Gulendam Bozdayi

Molecular epidemiology of hepatitis B, C and D viruses in Turkish patients

Summary.Different genotypes of the hepatitis viruses may influence the clinical outcome of the disease. The distribution of genotypes may vary according to geographical regions. The aim of this study was to evaluate hepatitis B virus (HBV), hepatitis C virus (HCV) and hepatitis D virus (HDV) genotypes in Turkish patients with chronic hepatitis in a large cohort of patients. Genotyping was performed in 41, 59 and 365 patients with chronic hepatitis B, D and C, respectively, and 36 hemodialysis patients with chronic hepatitis C. Genotypes were determined by direct sequencing in hepatitis B and by polymerase chain reaction-restriction fragment length polymorphism in hepatitis C and D patients. In addition, HBV subtyping by multiplex PCR and subtype specific ELISA were performed in 83 and 71 HBsAg (+) blood donors, respectively. All hepatitis B (100%) and hepatitis D (100%) patients had genotype D and type I, respectively. HBsAg subtyping by two methods yielded that 99% of the patients were subtype ayw. S gene amino acid sequence in the 41 patients included for HBV genotyping revealed the ayw2 subtype. Genotype distribution of 365 patients with chronic C hepatitis were as follows: 306 (84%) patients genotype 1b, 43 (11%) patients genotype 1a, 10 (3%) patients genotype 2, 3 (1%) patients genotype 3, 3 (1%) patients genotype 4. Among 36 patients receiving hemodialysis, 28 (78%) patients had genotype 1b and 8 (22%) patients had genotype 1a. The study indicates that Turkish patients with chronic viral hepatitis show very little genotypic heterogeneity. Subtype ayw and the genotype D of HBV DNA, and the type I of HDV RNA represent almost 100% of related infections. The genotype 1b of HCV RNA was found to be significantly dominant in Turkish patients.

Diversity of human rotavirus G9 among children in Turkey

Between September 2004 and December 2005 a prospective study was conducted to understand the epidemiology of rotavirus infection among children with diarrhea attending two hospitals in Ankara, Turkey. Rotavirus was detected in 39.7% of the 322 stool samples and affected mainly children in the age group of 6–23 months. More than 70% and 39% of these cases occurred in children <2 and <1 year of age, respectively. In the temperate climate of Ankara rotavirus infection was prevalent throughout the year. Serotype G1P[8] was dominant followed by G9P[8]. In 38 samples a total of 5 electropherotypes were detected. All G9P[8] were of long electropherotype except one of short electropherotype. A proportion of G1 and G9 strains were in combination with P[6], P[4] or P nontypable. Mixed serotypes were responsible for 2.4% of the infections. A phylogenetic tree constructed with the deduced amino acid sequences of the VP7 gene showed that 16 Turkish G9 strains clustered with rotaviruses of lineage III. One G9 strain formed a new lineage, lineage IV with the Sri Lankan G9 rotaviruses. In the phylogenetic tree of the VP8* gene, the Turkish G9P[6] rotaviruses clustered with human strains of lineage Ia. Increased diversity of the G/P type combination and the presence of infection throughout the year in Turkey was a situation similar to developing countries. The occurrence of rotavirus infection at later age and low level of mixed infections in Turkey represented the situation of developed countries. This study suggests that diverse G9 rotaviruses are emerging in Turkey. J. Med. Virol. 80:733–740, 2008.

Distribution of secreted aspartyl proteinases using a polymerase chain reaction assay withSAP specific primers inCandida albicans isolates

Secreted aspartyl proteinase (Sap) distribution among differentC. albicans isolates was determined usingSAP-specific primers in polymerase chain reaction (PCR) assay.SAP1, SAP2, andSAP3 were detected in 13 of 40 (32.5 %),SAP4 in 38/40 (95 %),SAP5 were detected in 30/40 (75 %),SAP6 in 23/40 (57.5 %) ofC. albicans strains isolated from blood cultures.SAP1-SAP3 were detected in 37 of 40 (92.5 %),SAP4 were detected in 3/40 (7.5 %),SAP5 in 3/40 (7.5 %),SAP6 in 5/40 (12.5 %) ofC. albicans strains isolated from vaginal swab cultures. Sap1, Sap2 and Sap3 isoenzymes were found to be related to the vaginopathic potential ofC. albicans, Sap4, Sap5 and Sap6 isoenzymes were found to be correlated with systemic infections.

Molecular characterization of a human group C rotavirus detected first in Turkey.

The present study was done to find out the prevalence of group B and C rotavirus infections in children with diarrhea presented at two major hospitals in Ankara, Turkey. Group B rotavirus was not found in any samples. One of 122 samples was positive for group C rotavirus. Phylogenetic analysis of genes for nonstructural protein NSP4, and structural proteins VP4, VP6, and VP7 confirmed the human origin of this strain. Similar to other human group C rotaviruses, one N-glycosylation site was predicted at amino acid residue 67 on the VP7 of strain GUP188. The genes of strain GUP188 were closely related to those of human group C rotavirus strain from the UK (Bristol) for NSP4, China (208 and Wu82) for VP4 and VP6, and from Colombia (Javeriana) for VP7, indicating that the Turkish group C rotavirus was unique and can serve as an additional reference strain for the molecular epidemiology of group C rotaviruses.

Detection and molecular characterization of diarrhea causing viruses in single and mixed infections in children: A comparative study between Bangladesh and Turkey

The incidence and mortality caused by diarrhea differ among countries. The prevalence of different enteric viruses, their molecular characteristics, and infections with multiple viruses might affect the disease incidence and mortality caused by diarrhea. The objective of this study was to determine the distribution and molecular characteristics of enteric viruses in children with diarrhea in Turkey and Bangladesh. A total of 288 stool samples that were negative for group A rotavirus were collected from children aged <5 years with acute diarrhea who presented to hospitals in Turkey and Bangladesh. The samples were screened for human bocavirus (HBoV), astrovirus (HAstV), norovirus (NoV), and adenovirus (AdV). Phylogenetic analyses of the targeted virus genes were performed. In Turkey, viruses were detected in 87/150 samples (58%), which included 69 (79.3%) with single viruses and 18 (20.7%) with multiple viruses. AdV was the most common virus, followed by HBoV. In Bangladesh, viruses were detected in 123/138 samples (89.1%), which included 29 (23.6%) with single viruses and 94 (76.4%) with multiple viruses. NoV GII was the most common, followed by AdV. The dominant genotypes among the virus species were HBoV 2A, HAstV 1, NoV GI type 1, and AdV 40. For NoV GII, the Hunter variant of genotype 4 in Turkey and genotype 17 in Bangladesh were the most common among the sequenced strains. It was concluded that the distribution of the viruses associated with diarrhea in Turkish and Bangladeshi children was different. Enteric viruses and mixed infections were more prevalent in Bangladesh than in Turkey. J. Med. Virol. 86:1159–1168, 2014.

Staining characteristics of p16INK4a: Is there a correlation with lesion grade or high-risk human papilloma virus positivity?

Aim:  The aims of this study were to evaluate the efficiency of p16INK4a in showing cervical lesions and to determine any relationship between lesion grade and high‐risk human papilloma virus (HR‐HPV) infection and p16INK4a staining characteristics.

Circulating rotaviral RNA in children with rotavirus antigenemia

BackgroundRotavirus antigenemia is a common phenomenon in children with rotavirus diarrhea, but information is scarce on aspects of this phenomenon, such as genotype specificity, presence of intact viruses and correlation between genomic RNA and antigen concentration. Such information may help in understanding rotavirus pathogenesis and eventually be useful for diagnosis, treatment and prevention.Methods and findingsSerum samples were collected from children who presented at hospitals with diarrhea. Antigenemia was present in 162/250 (64.8%) samples from children with rotavirus diarrhea. No specific rotavirus genotype was found to be associated with antigenemia. Rotavirus particles could not be found by electron microscopy in concentrated serum from children with high levels of antigenemia. In passaged rotavirus suspension a significant correlation (r = 0.9559; P = 0.0029) was found between antigen level and viral copy number, but no significant correlation (r = 0.001480; P = 0.9919) was found between antigenemia level and viral copy number in serum. When intact rotavirus was treated with benzonase endonuclease, genomic double-stranded (ds) RNA was not degraded, but when sera of patients with antigenemia were treated with benzonase endonuclease, genomic dsRNA was degraded, indicating genomic dsRNA was free in sera and not inside virus capsid protein.ConclusionsAntigenemia is present in a significant number of patients with rotavirus diarrhea. Rotavirus viremia was absent in the children with rotavirus diarrhea who participated in our study, and was not indicated by the presence of antigenemia. The significance of circulating rotavirus antigen and genomic dsRNA in serum of patients with diarrhea deserves further study.

Molecular detection of cytomegalovirus, herpes simplex virus 2, human papillomavirus 16-18 in Turkish pregnants

OBJECTIVE Human cytomegalovirus (CMV) is the most common cause of viral intrauterine infections in the world. Herpes simplex virus type 2 (HSV-2) and human papillomavirus (HPV) are the main agents of viral sexually transmitted diseases, which cause genital ulcers and genital warts, respectively. HPV infection has been linked to the majority of the anogenital malignancies. The aim of this study was to detect the existence of CMV, HSV-2 and HPV type 16-18 in Turkish pregnants by using sensitive molecular assays. METHODS One hundred thirty-four women (18-41 years old; mean age ± SD: 27 ± 8) applied to outpatient clinic of Obstetrics and Gynecology, in between 18th - 22nd weeks of their pregnancy and a control group of 99 healthy women (15-39 years old; mean age ± SD: 24 ± 8) were included in the study. Cervical smear samples were used for DNA extraction. CMV, HSV-2 and HPV 16-18 detections were carried out by real time PCR and in house PCR method, respectively. RESULTS Three patients (3/134; 2.2%) were found to be positive for each HPV and HSV-2. Dual infection with HPV and HSV was found in just one patient. HPV 18 was detected in all positive samples. CMV was found to be positive in two patients (2/134; 1.4 %). CONCLUSION HPV, HSV and CMV must be screened due to high prevalence of these viruses in pregnants by using sensitive molecular methods.

Complete Genome Sequence of an MLB2 Astrovirus from a Turkish Child with Diarrhea

ABSTRACT Only two complete genome sequences of MLB2 astroviruses are available, one from an Indian child with diarrhea and another from plasma of an American child. Here we report the complete MLB2 genome sequence from a Turkish child with diarrhea. This MLB2 astrovirus genome sequence shows high nucleotide identity with the American MLB2.

Prevalence of human papillomavirus (HPV) and HPV-16 genotyping by real-time PCR in patients with several cervical pathologies

PURPOSE this study was planned to evaluate the prevalence of HPV (excepting type 16) and HPV 16 by real-time PCR in colposcopy patients and to interprete the results with age, age of first sexual intercourse (FSI), parity and Pap smear results. METHODS one hundred and two colposcopy patients (50 and 52 of the patients were classified as colposcopy positive and negative, respectively) applying to Gynecology clinic were included. HPV (excepting type 16) and HPV 16 were detected by realtime PCR using the L1 region. Real-time nested amplifications of MY09/11 products were done by GP5+/GP6+ primers and Cyanine-5 labeled HPV and HPV 16 DNA specific probe after HPV DNA extraction by phenol chloroform isoamylalcohol. RESULTS HPV (excepting type 16) and HPV 16 were positive in 12% and 18% of the colposcopy positive patients respectively. HPV (excepting type 16) and HPV 16 were positive in 5.7% and 3.8% of the colposcopy negative patients, respectively. CONCLUSION there was a statistically significant difference between colposcopy positive and colposcopy negative patients comparing HPV 16 with total HPV positivity (p = 0.021 for type 16 and p = 0.010 for total HPV) but there was not a statistically significant difference between colposcopy positive and colposcopy negative patients when we compared HPV (excepting type 16) positivity (p = 0.314). In conclusion, HPV detection and typing may be helpful for cervical cancer screening and prevention.