Browsing by Author "Arikan, A"

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    Comparison of Performance Characteristics of DxN VERIS System versus Qiagen PCR for HBV Genotype D and HCV Genotype 1b Quantification
    Sayan, M; Arikan, A; Sanlidag, T
    The Beckman Coulter DxN VERIS system is a fully automated, closed molecular diagnostic instrument for viral load quantification of hepatitis B virus and hepatitis C virus. In this study, the analytical performance of this new system was compared to routine diagnostic Qiagen PCR kit by using the same clinical samples. The DxN VERIS system demonstrated a high analytical performance. The DxN VERIS allows random access, which means that samples can be uploaded straight on to the system at any time; so, it provides an improvement of workflow, staff productivity and allows faster turn-around of viral load results.
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    Evaluation of the pol/S Gene Overlapping Mutations in Chronic Hepatitis B Patients in Northern Cyprus
    Arikan, A; Sayan, M; Sanlidag, T; Suer, K; Akcali, S; Guvenir, M
    Mutations associated with the pol and the S gene can emerge as a consequence of the high replication capacity and proofreading deficiencies of hepatitis B virus during replication. The current study was constructed to evaluate primary, partial, compensatory and the escape mutations in chronic hepatitis B patients in Northern Cyprus. The samples of HBsAg positive treatment naive 100 patients were involved in this study. HBV pol gene region was sequenced, amplified and HBV pol/S gene mutations were determined. The samples of thirty-two patients were excluded because of their low viral load (HBV < 1000 lu/ml). Among the sequenced 68 samples, there was a partial mutation (1.5%) and 36.7% displayed a resistance profile to lamivudine, adevofir, and telbivudine. Immune response escape, vaccine escape, HBIg and diagnosis escape mutations were determined in 24%, 10%, 6%, and 4% samples of the patients, respectively. Additionally, there were six different combined mutations. These data underscored that there is no concern for primary mutations in Northern Cyprus, however, we have identified a compensatory mutation (rtV173M) that may have primary mutation characteristics by combining with other mutation patterns. Additionally, HBsAg escape mutants demonstrated that detection of the S gene together with the pol gene mutations might be beneficial and important to monitor the surveillance of S variants.
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    Hepatitis B Virus Genotype E Infection in Turkey: The Detection of the First Case
    Sayan, M; Sanlidag, T; Akçali, S; Arikan, A
    Hepatitis B virus (HBV) infection is a global major health problem. Currently, 10 genotypes (A-J) of hepatitis B virus (HBV) are identified based on the nucleic acid sequence heterogeneity, and these genotypes have been shown to have distinct geographic distribution. Reports of the previous studies indicated that the genotype D is the predominant type among hepatitis B patients in different regions of Turkey. However, recent studies indicated that other HBV genotypes are also seen with an increasing rate. Although epidemiological and clinical information on genotype E infection is currently limited, it is known that genotype E infection is common in West and Central Africa. In this report, the first case of HBV genotype E infection in Turkey was presented. A 22-year-old Nigerian male employee who resided in Manisa for five years was admitted to Celal Bayar University Hospital Manisa, Turkey, for his routine check-up. Since HBsAg was found positive, other HBV markers were tested with a repeated serum sample. Laboratory findings were as follows; HBsAg (+), anti-HBs (-), HBeAg (-), anti-HBe (+), anti-HBc (+), anti-HCV (-), anti-HIV (-), ALT: 44 U/L and AST: 45 U/L. HBV-DNA level was detected as 700 IU/m1 by real-time PCR (Artus HBV QS RGQ Qiagen, Germany). HBV-DNA isolated from the serum sample of the patient was amplified by PCR and polymerase gene segment of HBV was directly sequenced. UPGMA method was used for phylogenetic analysis and Inno-LIPA HBV genotyping method (Innogenetics, Belgium) was performed to determine multiple HBV genotype infection. On the basis of those methods the genotype of the virus was identified as genotype E. The partial sequences of the HBV polymerase gene were loaded to the international DNA data bank (GenBank) for contribution to the global HBV surveillance. This report emphasized that besides genotype D the other HBV genotypes could be found in Turkey. Since the patient was an inactive HBsAg carrier before his residence in Turkey, this case was regarded as an imported HBV genotype E case. In conclusion, detection of different HBV genotypes, their epidemiology and molecular characteristics are important for both national and global HBV surveillance and better clinical approach.
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    Investigation of 2019-2020 Seasonal Influenza Activity at a University Hospital in Northern Cyprus
    Abujamous, SMA; Arikan, A; Guler, E; Suer, K; Sanlidag, T
    BACKGROUND/AIM: Influenza (flu) is a contagious respiratory disease caused by influenza viruses, which is more common in the late autumn, winter and early spring of the year. We aimed to estimate the rate of seasonal influenza A and B at Near East University Hospital in Northern Cyprus and to correlate the rate of the infection with the gender and age of the patients, and by month in which the infection occurred. MATERIALS AND METHODS: Nasopharyngeal swabs collected from 844 individuals with flu like symptoms who were admitted to our hospital between December 2019 and March 2020 were involved. ABONT Influenza A&B chromatographic immunoassay was used for the qualitative detection of Influenza A and B antigens. The rate of the infections was assessed among different ages, gender and by month. RESULTS: Among 844 individuals, 234 (27.7%) were positive for either Influenza A virus or Influenza B virus. Among these infected cases, 97 (11.5%) and 137 (16.2%) were positive for influenza A and B, respectively. Influenza B was more dominant especially in children between 5-14 years of age. The major group of cases infected with Influenza A were aged 0-4 years. The difference between either Influenza A (p=0.679) or B (p=0.255) positivity and gender was not statistically significant. However, the rate of Influenza B differed by the month in which it occurred (p=0.034), peaking in February. CONCLUSION: Our findings show that the rate of Influenza B was more dominant compared to the rate of Influenza A and age is an important factor in the rate of seasonal influenza. Therefore, early identification and investigation of influenza cases is critical to control human-human transmission.
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    Rapid identification of seasonal influenza A and B virus in nasopharyngeal specimens in Northern Cyprus
    Arikan, A; Arikan, A; Sanlidag, T; Sanlidag, T; Guler, E; Suer, K
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    Molecular Epidemiology of Hepatitis B Virus in Northern Cyprus
    Arikan, A; Sanlidag, T; Süer, K; Sayan, M; Akçali, S; Güler, E
    Identification of hepatitis B virus (HBV) strains and understanding of molecular epidemiological characteristics are important for the effective surveillance of HBV infections. Genotype D is dominant in studies performed in Turkey but it is known that cases infected with genotypes A, E, G and H also exists. In contrast, there are no data regarding the molecular epidemiologic characteristics of the HBV in Northern Cyprus. The aim of this study was to determine the distribution of genotypes and subgenotypes of HBV among the people living, educating and working in Northern Cyprus. A total of 160 cases (1.2%) who were HBsAg seropositive out of 13.892 subjects admitted to Nicosia, Near East University Hospital microbiology laboratory for the routine control and to blood center for donor screening tests between November 2011 to September 2014, were included in the study. HBV-DNA levels in the HBsAg positive cases were detected by real-time polymerase chain reaction and genotypes/subgenotypes were determined by sequence analysis of the viral pol gene (reverse transcriptase [rt] region, between 80-250. aminoacids). Sixty samples (60/160, 37.5%) were excluded from sequencing analysis due to negative and/or very low (<30 IU/ml) HBV-DNA levels, so 100 samples were included in sequence analysis. Ninety-six of those cases (13 female, 87 male; mean age: 35.51 +/- 12.88 years) were anti-HBc IgG, 95 were anti-HBe and five were HBeAg positive, with a mean HBV-DNA level of 5.36 x 106 +/- 3.58 x 107 IU/ml. As 32 (32%) samples yielded HBV-DNA level below the threshold of 1000 IU/ml, sequence analyses were unsuccesful, eventually 68 (68/160, 42.5%) samples could be phylogenetically analyzed. The distribution of HBV genotypes/subgenotypes were found as follows: 48 were (70.6%) D/D1; four were (5.9%) D/D2; one was (1.5%) D/D3, five were (7.4%) A/A1, two were (2.9%) A/A2 and eight were (11.8%) genotype E. Among the most frequent D1 strains, 60.4% (29/48) cases were from Turkish; single D/D3 strain from Benguela (Angola) and all eight genotype E strains were from Nigerian national cases. According to the data of this first study performed in TRNC on this subject, genotype D is dominant (53/68, 78%) in Northern Cyprus and consistent with the subgenotype distribution that is similar to Turkey and mediterranean basin. The prevalences of genotype A (7/68, 10.3%) and E (8/68, 11.8%) were also remarkable. In conclusion, although Northern Cyprus is an island country the heterogeneous distribution of HBV genotype/subgenotype may be contributed to the cosmopolitan characteristics of various populations from different countries who have come here for education, work or touristic purposes.
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    Investigation of the Correlation Between Anti-HCV Levels (S/Co) with HCV-RNA in the Diagnosis of Hepatitis C Virus (HCV) Infection
    Sanlidag, T; Akçali, S; Ecemis, T; Süer, K; Erbay Dündar, P; Arikan, A; Güvenir, M; Güler, E
    Detection of borderline and/or low positive anti-HCV results by enzyme immunoassay (EIA) leads to severe problems in routine laboratories and needs confirmation with nucleic acid amplification tests which can increase the cost. In EIA tests, if the ratio of sample to cut-off (S/Co) is >= 1, the sample is accepted as positive according to the manufacturers' instructions. Although over the last decade the application of S/Co values have also applied to HCV-RNA readings, the current study aims to determine whether the S/Co value is adequate and applicable for the anti-HCV EIA test, and to determine whether a correlation exists between HCV-RNA and HCV infections. A total of 658 cases (402 female, 256 male; mean age: 49.4 +/- 17.0 years) who were found anti-HCV positive between January 2011-July 2013 were included in the study. Anti-HCV tests were performed by chemiluminescent EIA (Architect i2000SR, Abbott, USA and LiaisonXL Murex, DiaSorin, Italy) and HCV-RNA by real-time PCR (Cobas Ampliprep/Cobas TaqMan HCV, Roche, USA). The mean S/Co value of the cases was 7.3 +/- 4.8 (range: 1.00-17.59) and mean HCV-RNA value was 2.3x10(5) +/- 2.1x10(6) copies/ml. When the anti-HCV S/Co value of varying ranges was compared with HCV-RNA readings a particular trend was noted. In the anti-HCV S/Co values of 1.0-4.0; 4.1-7.0; 7.1-10.0; 10.1-13.0; 13.1-16.0 and (3)16.1, HCV-RNA positivity rates were detected as 1.9%, 24.7%, 37.1%, 46.7%, 56.4% and 75%, respectively. Statistical analysis indicated an intermediate positive correlation (r=0.454) between anti-HCV ve HCV-RNA readings (p=0.000). An adequate S/Co value was accepted as 5.0 based on the ROC analysis, and this value gave a performance confidence level of 95.6% when determining whether a patient is HCV positive. Based on the data of this study it became evident that further EIA testing is not required if the S/Co value is >= 5.0, however if the S/Co value is less than 5.0, then further clinical analysis and revaluation of the patient is required.
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    Molecular Epidemiology of Hepatitis B Virus
    Arikan, A; Sanlidag, T
    In addition to high viral copy number during replication, HBV reverse transciptase also does not have a proofreading function, therefore, many HBV genotypes, subgenotypes, mutants and recombinants can emerge. To date, 10 HBV genotypes (A-J) and almost 40 subgenotypes have been identified. Genotype A is dominant in Northwest Europe, North America and Africa; genotype B and C are common in Asian countries; genotype C is more dominant in East and Southeast Asian countries. Genotype D is widespread in the whole world and is endemic in the Meditteranean area, the Middle East and Western Asia. Genotype E is dominant in Western Africa and genotype H has been found in Central and South America. Genotype G has been reported in France, Germany and America. The genotype H is found in Central America. Recently identified genotype I, a recombination of genotypes A, C and G, was isolated in Vietnam and Laos. The most recent genotype J was identified in the Ryukyu islands in Japan and this genotype has a relationship between gibon/orangutan genotypes and human genotype C. In this review, HBV genotypes and subgenotypes, their geographic distributions and clinical aspects were overviewed.
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    Analytical performance of DxN Veris system in the viral load quantification of Hepatitis C virus
    Sayan, M; Sayan, M; Sanlidag, T; Sanlidag, T; Arikan, A; Arikan, A
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    Determination of NS3 inhibitors drug resistance mutations in chronic Hepatitis C patients infected with genotype 1
    Sanlidag, T; Sanlidag, T; Sayan, M; Sayan, M; Akcali, S; Kasap, E; Buran, T; Arikan, A; Arikan, A
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    Attitudes of Medical Malpractice in Pediatric Surgery
    Arikan, A; Çinarli, S; Aykar, FS; Sayan, A
    Aim: The aim of this study was to evaluate the proportion of pediatric surgeons who committed medical malpractice (MM) while on duty in hospitals, whether this proportion changed according to age and experience, and if they reported MM or not, and to determine their level of knowledge related to the legal processes. Materials and Methods: A cross-sectional survey design was used with a two-part web-questionnaire developed by the authors. The webquestionnaire consisted of twenty-four questions and was prepared after a review of the relevant literature as required to address the aims of the study. Statistical analysis was conducted using SPSS 18.0. Results: One hundred and fifty-one pediatric surgeons answered the questionnaire; 46% were specialists, 87% were working in public hospitals, and 9% had never committed MM. The type of institution did not affect the occurrence of MM. The major factors that affected the occurrence of MM seemed to be lack of knowledge and experience alongside lack of attention. Working conditions and exhaustion played minor roles. While junior pediatric surgeons mostly committed MM in abdominal, urogenital, newborn and thoracic surgeries, the area was mostly newborn surgery for senior surgeons. Conclusion: Few MM cases were taken to court. Lack of experience, knowledge and attention play major roles in the occurrence of MM. MM cases should be archived meticulously.
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    Determination of Drug Resistance Mutations of NS3 Inhibitors in Chronic Hepatitis C Patients Infected with Genotype 1
    Sanlidag, T; Sayan, M; Akçali, S; Kasap, E; Buran, T; Arikan, A
    Direct-acting antiviral agents (DAA) such as NS3 protease inhibitors is the first class of drugs used for chronic hepatitis C (CHC) treatment. NS3 inhibitors (PI) with low genetic barrier have been approved to be used in the CHC genotype 1 infections, and in the treatment of compensated liver disease including cirrhosis together with pegile interferon and ribavirin. Consequently, the development of drug resistance during DAA treatment of CHC is a major problem. NS3 resistant variants can be detected before treatment as they can occurnaturally. The aim of this study was to investigate new and old generation NS3 inhibitors resistance mutations before DAA treatment in hepatitis C virus (HCV) that were isolated from CHC. The present study was conducted in 2015 and included 97 naive DAA patients infected with HCV genotype 1, who were diagnosed in Manisa and Kocaeli cities of Turkey. Magnetic particle based HCV RNA extraction and than RNA detection and quantification were performed using commercial real-time PCR assay QIASypmhony + Rotorgene Q/ArtusHCV QS-RGQ and COBAS Ampliprep/COBAS TaqMan HCV Tests. HCV NS3 viral protease genome region was amplified with PCR and mutation analysis was performed by Sanger dideoxy sequencing technique of NS3 protease codons (codon 32-185). HCV NS3 protease inhibitors; asunaprevir, boceprevir, faldaprevir, grazoprevir, pariteprevir, simeprevir and telaprevir were analysed for resistant mutations by Geno2pheno-HCV resistance tool. HCV was genotyped in all patients and 88 patients (n= 88/97, 91%) had genotype 1. Eight (n= 8/97, 8.2%) and 80 (n= 80/97, 82.4%) HCC patients were subgenotyped as 1a and 1b, respectively. Many aminoacid substitutions and resistance mutations were determined in 39/88 (44%) patients in the study group. Q80L, S122C/N, S138W were defined as potential substitutions (6/88 patients; 7%); R109K, R117C, S122G, I132V, I170V, N174S were described as potential resistance (34/88 patients; 39%); V36L, T54S, V55A, Q80H were characterized as resistance (7/88 patients; 8%) and Q80K, A156S were defined as high resistance (3/88 patients; 3%) mutations. Based on resistance and high resistance mutations, clinically significant mutations were defined in 10/88 (11%) of the patients. Our study shows that it is essential to analyse HCV NS3 protease inhibitors drug resistance before DAA treatment of CHC patients. On the other hand, our results pointed out that analysis of NS5A and NS5B genome region mutations may also be required in the near future.