Genotyping of hepatitis B virus isolated from chronic hepatitis B patients in the south of Turkey by DNA cycle-sequencing method

Serin, Mehmet Sami; Akkız, Hikmet; Abaylı, Bahri; Öksüz, Murat; Aslan, Gönül; Emekdaş, Gürol

doi:10.1016/j.diagmicrobio.2005.04.007

Cited by 11 publications

(5 citation statements)

References 23 publications

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“…Genotypes display a certain geographical distribution. Several studies showed genotype and subtype homogeneity in Turkey which is a middle-endemic country for HBV [Bozdayi et al, 2004;Sentü rker Gü ldas and Abaciog lu, 2004;Serin et al, 2005]. The present study was in agreement with these findings, showing D (subtype ayw) as the only HBV genotype in the studied population.…”

Section: Discussionsupporting

confidence: 95%

Naturally occurring MHR variants in Turkish patients infected with hepatitis B virus

Sayıner

Özcan

Sengonul

2008

Journal of Medical Virology

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Major B-cell epitopes are located at the major hydrophilic region (MHR) of hepatitis B virus (HBV) surface antigen (HBsAg). The genotypes, subtypes, and naturally occurring amino acid (aa) substitutions of MHR were analyzed in 81 Turkish adult patients (41 inactive HBsAg carriers and 40 patients with chronic hepatitis B) by direct sequencing of the S gene fragment. All the isolates were genotype D according to the phylogenetic analysis. The most common HBsAg subtype was ayw2, followed by ayw3 while one isolate specified ayw4 by encoding Leu127. MHR variants were detected in 22 of the 81 (27.2%) isolates. The prevalence was significantly higher in the chronic hepatitis B group (42.5%) compared to inactive HBsAg carriers (12.2%). Twenty-two samples had a total of 26 amino acid substitutions involving 14 positions. The majority of the patients had a single variation. Most of the amino acid substitutions were located at the HBs1 region of the MHR, while 9 of the 26 were in the classic "a" determinant (aa 124-147). When samples with "a" variants were evaluated by two different commercial HBsAg tests, only the isolate with Ser143Leu variation had a decreased reactivity in the assay using monoclonal antibodies for capture and detection. In conclusion, the findings of the study was in accordance with previous studies showing HBV genotype and subtype homogeneity (genotype D/ayw) in Turkey. Naturally occurring MHR and "a" determinant variants were common, especially among chronic hepatitis B patients. The influence of detected "a" variants on diagnostic assays was limited.

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Section: Discussionsupporting

confidence: 95%

Naturally occurring MHR variants in Turkish patients infected with hepatitis B virus

Sayıner

Özcan

Sengonul

2008

Journal of Medical Virology

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“…These later modifications may lead to erroneous results with RFLP methods [19,20]. Analysis of our sequences is in agreement with this methodological artefact.…”

Section: Discussionsupporting

confidence: 76%

Molecular analysis of HBV genotypes and subgenotypes in the Central-East region of Tunisia

Hannachi

Fredj

Bahri

et al. 2010

Virol J

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BackgroundIn Tunisia, country of intermediate endemicity for Hepatitis B virus (HBV) infection, most molecular studies on the virus have been carried out in the North of the country and little is known about other regions. The aim of this study was to determine HBV genotype and subgenotypes in Central-East Tunisia. A total of 217 HBs antigen positive patients were enrolled and determination of genotype was investigated in 130 patients with detectable HBV DNA. HBV genotyping methods were: PCR-RFLP on the pre-S region, a PCR using type-specific primers in the S region (TSP-PCR) and partial sequencing in the pre-S region.ResultsThree genotypes (D, B and A) were detected by the PCR-RFLP method and two (D and A) with the TSP-PCR method, the concordance between the two methods was 93%. Sequencing and phylogenetic analysis of 32 strains, retrieved the same genotype (D and A) for samples with concordant results and genotype D for samples with discordant results. The sequences of discordant genotypes had a restriction site in the pre-S gene which led to erroneous result by the PCR-RFLP method. Thus, prevalence of genotype D and A was 96% and 4%, respectively. Phylogenetic analysis showed the predominance of two subgenotypes D1 (55%) and D7 (41%). Only one strain clustered with D3 subgenotype (3%).ConclusionsPredominance of subgenotype D7 appears to occur in northern regions of Africa with transition to subgenotype D1 in the East of the continent. HBV genetic variability may lead to wrong results in rapid genotyping methods and sequence analysis is needed to clarify atypical results.

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“…Several studies have shown that genotype D of HBV represents almost all isolates from the Turkish patient population infected with HBV [10,28–30]. The present study showed that genotype D of HBV is still dominant among Turkish HBV‐infected patients.…”

Section: Discussionsupporting

confidence: 49%

Naturally occurring aminoâacid substitutions to nucleos(t)ide analogues in treatment naive Turkish patients with chronic hepatitis B

Sayan

Akhan

Meriç

2010

Journal of Viral Hepatitis

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Naturally occurring amino-acid substitutions in the hepatitis B virus (HBV) polymerase gene may be responsible for resistance to nucleoside/nucleotide (NUCs) analogues. To date, only pre-existing lamivudine resistance has been extensively studied. The aim of the present study was to determine the naturally occurring or pre-existing amino-acid substitutions related to NUCs in treatment naive Turkish patients with chronic hepatitis B (CHB). The investigation involved a total of 88 patients (65 males and 23 females; mean age, 34 years; range, 15-61 years) who were diagnosed with CHB between April 2008 and January 2009. According to HBeAg status, 66 patients were HBeAg-negative and 22 patients were HBeAg positive. Naturally occurring substitutions in the HBV polymerase region were detected by DNA sequencing in 17 (19%) and 30 (34%) patients, based on manual and geno2pheno tool database interpretation, respectively. Each amino-acid substitution appeared alone and included rtA194T, rtV214A, rtQ215S, rtI233V and rtN236T. The median values for viral load, ALT and AST were 3.3 log(10) (2.0-6.0) IU/mL, 36 (12-515) U/L and 27 (13-284) U/L, respectively, but these did not correlate with the observed amino-acid substitutions in the polymerase region. By direct sequencing, genotype D of HBV was found to still be dominant among Turkish patients. In conclusion, every patient who is diagnosed with CHB should be monitored before the start of treatment for more effective management of patient treatment options.

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Genotyping of hepatitis B virus isolated from chronic hepatitis B patients in the south of Turkey by DNA cycle-sequencing method

Cited by 11 publications

References 23 publications

Naturally occurring MHR variants in Turkish patients infected with hepatitis B virus

Naturally occurring MHR variants in Turkish patients infected with hepatitis B virus

Molecular analysis of HBV genotypes and subgenotypes in the Central-East region of Tunisia

Naturally occurring aminoâacid substitutions to nucleos(t)ide analogues in treatment naive Turkish patients with chronic hepatitis B

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Genotyping of hepatitis B virus isolated from chronic hepatitis B patients in the south of Turkey by DNA cycle-sequencing method

Cited by 11 publications

References 23 publications

Naturally occurring MHR variants in Turkish patients infected with hepatitis B virus

Naturally occurring MHR variants in Turkish patients infected with hepatitis B virus

Molecular analysis of HBV genotypes and subgenotypes in the Central-East region of Tunisia

Naturally occurring aminoâacid substitutions to nucleos(t)ide analogues in treatment naive Turkish patients with chronic hepatitis B

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Naturally occurring aminoâacid substitutions to nucleos(t)ide analogues in treatment naive Turkish patients with chronic hepatitis B