Human papillomavirus DNA testing with the urine sample is not yet available: the accuracy of two distinct kits.

OBJECTIVE: The aim of this study was to assess the results and efficiency of two real-time polymerase chain reaction procedures for detecting human papillomavirus utilizing urine samples. METHODS: This study comprised 151 patients who had previously tested positive for human papillomavirus in their cervical samples. Two different commercial real-time polymerase chain reaction techniques were used for identification and genotyping human papillomavirus in urine specimens. The urine samples of 151 patients were evaluated via the Roche Cobas test, and the urine samples of 91 patients were also evaluated via the Qiagen test. RESULTS: The overall consistency of urine and cervical swab specimens for the identification of human papillomavirus in Roche Cobas and Qiagen tests were 44.8 and 44%, respectively. The rates of positive human papillomavirus results from urine samples were 57 and 70.3%, respectively. The overall concordance among Roche Cobas and Qiagen tests utilizing urine samples for human papillomavirus type 16/18 was 84.3% with a kappa value of 0.675, and for other high-risk-human papillomavirus, it was 75.60% with a kappa value of 0.535. Roche Cobas showed high concordance with Qiagen test. CONCLUSION: human papillomavirus positivity was not detected in all urine samples. It is still inappropriate to recommend the use of urine liquid biopsy for the accurate and reliable detection of human papillomavirus. Due to the lack of a standardized tool, the utilization of urine samples as a screening human papillomavirus test remains a challenge.

The relationship between the clinical course of SARS-CoV-2 infections and ACE2 and TMPRSS2 expression and polymorphisms.

BACKGROUND: The viral spike (S) protein and host ACE2 and TMPRSS2 genetic variations may act as a barrier to viral infections or determine susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. OBJECTIVES: We investigated the relationship between the expression patterns and polymorphisms of the ACE2 and TMPRSS2 receptor genes associated with coronavirus disease 2019 (COVID-19) and the clinical course of SARS-CoV-2 infections. MATERIAL AND METHODS: We examined 147 COVID-19 patients (41 asymptomatic, 53 symptomatic and 53 cases treated in the intensive care unit (ICU)) and 33 healthy controls. The ACE2 and TMPRSS2 expression was determined using the One-Run RT-qPCR kit. Genotypic distributions of single nucleotide polymorphisms (SNPs) of ACE2 and TMPRSS2 were obtained using reverse transcription quantitative polymerase chain reaction (RT-qPCR). RESULTS: The expressions of ACE2 and TMPRSS2 were different between SARS-CoV-2-positive and -negative groups. The ACE2 rs714205GG genotype and G-allele showed significant differences in the asymptomatic SARS-CoV-2-positive group. A significant correlation was found between the expression of TMPRSS2 rs8134378GA, rs2070788GA, rs7364083GA, and rs9974589AC genotypes and SARS-CoV-2 positivity. The rs1978124 C-allele and rs8134378 A-allele expressions were significant in the symptomatic SARS-CoV-2-positive group. The TMPRSS2 rs2070788GA expression was different in all patient groups compared to the control group. There was a difference between SARS-CoV-2-positive and -negative groups regarding the CTTA haplotype formed by ACE2 variants. The AGCAG and AGAAG haplotypes formed by the TMPRSS2 variants were more common in the asymptomatic patient group than in other patient groups. CONCLUSIONS: Identifying the relationship between host genetic variants and COVID-19 susceptibility will contribute to further studies, enabling new vaccines and potential therapeutic approaches to be discovered.

Determination of the Relationship between Globus-Type Complaints and COVID-19 Anxiety in Adult Cases with COVID-19.

INTRODUCTION: Besides generalized symptoms, patients with COVID-19 also show otolaryngological (ENT) symptoms. Globus is one of these symptoms. Anxiety problems may accompany the disease, as well. This study investigated the relationship between globus symptoms and COVID-19 anxiety in patients diagnosed with COVID-19. METHODS: The Turkish version of Glasgow-Edinburgh Throat Scale (GETS-T) and Coronavirus Anxiety Scale (CAS) was used to investigation of the relationship between globus symptoms and COVID-19 anxiety in patients diagnosed with COVID-19. They responded to the GETS-T for the evaluation of throat symptoms and determination of their severity. Additionally, it examined the level of dysfunctional anxiety associated with the coronavirus in COVID-19 patients by using the CAS. Data were collected through telephone interviews. There were 220 participants in a prospective cross-sectional study (110 COVID-19 patients and 110 non-COVID-19). RESULTS: Results show the GETS-T total score to be significantly higher in the COVID-19 group than in the non-COVID-19 group (p < 0.001). As the GETS-T total score increased, CAS total score also increased significantly in the COVID-19 group. Total scores of GETS-T and CAS were found to be lower in the post-acute period than in the acute period in the COVID-19 group (p < 0.001). CONCLUSION: This study confirms that globus-type symptoms may be present in the clinical appearance of COVID-19 infection. In addition, the results support the opinion held in the academic literature that there are positive correlations between globus sensation and psychosomatic etiology. Furthermore, the study concludes that the symptoms generalized as globus-type symptoms, which include sore throat, the feeling that something is stuck in the throat, and the inability to clear the throat, decrease and almost disappear after the first month of the disease.

Human papillomavirus DNA testing with the urine sample is not yet available: the accuracy of two distinct kits

SUMMARY OBJECTIVE: The aim of this study was to assess the results and efficiency of two real-time polymerase chain reaction procedures for detecting human papillomavirus utilizing urine samples. METHODS: This study comprised 151 patients who had previously tested positive for human papillomavirus in their cervical samples. Two different commercial real-time polymerase chain reaction techniques were used for identification and genotyping human papillomavirus in urine specimens. The urine samples of 151 patients were evaluated via the Roche Cobas test, and the urine samples of 91 patients were also evaluated via the Qiagen test. RESULTS: The overall consistency of urine and cervical swab specimens for the identification of human papillomavirus in Roche Cobas and Qiagen tests were 44.8 and 44%, respectively. The rates of positive human papillomavirus results from urine samples were 57 and 70.3%, respectively. The overall concordance among Roche Cobas and Qiagen tests utilizing urine samples for human papillomavirus type 16/18 was 84.3% with a kappa value of 0.675, and for other high-risk-human papillomavirus, it was 75.60% with a kappa value of 0.535. Roche Cobas showed high concordance with Qiagen test. CONCLUSION: human papillomavirus positivity was not detected in all urine samples. It is still inappropriate to recommend the use of urine liquid biopsy for the accurate and reliable detection of human papillomavirus. Due to the lack of a standardized tool, the utilization of urine samples as a screening human papillomavirus test remains a challenge.

Assessing neutrophil-derived ROS production at the bedside: a potential prognostic tool in severe COVID-19 cases.

PURPOSE: A prompt and effective immune response is required for clearance of pathogens but exaggerated states of inflammation can cause extensive collateral damage to the host. We have previously used a rapid near-patient assay that measures the functional capacity of neutrophils to produce reactive oxygen species (ROS) to show that values are elevated in patients with severe COVID-19 or sepsis. Here, we assess the utility of longitudinal ROS measurements to monitor and predict mortality outcome for patients with COVID-19 infection being treated in an ICU setting. METHODS: We used the Leukocyte ImmunoTest™ (LIT™) to quantify neutrophil ROS release using a small volume (10 µL) of capillary blood in a portable, rapid (10-min) format. RESULTS: ROS values (LIT score) and ROS levels assessed in relation to neutrophil count (LIT/N) were both markedly elevated in the patient group. Furthermore, these correlated strongly with peripheral neutrophil count and CRP value. Serial measurement of neutrophil or CRP values were not able to reliably predict mortality within the study. In contrast, LIT and LIT/N values started to decline at 7 and 5 days, respectively, in patients who survived ICU admission and this increment increased further thereafter. CONCLUSIONS: This study raises the possibility of LIT and LIT/N to be used as a predictive clinical tool for patients with severe COVID-19 and argues for its assessment to inform on prognosis, and potentially guide treatment pathways, in other disorders associated with neutrophil activation. TAKE-HOME MESSAGE: A longitudinal study of 44 severe COVID-19 patients in the ICU of a leading teaching hospital has demonstrated the prognostic potential of a rapid bedside assay of neutrophil-derived reactive oxygen species (ROS). Assessment of changes in ROS production, as measured using the Leukocyte ImmunoTest™, shows that ROS production generally declined back to normal levels for patients who survived, but remained elevated for those patients who did not survive.

Is diagnostic performance of SARS-CoV-2 detection dogs reduced -due to virus variation- over the time?

Medical detection dogs have a high potential for use as alternative diagnostic tools not only for organic diseases, but also for infectious diseases. However, new variants emerging over time may affect the accuracy and sensitivity of diagnostic methods including medical detection dogs in case of viral pandemics. To the best of our knowledge, this is a pioneer study aimed to investigate diagnostic performances and generalization ability of SARS-CoV-2 detection dogs against the new variant after being trained with the original virus. Two SARS-CoV-2 detection dogs were used in this study. In total, 1002 samples including the Omicron variant were introduced to the dogs using a double-blinded design. Two different refresher training sessions were conducted to train the dogs to identify the scent of the Omicron variant. In the first refreshment training, mixed samples (original virus and Omicron variant) were used. The diagnostic performances of the dogs were significantly increased only after the second refreshment training where only the Omicron variant was introduced. This study illustrates that diagnostic performances of SARS-CoV-2 detection dogs were not consistent over time with the emerging new variants. Thus, refreshment training with new variant(s) should be conducted with every new variant which may affect the diagnostic performances of those dogs in such infectious outbreaks.

Erratum: Evaluation of prevalence and risk factors for bloodstream infection in severe coronavirus disease 2019 (COVID-19) patients - CORRIGENDUM.

[This corrects the article DOI: 10.1017/ash.2021.254.].

The Prognostic Value of Lung Injury and Fibrosis Markers, KL-6, TGF-ß1, FGF-2 in COVID-19 Patients.

Background: Biomarkers of lung injury and interstitial fibrosis give insight about the extent of involvement and prognosis in well-known interstitial lung diseases (ILD). Serum Krebs von den Lungen-6 (KL-6) reflects direct alveolar injury and, transforming growth factor-beta1 (TGF-ß1) and fibroblast growth factor-2 (FGF-2) are principal mediators of fibrosis in ILD and in almost all fibrotic diseases. In this sense, we aimed to assess associations of these biomarkers with traditional inflammatory markers and clinical course of COVID-19. Methods: Patients with COVID-19 who had confirmed diagnosis with SARS-CoV-2 nucleic acid RT-PCR were enrolled and followed up prospectively with a standardized approach one month after diagnosis. Patients were divided into severe and non-severe groups according to National Institutes of Health criteria. Outcome was assessed for the requirement of intensive care unit (ICU) admission, long term respiratory support and death. Blood samples were collected at enrollment and serum levels of KL-6, TGF-ß1, FGF-2 were determined by ELISA. Association between these markers with other prognostic markers and prognosis were analyzed. Results: Overall 31 severe and 28 non-severe COVID-19 patients were enrolled and were compared with healthy control subjects (n = 30). Serum KL-6 levels in COVID-19 patients were significantly higher (median [IQR]; 11.54 [4.86] vs 8.54 [3.98] ng/mL, P = .001] and FGF-2 levels were lower (median [IQR]; 76.84 [98.2] vs 101.62 [210.6] pg/mL) compared to healthy control group. A significant correlation was found between KL-6 values and CRP, fibrinogen, d-dimer and lymphocyte counts. However, we did not find an association between these markers and subsequent severity of COVID-19, mortality and long-term prognosis. Conclusions: Serum KL-6 levels were significantly elevated at the diagnosis of COVID-19 and correlated well with the other traditional prognostic inflammatory markers. Serum levels of principal fibrosis mediators, TGF-ß1, FGF-2, were not elevated at diagnosis of COVID-19, therefore did not help to anticipate long term prognosis.

Immunogenicity and safety of the CoronaVac and BNT162b2 Covid-19 vaccine in patients with inflammatory rheumatic diseases and healthy adults: comparison of different vaccines.

OBJECTIVES: To determine the seroconversion (SC) rate after CoronaVac and BNT162b2 vaccines in adults with inflammatory rheumatic disease (IRD). METHODS: Patients who were followed up with IRD and who received two doses of either CoronaVac or BNT162b2 vaccines were included in this prospective observational single-center study. Subjects with two doses of CoronaVac or BNT162b2 without known IRD were included in the healthy controls. The blood samples were taken at a minimum of two and a maximum of 12 weeks after the second dose of vaccine. RESULTS: A total of 81 patients with IRD (61 CoronaVac, 20 BNT162b2) and 100 healthy controls (70 CoronaVac, 30 BNT162b2) were included. The SC rate was slightly lower among patients with IRD versus controls (84 vs 97%, p = 0.002). The SC rate was 100% in all participants who received BNT162b2 both in the patient and control group. The IgG antibody level after CoronaVac in the patient group was significantly lower than both the BNT162b2 (p = 0.031) and the healthy group (p < 0.001). Among patients with IRD, those on rituximab (RTX) (12/81,14.8%) had significantly less SC rate (5/12, 41.7%). The median neutralizing antibody titers were significantly higher in patients with BNT162b2 compared with CoronaVac (1.97 vs. 16.34, p < 0.001). CONCLUSIONS: This study showed that all patients with BNT162b2 vaccine developed immunogenicity in patients with IRD, while there was a decreased antibody response with CoronaVac vaccine compared to that of BNT162b2. In particular, RTX significantly reduces the SC rate.

Evaluation of prevalance and risk factors for bloodstream infection in severe coronavirus disease 2019 (COVID-19) patients.

Objectives: In this study, we sought to determine the prevalence of bloodstream infection (BSI) in severe coronavirus disease 2019 (COVID-19) patients and to determine the risk factors of BSI in critical COVID-19 patients. Design: Retrospective, descriptive study between March 2020 and January 2021. Setting: An 1,007-bed university hospital. Participants: Patients who were hospitalized due to severe COVID-19 disease and had an aerobic blood culture taken at least once during hospitalization. Methods: Case definitions were made according to National Institutes of Health clinical definitions. According to the blood culture results, the patients were grouped as with and without BSIs, and compared for BSIs risk factors. Results: In total, 195 patients were included in the study. Blood culture positivity was detected in 76 (39.0%) of 196 patients. Excluding blood culture positivity considered as contamination, the prevalence of BSI in all severe COVID-19 cases was 18.5% (n = 36). In intensive care unit patients the prevalence of BSI was 30.6% (n = 26). In multivariate analyses, central venous catheter (odds ratio [OR], 8.17; 95% confidence interval [CI], 2.46-27.1; P < .01) and hospitalization in the multibed intensive care unit (OR, 4.28; 95% CI, 1.28-14.3; P < .01) were risk factors associated with the acquisition of BSI. Conclusion: The prevalence of BSI in COVID-19 patients is particularly high in critically ill patients. The central venous catheter and multibed intensive care follow-up are risk factors for BSI. BSIs can be reduced by increasing compliance to infection control measures and central venous catheter insertion-care procedures. The use of single-bed intensive care units where compliance can be achieved more effectively is important for the prevention of BSIs.

Retrospective evaluation of viral respiratory tract infections in a university hospital in Ankara, Turkey (2016-2019).

INTRODUCTION: Viruses are responsible for two-thirds of all acute respiratory tract infections. This study aims to retrospectively detect respiratory tract viruses in patients from all age groups who visited the hospital. METHODOLOGY: A total of 1592 samples from 1416 patients with respiratory tract symptoms were sent from several clinics to the Molecular Microbiology Laboratory at Gazi University Hospital from February 2016 to January 2019. Nucleic acid extraction from nasopharyngeal swabs, throat swabs or bronchoalveolar lavage (BAL) samples sent to our laboratory was done using a commercial automated system. Extracted nucleic acids were amplified by a commercial multiplex-real time Polymerase Chain Reaction (PCR) method, which can detect 18 viral respiratory pathogens. RESULTS: Among 1592 samples, 914 (57.4%) were positive for respiratory viruses. The most prevalent were rhinovirus (25.2%) and influenza A virus (12.1%), the least prevalent was the bocavirus (2.6%). Rhinovirus was the most detected as a single agent (21.2%, 194/914) among all positive cases, followed by coronavirus (9.3%, 85/914). The detection rates of coronavirus, human adenovirus, respiratory syncytial virus A/B, human parainfluenza viruses, human metapneumovirus-A/B, human parechovirus, enterovirus and influenza B virus were 9.9%, 8%, 7.7%, 5%, 3.4%, 3.1%, 3%, and 2.8%, respectively. CONCLUSIONS: The most detected viral agents in our study were influenza A virus and rhinovirus. Laboratory diagnosis of respiratory viruses is helpful to prevent unnecessary antibiotic use and is essential in routine diagnostics for antiviral treatment. Multiplex Real-time PCR method is fast and useful for the diagnosis of viral respiratory infections.

The prevalence and distribution of human papillomavirus in 4267 Turkish women with or without cervical lesions: A hospital-based study.

In the present study, it was aimed to screen the genotypes of human papillomavirus (HPV) retrospectively in women with gynecological symptoms who were admitted to a tertiary care university hospital in Ankara, Turkey. A total of 4267 cervical swab samples of women aged 18-79 years were sent to Medical Virology Laboratory from January 2017 to November 2020. Nucleic acid extraction and amplification of samples were done by an automated system. The test can detect 14 high-risk HPV (HR-HPV) types in a single analysis that performs a real-time polymerase chain reaction, by providing individual results on the highest-risk genotypes HPV 16 and HPV 18 and pooled results on other high-risk genotypes (OHR-HPV) (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68). HPV DNA positivity was detected in 14.2% (605/4267) of the samples. HPV type 16 and type 18 were detected in 2.4% and 0.7% of the samples, respectively. OHR-HPV types were found in 8.8% of the samples. Of the 1.9% and 0.4% samples had mixed types with type 16+ OHR-HPV and type 18+ OHR-HPV, respectively. The results of this study presented the rates of HR-HPV genotypes of a university hospital in Ankara, over a 4-year period. It was observed that the positivity rate of type 18 is decreasing and some OHR-HPV types are increasing. HPV vaccination is not in the national immunization program in Turkey yet, however, HPV vaccines are available and the vaccination rates for women are increasing.

Hepatitis E Infection in Solid Organ Transplant Recipients in Turkey.

BACKGROUND: Hepatitis E virus is a re-emerging pathogen with an increase in human cases that can lead to chronic infection in immunosuppressed patients. Turkey is located between Asia and Europe, 2 regions with distinct epidemiological and clinical features of hepatitis E virus infection. This multicenter cross-sectional study aimed to investigate the prevalence of hepatitis E virus infection in liver and kidney transplant recipients in Turkey and to determine the role of possible transmission factors. METHODS: A total of 485 plasma samples of solid organ recipients were collected from 7 transplantation centers in Turkey. Samples were tested for anti-hepatitis E virus immunoglobin M, immunoglobin G, and hepatitis E virus ribonucleic acid. Water- and food-related risk factors were evaluated by a questionnaire. RESULTS: Samples of 300 kidney and 185 liver recipients were collected. Hepatitis E virus ribonucleic acid was tested in 472 samples and none were positive. Anti-hepatitis E virus immunoglobin G and immunoglobin M were detected in 84 (17.3%) and 3 (0.6%) patients, respectively. Seropositivity was associated with older age, male gender, being a liver recipient, and being infected with hepatitis B virus and/or hepatitis C virus. None of the patients under the age of 30 were seropositive. Hepatitis E virus immunoglobin G prevalence was higher in the Central East and Southeast Anatolia. Eating raw meat was the only independent variable associated with hepatitis E virus seropositivity. CONCLUSION: This is the first prevalence study of hepatitis E virus infection in solid organ recipients in Turkey. Anti-hepatitis E virus immunoglobin G prevalence was 17.3% which was higher than the previously reported rate in blood donors. Seropositivity was significantly higher in liver recipients. Despite the high antibody prevalence, none of the patients were viremic.

[Investigation of Group A Rotavirus G10, G12 Genotypes Emerging in Patients with Acute Gastroenteritis in a Tertiary Care Hospital]. / Hastanemize Basvuran Akut Gastroenteritli Hastalarda Yeni Görülmeye Baslayan A Grubu Rotavirüs G10, G12 Genotiplerinin Arastirilmasi.

Rotaviruses are the most common cause of viral gastroenteritis with the highest mortality and morbidity rates in children aged 0-5 years. The aim of this study was to determine the frequency of rotavirus infection in patients whose stool samples were sent to microbiology laboratory to investigate the etiology of diarrhea, to investigate the rotavirus genotypes that are common in our region and G10, G12 genotypes that have recently become common in the world. Fecal samples of 476 patients aged between 0-92 years who applied between November 2016 and February 2018 were studied via immunochromatographic rapid test and enzyme-linked immunosorbent assay (ELISA) methods. ELISA positive samples were studied by nested reverse transcriptase chain reaction (RT-PCR) and genotyped by agarose gel electrophoresis. Rotavirus was found positive in 18.3% and 17% of stool samples by immunochromatographic test and ELISA, respectively. All ELISA positive samples were also detected as positive by RT-PCR. 18.5% of female patients and 15.7% of male patients were found to be positive and rotavirus positivity was not statistically significant between genders. The frequency of rotavirus in different age groups was 23.5% (6-12 years), 17.3% (13-24 months) and 16% (25-36 months). It was determined that rotavirus cases were most common in the spring. G1, G2, G3, G4, G9, G10, and G12 were detected in 37%, 7.4%, 16.1%, 6.2%, 9.9%, 2.5%, 26% of the samples, respectively. G12 was the most common genotype after G1. The most common G and P genotype combination was G1P[8] (17.2%). This was followed by G12P[8] (11.11%) and G3P[8] (11.11%). P[8] (53%) was found to be the dominant P genotype. In this study, it was observed that rotavirus, which is the cause of childhood diarrhea, can also be encountered in advanced ages and even new genotypes that infect humans worldwide may also be the causative agents. Therefore, we concluded that it is important to investigate new genotypes such as G10 and G12 in molecular epidemiological studies.

[Investigation of HTLV-I/II Seroprevalance of Patients with HIV Positivity being Monitored by Real-Time RT-PCR]. / HIV Pozitifligi Gerçek Zamanli RT-PCR ile Takip Edilen Hastalarin HTLV-I/II Seroprevalansinin Arastirilmasi.

Human T-lymphotropic virus-I/II (HTLV-I/II) and human immun viruses (HIVs), that have similar genomic characteristics also share the same transmission routes and infect T lymphocytes. Regarding this epidemiological similarity, HIV and HTLV infections can be seen together. HIV and HTLV-I/II coinfection occurs with variable frequencies in different populations and geographic regions. There are not any population-based studies carried out defining the number of individuals coinfected with HIV and HTLV-I/II in Turkey. The aim of this study was to determine the seropositivity rates of HTLV-I/II in patients whose HIV viral load was monitored in Gazi University Faculty of Medicine Medical Virology Laboratory Forty-seven HIV positive cases followed-up in Medical Virology Laboratory for HIV viral load monitoring between May 2017-January 2019 were included in the study. HIV seropositivity of the samples was confirmed by the chemiluminescence microparticle immunoassay method. HIV viral load values of the samples were evaluated by real-time reverse transcriptase polymerase chain reaction. The samples were screened for antibodies against HTLV-I/II using chemiluminescent microparticle immunoassay. The study population range was between 19 to 60 years of age. Among the study population, 39 (83%) patients were male and 8 (17%) patients were female. Of 47 samples, 18 samples (38.3%) had viral load of <1000 copies/ml, 10 samples (21.3%) had viral load of 1000-10000 copies/ml, 19 samples (40.4%) had viral load of ≥10000 copies/ml. HTLV serology was negative in all samples included in the study. CD4+ results were available for 42 patients and the CD4+ results of five patients could not be studied. Co-infection with different retroviruses is a well-known fact which should be thoroughly examined. HTLV-I co-infection leads to faster progression of the disease in HIV-1 positive patients. Although it is known that the co-infection has a significant effect on the progression of the disease, there are very few centers in the world and in our country that routinely perform HTLV testing in HIV-positive patients. We think that in order to evaluate the clinical and microbiological importance of the coinfection of retroviruses with each other and to determine the frequency of these infections together, there is a need for studies involving a larger number of patients, including detailed clinical backgrounds of individuals, and that the importance of this issue should be realized at the same time.

Genomic characterization of SARS-CoV-2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins.

Novel mutations have been emerging in the genome of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2); consequently, the evolving of more virulent and treatment resistance strains have the potential to increase transmissibility and mortality rates. The characterization of full-length SARS-CoV-2 genomes is critical for understanding the origin and transmission pathways of the virus, as well as identifying mutations that affect the transmissibility and pathogenicity of the virus. We present an analysis of the mutation pattern and clade distribution of full-length SARS-CoV-2 genome sequences obtained from specimens tested at Gazi University Medical Virology Laboratory. Viral RNA was extracted from nasopharyngeal specimens. Next-generation sequencing libraries were prepared and sequenced on Illumina iSeq 100 platform. Raw sequencing data were processed to obtain full-length genome sequences and variant calling was performed to analyze amino acid changes. Clade distribution was determined to understand the phylogenetic background in relation to global data. A total of 293 distinct mutations were identified, of which 152 missense, 124 synonymous, 12 noncoding, and 5 deletions. The most frequent mutations were P323L (nsp12), D614G (ORF2/S), and 2421C>T (5'-untranslated region) found simultaneously in all sequences. Novel mutations were found in nsp12 (V111A, H133R, Y453C, M626K) and ORF2/S (R995G, V1068L). Nine different Pangolin lineages were detected. The most frequently assigned lineage was B.1.1 (17 sequences), followed by B.1 (7 sequences) and B.1.1.36 (3 sequences). Sequence information is essential for revealing genomic diversity. Mutations might have significant functional implications and analysis of these mutations provides valuable information for therapeutic and vaccine development studies. Our findings point to the introduction of the virus into Turkey through various sources and the subsequent spread of several key variants.

Relationship between chest computed tomography findings and clinical conditions of coronavirus disease (COVID-19): A multicentre experience.

AIMS: This study aimed to investigate the clinical and chest computed tomography (CT) features associated with clinical parameters for coronavirus disease (COVID-19) in the capital of Turkey, Ankara. MATERIALS AND METHODS: Epidemiological, clinical features, laboratory findings and radiological characteristics of 1563 hospitalised patients with COVID-19 in Ankara were collected, reviewed and analysed in this study. The risk factors associated with disease severity were investigated. RESULTS: Non-severe (1214; 77.7%) and severe cases (349; 22.3%) were enrolled in the study. Compared with the non-severe group, the severe group were significantly older and had more comorbidities (ie, hypertension, diabetes mellitus, cardiovascular disease and chronic kidney disease). Smoking was more common in the severe group. Severe patients had higher respiratory rates and higher incidences of cough and dyspnoea compared with non-severe patients. Compared with the non-severe patients, the severe patients had increased C-reactive protein (CRP), procalcitonin, neutrophil to lymphocyte ratio (NLR) and CRP/albumin ratio and decreased albumin. The occurrence rates of consolidation, subpleural sparing, crazy-paving pattern, cavity, halo sign, reversed halo sign, air bronchogram, pleural thickening, micronodule, subpleural curvilinear line and multilobar and bilateral involvement in the CT finding of the severe patients were significantly higher than those of the non-severe patients. CONCLUSIONS: Many factors are related to the severity of COVID-19, which can help clinicians judge the severity of the patient and evaluate the prognosis. This cohort study revealed that male sex, age (≥55 years), patients with any comorbidities, especially those with cardiovascular disease, dyspnoea, increased CRP, D-dimer and NLR, and decreased lymphocyte count and CT findings of consolidation and multilobar involvement were predictors of severe COVID-19.

Determination and Role of Epstein-Barr Virus in Patients With Lymphoproliferative Disorders.

INTRODUCTION: Epstein-Barr virus (EBV) is associated with different types of human malignancies, including Burkitt lymphoma, nasopharyngeal carcinoma, and lymphomas. We retrospectively investigated the presence of EBV-DNA by real-time PCR in clinical samples of patients diagnosed as having hematologic malignancies while investigating the cause of lymphoproliferative disorders, and investigated its relationship to clinical manifestations. PATIENTS AND METHODS: Fifty clinical samples sent to Gazi University's hematology clinics between November 2013 and March 2018 were included. EBV-DNA was investigated by real-time PCR method, and EBV-IgM and EBV-IgG antibodies were investigated by ELISA. RESULTS: Fifty serum samples were investigated, and 10% (5/50) EBV-DNA positivity was determined in patients. Of the 5 patients with EBV-DNA positivity, 2 had acute lymphoblastic leukemia, 1 lymphoma, 1 T-cell lymphoma, and 1 B-cell lymphoma. Concomitant EBV-DNA and viral capsid antigen (VCA)-IgM positivity was not detected. The VCA-lgM test results of the all EBV-DNA-positive patients were negative and VCA-IgG positive (except for 1 patient). Regarding virus load, of the 5 samples, 2, 1, 1, and 1 of the samples had a virus load of 102, 103, 104, and 105 copies/mL, respectively. CONCLUSION: EBV infection is threatening in patients with hematologic malignancies and are diagnosed by serologic and molecular methods. As a result of the study, we suggest that the detection of EBV-DNA by real-time PCR in patients being admitted with lymphoproliferative diseases and diagnosed as acute lymphoblastic leukemia and lymphomas may be useful in follow-up and treatment.

Early predictors of acute kidney injury in COVID-19 patients.

AIM: This study aims to determine the frequency of COVID-19 related AKI and to identify the early predictors of AKI. METHODS: This study is a single-center, retrospective, observational study. Hospitalized COVID-19 patients between 24/03/2020 and 31/05/2020 were included in the study. All patients were evaluated for renal dysfunctions with urine dipstick, protein/creatinine ratio, albumin/creatinine ratio in spot urine, serum cystatin C, serum creatinine level on hospital admission, and 28th day of hospital admission. To assess the utility of these parameters to predict AKI, a receiver-operating characteristic curve was generated and the area under the curve (AUC) was calculated. RESULTS: 348 patients were included. The average incidence of AKI was 4.9% (n = 17). The incidence of AKI in mild, moderate and severe COVID-19 cases was 1.3% (n = 4), 9.0% (n = 3) and 76.9% (n = 10), respectively. Proteinuria was detected in 7.8% (n = 27) of patients with a urine dipstick test. In spot urine analysis, proteinuria was found in 20.1% (n = 70) of patients. The frequency of persistent proteinuria was 5.2% (n = 18). The AUC alue of serum cystatin C, D-dimer and albumin/creatinine ratio to predict COVID-19 related AKI were 0.96 (0.90 to 1.0), 0.94 (0.89-0.98), and 0.95 (0.91-0.98). CONCLUSION: In COVID-19 patients with normal serum creatinine levels on hospital admission, albuminuria, serum cystatin C and D-dimer levels may be an early predictor of COVID-19 related AKI and these patients should be monitored closely for AKI. Since the sample size in the AKI group was small, our study results should be confirmed with larger cohort studies.

The prognostic role of neopterin in COVID-19 patients.

In Coronavirus disease-2019 (COVID-19) cases, hyper inflammation is associated with the severity of the disease. High levels of circulating cytokines were reported in severe COVID-19 patients. Neopterin produced by macrophages on stimulation with interferon-gamma, which is an important cytokine in the antiviral immune response, hence it can be used to predict the severity of disease in COVID-19 cases. In this study, it was aimed to determine the prognostic value of the neopterin for the prediction of severe disease in patients with COVID-19. This single-center, prospective study was conducted in hospitalized COVID-19 patients and healthy volunteers. Severe and mild COVID-19 cases were compared in terms of clinical and laboratory findings as well as serum neopterin levels on hospital admission. To assess the prognostic utility of neopterin between the severe and mild COVID-19 groups, a receiver-operating characteristic (ROC) curve was generated, and the area under the curve (AUC) was calculated. The median serum neopterin level was four times higher in COVID-19 patients than the healthy controls (46 vs. 12 nmol/L; p < .001). The AUC value of serum neopterin was 0.914 (95% confidence interval, 0.85-0.97). The sensitivity and specificity of serum neopterin for the cut-off value of 90 nmol/L to identify severe COVID-19 cases were 100% and 76%, respectively. Serum neopterin levels on hospitalization were significantly higher in severe COVID-19 disease than mild COVID-19 patients. Neopterin levels can be used as an early prognostic biomarker for COVID-19 on admission.