Pre-infection antibody levels of vaccinated healthcare workers with SARS-CoV-2 breakthrough infection: A nested case-control study.

AIM: To evaluate anti-RBD IgG antibody levels and neutralizing antibody titers between the health care workers (HCWs) with breakthrough SARS-CoV-2 infection and controls. METHODS: In this nested case-case control study, we followed 548 vaccinated HCWs with homologous (only with inactivated vaccine) or heterologous (both with inactivated and BNT162b2 vaccine) vaccination for 11 months, prospectively. We obtained blood samples from the participants for quantitative anti-RBD IgG and surrogate neutralization test. The participants with SARS-CoV-2 PCR positivity (at least 14 days after the last vaccination) were considered breakthrough infection. We chose 1:2 matched controls from the cohort, according to age, sex and vaccination status. We used R version 4.0.2 for the statistical analysis. RESULTS: Sixty-five cases and 130 controls were included in the study. The number of the breakthrough infections in HCWs were correlated with the pandemic waves in Türkiye and peaked during Omicron outbreak. The median age of the cases was 39 and 78.5% were female. The cases had more comorbidities than controls, significantly (p = 0.021). All cases experienced no or mild symptoms and recovered completely. Both pre-infection anti-RBD antibody and neutralizing antibody titers did not differ between cases and matched controls (p = 0.767, p = 0.628). CONCLUSION: In this study, we showed that there was no comparable difference in humoral response after homologous or heterologous vaccination between the cases of breakthrough infection and matched controls. Compliance with infection control measures should be ensured, in combination with vaccination.

Can Some Viral Respiratory Infections Observed Before the Pandemic Announcement Be Related to SARS-CoV-2?

OBJECTIVE: There have been doubts that SARS-CoV-2 has been circulating before the first case was announced. The aim of this study was to evaluate the possibility of COVID-19 in some cases diagnosed to be viral respiratory tract infection in the pre-pandemic period in our center. MATERIAL AND METHODS: Patients who were admitted to our hospital's pulmonary diseases, infectious diseases, and intensive care clinics with the diagnosis of viral respiratory system infection within a 6-month period between October 2019 and March 12, 2020, were screened. Around 248 archived respiratory samples from these patients were analyzed for SARS-CoV-2 ribonucleic acid by real-timequantitative polymerase chain reaction. The clinical, laboratory, and radiological data of the patients were evaluated. RESULTS: The mean age of the study group was 47.5 (18-89 years); 103 (41.5%) were female and 145 (58.4%) were male. The most common presenting symptoms were cough in 51.6% (n = 128), fever in 42.7% (n = 106), and sputum in 27.0% (n = 67). Sixty-nine percent (n = 172) of the patients were pre-diagnosed to have upper respiratory tract infection and 22.0% (n = 55) had pneumonia, one-third of the patients (n = 84, 33.8%) were followed in the service. Respiratory viruses other than SARS-CoV-2 were detected in 123 (49.6%) patients. Influenza virus (31.9%), rhinovirus (10.5%), and human metapneumovirus (6.5%) were the most common pathogens, while none of the samples were positive for SARS-CoV-2 RNA. Findings that could be significant for COVID-19 pneumonia were detected in the thorax computed tomography of 7 cases. CONCLUSION: The negative SARS-CoV-2 real-time-quantitative polymerase chain reaction results in the respiratory samples of the cases followed up in our hospital for viral pneumonia during the pre-pandemic period support that there was no COVID-19 among our cases during the period in question. However, if clinical suspicion arises, both SARS and non-SARS respiratory viral pathogens should be considered for differential diagnosis.

Existence of SARS-Cov-2 in the Peritoneal Fluid.

OBJECTIVE: To determine the existence of SARS-CoV-2 in the peritoneal fluid to assess the risk of exposure through surgical smoke and aerosolization threatening healthcare workers during abdominal surgery. BACKGROUND: SARS-CoV-2 is a respiratory virus and possible ways of viral transmission are respiratory droplets, close contact, and fecal-oral route. Surgeries pose risk for healthcare workers due to the close contact with patients. Aerosolized particles may be inhaled via the leaked CO2 during laparoscopic procedures and surgical smoke produced by electrocautery. METHODS: All the data of 8 patients, who were tested positive for COVID-19, were collected between August 31, 2020 and April 30, 2021. Recorded clinicopathologic data included age, symptoms, radiological and laboratory findings, antiviral treatment before surgery, type of surgery and existence of the virus in the peritoneal fluid. Nasopharyngeal swab RT-PCR was used for the diagnosis. COVID-19 existence in the peritoneal fluid was determined by RT-PCR test as well. RESULTS: All 8 COVID-19 positive patients were pregnant, and surgeries were cesarean sections. 1 of the 8 patients was febrile during surgery. Also only 1 patient had pulmonary radiological findings specifically indicating COVID-19 infection. Laboratory findings were as follows: 4 of 8 had lymphopenia and all had elevated D-dimer levels. Peritoneal and amniotic fluid samples of all patients were negative for SARS-CoV-2. CONCLUSION: SARS-CoV-2 exposure due to aerosolization or surgical fumes does not seem to be likely, provided the necessary precautions are taken.

OBJETIVO: Determinar a existência de SARS-CoV-2 no fluido peritoneal para avaliar o risco de exposição através da fumaça cirúrgica e aerossolização que ameaçam os profissionais de saúde durante a cirurgia abdominal. CONTEXTO: O SARS-CoV-2 é um vírus respiratório e as possíveis formas de transmissão viral são gotículas respiratórias, contato próximo e rota fecal-oral. As cirurgias representam risco para os profissionais de saúde devido ao contato próximo com os pacientes. As partículas aerossolizadas podem ser inaladas através do CO2 vazado durante os procedimentos laparoscópicos e a fumaça cirúrgica produzida pela eletrocauterização. MéTODOS: Todos os dados de 8 pacientes, que foram testados positivos para COVID-19, foram coletados entre 31 de agosto de 2020 e 30 de abril de 2021. Dados clinicopatológicos registrados incluíam idade, sintomas, achados radiológicos e laboratoriais, tratamento antiviral antes da cirurgia, tipo de cirurgia e existência do vírus no fluido peritoneal. O diagnóstico foi feito através do swab nasofaríngeo RT-PCR. A existência de COVID-19 no fluido peritoneal foi determinada pelo teste de RT-PCR também. RESULTADOS: Todas as 8 pacientes positivas para COVID-19 estavam grávidas, e as cirurgias eram cesarianas. 1 das 8 pacientes estava com febre durante a cirurgia. Também apenas 1 paciente tinha achados radiológicos pulmonares especificamente indicando infecção por COVID-19. Os achados laboratoriais foram os seguintes: 4 de 8 tinham linfopenia e todas apresentavam níveis elevados de D-dímero. Amostras de fluido peritoneal e líquido amniótico de todas as pacientes foram negativas para SARS-CoV-2. CONCLUSãO: A exposição ao SARS-CoV-2 devido à aerossolização ou fumaças cirúrgicas não parece ser provável, desde que sejam tomadas as precauções necessárias.

Existence of SARS-Cov-2 in the Peritoneal Fluid / Existência de SARS-Cov-2 no líquido peritoneal

Abstract Objective To determine the existence of SARS-CoV-2 in the peritoneal fluid to assess the risk of exposure through surgical smoke and aerosolization threatening healthcare workers during abdominal surgery. Background SARS-CoV-2 is a respiratory virus and possible ways of viral transmission are respiratory droplets, close contact, and fecal-oral route. Surgeries pose risk for healthcare workers due to the close contact with patients. Aerosolized particles may be inhaled via the leaked CO2 during laparoscopic procedures and surgical smoke produced by electrocautery. Methods All the data of 8 patients, who were tested positive for COVID-19, were collected between August 31, 2020 and April 30, 2021. Recorded clinicopathologic data included age, symptoms, radiological and laboratory findings, antiviral treatment before surgery, type of surgery and existence of the virus in the peritoneal fluid. Nasopharyngeal swab RT-PCR was used for the diagnosis. COVID-19 existence in the peritoneal fluid was determined by RT-PCR test as well. Results All 8 COVID-19 positive patients were pregnant, and surgeries were cesarean sections. 1 of the 8 patients was febrile during surgery. Also only 1 patient had pulmonary radiological findings specifically indicating COVID-19 infection. Laboratory findings were as follows: 4 of 8 had lymphopenia and all had elevated D-dimer levels. Peritoneal and amniotic fluid samples of all patients were negative for SARS-CoV-2. Conclusion SARS-CoV-2 exposure due to aerosolization or surgical fumes does not seem to be likely, provided the necessary precautions are taken.

Resumo Objetivo Determinar a existência de SARS-CoV-2 no fluido peritoneal para avaliar o risco de exposição através da fumaça cirúrgica e aerossolização que ameaçam os profissionais de saúde durante a cirurgia abdominal. Contexto O SARS-CoV-2 é um vírus respiratório e as possíveis formas de transmissão viral são gotículas respiratórias, contato próximo e rota fecal-oral. As cirurgias representam risco para os profissionais de saúde devido ao contato próximo com os pacientes. As partículas aerossolizadas podem ser inaladas através do CO2 vazado durante os procedimentos laparoscópicos e a fumaça cirúrgica produzida pela eletrocauterização. Métodos Todos os dados de 8 pacientes, que foram testados positivos para COVID-19, foram coletados entre 31 de agosto de 2020 e 30 de abril de 2021. Dados clinicopatológicos registrados incluíam idade, sintomas, achados radiológicos e laboratoriais, tratamento antiviral antes da cirurgia, tipo de cirurgia e existência do vírus no fluido peritoneal. O diagnóstico foi feito através do swab nasofaríngeo RT-PCR. A existência de COVID-19 no fluido peritoneal foi determinada pelo teste de RT-PCR também. Resultados Todas as 8 pacientes positivas para COVID-19 estavam grávidas, e as cirurgias eram cesarianas. 1 das 8 pacientes estava com febre durante a cirurgia. Também apenas 1 paciente tinha achados radiológicos pulmonares especificamente indicando infecção por COVID-19. Os achados laboratoriais foram os seguintes: 4 de 8 tinham linfopenia e todas apresentavam níveis elevados de D-dímero. Amostras de fluido peritoneal e líquido amniótico de todas as pacientes foram negativas para SARS-CoV-2. Conclusão A exposição ao SARS-CoV-2 devido à aerossolização ou fumaças cirúrgicas não parece ser provável, desde que sejam tomadas as precauções necessárias.

Evaluation of abdominal computed tomography findings in patients with COVID-19: a multicenter study

PURPOSE: To evaluate the frequency of abdominal computed tomography (CT) findings in patients with coronavirus disease-2019 (COVID-19) and interrogate the relationship between abdominal CT findings and patient demographic features, clinical findings, and laboratory test results as well as the CT atherosclerosis score in the abdominal aorta. METHODS: This study was designed as a multicenter retrospective study. The abdominal CT findings of 1.181 patients with positive abdominal symptoms from 26 tertiary medical centers with a positive polymerase chain-reaction test for severe acute respiratory syndrome coronavirus 2 were reviewed. The frequency of ischemic and non-ischemic CT findings as well as the association between CT findings, clinical features, and abdominal aortic calcific atherosclerosis score (AA-CAS) were recorded. RESULTS: Ischemic and non-ischemic abdominal CT findings were detected in 240 (20.3%) and 328 (27.7%) patients, respectively. In 147 patients (12.4%), intra-abdominal malignancy was present. The most frequent ischemic abdominal CT findings were bowel wall thickening (n = 120; 10.2%) and perivascular infiltration (n = 40; 3.4%). As for non-ischemic findings, colitis (n = 91; 7.7%) and small bowel inflammation (n = 73; 6.2%) constituted the most frequent disease processes. The duration of hospital stay was found to be higher in patients with abdominal CT findings than in patients without any positive findings (13.8 ± 13 vs. 10.4 ± 12.8 days, P < 0.001). The frequency of abdominal CT findings was significantly higher in patients who did not survive the infection than in patients who were discharged after recovery (41.7% vs. 27.4%, P < 0.001). Increased AA-CAS was found to be associated with a higher risk of ischemic conditions in abdominal CT examinations. CONCLUSION: Abdominal symptoms in patients with COVID-19 are usually associated with positive CT findings. The presence of ischemic findings on CT correlates with poor COVID-19 outcomes. A high AA-CAS is associated with abdominal ischemic findings in patients with COVID-19.

Electromechanical RT-LAMP device for portable SARS-CoV-2 detection.

Rapid point-of-care tests for infectious diseases are essential, especially in pandemic conditions. We have developed a point-of-care electromechanical device to detect SARS-CoV-2 viral RNA using the reverse-transcription loop-mediated isothermal amplification (RT-LAMP) principle. The developed device can detect SARS-CoV-2 viral RNA down to 103 copies/mL and from a low amount of sample volumes (2 µL) in less than an hour of standalone operation without the need for professional labor and equipment. Integrated Peltier elements in the device keep the sample at a constant temperature, and an integrated camera allows automated monitoring of LAMP reaction in a stirring sample by using colorimetric analysis of unfocused sample images in the hue/saturation/value color space. This palm-fitting, portable and low-cost device does not require a fully focused sample image for analysis, and the operation could be stopped automatically through image analysis when the positive test results are obtained. Hence, viral infections can be detected with the portable device produced without the need for long, expensive, and labor-intensive tests and equipment, which can make the viral tests disseminated at the point-of-care.

Evaluation of SARS-CoV-2 antibody persistence and viral spread in stool: a long-term care experience before COVID-19 vaccination.

BACKGROUND: Due to elderly residents, nursing homes/assisted living facilities were the most affected places in COVID-19 pandemic. Besides symptomatic patients, asymptomatic patients were detected during routine screening. AIM: This study aims to determine the factors that affect antibody response and viral shedding in stool samples after natural exposure to the virus in residents and staff who recovered from COVID-19 before the vaccine was available. METHODS: This prospective cross-sectional study was conducted at the nation's highest-capacity Residential and Nursing Home. Blood samples were collected between December 15, 2020 and January 15, 2021 from participating residents and staff for anti-SARS-CoV-2 antibody testing. Stool samples were obtained for SARS-CoV-2 PCR testing 2 months after COVID-19. The Social Sciences (SPSS) program version 15.0 was used for statistical analysis. The Mann-Whitney U test compared SARS-CoV-2 antibody concentration between two groups. RESULTS: Four hundred sixty-four (52.3%) residents and 424 (47.7%) staff participated. Entirely 259 (29.2%) participants were anti-SARS-CoV-2 IgG (+) and 255 (28.7%) were SARS-CoV-2 PCR (+). Both antibody and PCR positivity was detected in 196 (76.9%). In PCR (-) group, 63 (10.0%) participants were SARS-CoV-2 IgG (+). Antibody titers were found highest in SARS-CoV-2 PCR (+) male residents. SARS-CoV-2 IgG titers were significantly high in SARS-CoV-2 PCR (+) and hospitalized participants regardless of age. Stool samples were obtained from 61(23.9%) participants and were found negative. CONCLUSION: A durable SARS-CoV-2 IgG antibody response was monitored at least 9 months after the participants were diagnosed with COVID-19. SARS-CoV-2 antibody positivity was detected 76.9% in PCR (+) and 10.0% in PCR (-) participants. Knowing the duration of detectable antibodies is an important finding for developing disease prevention and public health strategies.

Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection.

Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor™ Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor™ SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9%) were positive and 98 (22.1%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor™. Antigen Rapid Test Kit was 80.3% whereas specificity was found to be 87.8%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7%, while it increased to 95.7% in samples 20 ≤ Ct < 25 and reached 100% in samples with Ct values below 20. RapidFor™ SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.

Distribution of Viral Respiratory Pathogens During the COVID-19 Pandemic: A Single-Center Pediatric Study from Turkey.

OBJECTIVE: To evaluate the distribution and characteristics of respiratory viral pathogens and to assess the epidemiological data, clinical features, and prognoses of infected children in a pediatric emergency department during the COVID-19 pandemic. MATERIALS AND METHODS: Between September 1, 2020, and April 30, 2021, patients aged between 0 and 18 years arrived at the pediatric emergency department and were tested by nasopharyngeal/tracheal specimen polymerase chain reaction for both SARS-CoV-2 and other viral respiratory pathogens. Demographics, symptoms, laboratory and radiologic investigations, respiratory viruses detected by PCR, presence of co-infection and co-infecting viruses, need for respiratory support, hospitalization, length of hospital stay, and prognosis were recorded. RESULTS: There were 327 patients for whom PCR tests were performed and 118 (36.0%) of them had positive results for SARS-CoV-2 and/or other respiratory viruses. Rhinovirus was the most commonly detected pathogen with 74 (62.7%) cases, followed by enterovirus with 38 (32.2%) and adenovirus with 20 (16.9%) cases. There was no detection of influenza virus or respiratory syncytial. SARS-CoV-2 PCR results were positive in 14 (11.9%) cases and there was only 1 coinfection of SARS-CoV-2 occurring together with rhinovirus. For 43 (36.4%) patients, there was co-infection, and among co-infections, the most common was that of rhinovirus and enterovirus, seen in 37 (86.0%) cases. CONCLUSION: A decrease was observed in the positivity rate of respiratory viral pathogens, while no cases of influenza virus or respiratory syncytial virus were observed in our study. Circulating viruses may change due to multifactorial approaches during the COVID-19 pandemic.

Correlation of Treponemal Chemiluminescent Microparticle Immunoassay Screening Test Signal Strength Values With Reactivity of Confirmatory Testing.

BACKGROUND: Automated chemiluminescent microparticle immunoassays (CMIAs) are the most common first step at high-volume laboratories for syphilis screening. If the initial screening test is reactive, 1 more treponemal test is required, resulting in increased cost. In this multicenter study, we aimed to determine the correlation between the CMIA signal-to-cutoff ratio (S/Co) and the confirmatory tests to reduce unnecessary confirmatory testing. METHODS: Eight hospitals from 5 provinces participated in this study. All laboratories used Architect Syphilis TP CMIA (Abbott Diagnostics, Abbott Park, IL) for initial screening. Treponema pallidum hemagglutination (TPHA), rapid plasma reagin (RPR), and fluorescent treponemal antibody absorption (FTA-ABS) were used as confirmatory tests according to the reverse or European Centre for Disease Prevention and Control algorithms. A receiver operating characteristic analysis was used to determine the optimal S/Co ratio to predict the confirmation results. RESULTS: We evaluated 129,346 serum samples screened by CMIA between January 2018 and December 2020. A total of 2468 samples were reactive; 2247 (91%) of them were confirmed to be positive and 221 (9%) were negative. Of the 2468 reactive specimens, 1747 (70.8%) had an S/Co ratio ≥10.4. When the S/Co ratios were ≥7.2 and ≥10.4, the specificity values were determined to be 95% and 100%, respectively. In a subgroup of 75 CMIA-positive patients, FTA-ABS was performed and 62 were positive. Among these FTA-ABS-positive patients, 24 had an S/Co ratio <10.4, and negative TPHA and RPR. CONCLUSIONS: We propose a potentially cost-effective reverse screening algorithm with a treponemal CMIA S/Co ratio ≥10.4, obviating the need for secondary treponemal testing in about 71% of the screening-reactive samples. This would substantially reduce the confirmatory testing volume and laboratory expenses. However, in high-risk group patients with CMIA positive results, S/Co ratio <10.4, and negative TPHA and RPR, FTA-ABS may be used for confirmation.

An analysis of antibody response following the second dose of CoronaVac and humoral response after booster dose with BNT162b2 or CoronaVac among healthcare workers in Turkey.

Limited data are available on the short- to midterm levels of antibodies to the CoronaVac vaccine and quantitative change in humoral response after homologous or heterologous booster doses. In this prospective cohort study, we evaluated the anti-receptor-binding domain (RBD) immunoglobulin G (IgG) levels after two doses of CoronaVac and heterologous/homologous booster administration among healthcare workers in a university hospital in Turkey. Quantitative anti-RBD IgG antibody levels were measured at first and fourth months in 560 healthcare workers who had completed two doses of CoronaVac vaccine, and within 2 months after the third dose of CoronaVac or BNT162b2. Participants were asked to complete a questionnaire during the first blood draw. The seropositivity rate was 98.9% and 89.1%, and the median antibody level was 469.2 AU/ml and 166.5 AU/ml at first and fourth month, respectively. In the fourth month, a mean reduction of 61.4% ± 20% in antibody levels was observed in 79.8% of the participants. The presence of chronic disease (odds ratio [OR]: 1.76, 95% confidence interval [CI]: 1.15-2.69) and being in the 36-50 age group (OR: 2.11, 95% CI: 1.39-3.19) were identified as independent predictors for low antibody response. The antibody level increased 104.8-fold (median: 17 609.4 vs. 168 AU/ml) and 8.7-fold (median: 1237.9 vs. 141.4 AU/ml) in the participants who received BNT162b2 and CoronaVac, respectively. During the follow-up, 25 healthcare workers (4.5%) were infected with severe acute respiratory syndrome coronavirus 2. Considering the waning immunity and circulating variants, a single booster dose of messenger RNA vaccine seems reasonable after the inactivated vaccine especially in risk groups.

Evaluation of COVID-19 antibody response with using three different tests.

BACKGROUND AND OBJECTIVES: In this study, the performance of three different commercial antibody assays for COVID-19 was examined and parameters affecting the antibody response were investigated. The correlation of patients' chest CT results, procalcitonin, CRP, and D-dimer levels with the antibody response were retrospectively evaluated. MATERIALS AND METHODS: COVID-19 antibodies were detected by three commercially available assays in each patient. Two of the assays were rapid immunochromatographic tests and - one was an ELISA-based IgG assay. SARS-CoV-2 RNA was tested by "COVID-19 RT-qPCR Detection Kit" using nasopharyngeal swab samples. The results of antibody tests were compared with each other, RT-qPCR, Biochemical parameters and chest CT findings. RESULTS: RT-qPCR was positive in 46.6% (41/88) of the evaluated patients among which 77.3% (68/88) were healthcare workers. Seventeen (41.4%) of viral RNA positive patients had a positive antibody result with at least two assays. Both of the rapid immunochromatographic tests had identical sensitivity of 36.6% and specificity of 100%, compared to RT-qPCR assay; while the sensitivity of the ELISA based Euroimmune test was 43.9%, and the specificity was 95.7%. The sensitivity and specificity of the immunochromatographic tests were 75% and 100% respectively, compared to ELISA test result. There was a correlation between antibody positivity and old age and male gender. The presence of typical chest CT findings increased the antibody positivity 13.62 times. Antibody positivity was also increased with the decrease in Ct value of the PCR assay. There was no significant relationship between the biochemical parameters (CRP, D-dimer and procalcitonin values) and the antibody or RT-qPCR results. CONCLUSION: There was a correlation between antibody response and male gender, older age, presence of symptoms, typical chest CT findings and low PCR-Ct value.

Evaluation of Abbott Architect, Siemens Immulite, bioMerieux Vidas, and Euroimmune assays for determination of Epstein-Barr virus serological diagnosis.

Serological tests detecting antibodies for Epstein-Barr virus (EBV) antigens are frequently used to define infection status. Several new automated assays are available for this purpose. We compared the performance of Architect, Immulite, Vidas, and Euroimmune immunofluorescence assays (IFA)/enzyme-linked immunosorbent assays (ELISA) for the detection of EBV viral capsid antigen (VCA) immunoglobulin M (IgM), VCA IgG, Epstein-Barr nuclear antigen (EBNA)-1 IgG. The routine diagnosis of EBV in our laboratory is done by anti-EBV VCA IgM IFT, anti-EBV VCA IgG IFT, and anti-EBNA-1 IgG ELISA (Euroimmune) Kits. Samples were tested with EBV Kits of Architect, Immulite, and Vidas for anti-VCA IgM, anti-VCA IgG, and anti-EBNA-1 IgG. The agreement between assays was calculated for each marker individually and for the determination of the EBV infection profile, based on the combination of three markers. BIOCHIP Sequence EBV (Avidity test) and/or EUROLINE EBV Profile 2 (IgG/IgM) were used as confirmatory assays to resolve discrepancies. The best concordance for VCA IgM detection was between Immulite and Vidas; for VCA IgG and EBNA-1 IgG were between Architect and Vidas. The sensitivities and specificities for VCA IgM were 97% and 88% for IFA, 100% and 94% for Architect, 100% and 99% for Vidas, and 100% and 100% for Immulite, respectively. The most problematic marker was EBNA-1 IgG with a 68.1% specificity by Immulite. Vidas panel had a perfect performance (100%) for determining all EBV profiles. Overall, evaluated assays had comparable performance. There were more discordant VCA IgG and EBNA-1 IgG results than VCA IgM results. The agreement between Architect and Vidas was better than other assays.

[Analysis of Nucleotide Changes in RT-PCR Primer/Probe Binding Regions in SARS-CoV-2 Isolates Reported from Turkey]. / Türkiye'den Bildirilen Sars-CoV-2 Izolatlarinda RT-PCR Primer/Prob Baglanma Bölgelerindeki Nükleotit Degisimlerinin Analizi.

The SARS-CoV-2 virus, which caused the COVID-19 epidemic, caused more than 55 million cases and nearly 1.5 million deaths worldwide. For the microbiological diagnosis of the disease, the most valid method is detecting the presence of the viral genome by real-time reverse transcription polymerase chain reaction (rRT-PCR). However, due to the nature of the RNA viruses, frequent mutations may affect the sensitivity of the analyses made on the genetic material of the virus, such as PCR. In this study, we aimed to investigate the mutations in the primer-probe binding regions of the rRT-PCR panels used in COVID-19 diagnosis. SARS-CoV-2 whole genome sequence data (n= 194) isolated from COVID-19 cases in Turkey and uploaded on GISAID database from the centers in Istanbul (n= 78), Ankara (n= 58), Kars (n= 47), Bursa (n= 2), Adiyaman (n= 2), Erciyes (n= 1) and Kocaeli (n= 1) between March 17-September 14, 2020 were analyzed. In order to determine the nucleotide changes, SARS-CoV-2 sequences from Turkey were compared to the reference genome sequence (NC_045512.1) present in "GenBank" website. The constructed data set was aligned using the MAFFT program and was checked manually if the sequences were in the same frame by using the AliView program. Primer-probe binding sites of the thirteen SARS-CoV-2 rRT-PCR panels from seven different institutes (US CDC, China CDC, Charite CDC, Pasteur, HKU, Thailand, NIID) that are being used in COVID-19 diagnosis were evaluated in terms of nucleotide changes within the corresponding regions compared to the reference genome. Sequence diversities in the viral genomes were determined via positional nucleotide numerical calculator and entropy calculator modules and nucleotide and entropy changes in primer-probe binding regions for each rRT-PCR panel were examined. Among thirteen different primer-probe panels, nucleotide changes in the target regions of the seven primer-probe panels were determined. When viral sequences with nucleotide changes in the primer-probe binding regions were examined, the most common changes were observed in the "China CDC" N-forward primer and "US CDC" N3-forward primer binding regions. It is important that the kits to be used as diagnostic tests are designed specific to the regions with less nucleotide changes. Nucleotide changes may not be critical for DNA amplification for most PCR panels, but should be carefully monitored as they may affect the sensitivity of the assay. If the risk of alteration of the designed region is high, the primer - probe binding sites should be checked frequently and updated when necessary.

Evaluation of COVID-19 Disease and the Effect of Trends in Intervention Measures: The Pediatric Perspective from a Tertiary Care Hospital in Turkey.

BACKGROUND: COVID-19 is an emerging disease of global public health concern. AIMS: To evaluate the epidemiological, clinical, laboratory, and radiologic findings and the clinical outcomes of children who were diagnosed with SARS-CoV-2 by polymerase chain reaction (PCR), and to evaluate the effect of the trends in intervention measures. STUDY DESIGN: Between April 2, 2020 and January 16, 2021, children aged 0-18 years who had presented at the pediatric emergency department and were diagnosed with confirmed SARS-CoV-2 by PCR were enrolled. METHODS: Details on demographics, epidemiologic characteristics, clinical findings, laboratory data, and radiologic investigations, hospital admissions, and prognosis were recorded. According to clinical severity, patients were divided into 5 groups as asymptomatic, mild, moderate, severe, or critical. We classified the outbreak into 3 periods. The first was between April 2, 2020, the date when the first pediatric case of our hospital was detected, and June 1, 2020, when restrictive measures were relaxed. The second period was between June 1, 2020 and November 15, 2020, when restrictive measures were reimplemented. The third period was between November 15, 2020 and January 16, 2021. RESULTS: A total of 600 patients [median age: 10.3 years (IQR: 4.4-15.1); 304 females] were enrolled. Among them, 25.0% were asymptomatic, while the 3 most common symptoms among symptomatic cases were fever, cough, and fatigue. There was contact with a COVID-19 PCRpositive individual in 73.5% of the cases, with 76.6% of those being a household contact. There were 23 (3.9%) moderate, severe, or critical cases in terms of clinical severity. The presence of chronic disease, a pathological physical chest examination, and procalcitonin levels of >0.05 ng/mL were identified as predictors of being moderate, severe, or critical. Twenty-four (4.0%) patients were admitted to the hospital; 14 (2.3%) to the ward and 10 (1.6%) to the pediatric intensive care unit. In the second intervention period, we observed a rapidly increasing number of new cases daily, especially in August. From September, an increase was observed, being particularly marked from October to November 18. Since then, there was a decrease in the daily number of cases. CONCLUSION: The majority of the cases were asymptomatic or had a mild clinical presentation. The presence of chronic disease, a pathological physical chest examination, and procalcitonin levels of >0.05 ng/mL were identified as predictors of being moderate, severe, or critical in terms of clinical severity. Strict intervention measures seem to be effective in containing the spread of COVID-19.

[Evaluation of SARS-CoV-2 PCR Positive Cases in the Pediatric Emergency Department]. / Çocuk Acil Serviste SARS-CoV-2 PCR Pozitif Saptanan Olgularin Degerlendirilmesi.

In December 2019, a previously unknown type of coronavirus was detected in China and named as "severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)". The World Health Organization has named the SARS-CoV-2 related as coronavirus disease-2019 (COVID-19) and declared it as a pandemic. There is a limited data about the COVID-19 disease for the pediatric patients. In this study, it was aimed to evaluate the epidemiological, clinical, laboratory and radiologic findings, treatment and clinical outcomes of patients admitted to the pediatric emergency department with the suspicion of COVID-19. Between March 11 and June 16, 2020, patients aged between 1 month-18 years admitted to the pediatric emergency department and who have an indication for sampling for the polymerase chain reaction (PCR) method with the suspicion of COVID-19 according to the current guidelines published by the Ministry of Health were included in the study. The demographic characteristics, symptoms, durations and the history of contact with the suspected/definite COVID-19 cases were questioned in the patients with positive results. Physical examination, laboratory and imaging data of the patients were recorded. According to clinical severity, patients were divided into five groups. Treatment methods, ward/intensive care unit admission, length of stay at hospital, and prognosis were recorded. Of the 237 patients included in the study, 45 (18.9%) of the samples were positive and 192 (81.1%) were negative. There was a history of contact with COVID-19 positive case in 38 (85.6%) of COVID-19 PCR positive patients. The mean time for onset of symptoms after contact was 3.5 ± 1.7 days. Twenty-one of the patients (46.6%) were asymptomatic and the most common symptom was fever (34.1%) and cough (27.3%). Of the patients whose laboratory tests were requested, lymphopenia wasdetected in 50% and 52.3% of procalcitonin, 23.5% of C-reactive protein and 64.7% of D-dimer values were found to be high. Chest radiography was obtained from 45.4% of the patients; 90.0% were evaluated as normal, bronchovascular change, pleural effusion and consolidation were detected in one of each (5.0%) patient. Thorax computed tomography (CT) was obtained from 4 (9.0%) patients. One patient had normal CT findings, two patients had consolidation, one patient had peripheral ground-glass appearance and one patient had pleural effusion. Antibiotics were started in 38.6% of the patients and the most commonly used antibiotic was azithromycin (34.1%). Oseltamivir was started in one (2.3%) patient, and 10 (24.7%) patients were treated with hydroxychloroquine. There were no serious and critical cases according to the clinical severity. Pediatric patients constitute a small part of COVID-19 individuals in the community, and a significant part of them are asymptomatic, and patients who are symptomatic present with a mild clinic. In our study, most of the patients had a history of contact with COVID-19 positive cases, therefore, it should be questioned when evaluating a pediatric patient. There were no specific findings for COVID-19 positive patients in terms of laboratory and radiology.

COVID-19 S: A new proposal for diagnosis and structured reporting of COVID-19 on computed tomography imaging.

PURPOSE: Because of the widespread use of CT in the diagnosis of COVID 19, indeterminate presentations such as single, few or unilateral lesions amount to a considerable number. We aimed to develop a new classification and structured reporting system on CT imaging (COVID-19 S) that would facilitate the diagnosis of COVID-19 in the most accurate way. METHODS: Our retrospective cohort included 803 patients with a chest CT scan upon suspicion of COVID 19. The patients' history, physical examination, CT findings, RT PCR, and other laboratory test results were reviewed, and a final diagnosis was made as COVID 19 or non-COVID 19. Chest CT scans were classified according to the COVID 19 S CT diagnosis criteria. Cohen's kappa analysis was used. RESULTS: Final clinical diagnosis was COVID-19 in 98 patients (12%). According to the COVID-19 S CT diagnosis criteria, the number of patients in the normal, compatible with COVID 19, indeterminate and alternative diagnosis groups were 581 (72.3%), 97 (12.1%), 16 (2.0%) and 109 (13.6%). When the indeterminate group was combined with the group compatible with COVID 19, the sensitivity and specificity of COVID-19 S were 99.0% and 87.1%, with 85.8% positive predictive value (PPV) and 99.1% negative predictive value (NPV). When the indeterminate group was combined with the alternative diagnosis group, the sensitivity and specificity of COVID-19 S were 93.9% and 96.0%, with 94.8% PPV and 95.2% NPV. CONCLUSION: COVID-19 S CT classification system may meet the needs of radiologists in distinguishing COVID-19 from pneumonia of other etiologies and help optimize patient management and disease control in this pandemic by the use of structured reporting.

[A Case of Congenital Syphilis and Prozone Phenomenon]. / Konjenital Sifilis Olgusu ve Prozon Fenomeni.

The screening for syphilis during pregnancy is important to prevent intrauterine transmission and complications. Prozone phenomenon may cause a false negative result in non-treponemal syphilis tests, which complicates an accurate diagnosis. In this case report a newborn syphilis case was presented to emphasize the importance of reverse algorithm in diagnosis and the prozone phenomenon which can cause problems in rapid plasma reagin (RPR) test. The 2920 g infant patient was born from a 24-year-old mother with no known diseases, at the 35th week of gestation by cesarean section due to premature rupture of membranes. The initial physical examination of the newborn revealed erythema and exfoliation of the bilateral hands and feet. Laboratory results revealed CRP: 90 mg/L, WBC: 19.2 x 103/µl, hemoglobin: 9.5 g/dl, platelet count: 214 x 103/µl, HIV-Ag/Ab: non-reactive, anti-Toxoplasma gondii IgM and IgG: negative, anti-cytomegalovirus IgM: negative, anti-cytomegalovirus IgG: positive (128.7 AU/ml), anti-Rubella IgM: negative, anti-Rubella IgG: positive (26 IU/ml), anti-Treponema pallidum (anti-T.pallidum) antibody [IgM and IgG by the chemiluminescence microparticle enzyme immunoassay (Architect Syphilis TP; Abbott Japan Co, Japan)]: positive (Signal Cut Off value (S/CO): 28.35), and RPR (Omega Diagnostics, UK): negative. All of the above ELISA tests were performed by using Architect (Abbott Diagnostics, Wiesbaden, Germany) kits. When the RPR test was repeated with serial dilutions of the serum in order to detect prozone phenomenon, positive reaction was detected starting from 1:2 and ending at 1:64 dilution. It was determined that the mother was not tested for syphilis during her pregnancy. When both the mother and the father were tested for syphilis, the mother's anti-T.pallidum total antibody test result was reactive (S/CO: 30.52) and the RPR was positive at 1:32 dilution, while the father's anti-T.pallidum total antibody test result was reactive (S/CO: 16.05) and the RPR was negative. A four-fold difference between the maternal and infant RPR dilutions is required by the guidelines for a laboratory diagnosis of congenital syphilis. Although this criterion was not met in the newborn, the case was accepted as congenital syphilis due to clinical findings. Congenital syphilis must be considered in the differential diagnosis in the presence of skin manifestations at the birth and early neonatal period. Accurate and early diagnosis of the disease is important to start appropriate treatment and prevent complications. As described in the presented case, the use of reverse syphilis test algorithm will enable to reach the correct diagnosis of the infection. If the result of the treponemal test is positive and the RPR test is negative, prozone phenomenon should be considered and the RPR test should be repeated with serial serum dilutions.

Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients.

Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent-specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real-time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8-year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016-2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season.

Comparison of polymerase chain reaction-restriction enzyme analysis method and DNA sequence analysis results in the identification of non-tuberculous mycobacteria.

The typing of non-tuberculous mycobacteria (NTM) is important from a clinical and epidemiological perspective. The polymerase chain reaction-restriction enzyme analysis (PRA) method and DNA sequence analysis method were utilized to target a gene region that codes the 65-kDa heat-shock protein for typing 150 suspected NTM samples isolated from the respiratory tract. Mycobacterium abscessus, Mycobacterium xenopi, Mycobacterium fortuitum, and Mycobacterium peregrinum were most frequently found by both methods. Six isolates that could not be defined by the PRA method were defined as Nocardia cyriacigeorgica, Nocardia abscessus, and Mycobacterium intracellulare by DNA sequence analysis. Discordance between the results of the two methods was observed for only one isolate. The isolate that was defined as Mycobacterium gordonae type 6 by the PRA method was defined as Mycobacterium senegalense by sequence analysis. The PRA method is simple and gives rapid results. Compared with DNA sequence analysis, it gives consistent and reliable results up to a ratio of 90%. DNA sequence analysis is the gold standard method in which all strains can be defined. However, given our laboratory conditions, its disadvantage is that it takes longer to reach a diagnosis than through the PRA method.