A rapid and reliable genotyping method for hepatitis B virus genotypes (A–H) using type-specific primers

Farazmandfar, Touraj; Haghshenas, Mohammad Reza; Janbabai, Ghasem; Azadeh, Hossein; Sharifian, Rayka; Taghipour, Mehrdad

doi:10.1016/j.jviromet.2012.01.025

Cited by 11 publications

(6 citation statements)

References 13 publications

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“…The PCR for HBV is one of the most used methods, with complete or partial genome sequencing as a clinical tool for the determination of HBV genotypes. The costs of reagents and labor, however, are high (2,5,8) . In research activities, sequencing is used for analysis of mutations in the genome of HBV.…”

Section: Discussionmentioning

confidence: 99%

“…Genotyping of HBV is important to elucidate the differences in diversity of sequences and viral phylogeny (23) . Several methods have been used for genotyping of HBV, including sequencing, PCR with probes, RFLP analysis, colorimetric test for detecting point mutations, ligase chain reaction, mass spectrometry and enzyme-linked immunosorbent assay for genotype-specific epitopes (8,11) . The main genotyping systems that have been developed are based on the polymerase chain reaction.…”

Section: Discussionmentioning

confidence: 99%

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Melting Curve Analysis for the Screening of Hepatitis B Virus Genotypes A, D and F in Patients From a General Hospital in Southern Brazil

Becker

Filho

Mattos

et al. 2013

Arq. Gastroenterol.

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-Context -Hepatitis B virus (HBV) can cause fulminant hepatitis, cirrhosis and hepatocellular carcinoma, and is one of the most common causes of acute and chronic liver failure. The genetic variants of HBV can be decisive for the evolution of these diseases as well as for the election of therapy. Objectives -The aim of this study was to evaluate and standardize an in house methodology based on the analysis of the melting curve polymerase chain reaction (PCR) of real-time (qPCR) to screen for genotypes A, D and F of HBV in patients from a hospital in Rio Grande do Sul, Brazil. Methods -We evaluated 104 patients presumably with HBV chronic infection. Viral DNA was extracted from plasma and viral genotypes and different mutations were determined using PCR-based protocols. Results -A PCR-based methodology was standardized for the analysis of genotypes A, D and F of HBV. The technique was based in a nested PCR with the final step consisting of a multiplex real-time PCR, using the melting curve as a tool for the differentiation of fragments. A higher frequency of genotype D (44.4%), followed by genotype A (22.2%) and genotype F (3.7%) was observed. Conclusion -The standardized assay, a nested PCR-multiplex qPCR using specific primers, provides a rapid and accurate method for the differentiation of HBV genotypes that are more frequent in Southern Brazil -A, D and F. This method can be applied in the clinical practice.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Melting Curve Analysis for the Screening of Hepatitis B Virus Genotypes A, D and F in Patients From a General Hospital in Southern Brazil

Becker

Filho

Mattos

et al. 2013

Arq. Gastroenterol.

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“…The PCR protocol included one initial denaturation at 95 o C for 4 min, 10 cycles (15 sec at 95 o C, 50 sec at 65 o C and 40 sec at 72 o C) followed by 25 cycles (20 sec at 95 o C, 50 sec at 58 o C and 50 sec at 72 o C), with a final extension at 72 o C for 5 min. The PCR products, after staining with safe stain, were subjected to electrophoresis and photographed under a UV transilluminator (UVITEC, Cambridge, UK) as described previously ( 14 ). The two alleles of HLA-DQA1*0102 and HLA-DQB1*0602 are identified by lack of a portion of intron 3.…”

Section: Methodsmentioning

confidence: 99%

Relationship between human leukocyte antigen (HLA)-DQA10102/HLA-DQB10602 polymorphism and preeclampsia

Mohammadi

Farazmandfar

Shahbazi

2017

IJRM

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Background: Preeclampsia is a condition associated with systemic disorders in the mother and the fetus. However, the exact causes of preeclampsia are unknown, but several genetics and environmental factors play role in development of this disease. Major histocompatibility complex role is very important during pregnancy through which the fetus is not rejected by mother's immune system. Objective: In this study, we investigated the relationship of the human leukocyte antigen (HLA)-DQA1*0102/HLA-DQB1*0602 polymorphism with preeclampsia. Materials and Methods: Genomic DNA of 181 pregnant women with a history of preeclampsia as the case group and 228 pregnant women with no history of preeclampsia as the controls were extracted. The HLA-DQA1*0102/HLA-DQB1*0602 polymorphisms of all DNA samples were identified by the SSP-PCR method. Frequencies difference of variables between case and control groups were calculated by Chi-square test. The ethnic origin of the participants in this study was extracted from their medical records. Results: There was a significant association between preeclampsia and Sistani ethnic group (p=0.031). Moreover, there was a significant association between preeclampsia and frequencies of allele HLA-DQB1*0602 (p<0.001), and genotypes of heterozygote (+0102/-0602) (p<0.001) and negative homozygote (-0102/-0602) (p=0.005). There also was an association between allele HLA-DQB1*0602 and preeclampsia in Fars ethnic group (p=0.028). Conclusion: It seems that immune incompatibility may have an important role in preeclampsia predisposition. According to our results, the lack of locus HLA-DQB1*0602 may be a risk factor for preeclampsia.

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“…These methods include restriction fragment length polymorphisms (RFLP) [60], PCR with specific primers for single genotypes [61], multiplex-PCR for many HBV genotypes [62,63] and on hybridization technologies [64] or real time quantification and genotyping [65] or Mass spectrometry [66]. The gold standard method for HBV genotyping is a complete genome sequencing followed by phylogenetic analysis of the sequence divergence [9,52].…”

Section: Hbv Genotypingmentioning

confidence: 99%

Hepatitis B Virus Genetic Diversity: Disease Pathogenesis

Jayalakshmi¹,

Kalyanaraman²,

Pitchappan³

2013

Viral Replication

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A rapid and reliable genotyping method for hepatitis B virus genotypes (A–H) using type-specific primers

Cited by 11 publications

References 13 publications

Melting Curve Analysis for the Screening of Hepatitis B Virus Genotypes A, D and F in Patients From a General Hospital in Southern Brazil

Melting Curve Analysis for the Screening of Hepatitis B Virus Genotypes A, D and F in Patients From a General Hospital in Southern Brazil

Relationship between human leukocyte antigen (HLA)-DQA10102/HLA-DQB10602 polymorphism and preeclampsia

Hepatitis B Virus Genetic Diversity: Disease Pathogenesis

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A rapid and reliable genotyping method for hepatitis B virus genotypes (A–H) using type-specific primers

Cited by 11 publications

References 13 publications

Melting Curve Analysis for the Screening of Hepatitis B Virus Genotypes A, D and F in Patients From a General Hospital in Southern Brazil

Melting Curve Analysis for the Screening of Hepatitis B Virus Genotypes A, D and F in Patients From a General Hospital in Southern Brazil

Relationship between human leukocyte antigen (HLA)-DQA1*0102/HLA-DQB1*0602 polymorphism and preeclampsia

Hepatitis B Virus Genetic Diversity: Disease Pathogenesis

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Product

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Relationship between human leukocyte antigen (HLA)-DQA10102/HLA-DQB10602 polymorphism and preeclampsia