Positive Real-time Reverse Transcription Polymerase Chain Reaction Research Articles

New onset or recurrence of uveitis following COVID-19 infection

BackgroundWhile the 2019 novel coronavirus disease (COVID-19) pandemic has resulted in millions of cases worldwide, there is increasing recognition of a wide range of ocular manifestations associated with the virus, including uveitis. Uveitis is an inflammatory condition of the uveal tract of the eye that can lead to permanent vision loss if not treated promptly. Here we report a retrospective observational study of patients who presented with new onset or recurrent uveitis following COVID-19 infection.MethodsThis is a retrospective observational study conducted at the Beijing Tongren Hospital. We identified patients who presented with symptoms of non-infectious active uveitis with positive real-time reverse transcription polymerase chain reaction (RT-PCR) of COVID-19 within 4 weeks. All patients received ophthalmic examinations, including anterior and posterior segment imaging, to assess the extent of ocular involvement.ResultsThe 18 patients with a total of 33 eyes included in this study presented with symptoms of active uveitis within 4 weeks of their positive COVID-19 RT-PCR test. Among them, 9 patients presented with the development of uveitis following COVID-19 infection, and 9 patients had relapsed uveitis after COVID-19 infection. Treatment with corticosteroids resulted in improvement of symptoms and resolution of inflammation in all cases. In this study, all patients did not experience any adverse drug reactions during treatment.ConclusionOur observational study highlights the potential for new onset or recurrence of uveitis following COVID-19 infection.Trial registrationhttps://www.chictr.org.cn/; identifier: ChiCTR2100044365, date: 03/17/2023.

Investigation of SARS-CoV-2 in vaginal secretions of women with coronavirus disease 2019

Abstract Objectives The present study investigates the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the vaginal swabs of female patients diagnosed with coronavirus disease 2019 (COVID-19) based on a positive real-time reverse transcription polymerase chain reaction (RT-PCR) test on a combined throat and nasopharyngeal swab. Methods This study included 48 female patients hospitalized in two tertiary hospitals diagnosed with COVID-19 based on a positive RT-PCR test of the combined throat and nasopharyngeal swab samples, along with clinical and radiological findings. The IBM SPSS software package was used for the statistical analysis of the study data. Results SARS-CoV-2 positivity was detected in only one patient (2.08 %) in the present study from RT-PCR tests of vaginal swab samples. This patient was a 64-year-old, postmenopausal woman who tested positive for SARS-CoV-2 in a RT-PCR test of a vaginal swab sample six days after having tested positive in an RT-PCR test of a combined throat and nasopharyngeal swab. The patient’s partner also tested positive for SARS-CoV-2 in an RT-PCR of a combined throat and nasopharyngeal swab. Conclusions The present study is the first to report the presence of SARS-CoV-2 in vaginal secretions in Türkiye. The authors believe there is a need for studies investigating the presence of SARS-CoV-2 in the semen samples of the male partners of female patients to establish whether the presence of SARS-CoV-2 in vaginal secretions can play a role in the transmission of the virus.

Association between time of onset and Omicron BA.2 RNA clearance time in children: a retrospective cohort study.

The association between the time of onset [time from the date of detection of a positive real-time reverse-transcription polymerase chain reaction (RT-PCR) to the date of detection of a positive RT-PCR in the first child] and viral RNA clearance time (time from first positive RT-PCR to two consecutive negative RT-PCR) remains unclear. Our study aimed to evaluate their association. That can provide a reference for the number of nucleic acid tests. We conducted a retrospective analysis of children diagnosed with Omicron BA.2 infection at Fujian Medical University Affiliated First Quanzhou Hospital between March 14, 2022 (date the first child in the outbreak was found positive for RT-PCR) and April 9, 2022 (date the last child was found positive for RT-PCR). We used the electronic medical record to extract demographic data, symptoms, radiology and laboratory findings, treatments, and viral RNA clearance time. The 282 children were divided equally into 3 groups according to the time of onset. We calculated the factors affecting viral RNA clearance time by univariate and multivariate analysis. We used the generalized additive model to investigate the relationship between the time of onset and viral RNA clearance time. 46.45% of children were female. Fever (62.06%) and cough (15.60%) were the dominant onset symptoms. We found no serious cases and all children were cured. The median time to viral RNA clearance was 14 days (IQR 12-17 days), with a range of 5 to 35 days. After adjustment for potential confounders, the viral RNA clearance time was reduced by 2.45 (95% CI: 0.85, 4.04) days in the 7-10 days group and by 4.62 (95% CI: 2.38, 6.14) days in > 10 days group compared to the ≤6 days group. There was a non-linear association between the time of onset and viral RNA clearance time. Time of onset was non-linearly associated with Omicron BA.2 RNA clearance time. During the first 10 days of the outbreak, viral RNA clearance time decreased with increasing onset date. After 10 days of the outbreak, viral RNA clearance time did not decrease with increasing onset date.

Real-world assessment of the clinical performance of COVID-VIRO ALL IN rapid SARS-CoV-2 antigen test.

Since the external validation of severe acute respiratory syndrome coronavirus 2 antigen rapid diagnostic tests (SARS-CoV-2 RDT-Ags) is a necessary requisite before they can be introduced into routine clinical practice, this study reports the results of a real-world assessment of the clinical performance of the new COVID-VIRO ALL IN device. The study population consisted in 165 outpatients (median age: 43years, range: 14-68years; 66.1% females) who had paired nasal and nasopharyngeal samples collected upon hospital presentation. The samples were concomitantly tested with the AAZ-LMB COVID-VIRO ALL IN SARS-CoV-2 RDT-Ag and with Cepheid Xpert Xpress SARS-CoV-2 real-time reverse transcription polymerase chain reaction (RT-PCR). The number of subjects with positive RT-PCR results (i.e.,mean Ct value <45) was 116 (70.3%), 109 (66.1%) and 86 (52.1%) with mean Ct values <37 and <30, respectively. In all RT-PCR positive samples, COVID-VIRO ALL IN displayed 78.8% agreement, 0.698 sensitivity, 1.000 specificity, 0.583 negative predictive value (NPV) and 1.000 positive predictive value (PPV) compared to RT-PCR. The median Ct value of samples testing positive with COVID-VIRO ALL IN was significantly lower than those testing negative (22.8 vs. 32.2; p<0.001). In samples with high viral load (i.e.,Ct value <30), COVID-VIRO ALL IN displayed 92.1% agreement, 0.895 sensitivity, 0.949 specificity, 0.983 NPV and 0.951 PPV compared to RT-PCR. Although the diagnostic performance of COVID-VIRO ALL IN do not exactly match those of the manufacturer, its high NPV in high viral load samples would enable fast-track and rapid identification of highly contagious subjects.

Association of COVID-19 Real-Time Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Cycle Threshold Value With Surrogate Markers of Disease Severity.

Introduction The cycle threshold (Ct) value in real-time reverse transcription-polymerase chain reaction (RT-PCR) serves as a criterion to diagnose coronavirus disease 2019 (COVID-19) and is inversely proportional to viral load. Levels of inflammatory markers such as aspartate aminotransferase (AST), ferritin, D-dimer, high sensitivity C-reactive protein (hs-CRP), and lactate dehydrogenase (LDH) are used as quantitative measures of COVID-19 severity. We examined the association between these markers and Ct values. Methodology This retrospective data analysis included 400 patients with positive RT-PCR results for COVID-19 who were admitted to a tertiary care hospital. Clinical and biochemical data were accessed from the hospital information management system. Associations of clinical parameters and markers of disease severity (e.g., polymorph, AST, hs-CRP, D-dimer, LDH, and ferritin levels) with Ct values were assessed. Observations LDH, ferritin, D-dimer, and hs-CRP were found to be significantly higher in moderate and severe groups than in the mild COVID-19 group. AST, ferritin, and hs-CRP levels were also significantly higher in severe COVID-19 subjects, compared to moderate COVID-19 subjects.Ct values for the E (envelop) gene and ORF (open reading frame) 1b gene were found to be significantly higher in those with severe COVID-19. Polymorph counts in subjects with Ct values of 25 or higher were significantly increased, compared to those with Ct values under 30. LDH, D-dimer, and hs-CRP levels in subjects with Ct values over 30 were significantly lower than for those with Ct values under 30. Ferritin was the best independent predictor of non-survival in study subjects, with an area under the curve (AUC) of 85.5% (95% confidence interval = 73.2-95.9). The Ct value for the E gene had an AUC of 75.1%, and the ORF1b gene had an AUC of 64.5%. However, no significant correlation was detected between any parameter and Ct value. Conclusion Polymorph, LDH, ferritin, D-dimer, and hs-CRP levels were significantly elevated in subjects with low E gene Ct values. Also, these subjects were at risk of severe disease and fatality. Ct values for the E gene thus could serve as an early indicator for patients at risk of severe disease and death.

Comparison of sputum specimens and nasopharyngeal swab specimens for diagnosis of acute human metapneumovirus-related lower respiratory tract infections in adults.

To detect human metapneumovirus, tests besides reverse transcription-polymerase chain reaction (RT-PCR) on nasopharyngeal swab specimens are less accessible. Immunochromatography assays are rapid and simple without the need of any special equipment but sometimes are insufficiently sensitive. This study describes the usefulness of immunochromatography assays to detect human metapneumovirus in adult patients with human metapneumovirus-related acute lower respiratory tract infection using sputum specimens. This prospective single-center study enrolled adults and adolescents aged ≥16 years with signs and symptoms of an acute respiratory illness who were diagnosed with acute lower respiratory tract infection. The presence of human metapneumovirus infection was confirmed by seroconversion. Immunochromatography assays and real-time RT-PCR were performed to compare the efficacy of nasopharyngeal swab specimens and sputum specimens. Comparative results were obtained via McNemar's test. Overall, 337 patients were recruited in this study; 63 (18.7%) patients were seroconverted. Sputum specimens showed significantly higher positivity rates than nasopharyngeal swab specimens with both immunochromatography assays (p=0.0008) and real-time RT-PCR (p=0.014). Among 29 patients with pneumonia who had concordant positive real-time RT-PCR results for both nasopharyngeal swab specimens and sputum specimens, 21 (72.4%) had a higher viral load in the sputum specimens. Sputum specimens are more useful in detecting human metapneumovirus than nasopharyngeal swab specimens in adult patients with acute lower respiratory tract infection.

Detection of SARS-CoV-2 contamination in the operating room and birthing room setting: a cross-sectional study.

Background:The exposure risks to front-line health care workers caring for patients with SARS-CoV-2 infection undergoing surgery or obstetric delivery are unclear, and an understanding of sample types that may harbour virus is important for evaluating risk. We sought to determine whether SARS-CoV-2 viral RNA from patients with SARS-CoV-2 infection undergoing surgery or obstetric delivery was present in the peritoneal cavity of male and female patients, in the female reproductive tract, in the environment of the surgery or delivery suite (surgical instruments or equipment used, air or floors), and inside the masks of the attending health care workers.Methods:We conducted a cross-sectional study from November 2020 to May 2021 at 2 tertiary academic Toronto hospitals, during urgent surgeries or obstetric deliveries for patients with SARS-CoV-2 infection. The presence of SARS-CoV-2 viral RNA in patient, environmental and air samples was identified by real-time reverse transcription polymerase chain reaction (RT-PCR). Air samples were collected using both active and passive sampling techniques. The primary outcome was the proportion of health care workers’ masks positive for SARS-CoV-2 RNA. We included adult patients with positive RT-PCR nasal swab undergoing obstetric delivery or urgent surgery (from across all surgical specialties).Results:A total of 32 patients (age 20–88 yr) were included. Nine patients had obstetric deliveries (6 cesarean deliveries), and 23 patients (14 male) required urgent surgery from the orthopedic or trauma, general surgery, burn, plastic surgery, cardiac surgery, neurosurgery, vascular surgery, gastroenterology and gynecologic oncology divisions. SARS-CoV-2 RNA was detected in 20 of 332 (6%) patient and environmental samples collected: 4 of 24 (17%) patient samples, 5 of 60 (8%) floor samples, 1 of 54 (2%) air samples, 10 of 23 (43%) surgical instrument or equipment samples, 0 of 24 cautery filter samples and 0 of 143 (95% confidence interval 0–0.026) inner surface of mask samples.Interpretation:During the study period of November 2020 to May 2021, we found evidence of SARS-CoV-2 RNA in a small but important number of samples obtained in the surgical and obstetric operative environment. The finding of no detectable virus inside the masks worn by the health care teams would suggest a low risk of infection for health care workers using appropriate personal protective equipment.

SARS-CoV-2 Reverse Transcription-Polymerase Chain Reaction Positivity and Seroprevalence among Health Care Workers in a Referral Cancer Institute: A Cross-sectional Study

BACKGROUND: During the ongoing coronavirus disease 2019 pandemic, healthcare workers (HCWs) are presumed to be at increased risk of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), transmitting the infection to vulnerable patients if they are not timeously isolated. AIM: This study aimed to determine the point prevalence of SARS-CoV-2 infection in a cohort of HCWs providing oncology services. METHODS AND RESULTS: HCWs in a large referral cancer hospital in Egypt were tested using real-time reverse transcription-polymerase chain reaction (RT-PCR) on nasopharyngeal swabs, and immunochromatography-based rapid serological test (RST). Clinical and epidemiological data were collected. In 2020, 999 HCWs were screened, of whom 86 tested positive for SARS-CoV-2 by RT-PCR (8.6%) and 127 subjects were seropositive for antibodies against SARS-CoV-2 by RST (12.8%). Immunoglobulin M seroprevalence demonstrated considerable concordance with RT-PCR positivity (sensitivity 82.14% and specificity 96.71%). Most HCWs (&gt;95%) reported adherence to personal protective equipment. Patient transporters/cleaner were the group with the highest frequency of positive RT-PCR (19%) whereas laboratory and radiology technicians displayed the lowest frequency. Fever, dry cough, rhinorrhea, shortness of breath, fatigue and diarrhea were significantly associated with RT-PCR positivity, with increased likelihood of being positive with the presence of five or six simultaneous symptoms. CONCLUSIONS: The point prevalence of SARS-CoV-2 infection in screened HCWs is 8.6% by RT-PCR and seroprevalence is 12.8% by RST. Strict measures should be implemented to minimize transmission within healthcare settings and to the community. Our data support the importance of HCWs screening for SARS-CoV-2, taking in account the significant proportion of asymptomatic carriers.

Evaluation of human coronavirus OC43 and SARS-COV-2 in children with respiratory tract infection during the COVID-19 pandemic.

The coronavirus disease 2019 (COVID‐19) pandemic is an overwhelming crisis across the world. Human Coronavirus OC43 (HCoV‐OC43) is a Betacoronavirus responsible mostly for mild respiratory symptoms. Since the presentations of HCoV‐OC43 and severe acute respiratory syndrome coronavirus 2 (SARS‐COV‐2) are believed to resemble a lot, the aim of this study was to evaluate the frequency and characteristics of HCoV‐OC43 in the current pandemic and the rate of coinfection for the two viruses. One hundred and seventeen patients referred to Children's Medical Center, Tehran, Iran with respiratory symptoms were included. Real‐time reverse transcription‐polymerase chain reaction (RT‐PCR) methods were performed for the detection of HCoV‐OC43 and SARS‐COV‐2. Totally, 23 (20%) had a positive RT‐PCR for HCoV‐OC43 and 25 (21%) were positive for SARS‐COV‐2. Two patients (2%) had a positive PCR for both HCoV‐OC43 and SARS‐COV‐2. The two groups showed significant differences in having contact with family members with suspected or confirmed COVID‐19 (p = 0.017), fever (p = 0.02), edema (p = 0.036), vomiting (p < 0.001), abdominal complaints (p = 0.005), and myalgia (p = 0.02). The median level of lymphocyte count in patients with HCoV‐OC43 was significantly lower than patients with SARS‐COV‐2 infection (p = 0.039). The same frequency of SARS‐COV‐2 and HCoV‐OC43 was found in children with respiratory symptoms during the COVID‐19 pandemic. The rate of coinfection of SARS‐COV‐2 with HCoV‐OC43 in our study was 0.08. Further research into the cocirculation of endemic coronaviruses, such as HCoV‐OC43 and SARS‐CoV2, in different regions, is highly recommended. Attempts to determine the geographic distribution and recruit more flexible test panel designs are also highly recommended.

Prolonged viral shedding of SARS-CoV-2 in two immunocompromised patients, a case report

BackgroundThe duration of viable Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) shedding in immunocompromised patients is still unknown. This case report describes the duration of viable SARS-CoV-2 in two immunocompromised patients with completely different clinical courses and further addresses the immunological aspects.Case presentationsOropharyngeal swaps were collected continuously during hospitalization for two immunocompromised patients infected with SARS-CoV-2 and sent for analysis to real timereverse transcription polymerase chain reaction (RT-PCR), viral culture assessed by plaque assay and full genome sequencing. Blood samples for flow cytometry and further immunological analysis were taken once during admission. One patient was without symptoms of Coronavirus disease 2019 (COVID-19) whereas the other had severe respiratory symptoms requiring a stay at an intensive care unit (ICU) and treatment with remdesivir and dexamethasone. Despite their difference in clinical courses, they both continuously shed SARS-CoV-2 with high viral loads in culture. Both patients had undetectable anti SARS-CoV-2 IgG levels about 2 weeks after the first positive real time RT-PCR test of SARS-CoV-2, marked expansions of virus reactive CD8+ T cells but cellular markers indicative of attenuated humoral immunity.ConclusionsOur case illustrates the importance of distinguishing isolation guidelines for patients infected with SARS-CoV-2 according to their immunological status. Furthermore, it demonstrates the need for immune markers relating to viral shedding in immunocompromised patients.

Suspected COVID-19 Reinfections at a Tertiary Care Center, Iowa 2020

Background: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 RNA can be detected by real-time reverse-transcription polymerase chain reaction (RT-PCR) for several weeks after infection. Discerning persistent RT-PCR positivity versus reinfection is challenging and the frequency of COVID-19 reinfections is unknown. We aimed to determine the frequency of clinically suspected reinfection in our center and confirm reinfection using viral whole-genome sequencing (WGS). Methods: The University of Iowa Hospitals and Clinics (UIHC) is an 811-bed academic medical center. Patients with respiratory complaints undergo COVID-19 RT-PCR using nasopharyngeal swabs. The RT-PCR (TaqPath COVID-19 Combo kit) uses 3 targets (ORF1ab, S gene, and N gene). We identified patients with previous laboratory-confirmed COVID-19 who sought care for new respiratory complaints and underwent a repeated SARS-CoV-2 test at least 45 days from their first positive test. We then identified patients with median RT-PCR cycle threshold (Ct) values. Results: During the study period, 13,603 patients had a SARS-CoV-2– positive RT-PCR. Of these, 296 (2.2%) had a clinical visit for new onset of symptoms and a repeated RT-PCR assay &gt;45 days from the first test. Moreover, 29 patients (9.8%) had a positive RT-PCR assay in the repeated testing. Ct values were available for samples from 25 patients; 7 (28%) had Ct values. Conclusions: In patients with a recent history of COVID-19 infection, repeated testing for respiratory symptoms was infrequent. Some had a SARS-CoV-2–positive RT-PCR assay on repeated testing, but only 1 in 4 had Ct values suggestive of a reinfection. We confirmed 1 case of reinfection using WGS.Funding: NoDisclosures: None

Factors Associated with False Negative and False Positive RT-PCR Test Results for COVID-19 Detection

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread rapidly and developed the current pandemic and the stressful lifestyle in addition with extreme pressure on people was the consequence of its increasing mortality rate. Since COVID-19 is highly infectious, it is crucial to diagnose the disease timely and initiate preventive measures to control the epidemic. Therefore, the need for accurate detection of this virus has been increased dramatically. Real-Time reverse-transcription Polymerase Chain Reaction (RT-PCR) tests are considered a gold standard to detect SARS-CoV-2 RNA. Besides, the recent pandemic has posed the most serious challenge in PCR applications to date. Although RT-PCR has great accuracy, some factors can reduce the efficiency of this test. Time of testing and type of sample are typical elements that may cause false negative results. Furthermore, false positive cases would be the result of contamination and unoptimized primers. In this paper, the relevant factors creating false positive and false negative results have been investigated in depth to increase the awareness of clinicians.

Evaluation of a rapid diagnostic test for detection of SARS-CoV-2 antigen in nasopharyngeal swabs

Background and aims: Rapid and accurate diagnosis is essential to limit the spread of SARS-CoV-2 and for patient’s management. Currently, real-time reverse transcription polymerase chain reaction (RT-PCR) is the recommended laboratory test to detect SARS-CoV-2. However, the requirement of special instruments and skilled personnel have limited the use of this technique. Recently, several rapid antigen detection tests have been developed and used as frontline. The aim of this work was to assess the performances of STANDARD F COVID-19 Ag FIA Kit, a rapid fluorescence immunoassay for the detection of SARS-CoV-2 nucleoprotein antigens, in comparison to RT-PCR.Materials and methods: Twenty-three nasopharyngeal swabs were collected and tested. Results: Among the 20 positive RT-PCR samples, 9 were detected by the immunofluorescence assay, reporting an overall sensitivity of 45%. The sensitivity increased to 64% in the case of a high viral load, where all three target genes, RdRp, N, and E, were detected by RT-PCR. Conclusions: A better antigen detection rate is associated with low Cycle threshold values which are inversely related to the viral load. STANDARD F COVID-19 Ag test cannot be considered as the frontline assay for COVID-19 diagnosis, but it might be used in association with clinical signs of patients to reduce the number of RT-PCR testing.

Sinonasal manifestations and dynamic profile of RT-PCR results for SARS-CoV-2 in COVID-19 patients.

Sinonasal symptoms were usually reported to appear initially, yielding the symptoms important for the early detection of coronavirus disease 2019 (COVID-19). This study was conducted retrospectively to investigate the detailed sinonasal manifestations and dynamic profile of real-time reverse transcription polymerase chain reaction (RT-PCR) results for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in COVID-19 patients longitudinally. This retrospective study included 11 consecutive patients. The prevalence, timing and severity of sinonasal manifestations were analyzed. Oropharyngeal, nasal, sputum and stool specimens were collected to detect RT-PCR for SARS-CoV-2 over COVID-19 period. Among the 11 patients, 6 (54.5%) were female, and the median age was 51 (IQR, 36-62) years. Seven patients (63.6%) experienced sinonasal symptoms, with 6 (54.5%) exhibiting sinonasal symptoms on the onset day. Seven patients (63.6%) demonstrated nasal obstruction, 5 (45.5%) had rhinorrhea, and 4 (36.4%) exhibited olfactory dysfunction. All six patients with sinonasal symptoms on the onset day had non-severe infections. Most patients (85.7%) with sinonasal symptoms had non-severe infections. Sinonasal symptoms commonly appeared early. The positive RT-PCR rate for SARS-CoV-2 in various specimens was highest in the first week (73.3%), then gradually decreased over the disease course, but 3 patients (27.3%) had experienced a long-lasting fluctuated positive RT-PCR results since 29 days of illness in both groups, especially for two patients with airway comorbidities. Sinonasal symptoms were more prevalent in patients with mild or moderate COVID-19 and usually appeared early. In addition, regular nucleic acid testing for SARS-CoV-2 should be considered for COVID-19 patients with certain airway comorbidities.

Arterial abnormalities identified in kidneys transplanted into children during the COVID-19 pandemic.

Graft artery stenosis can have a significant short- and long-term negative impact on renal graft function. From the beginning of the COVID-19 pandemic, we noticed an unusual number of graft arterial anomalies following kidney transplant (KTx) in children. Nine children received a KTx at our center between February and July 2020, eight boys and one girl, of median age of 10years. Seven presented Doppler features suggesting arterial stenosis, with an unusual extensive pattern. For comparison, over the previous 5-year period, persistent spectral Doppler arterial anomalies (focal anastomotic stenoses) following KTx were seen in 5% of children at our center. We retrospectively evidenced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in five of seven children with arterial stenosis. The remaining two patients had received a graft from a deceased adolescent donor with a positive serology at D0. These data led us to suspect immune postviral graft vasculitis, triggered by SARS-CoV-2. Because the diagnosis of COVID-19 is challenging in children, we recommend pretransplant monitoring of graft recipients and their parents by monthly RT-PCR and serology. We suggest balancing the risk of postviral graft vasculitis against the risk of prolonged dialysis when considering transplantation in a child during the pandemic.

Yeni Koronavirüs Hastalığının (Covid-19) Klinik, Laboratuvar ve Radyolojik Sonuçlarının İncelenmesi

Covid-19, which emerged in China in December 2019 and spread to the whole world in a short time, has been a serious public health problem threatening humanity. In this study, we aimed to reveal demographic, clinical, laboratory and radiological features of patients diagnosed with Covid-19. The study is a retrospective cross-sectional study consisting of patients who were hospitalized in health institutions in Bolu, Turkey between 11.03.2020 and 19.04.2020 with a definitive or probable diagnosis of Covid-19. The number of patients in the study was 262. The mean age of the patients participating in the study was 57.39 ± 19.85, the youngest patient was 19 and the oldest was 94 years old. Of the patients, 40.1% was between the ages of 18-50, 59.9% were over 50 years old. 55.3% of the patients were women and 44.7% were men. Most common symptoms were fever (75.6%), cough (71.8%) and dyspnea (46.9%). Elevated CRP (in 71.3%), elevated LDH (in 56.9%), elevated D-DIMER (in 56.4%) and lymphopenia (in 30.5) were most detected laboratory abnormalities. The result of the real-time reverse-transcription polymerase chain reaction (RT-PCR) test was positive in 35.5% of 262 patients. 88.5% of the patients had chest CT findings compatible with Covid-19. Additionally, 24% had both positive RT-PCR results and CT findings compatible with Covid-19. Expected findings were found to be in older patients more than younger ones. We suggest that clinical features, laboratory abnormalities and radiological findings can be used to provide an early diagnosis and treatment of Covid-19.

Structured reporting in portable chest radiographs: An essential tool in the diagnosis of COVID-19

PurposeTo date, the majority of chest imaging studies in COVID-19 pneumonia have focused on CT. Evidence for the utility of chest radiographs (CXRs) in this population is less robust. Our objectives were to develop a systematic approach for reporting likelihood of COVID-19 pneumonia on CXRs, to measure the interobserver variability of this approach and to evaluate the diagnostic performance of CXRs compared to real-time reverse transcription polymerase chain reaction (RT-PCR). MethodRetrospective review of patients suspected of having COVID-19 pneumonia who attended our emergency department and underwent both CXR and a RT-PCR were included. Two radiologists reviewed the CXRs, blind to the RT-PCR, and classified them according to a structured reporting template with five categories (Characteristic, High Suspicion, Indeterminate, Unlikely and Normal) which we devised. For analysis of diagnostic accuracy, Characteristic and High Suspicion CXRs were considered positive and the remaining categories negative. Concordance between the two assessors was also measured. ResultsOf 582 patients (51 +/- 20 years), 143/582 (24.6 %) had a positive RT-PCR. The absolute concordance between the two assessors was 71.1 % (414/582) with a Fleiss-Cohen-weighted Cohen’s κ of 0.81 (95 % confidence interval, 0.78-0.85). A patient with a positive CXR had an 88 % (95 % CI 80–96 %) probability of having a positive RT-PCR during a period of high incidence, early in the COVID-19 pandemic. ConclusionUsing a structured approach, a positive CXR had a high likelihood of predicting a positive RT-PCR, with good interrater reliability. CXRs can be useful in identifying new cases of COVID-19.

Diagnostic performance of the BinaxNow Influenza A&B rapid antigen test in ED patients

ObjectiveThe objective of this study is to evaluate the diagnostic performance of the BinaxNow Influenza A&B rapid antigen test (RAT) in emergency department (ED) patients. MethodsWe prospectively enrolled a systematic sample of ED patients older than 6 months with acute respiratory symptoms or nonlocalizing fever during 3 consecutive influenza seasons (2008-2011). Nasal and throat swabs collected by research personnel were tested for influenza by real-time reverse transcription–polymerase chain reaction (RT-PCR). Clinicians independently ordered RATs during clinical care; these specimens were collected by clinical staff and tested for influenza using the BinaxNow RAT. Patients with both a research RT-PCR and clinical RAT were included in the study. Rapid antigen test diagnostic performance was evaluated using RT-PCR as a criterion standard, with preplanned, stratified analysis for subject age, duration of symptoms, influenza subtype, and polymerase chain reaction cycle threshold, which provides a semiquantitative estimate of viral load. ResultsOf 561 subjects enrolled, 131 (23.4%) had a positive RT-PCR, and 37 (6.6%) had a positive RAT. Overall, RAT performance included sensitivity of 24.4% (95% confidence interval [CI], 17.5%-32.9%), specificity of 98.8% (95% CI, 97.1%-99.6%), positive predictive value of 86.5% (95% CI, 70.4%-94.9%), negative predictive value of 81.1% (95% CI, 77.4%-84.3%). Rapid antigen test sensitivities were low for all categories of subject age, symptom duration, influenza subtype, and cycle threshold. ConclusionThe BinaxNow RAT demonstrated high specificity and poor sensitivity in ED patients selected by treating clinicians for influenza testing. A negative RAT is a poor predictor for the absence of influenza in the ED and should not be used as a criterion to withhold antiviral medications.

Development and Validation of RT-PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples

SummaryTwo tests were developed that allow the detection and genotyping of infectious bronchitis virus (IBV) and other closely related gammacoronaviruses. The first test employs a one‐step, reverse transcription‐polymerase chain reaction (RT‐PCR) assay in which the amplification is monitored in real time using a TaqMan® probe. This real‐time RT‐PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls’ eggs. A total of 323 field samples were tested; 176 samples were positive using the real‐time RT‐PCR method, but only three were positive by virus isolation. Sequencing was used to confirm the positive real‐time RT‐PCR results for a subset of samples. The test is suitable for swabs and post‐mortem samples and has been shown to be highly sensitive and specific. The second test, a genotyping method, was developed for identification of the strain of IBV present in field samples based on nucleotide variations within the gene encoding the S1 subunit of the surface spike (S) glycoprotein. This method was developed to provide a tool to inform vaccination decisions and for ongoing surveillance to detect new and emerging strains of IBV within the UK. The performance of the test was evaluated using laboratory isolates of IBV and field samples. Both tests are suitable for use in a high‐throughput diagnostic laboratory.