Kenan Sener

First molecular characterization of a Turkish orf virus strain from a human based on a partial B2L sequence

Cases of orf virus infection in human in Turkey have been reported for many years. Scab material from a man was found positive by PCR using pan-parapox-specific primers for parapoxvirus infection. The amplicon was purified and sequenced. The present study provides for the first time a phylogenetic analysis of parapoxviruses from Turkey. The partial B2L gene sequence of a Turkish orf virus from a human presented here may be useful for characterization of parapoxvirus infections in Turkey based on the phylogenetic analysis studies.

Stability of hepatitis C virus RNA in blood samples by TaqMan real-time PCR.

The storage conditions of blood samples for reliable results are very important in hepatitis C virus (HCV) RNA amplification tests used in routine HCV analyses. According to many studies, storage conditions could affect the RNA stability for HCV RNA detection. We have studied HCV RNA stability in blood samples stored at 4°C. Nineteen blood samples containing different HCV RNA levels were stored at 4°C and they were then analyzed by TaqMAN real‐time PCR method. HCV RNA levels remained almost stable (100%) at least for five weeks at this storage condition. However, among them, the stability period was up to 11 weeks in two of the samples. As with these findings, there was a slightly significant correlation between the positivity time and the beginning HCV RNA levels (r=0.474, P=0.040). We conclude that, blood samples can be stored at 4°C for five weeks without any significant difference in detected HCV RNA level by using TaqMan real‐time PCR. J. Clin. Lab. Anal. 24:134–138, 2010.

Congenital cytomegalovirus infections and glycoprotein B genotypes in live-born infants: a prevalence study in Turkey

Abstract Background: Cytomegalovirus (CMV) infections are the leading cause of infectious hearing loss and central nervous system disease among children worldwide. In this study, we aimed to determine the birth prevalence of congenital CMV infection in live-born infants in Turkey. Methods: In total, 944 consecutive live-born infants born from 926 pregnant women were included in this study. CMV-DNA was investigated in saliva samples of all newborns within the first 3 days after birth using TaqMan-based real-time PCR. Results: The birth prevalence of congenital CMV infection in live-born infants was 1.91% (18/944), and all congenitally infected infants were asymptomatic at birth. The prevalence of congenital CMV infection was 16.7% (3/18) in twin pregnancies and 1.32% (12/908) in single pregnancies (p = 0.002). Genotyping analysis showed glycoprotein B-1 (gB1) to be the most frequently detected genotype at 83.3%. Conclusion: The study results suggest that the majority of congenital CMV infection in Turkey occurs following nonprimary maternal infection. We believe that congenital CMV infection and its long-term effects have been underestimated in our country, as infected infants are usually asymptomatic at birth.

Preservative solution for skeletal muscle biopsy samples

Context : Muscle biopsy samples must be frozen with liquid nitrogen immediately after excision and maintained at -80 o C until analysis. Because of this requirement for tissue processing, patients with neuromuscular diseases often have to travel to centers with on-site muscle pathology laboratories for muscle biopsy sample excision to ensure that samples are properly preserved. Aim: Here, we developed a preservative solution and examined its protectiveness on striated muscle tissues for a minimum of the length of time that would be required to reach a specific muscle pathology laboratory. Materials and Methods: A preservative solution called Kurt-Ozcan (KO) solution was prepared. Eight healthy Sprague-Dawley rats were sacrificed; striated muscle tissue samples were collected and divided into six different groups. Muscle tissue samples were separated into groups for morphological, enzyme histochemical, molecular, and biochemical analysis. Statistical method used: Chi-square and Kruskal Wallis tests. Results: Samples kept in the KO and University of Wisconsin (UW) solutions exhibited very good morphological scores at 3, 6, and 18 hours, but artificial changes were observed at 24 hours. Similar findings were observed for the evaluated enzyme activities. There were no differences between the control group and the samples kept in the KO or UW solution at 3, 6, and 18 hours for morphological, enzyme histochemical, and biochemical features. The messenger ribonucleic acid (mRNA) of β-actin gene was protected up to 6 hours in the KO and UW solutions. Conclusion: The KO solution protects the morphological, enzyme histochemical, and biochemical features of striated muscle tissue of healthy rats for 18 hours and preserves the mRNA for 6 hours.

The comparative results of three different real-time PCR assays: MY09/11 primers failed to detect multiple infections -

HPV-DNA testing is widely used worldwide today and it has become an important part of cervical cancer screening programs. The aim of this study is re-evaluating the effectiveness of MY09/11 consensus primer system, which is one of the most widely used HPV-DNA tests, by using a different approach. In this study, MY09/11 consensus PCR and two different TaqMan-based type-specific PCR assays were used for investigation of the presence of 17 different HPV types in cervical smear samples. Of the 470 samples, 33.2% (156/470) were HPV-DNA positive by at least one of the three methods and remains were negative by all methods. A total of 220 different HPV isolates were identified in 149 samples by the type specific PCR, while the nine samples were positive by consensus PCR only. A single HPV type was detected in 64.4% (96/149) of the genotyped samples, and multiple HPV types were detected in the remaining 35.6% (53/149). MY09/11 PCR failed to detect 21.2% (33/156) of all HPV-DNA positive samples and the rates of false negative results were 18.75% (18/96) and 28.3% (15/53) in single and multiple infections, respectively. We conclude that highly sensitive type-specific PCR tests may be a useful tool for screening of cervical cancer.