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    Analysis of Hepatitis B Virus (HBV) preS1, preS2 and S Gene Regions from Patient Groups Infected with HBV Genotype D
    (Ankara Microbiology Soc, 2018) Karatas, Eylem; Erensoy, Selda; Akarca, Ulus Salih; Sertoz, Ruchan
    Mutations in preS and S gene regions of hepatitis B virus genome may cause immune escape and diagnostic escape HBV mutants. The aim of this study was to determine preS1, preS2 and S gene regions of HBV from HBV infected patient groups by sequence analysis and contribute to the relevant literature. Nucleic acid sequence analysis of preS and S genes of HBV PCR products from 56 archived plasma samples sent to Ege University Faculty of Medicine Medical Microbiology Department Molecular Virology laboratory, for HBV tests were determined by chain termination reaction. Amino acid (aa) sequences were compared with the reference sequences obtained from GenBank. Plasma samples belonged to four groups of patients: A- Chronic HBV infected patients with typical HBV serological profiles (22 samples), B-HBV infected patients with atypical HBV serological profiles (26 samples), C- HBV re-infected patients after liver transplantation (5 samples), D- Seroconversion phase following acute HBV infection (3 samples). One of two vaccine escape mutant samples was also diagnostic escape mutant; the other diagnostic escape mutant was isolated from anti-HBc positive sample. All of the sequences were determined as genotype D. HBsAg subtypes were determined as; two ayw1, six ayw3, two mix, 46 ayw2. Among the 304 codons analysed between preS 33rd and S 162nd amino acids; aa variants were determinedin 105 codons (34.5%). Sequences can be found in GenBank with accession numbers FJ001941-FJ001996. At least one aa variation was detected in 48 of 56 samples (85.7%). The amino acid variants were as follows; PreS1: A33T, A39T, P41 K, D44del, D5ON, T51P, D54N, L65P/M, F67L, W77T, A81 S, Q82E, I84T, L851/M, Q86H/T, L88S, A90T/V, N91K/del, A95P, S96A, T97I/A, N98K, Q100K, S101T, S109T, P110S, N114D/E, PreS2: M1V, Q2R, S5H, F8S, H9Q, Q13L, D14N, R16K, R18K, G19S/D, F22L/S, S28T, G30E, N33T, V39A, P41H/L, I42T/L, I45T, F46Y, S47L, R48K, I49T, D51V/G, P52L, A53V, L54R/G, N55K; S gene: E2D, I4F, F8L, G10A, V14A, F20S, L22del, R24K, P29L, Q30K, N40S, F41del, G44E, T45L, T46P, V47A, L49R, Q54R, P56L, S64F, P70A, M75I, C76Y, R79H, I81T, F83C, L88P, L94S, Y100F, Q101H/R, M103L, L104F, L109I/M, I110L, G112S/R, S113N/P, S114A/del, T115I, T116N, T118A/K, P120A/T, T123A, in "a" determinant; T126I, Q129H/R, T131N, M133T, Y134N, S136Y, S143L/M/T, D144E, G145A/R. Deletions were also found in all three preS/S gene regions. The highest number of aa variations were detectedin the isolated anti-HBc positive sample (in 24 codons), followed by liver transplant group (8-13 codons). Point mutation was detected in the preS2/S promoter CCAAT box. Major hydrophilic region (MHR) variants were determined in 41.1% of 56 samples. The highest number of MHR variants belonged to atypical HBV serological profile group (group B; 61.5%) and liver transplantation group with HBV re-infection (all C group). Among the diagnostic escape and immune escape mutant (anti-HBs positive) samples, reported MHR and "a" determinant mutations were detected. In conclusion, the study population carries HBV preS/S variants; MHR and "a" determinant variant rates are high among diagnostic or immune escape mutants. It is important to evaluate the mutant detection performance of HBsAg tests.
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    Comparison of immunofluorescence assay and multiplexed microparticle-based immunoassay for detecting
    (Elsevier Science Bv, 2008) Zeytinoglu, Aysin; Altuglu, Imre; Karatas, Eylem; Sertoz, Ruchan Yazan
    A new multiplexed microparticle-based immunoassay was compared with the immunofluorescence assay that is used widely for detecting EBV-specific antibodies in immunocompetent patients. Serum samples of 162 patients submitted for routine EBV diagnosis were tested for viral capsid antigen IgM, viral capsid antigen IgG and serological profile interpretations with both systems. The result concordances were 94.2%, 93.6%, and 92.1%, respectively. Multiplexed microparticle-based immunoassay can be an alternative to immunofluorescence assay especially in laboratories receiving large numbers of samples. (C) 2007 Elsevier B.V. All rights reserved.
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    Comparison of the "ProDect BCS RV CHIP" assay with the combination of shell vial cell culture and immunofluorescence antibody test for the detection of respiratory viruses
    (Elsevier Science Bv, 2007) Cicek, Candan; Gulen, Figen; Karatas, Eylem; Demir, Esen; Tanac, Remziye; Bacakoglu, Feza; Bilgic, Altinay
    In the present study, a multiplex reverse transcriptase polymerase chain reaction combined with a chip hybridization assay (ProDect BCS RV CHIP) was evaluated as an alternative to the combination of immunofluorescent antibody test and shell vial cell culture considered as gold standard for the detection of respiratory viruses. Among 100 specimens, 40 were positive using the combination of immunofluorescent antibody test and shell vial cell culture assay in which 9 of them were infected by two different viruses (27 parainfluenza virus type 3, 10 adenovirus, 9 respiratory, syncytial virus. 2 influenza type B, and 1 influenza type A). ProDect BCS RV CHIP detected only 10 positive specimens in which one of them was infected by two different viruses (5 respiratory syncytial virus, 3 parainfluenza virus type 3, 2 adenovirus, and I influenza virus type B). The sensitivity. specificity, PPV. NPV and diagnostic accuracy of ProDect BCS RV CHIP were 25.0%, 100%, 100%, 66.6%, and 70.0%, respectively, compared to the combination of shell vial cell culture and immunofluorescent antibody test. As a result, the specificity of ProDect BCS RV CHIP is high. however. the sensitivity (25%) of the assay is not sufficient for routine laboratory use. (C) 2007 Elsevier B.V. All rights reserved.
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    Genotyping of rifampin-resistant Mycobacterium tuberculosis isolates by mycobacterial interspersed repetitive unit - variable number tandem repeat (MIRU-VNTR) analysis
    (Ankara Microbiology Soc, 2007) Cavusoglu, Cengiz; Karatas, Eylem; Soeyler, Ilknur
    Molecular typing methods have greatly enhanced our understanding on epidemiology of tuberculosis and allowed us to identify outbreaks and intertransmission within populations. Recently, a set of 12 variable-number tandem repeat (VNTR), designated mycobacterial interspersed repetitive units (MIRU), has been described as being useful for the typing of M.tuberculosis. In this study, 26 rifampin (RIF) resistant M.tuberculosis isolates with known IS6110-RFLP patterns obtained from 26 different patients in Aegean Region were typed by MIRU-VNTR and the data were compared with IS6110-RFLP results. The results showed that in most isolates the clustering on the basis of IS6110 RFLP typing and that on the basis of MIRU-VNTR typing were in agreement. It was also determined that the loci including MIRU 16, MIRU 40, MIRU 26, MIRU 10, MIRU 04 and MIRU 31, respectively, have the highest allelic diversities and discriminatory power. In conclusion, since the discrimination level of conventional MIRU-VNTR including 12 loci might be variable, by the use of additional loci which present high degree of allelic differentiation, this method would be reliable for the epidemiologic studies.