High-Risk Human Papilloma Virus Genotype Distribution and Correlation with Cervical Cytomorphological Data in Turkish and Immigrant Women in Mersin Province.

Human papilloma virus (HPV) is the most common sexually transmitted viral agent in the world and the most common cause of cervical cancer. HPV prevalence and genotype distribution vary by region and demographic data. In a province in the south of Turkey that constantly receives immigration, we aimed to determine the prevalence of high-risk HPV (HR-HPV) genotypes, evaluate the compatibility between cervical Pap smear cytology results patients and HR-HPVs, and make an up-to-date contribution to the elucidation of epidemiological data. In this single-centre study, a total of 12,641 women aged 18 and over were evaluated retrospectively from January 2019 to July 2022. HPV detection and genotyping were analysed by the PCR method. Bethesda scoring was used for Pap smear cytological evaluation. The overall prevalence of HR-HPV was 12.6% (12.7% in Turkish women, 11.2% in foreign women). Among the typed HPVs that were detected, HPV-16 (31%) was found first, followed by HPV-18 (8%). The prevalence of HR-HPV was higher in women with abnormal cytology (977/1762, 55.4%) than in women with normal cytology (620/10879, 5.7%) (p<0.001). Turkey doesn't yet have a national HPV immunisation program. We think that determining the specific regional frequency of other HR-HPVs separately will be useful in the follow-up of the natural course of the type-specific infection and in vaccine studies in the future.

Determination of hepatitis C virus viremia and genotype distribution in Turkish citizens and immigrants from 2018 to 2022.

Hepatitis C virus (HCV) infection is an important public health problem with potential risk for Turkey. In order to contribute to the epidemiological data, we aimed to investigate the changes in seroprevalence, viremia rates, and genotypes in the last five years in HCV patients in the southern region of Turkey, which has received heavy migration in recent years, according to demographic criteria. In our study, we analyzed the results retrospectively with demographic data. Conducted at a single center, the study involved 259,875 anti-HCV antibody tests administered between January 2018 and July 2022. The study revealed a prevalence of 0.5% for HCV antibody positivity and a viremia prevalence of 0.1%. Among Turkish nationals, the most common genotypes were GT1 (65.1%), while foreign nationals, mainly of Syrian and Ukrainian origin, showed GT4 (52.3%) as the predominant genotype (p<0.001 for both). Although GT2 (7.4% vs. 4.5%) and GT3 (23.3% vs. 13.6%) were relatively higher in Turkish nationals compared to foreign nationals, the difference was not statistically significant (p=0.750 and p=0.154, respectively). This highlights the importance of continuous monitoring and public health efforts to address the potential impact of these demographic shifts on HCV epidemiology in the region.

Pooling Strategy for Detection of SARS-CoV-2 RNA by Real-Time RT-PCR: Comparison of Pooling 5 and 10 Samples.

BACKGROUND: We evaluated whether it was appropriate to screen SARS-CoV-2 in sample pools of 5 and 10. This study was aimed to evaluate whether the pooling strategy would be an appropriate strategy for SARS-CoV-2 screening. METHODS: In the study, 5 and 10 sample pools were formed using 720 nasopharyngeal swab samples, of which 72 were positive, and 648 were negative. The samples were analyzed in three groups according to their Ct values as high, medium, and low viral load. SARS-CoV-2 RNA in nasopharyngeal swab samples was detected by the real-time PCR method on the Bio-Rad platform. RESULTS: The sensitivity of 5-sample pooling was 77.8%, and the sensitivity of 10-sample pooling was 75%. The false-negative rate was 22.2% in 5 sample poolings and 25% in 10 sample poolings. Out of the samples with medium and high viral loads, none of the positive samples were lost in either pool. In pools containing both 5 samples and 10 samples, the individual mean Ct values of the samples detected as false-negative were significantly higher (low viral load) than those of the other samples (p < 0.001). CONCLUSIONS: In this study, 5 and 10 pooling seems useful in detecting patients with medium and high viral loads. Pooling strategies that allow mass screening of SARS-CoV-2 can contribute to early detection of patients at high risk of SARS-CoV-2 transmission in low prevalence areas, as well as timely public health interventions.

Determination of Low IgG Class Antibody Avidity Percentage by IgM Levels Specific to Toxoplasma Gondii.

BACKGROUND: Ig (Immunglobulin) M detection and low avidity index are markers of recent infection in differentiating acute and chronic stages of Toxoplasma gondii (T. gondii) infections. In this study, we aimed to evaluate whether the anti-T. gondii IgM antibody index threshold value could be a predictive factor in the estimation of low avidity and its use in improving the diagnosis of early toxoplasma infection. METHODS: Anti-T. gondii IgM, IgG antibody and IgG avidity results were analyzed. Anti-T. gondii IgG and IgM antibodies in blood samples were studied with chemiluminescent microparticle immunoassay (CMIA), and IgG avidity test was performed with Enzyme Linked Fluorescent Assay (ELFA) technique. RESULTS: The overall seroprevalence of anti-T. gondii antibodies (IgG and/or IgM) was 19.4%. Of the 64 patients whose avidity tests were studied, 47 (73.4%) were female. Twenty seven (57.4%) of the women were pregnant. In the IgG avidity test, 7.8% low avidity was detected. Low avidity was detected in only 4 (15.4%) of 26 IgM positive cases. IgM analysis of a case (6-month-old baby) with low avidity was found to be negative. In the prediction of low avidity, the assay's IgM positivity cutoff value was ≥ 0.6, its sensitivity, specificity, positive predictive value, and negative predictive value were 80%, 62.7%, 2.3%, and 99.7%, respectively. With Architect, 37.3% of samples were false positive. Determining the IgM index cutoff value was unsuccessful in distinguishing low avidity. The area under the ROC curve was 0.574 (p = 0.60). CONCLUSIONS: In our study, the positive predictive value of the IgM test kit in estimating low avidity was low and the false positivity rate was 37.3%. It is thought that the index cutoff value of the anti-T. gondii IgM antibody test kit cannot be considered as a good predictor of recent infection. Studies with larger patient groups are needed.

Assessment of index value performance of enzyme immunoassay test in predicting the diagnosis of human brucellosis.

INTRODUCTION: Clinical presentation of brucellosis is variable. Therefore, it must be confirmed with laboratory findings. Standard tube agglutination test (STAT) is commonly used for diagnosis of brucellosis. ELISA tests differentiate between IgM and IgG antibodies. However, there are evidences revealing that they do not have sufficient specificity. This study aimed to determine an ELISA optimal index value in the diagnosis of brucellosis. METHODOLOGY: Brucella STAT and ELISA IgM/IgG tests of patients admitted to the hospital with signs and symptoms of brucellosis between January 2017 and December 2019 were evaluated in the Microbiology Laboratory. RESULTS: ELISA IgM and IgG serum median index value was significantly higher in STAT positive (1 ≥ 1:160) group (p < 0.001 for both). By ROC analysis of 117 patients, when the IgM index value was determined to be 2.44, the sensitivity, specificity, positive and negative predictive values were 85.7%, 71.4%, 60%, and 90.9%, respectively, and when the IgG index 7.85 was determined, these values were 85.7%, 53.7%, 36.7%, and 92.3%, respectively was detected. CONCLUSIONS: In this study, it was revealed that Vircell Brucella had a good clinical diagnostic performance for index value of 2.44 for IgM test kit and 7.95 for IgG test kit. If the diagnosis of brucellosis is correctly predicted with index values in Brucella IgM and IgG tests before STAT analysis, they can be used in the process of clinical decision. In addition to the results of Brucella ELISA, reporting index values and determining optimal index values for each laboratory can help the diagnosis of brucellosis.

Hepatitis C virus genotypes and viremia in a tertiary hospital in Istanbul, Turkey.

INTRODUCTION: The World Health Organization estimates that 71 million people with chronic HCV infection lived worldwide in 2015. HCV is a globally prevalent pathogen, that genotype1 is the most common. In this study, the prevalence of anti-HCV, distributions of HCV genotype, and viremia rates in patients with chronic hepatitis C were evaluated. METHODOLOGY: In this retrospective single-center study, anti-HCV results of 197,081 patients were evaluated between 2017 and 2020. Quantitative HCV-RNA PCR tests were performed on the Rotor-Gene Q real-time PCR instrument. HCV genotypes determination of 546 samples was carried out with the Gen-C 2.0 Reverse Hybridization strip and HCV Genotype Plus Real-TM kit. RESULTS: The prevalence of anti-HCV was 0.95% and viremic HCV infection was 0.3% (610/197,081). HCV viremia rate was 33.17%. HCV viremia rate was highest in 2017 (52.36%) and the lowest in 2020 (18.3%) (p < 0.001). Genotype1 (72%) was the most common genotype, followed by genotype3 (14.1%), and genotype4 (8.8%). The most common subtypes were determined as genotype1b (56.2%) and genotype1a (13.2%). The viral load was higher in patients infected with genotype5. CONCLUSIONS: In this study, the rate of viremic HCV infection was found to be 0.3%. This rate was lower than the worldwide rate of HCV viremia. The distribution of HCV genotypes was like the global data. The identification of circulating genotypes and subtypes is essential for epidemiological purposes and remains important in the choice of treatment in patients with chronic HCV.

Evaluation of the relationship between progression and SARS-CoV-2 viral load in COVID-19 cases in Ankara, Turkey.

INTRODUCTION: Patients infected with SARS-CoV-2 may present with varying clinical pictures. This study aimed to examine the relationship between viral load cycle threshold value, clinical prognosis and other laboratory parameters in initial swab samples on the day of hospitalization. METHODOLOGY: This retrospective and cross-sectional study included 112 patients, who were diagnosed with SARS-CoV-2 via the Bio-Rad CFX96 TouchTM system. Cycle threshold values for the RdRp gene obtained from reverse transcriptase polymerase chain reaction positive patients were recorded. RESULTS: The mean age of the 112 patients was 47.57 ± 17 years. No relationship was found in symptoms, pneumonia, oxygen need, follow-up in intensive care unit, and mortality between patient groups with cycle threshold values of < 30 and ≥ 30. Frequencies of thrombocytopenia (50%) and elevated LDH levels were higher in patients with cycle threshold values of ≥ 30 (p = 0.02 and p = 0.04, respectively). There was a weak but significant correlation between cycle threshold values and CRP levels (Pearson's r = 0.207, p = 0.029). CONCLUSIONS: Symptoms or clinical prognosis were not significantly related to the SARS-CoV-2 viral load levels tested at admission or for the first time within the scope of this study. Thrombocytopenia and elevated LDH rates were higher in patients with cycle threshold values of ≥ 30. A weak but significant correlation was found between the viral load and CRP levels. Large-scale studies are needed to further elucidate this subject matter.

Could serum thrombocyte/lymphocyte (TLR), neutrophil/lymphocyte (NLR) and neutrophil/albumin (NAR) ratios be indicators of hospitalization and mortality in COVID-19?

Background and Objectives: Neutrophil / lymphocyte (NLR) and thrombocyte / lymphocyte ratios (TLR) are also a guiding factors in the prognostic evaluation of infectious diseases. Another parameter to determine inflammation and prognosis is albumin. This study was aimed to determine whether TLR, NLR and neutrophil / albumin ratios (NAR) are effective in predicting the severity and course of Corona Virus Disease-2019 (COVID-19). Materials and Methods: In this retrospective and cross-sectional study, a total of 1597 patients who were admitted to our hospital between 15.03.2020-1.06.2020, diagnosed with COVID-19 were evaluated. Results: In the estimation of the decision for hospitalization, TLR, NLR and NAR AUROC values were 0.596, 0.634, 0.602 for cutoff values 123.7, 2.3 and 839.5, respectively. In predicting mortality, TLR, NLR and NAR AURO sample size can be specified C values were 0.674, 0.821, 0.787 for cutoff values 168.1, 5.2 and 1303.4, respectively (p <0.001 for all). Conclusion: In our study, it was determined that TLR, NLR and NAR are independent predictors in making the decision of hospitalization and in determining the prognosis in patients who are decided to be hospitalized.

Investigation of Viral Load Cycle Threshold Values in Patients with SARS-CoV-2 Associated Pneumonia with Real-Time PCR Method.

INTRODUCTION: In this study, we aimed investigate the relationship of SARS-CoV-2 viral load cycle threshold (Ct) values with pneumonia. METHODOLOGY: A total of 158 patients in whom SARS-CoV-2 was confirmed in upper respiratory tract (URT) samples with molecular method and who had computed tomography (CT) of the chest, between April 2020 and June 2020 were included in this retrospective cross-sectional study. RESULTS: Mean age of 158 PCR positive patients was 45.22 ± 17.89 and 60.8% of them were male. Pneumonia was detected in 40.5% of the patients on their chest CT. A weak but significant correlation was found between SARS-CoV-2 Ct value detected with PCR in analysis of oropharyngeal/ nasopharyngeal (OP/NP) samples and chest CT score (Pearson's r: 0.197, p = 0.01). No correlation was found between the first detected viral load Ct value and age, gender and mortality. There was no significant correlation between chest CT score and mortality. While the areas remaining under ROC curve for Ct value in analysis of OP/NP samples in prediction of chest CT score ≥ 1, ≥ 5 and ≥ 10 were 0.564, 0.640 and 0.703 respectively. CONCLUSIONS: We found that the amount of SARS-CoV-2 viral load (inverse relationship with Ct) detected in OP/NP samples of patients with COVID-19 pneumonia did not reflect the increasing severity of pulmonary lesions on chest CT. Although primary target of SARS-CoV-2 is all epithelial cells of the respiratory tract we believe studies comparing viral loads in lower respiratory tract samples are needed to determine the severity of pulmonary disease.

Human Papillomavirus Prevalence and Genotype Distribution in Cervical Swab Samples in Istanbul, Turkey.

INTRODUCTION: Human papillomavirus (HPV) is the most common sexually transmitted infection agent worldwide and, with high-risk (HR) HPV genotypes, is the main factor for development of cervical cancer. This study aimed to assess the prevalence of HPV and distribution of HR-HPV genotypes in cervical swab samples and compare them with demographic and clinical data. METHODOLOGY: Cervical swab samples of 2,285 women between the age of 17 and 76 were assessed between January 2018 and October 2020 in order to obtain the data of Turkey. Fifteen different HR-HPV genotypes were determined using multiplex real-time polymerase chain reaction test. RESULTS: HPV was positive in 36.3% (829/2,285) of DNA samples. Prevalence of multiple HR-HPV infection was 40.7%. Of the women, 30.9% (256/829) were infected with HPV16, 14.6% (121/829) with HPV39, and 14.2% (118/829) with HPV51. The most frequently detected genotypes with HPV16 were HPV31, HPV39 and HPV52, respectively. In women with cervical dysplasia, HPV16, 31, and 39 were the most common, and in women with genital warts, HPV16, 59 and 66 were most common, respectively. The highest HR-HPV prevalence was detected in the 17-34 age group (44.1%) (p < 0.001). CONCLUSIONS: The prevalence of HR-HPV was 36.3% in this study. High prevalence (44.1%) especially in young women was consistent with findings in literature. The most common HR-HPV genotypes were HPV16, 39 and 51, respectively. Determining the prevalence and genotypes of HR-HPV playing role in the etiology of cervical cancer will be guiding for measures on prevention of cervical cancer and research on preventive vaccines.

Evaluation of Human Papillomavirus Genotype Distribution in Cervical Samples.

BACKGROUND: The most common sexually transmitted infection in the world is human papillomavirus (HPV). HPV types 16 and 18 are responsible for 60-80% of cervical cancers and precancerous cervical lesions worldwide. AIM: In this study, it was aimed to evaluate the correlation of HPV genotype distribution with cervical cytology results in cervical smear samples and to contribute to HPV epidemiology. MATERIALS AND METHODS: This study included 72 female patients. For detection of the HPV genotypes, a multiplex real-time polymerase chain reaction (PCR) method that could detect more than 25 different HPV types was used. The cervical cytology and histopathology results of the patients were also evaluated simultaneously. RESULTS: The frequency of high-risk HPV was 35% (25/72). The most common types were HPV51 (10%), HPV16 (8%), and HPV66 (8%), respectively. The most common type HPV51 and multiple HPV types were seen in 21-34 age groups. HPV DNA was detected in 21 of 43 samples that had cervical smear diagnosis grouping. Twelve samples (26%) had normal cytology. Low grade squamous intraepithelial lesions were the most common cytological diagnosis in HPV DNA positive samples. The most common HPV types in the patients diagnosed low grade squamous intraepithelial lesions and high grade squamous intraepithelial lesions were HPV16 and HPV52. CONCLUSIONS: In this study, the frequency of high-risk HPV genotypes was 35% as similar to reports of the other studies conducted in our country. The most common types were HPV51, HPV16, and HPV66, respectively. The follow-up of patients with HPV51 infection in our area could help to improve the natural course of the disease and effective prevention programs.

Diagnostic significance of cytomegalovirus DNA quantitation in gastrointestinal biopsies: comparison with histopathological data and blood cytomegalovirus DNA.

OBJECTIVES: This study aims to improve the diagnosis of gastrointestinal (GI) cytomegalovirus (CMV) disease. It presents the results of a novel study in which CMV blood viral load (BVL), tissue viral load (TVL) determined by PCR and hematoxylin-eosin (HE)/immunohistochemistry (IHC) results of GI biopsies are examined comparatively. METHODS: CMV DNA was investigated by quantitative real-time PCR in blood and GI biopsy specimens of 76 patients suspected of CMV disease. Biopsies were also performed HE/IHC stainings in the pathology laboratory. RESULTS: This study included 76 patients whose median age was 34.5 years and 58% (44) were male. Tissue CMV PCR positivity was detected in the highest colon (40/53;75.5%) samples. HE, IHC, blood and tissue CMV PCR positivity rates of all samples were 15.8, 25, 50 and 71.1%, respectively. When IHC was used as the gold standard test for ROC analysis, the optimal cutoff values for the maximum sensitivity and specificity for BVL and TVL were 1.91 log10 copies/ml and 3.82 log10 copies/mg, respectively. Sensitivity and specificity for the cutoff value of tissue CMV DNA were 78.9 and 74.3%, respectively (P < 0.001). CONCLUSION: In this study, CMV DNA was detected in 71.1% of the tissue samples of the cases by PCR. Since the sensitivity of the histopathological examinations accepted as the gold standard is low, simultaneous with the histopathological examinations, determination of BVL, TVL and the identification of optimal cutoff values have been shown to support the diagnosis of GI CMV disease.

Investigation of human bocavirus in pediatric patients with respiratory tract infection.

INTRODUCTION: Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family. This study aimed to investigate the incidence of HBoV and co-infections in pediatric patients with symptoms of viral respiratory tract infection. METHODOLOGY: This study included 2,310 patients between the ages of 0-18 in whom HBoV and other respiratory tract viral pathogens were analyzed in nasopharyngeal swab specimens. RESULTS: In the pediatric age group, HBoV was found in 4.5% (105/2310) of the patients and higher in children between the ages of 1 and 5. Mixed infection was detected in 43.8% (46/105) of HBoV positive patients (p = 0.10). Mono and mixed infection rates were higher in outpatients than in inpatients (p < 0.05). Respiratory syncytial virus was significantly higher than the other respiratory viral pathogens (p < 0.001). CONCLUSIONS: This study is important as it is one of the rare studies performed on the incidence of HBoV in the Marmara region. In pediatric age group, the incidence of HBoV was found 4.5%. The incidence rate of HBoV in this study was similar to those in studies around the world, but close to low rates. The incidence of HBoV was found higher especially among children between the ages of 1-5 in this study. In addition to the incidence of HBoV, accompanying co-infections in the pediatric age group were also investigated in this study. Since concurrence of RSV, HRV and hMPV with HBoV was the most common it must be considered that there may be more than one agents in patients with symptoms of respiratory tract infection.