitutions (RASs) in Saudi Arabia patients. A total of 17 GT4 patients was analyzed. Sequence analysis of NS3, NS5A and NS5B regions was performed by direct sequencing. In addition, phylogenetic analysis was used to determine genetic subtypes, RAS and polymorphisms. Nine patients were infected by a GT4a, one with GT4o, 3 with GT4d. The remaining four patients were infected with a recombinant virus (GT4a+GT4o in three patients, GT4c+GT4d in a patient). Natural RASs were found in six patients (35%), including three infected by GT4a, two by GT4a+GT4o and one patient infected by GT4c+GT4d. In particular, NS3-RAS V170I was demonstrated in three patients, while NS5A-RASs (L28M, L30R, L28M+M31L) were detected in the remaining three patients. All patients were treated with sofosbuvir plus daclatasvir; three patients were lost to follow-up whereas 14 patients completed the treatment. A sustained virological response (SVR) was obtained in all but one patient carrying NS3-RAS V170I who later relapsed. GT4a is the most common subtype in this small cohort of Saudi Arabia patients infected with hepatitis C infection. Natural RASs were observed in about a third of patients, but only one of them showed a treatment failure.

scholarly journals Prevalence of Hepatitis C Virus Genotypes in the Southern Region, Saudi Arabia

2019 ◽  
Author(s):  
Abdullah M AlKahtani ◽  
Meaad N Alsultan ◽  
Abdulrahim R Hakami ◽  
Mohammad Alamri
Keyword(s):  
Saudi Arabia ◽  
Viral Load ◽  
Blood Transfusion ◽  
Blood Donation ◽  
Direct Sequencing ◽  
Southern Region ◽  
Genotype 1 ◽  
Genotype 4 ◽  
Genotype 2 ◽  
History Of

ABSTRACTAimThe aim of this study was to investigate the prevalence of HCV genotypes in the Southern Region, Saudi Arabia.Materials & methodsA total of 76 HCV-positive individuals were selected for this study, including 34 males and 42 females, both acute and chronic patients. All HCV isolates were genotyped by direct sequencing of the 5’UTR region. The Chemistry profile, viral load and history of blood transfusion were collected from the hospital record.ResultsThe most common genotype was gt 4 (48.7%) followed by gt 1 (34.2%) and gt 3 (14.5%). Genotype 2 (2.6%) was only found in elderly male individuals. Patients with history of blood transfusion showed a high percentage of genotype 1 compared to the total number of all patients with genotype 1 (23% and 11% respectively). Biochemical assay showed high level of ALT particularly in genotype 4. No significant relationship was observed between HCV genotype and AST level between genotypes. The viral load was higher in HCV patients received blood transfusion than other genotypes.ConclusionThe prevalence of genotypes in this study confirmed the observation of other investigations, but no link was found between sex and genotype. There might be an association between blood donation in the past and infections with genotype 1.

Genetic Diversity and Drug Resistance of HIV-1 CRF55_01B in Guangdong, China

2020 ◽  
Vol 18 (3) ◽  
pp. 210-218
Author(s):  
Guolong Yu ◽  
Yan Li ◽  
Xuhe Huang ◽  
Pingping Zhou ◽  
Jin Yan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Reverse Transcriptase ◽  
Phylogenetic Analyses ◽  
Resistance Mutations ◽  
Protease Inhibition ◽  
Subtype B ◽  
Primary Drug Resistance ◽  
Hiv 1 ◽  
Primary Drug

Background: HIV-1 CRF55_01B was first reported in 2013. At present, no report is available regarding this new clade’s polymorphisms in its functionally critical regions protease and reverse transcriptase. Objective: To identify the diversity difference in protease and reverse transcriptase between CRF55_01B and its parental clades CRF01_AE and subtype B; and to investigate CRF55_01B’s drug resistance mutations associated with the protease inhibition and reverse transcriptase inhibition. Methods: HIV-1 RNA was extracted from plasma derived from a MSM population. The reverse transcription and nested PCR amplification were performed following our in-house PCR procedure. Genotyping and drug resistant-associated mutations and polymorphisms were identified based on polygenetic analyses and the usage of the HIV Drug Resistance Database, respectively. Results: A total of 9.24 % of the identified CRF55_01B sequences bear the primary drug resistance. CRF55_01B contains polymorphisms I13I/V, G16E and E35D that differ from those in CRF01_AE. Among the 11 polymorphisms in the RT region, seven were statistically different from CRF01_AE’s. Another three polymorphisms, R211K (98.3%), F214L (98.3%), and V245A/E (98.3 %.), were identified in the RT region and they all were statistically different with that of the subtype B. The V179E/D mutation, responsible for 100% potential low-level drug resistance, was found in all CRF55_01B sequences. Lastly, the phylogenetic analyses demonstrated 18 distinct clusters that account for 35% of the samples. Conclusions: CRF55_01B’s pol has different genetic diversity comparing to its counterpart in CRF55_01B’s parental clades. CRF55_01B has a high primary drug resistance presence and the V179E/D mutation may confer more vulnerability to drug resistance.

scholarly journals Molecular Identification of Trypanosoma evansi Isolated from Arabian Camels (Camelus dromedarius) in Riyadh and Al-Qassim, Saudi Arabia

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1149
Author(s):  
Dina M. Metwally ◽  
Isra M. Al-Turaiki ◽  
Najwa Altwaijry ◽  
Samia Q. Alghamdi ◽  
Abdullah D. Alanazi
Keyword(s):  
Saudi Arabia ◽  
Infection Rate ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Trypanosoma Evansi ◽  
Camelus Dromedarius ◽  
18S Ribosomal Rna ◽  
18S Ribosomal Rna Gene ◽  
Polymerase Chain ◽  
Pcr Targeting

We analyzed the blood from 400 one-humped camels, Camelus dromedarius (C. dromedarius), in Riyadh and Al-Qassim, Saudi Arabia to determine if they were infected with the parasite Trypanosoma spp. Polymerase chain reaction (PCR) targeting the internal transcribed spacer 1 (ITS1) gene was used to detect the prevalence of Trypanosoma spp. in the camels. Trypanosoma evansi (T. evansi) was detected in 79 of 200 camels in Riyadh, an infection rate of 39.5%, and in 92 of 200 camels in Al-Qassim, an infection rate of 46%. Sequence and phylogenetic analyses revealed that the isolated T. evansi was closely related to the T. evansi that was detected in C. dromedarius in Egypt and the T. evansi strain B15.1 18S ribosomal RNA gene identified from buffalo in Thailand. A BLAST search revealed that the sequences are also similar to those of T. evansi from beef cattle in Thailand and to T. brucei B8/18 18S ribosomal RNA from pigs in Nigeria.

scholarly journals Molecular Analysis of Targeted Insecticide Resistance Gene Mutations in Field-Caught Mosquitos of Medical Importance From Saudi Arabia

2021 ◽  
Author(s):  
Yuan Fang ◽  
Ernest Tambo ◽  
Jing-Bo Xue ◽  
Yi Zhang ◽  
Xiao-Nong Zhou ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Insecticide Resistance ◽  
Resistance Gene ◽  
Phylogenetic Analyses ◽  
Gene Mutations ◽  
Mosquito Vector ◽  
Dengue Disease ◽  
The Status ◽  
History Of ◽  
Exon 20

Abstract Gene mutations on target sites can be a valuable indicator of the status of insecticide resistance. Jeddah, a global commercial and major port-of-entry city, is bearing the brunt of dengue disease burden in Saudi Arabia. In the current study, six genotypes of three codon combinations (989, 1016, and 1534) were observed on voltage-gated sodium channel (VGSC) gene in Jeddah’s Aedes aegypti population, with PGF/PGC as the dominant one. Two types of introns between exon 20 and 21 on VGSC have been identified for the first time in Ae. aegypti in Saudi Arabia. Statistical and phylogenetic analyses showed that the intron type was significantly associated with the 1016 allele and may reflect the history of insecticide treatment in different continents. In addition, fixation of the L1014F allele on VGSC and G119S on acetylcholinesterase 1 gene was detected in local Culex quinquefasciatus populations, with frequencies of 95.24 and 100%, respectively. To the best of our knowledge, this is the first report of resistant-associated mutations in field-caught Cx. quinquefasciatus in Saudi Arabia. The high prevalence of insecticide resistance gene mutations in local primary mosquito vector species highlights the urgent need to carry out comprehensive insecticide resistance surveillance in Saudi Arabia.

Impact of genotypic diversity on selection of subtype-specific drug resistance profiles during raltegravir-based therapy in individuals infected with B and BF recombinant HIV-1 strains

2020 ◽  
Vol 75 (6) ◽  
pp. 1567-1574
Author(s):  
Daniela Sánchez ◽  
Solange Arazi Caillaud ◽  
Ines Zapiola ◽  
Silvina Fernandez Giuliano ◽  
Rosa Bologna ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Current Knowledge ◽  
Phylogenetic Analyses ◽  
Genotypic Diversity ◽  
Resistance Testing ◽  
Cross Resistance ◽  
Resistance Mutations ◽  
Middle Income ◽  
Subtype B ◽  
Hiv 1

Abstract Background Current knowledge on HIV-1 resistance to integrase inhibitors (INIs) is based mostly on subtype B strains. This contrasts with the increasing use of INIs in low- and middle-income countries, where non-B subtypes predominate. Materials and methods HIV-1 drug resistance genotyping was performed in 30 HIV-1-infected individuals undergoing virological failure to raltegravir. Drug resistance mutations (DRMs) and HIV-1 subtype were characterized using Stanford HIVdb and phylogenetic analyses. Results Of the 30 integrase (IN) sequences, 14 were characterized as subtype F (47%), 8 as subtype B (27%), 7 as BF recombinants (23%) and 1 as a putative CRF05_DF (3%). In 25 cases (83%), protease and reverse transcriptase (PR-RT) sequences from the same individuals confirmed the presence of different BF recombinants. Stanford HIVdb genotyping was concordant with phylogenetic inference in 70% of IN and 60% of PR-RT sequences. INI DRMs differed between B and F IN subtypes, with Q148K/R/H, G140S and E138K/A being more prevalent in subtype B (63% versus 0%, P = 0.0021; 50% versus 0%, P = 0.0096; and 50% versus 0%, P = 0.0096, respectively). These differences were independent of the time on raltegravir therapy or viral load at the time of genotyping. INI DRMs in subtype F IN genomes predicted a lower level of resistance to raltegravir and no cross-resistance to second-generation INIs. Conclusions Alternative resistance pathways to raltegravir develop in subtypes B and F IN genomes, with implications for clinical practice. Evaluating the role of HIV-1 subtype in development and persistence of mutations that confer resistance to INIs will be important to improve algorithms for resistance testing and optimize the use of INIs.

A new microsporidian parasite, Heterosporis saurida n. sp. (Microsporidia) infecting the lizardfish, Saurida undosquamis from the Arabian Gulf, Saudi Arabia: ultrastructure and phylogeny

Parasitology ◽  
2012 ◽  
Vol 139 (4) ◽  
pp. 454-462 ◽  
Author(s):  
S. AL-QURAISHY ◽  
A. S. ABDEL-BAKI ◽  
H. AL-QAHTANI ◽  
M. DKHIL ◽  
G. CASAL ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Polar Filament ◽  
Phylogenetic Analyses ◽  
Abdominal Cavity ◽  
Arabian Gulf ◽  
Its Region ◽  
Rrna Genes ◽  
Microsporidian Parasite ◽  
Ultrastructural Characteristics ◽  
A New Species

SUMMARYA new microsporidian that infects the lizardfish Saurida undosquamis (Richardson, 1848) that are caught in the Arabian Gulf in Saudi Arabia is described here. This parasite invades the skeletal muscle of the abdominal cavity forming white, cyst-like structures containing numerous spores. The prevalence of the infection was 32·1% (135/420). The spores were oval to pyriform in shape and measured approximately 3·3 μm×2·0 μm. The developing spores were found within parasitophorous vacuoles. In mature spores, the polar filament was arranged into 5 coils in a row. Molecular analysis of the rRNA genes, including the ITS region, and phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference were performed. The ultrastructural characteristics and phylogenetic analyses support the recognition of a new species, herein named Heterosporis saurida n. sp.

scholarly journals Cocirculation of Four Infectious Bronchitis Virus Lineages in Broiler Chickens in the Eastern Region of Saudi Arabia from 2012 to 2014

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Abdullah I. A. Al-Mubarak ◽  
Anwar A. G. Al-Kubati
Keyword(s):  
Saudi Arabia ◽  
Middle East ◽  
Infectious Bronchitis Virus ◽  
Broiler Chickens ◽  
Direct Sequencing ◽  
Hypervariable Region ◽  
Economic Losses ◽  
Eastern Region ◽  
Infectious Bronchitis ◽  
First Time

Avian infectious bronchitis virus (IBV) is an evolving and dynamic virus that causes major economic losses for the poultry industry worldwide. Continuous evolution and emergence of new variants of this virus are the major challenges for controlling the disease with routine vaccination. Successful vaccination usually requires the use of a homologous vaccine, which in turn necessitates continuous investigation of the circulating strains. Herein, we performed a reverse transcriptase-polymerase chain reaction- (RT-PCR-) based investigation in broiler chicken flocks of the Eastern Region of Saudi Arabia. IBV was detected in 36.5% of the tested flocks (42 out of 115) from January 2012 to March 2014. Direct sequencing of hypervariable region-3 (HVR-3) of the Spike (S)-1 gene was performed, followed by phylogenetic analysis to determine the circulating IBV genotypes. Four lineages appear to coexist in this region, including the GI-13 or 4/91 IBV (31%), GI-16 or CK/CH/LDL/97I IBV (28.6%), GI-1 or Mass IBV (19%), and GI-23 or Middle East IBV (21.4%). The latter lineage include two subgroups: IS/720/99 IBV (16.7%) and IS/Variant2/98 IBV (4.7%). Some of the detections made in the 4/91 and Mass lineages are expected to belong to the vaccine strains. Lineages without a homologous vaccine in use (CK/CH/LDL/97I and Middle East) represent 50% of the isolates recovered in this study. Based on identity with the vaccine sequences, field observations, and frequent detection, these two lineages appear to be out of coverage of the IBV vaccines used in Saudi Arabia. This is the first time to identify Middle East lineage (IS/720/99 IBV and IS/Variant2/98 IBV) in the Eastern Region of Saudi Arabia.

scholarly journals Characterization of HIV-1 Integrase Gene and Resistance Associated Mutations Prior to Roll out of Integrase Inhibitors by Kenyan National HIV-Treatment Program in Kenya

2020 ◽  
Vol 30 (1) ◽  
Author(s):  
Mabeya Sepha ◽  
Nyamache Anthony ◽  
Ngugi Caroline ◽  
Nyerere Andrew ◽  
Lihana Raphael
Keyword(s):  
Drug Resistance ◽  
Direct Sequencing ◽  
Integrase Inhibitor ◽  
Hiv Treatment ◽  
Strand Transfer ◽  
Hiv Integrase ◽  
Integrase Inhibitors ◽  
Resistance Mutations ◽  
Integrase Gene ◽  
Hiv 1

BACKGROUND: Antiretroviral therapy containing an integrase strand transfer inhibitor plus two Nucleoside Reverse Transcriptase inhibitors has now been recommended for treatment of HIV-1-infected patients. This thus determined possible pre-existing integrase resistance associated mutations in the integrase gene prior to introduction of integrase inhibitors combination therapy in Kenya.METHODS: Drug experienced HIV patients were enrolled at Kisii Teaching and Referral in Kenya. Blood specimens from (33) patients were collected for direct sequencing of HIV-1 polintegrase genes. Drug resistance mutations were interpreted according to the Stanford algorithm and phylogenetically analysed using insilico tools.RESULTS: From pooled 188 Kenyan HIV integrase sequences that were analysed for drug resistance, no major mutations conferring resistance to integrase inhibitors were detected. However, polymorphic accessory mutations associated with reduced susceptibility of integrase inhibitors were observed in low frequency; M50I (12.2%), T97A (3.7%), S153YG, E92G (1.6%), G140S/A/C (1.1%) and E157Q (0.5%). Phylogenetic analysis (330 sequences revealed that HIV-1 subtype A1 accounted for majority of the infections, 26 (78.8%), followed by D, 5 (15.2%) and C, 2 (6%).CONCLUSION: The integrase inhibitors will be effective in Kenya where HIV-1 subtype A1 is still the most predominant. However, occurring polymorphisms may warrant further investigation among drug experienced individuals on dolutegravir combination or integrase inhibitor treatment. 

Identification of a point mutation in the ace1 gene of Therioaphis trifolli maculata and detection of insecticide resistance by a diagnostic PCR–RFLP assay

2015 ◽  
Vol 105 (6) ◽  
pp. 712-716
Author(s):  
E. AlSuhaibani ◽  
C.C. Voudouris ◽  
R. Al-Atiyat ◽  
A. Kotzamumin ◽  
J. Vontas ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Insecticide Resistance ◽  
Management Strategies ◽  
Resistance Management ◽  
Resistance Mutation ◽  
Resistance Mechanisms ◽  
Effective Control ◽  
Agricultural Pests ◽  
Resistance Mutations ◽  
Diagnostic Pcr

AbstractAphids are important agricultural pests worldwide. Their control is largely based on chemical insecticides. One species that shows important invasive abilities and host-plant-related differences is Therioaphis trifolii (Monell) (Hemiptera: Aphididae). T. trifolii maculata, also known as spotted alfalfa aphid (SAA), can be very injurious to alfalfa crops in certain regions, such as in Saudi Arabia for effective control it is essential to diagnose and monitor the resistance mechanisms in the SAA populations. In the present study, we analysed acetylcholinesterase (ace) target site insensitivity mechanisms. A 650 bp length DNA containing the putative acetylcholinesterase (ace1) precursor was obtained and compared with other Hemipteran species. The sequences of many individual aphids collected from alfalfa crops in Saudi Arabia were analysed for the presence of resistance mutations: no resistance mutations were found at the resistance mutation loci 302; however, the presence of a serine–phenylalanine substitution (S431F) was identified in one individual. The S431F substitution, has been shown to confer significant levels of both organophosphate and carbamate resistance in other aphid species, and is now found for the first time in T. trifolii. We subsequently developed a simple polymerase chain reaction–restriction fragment length polymorphism assays for the S431F mutation, using a TaqI restriction site destroyed by the S431F mutation. The novel diagnostic assay may support the implementation of Insecticide Resistance Management strategies, for the control of SAA in alfalfa crops in the Kingdom of Saudi Arabia, and other countries worldwide.

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