Real-time Reverse Transcription-polymerase Chain Reaction Test Research Articles

Performance of CO-RADS in the diagnosis of COVID-19 in hemodialysis patients.

Different data systems have been used to reach a common decision in the interpretation of chest computed tomography (CT) scans for the detection of COVID-19 infection. The aim of our study was to determine the usefulness of the COVID-19 Reporting and Data System (CO-RADS) for COVID-19 in patients undergoing hemodialysis. We included 90 hemodialysis patients who underwent chest CT and had samples available for real-time reverse transcription-polymerase chain reaction (RT-PCR). The files of the patients were retrospectively reviewed and the data were recorded. Image interpretation and CO-RADS staging were performed retrospectively by two radiologists experienced in COVID-19 patients, blinded to the RT-PCR results. The RT-PCR results were then compared with the CO-RADS stages obtained. The success of CO-RADS in diagnosing COVID-19 was evaluated according to its prediction of a positive RT-PCR result. At the same time, the relationship between CO-RADS stages and prognosis was also evaluated. Patients were divided into two groups according to the RT-PCR results, of which 38 (42.2%) had positive results. Validity tests of CO-RADS were performed according to the RT-PCR test. While 71.1% of patients with CO-RADS ≥4 were RT-PCR (+), 13.2% of patients with CO-RADS ≤2 were RT-PCR (+) (p < 0.001). CO-RADS ≥4 detected COVID-19 with 71.1% sensitivity and 51.9% specificity. ROC analysis confirmed the diagnostic performance of CO-RADS for predicting RT-PCR positivity with AUC = 0.73 (95% CI: 0.63-0.84). The relationship between CO-RADS stages and mortality was not significant (p = 0.21). CO-RADS is moderately sensitive and poorly specific for the diagnosis of COVID-19 in hemodialysis patients. In these patients, CO-RADS would be more useful to exclude other infections than to diagnose COVID-19.

Clinical performance of the ImmuneMed Dengue NS1 Ag Rapid I test for the diagnosis of dengue fever: a diagnostic accuracy study

Background: Dengue virus (DENV) is transmitted by mosquitoes and is becoming a global threat owing to an increase in the number of cases and mortality, especially in low- and middle-income tropical countries. Rapid and easy-to-use diagnostic tests are required to differentiate dengue fever from other febrile illnesses. Methods: We evaluated the clinical performance of the ImmuneMed Dengue NS1 Ag Rapid I test (ImmuneMed, Inc.) using positive and negative sera collected from patients with confirmed DENV infection and healthy individuals, respectively. The AccuPower® ZIKV (DENV, CHIKV) multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assay (Bioneer) was used as the reference standard to confirm DENV infection. Results: One hundred DENV-positive and 161 DENV-negative samples were evaluated. Overall, the sensitivity and specificity were 100% (95% confidence interval [CI], 96%–100%) and 100% (95% CI, 98%–100%), respectively. The sensitivity and specificity were 100% for both DENV-1 and DENV- 2. The sensitivity was the same (100%) for sera collected &lt; 3 days and ≥ 3 days from symptom onset. The performance of the ImmuneMed Dengue NS1 Ag Rapid I and realtime RT-PCR tests showed strong overall agreement. Conclusion: The ImmuneMed Dengue NS1 Ag Rapid I test was highly specific for DENV and as sensitive as RT-PCR. These findings suggest that the ImmuneMed Dengue NS1 Ag Rapid I test may be a useful point-of-care test for dengue fever.

Comparative study between gold standard real-time RT-PCR assay and rapid antigen test for detection of COVID-19 in Sylhet CMH

Background: The notorious pandemic coronavirus disease 2019 (COVID-19) has been spread all over the world. Its third pandemic wave has been completed and now a fourth wave is running over many countries. Almost 60 million people have been infected and more than 5.7 million people have died. Till now almost 1.2 million people have been infected and about 30000 people have died in Bangladesh from Covid-19. It has not only taken away human lives but also has put a tremendous impact on our society and economy. So early detection of this virus and isolating the patients have a significant role to control the disease. Henceforth there is an urgent need for simple, accurate and rapid identifications of C0VID -19. Rapid antigen tests can provide timely results, which is of particular importance in a primary setting. So, Performance of the Rapid antigen detection test (RAT) should be evaluated and compared with gold standard real-time reverse transcription-polymerase chain reaction (RT-PCR) test for diagnosis of COVID-19. Methods: Specimens were collected from both naso and oropharyngeal region from 1000 patients who reported to the flu centre in CMH Sylhet with the complaints of fever, cough &amp; headache for detection of COVID virus-2 RNA by rapid antigen (RAT) and RT-PCR test. We used real time RT-PCR kit (Sansure, Biotech china, gene RdRP &amp; N) and COVID-19 Ag Kit (Wondfo, Republic of China) for detection of COVID-19 RNA. Results: Out of 1000 samples 158 were positive and 842 were negative by real-time RT-PCR assay where 154 samples were positive, and 846 cases were negative by rapid antigen test for severe acute respiratory syndrome (SARS) CoV-2. The duration from the onset of symptoms to laboratory test in all suspected cases ranged from 0 to 02 days (with a median of 01 days). The rapid SARS-CoV-2 antigen detection tests sensitivity and specificity were 97.29% (95% CI, 90.06–99.89%) and 97.94% (95% CI, 97.26–98.57%), respectively. Seven samples were found negative in RAT but were found positive in RT-PCR, other three samples were found positive in RAT while they were found negative in RT-PCR. Conclusions: It is observed that most rapid antigen tests for COVID-19 are significantly comparable with RT-PCR tests and had enough sensitivity and specificity for 158 individuals, infected with severe acute respiratory syndrome-CoV-2.

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.

Diagnosis of COVID-19 obtained by rapid antigen test and reverse transcription–polymerase chain reaction in a medical college in Eastern India-a record-based observational descriptive study

Background: In December 2019 in Wuhan, China, a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared. Gradually, the virus started spreading around the world, which was life-threatening. Aims and Objectives: The study’s objective was to find out the positivity rate of infection, the category of patients included in the study, the percentage of positive and negative cases, comparison of rapid antigen detection in relation to real-time reverse transcription–polymerase chain reaction (RT-PCR) test, and rapid antigen detection test’s sensitivity and specificity. Materials and Methods: Eight hundred sixty-five patients’ samples and nasopharyngeal swabs were collected within 3 months as routine samples. Two hundred thirty-two samples were compared by both rapid antigen test (RAT) and RT-PCR. To rule out false negatives, those who tested negative for COVID-19 using a RAT underwent testing by RT-PCR. To rule out false positives, a small number of patients who tested positive for COVID-19 by RAT also underwent validation by RT-PCR test. Results: Two hundred thirty-two samples were obtained for rapid antigen detection, then RT-PCR testing. Both the results were compared. According to the findings, the positivity rate of COVID-19 infection was 0.86%. Two patients (0.86%) tested positive (either by one or both methods) and the number of patients who tested negative was 230 (99.14%). RAT sensitivity and specificity were 50% and 100%, respectively, compared to gold standard RT-PCR. The positive predictive value was 100% and the negative predictive value was 99%. Conclusion: We conclude that antigen detection methods are less sensitive than real-time RT-PCR but they can be used for COVID-19 mass screening and can be used as a quick diagnostic tool in remote locations without molecular testing facilities.

Efficacy of SARS-CoV-2 detection from used surgical masks compared with standard detection method

The real-time reverse transcription-polymerase chain reaction (RT-PCR) test is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. Proper specimen collection and obtaining a sufficient specimen are the most essential steps for laboratory diagnosis. The nasopharyngeal (NP) swab is recommended as the reference collection method. However, NP swab collection is invasive and uncomfortable for patients and poses some risk to healthcare workers. This study aimed to compare the efficacy of SARS-CoV-2 RNA detection from surgical masks with the NP swab method using RT-PCR testing. Of 269 patients, RT-PCR RNA from NP swabs was detected among 82 patients (30.5%) and was undetected among 187 patients (69.5%). All patients were tested for SARS-CoV-2 RNA from surgical masks. SARS-CoV-2 RNA was detected in 25/82 (30.5%) surgical mask filters, while undetected among 57 (69.5%). For the surgical mask with an average use time of 7.05 h, the sensitivity was 30.5%, the specificity was 100.0%, with positive predictive value of 100.0% and negative predictive value of 76.2%. Therefore, surgical masks could be an alternative non-invasive specimen source for SARS-CoV-2 RT-PCR testing. The results of our study suggest that the test could be employed after wearing surgical masks for at least 8-12 h, with increased sensitivity when used for more than 12 h.

COVID-19 scent dog research highlights and synthesis during the pandemic of December 2019-April 2023.

This review was undertaken to provide information concerning the advancement of research in the area of COVID-19 screening and testing during the worldwide pandemic from December 2019 through April 2023. In this review, we have examined the safety, effectiveness, and practicality of utilizing trained scent dogs in clinical and public situations for COVID-19 screening. Specifically, results of 29 trained scent dog screening peer-reviewed studies were compared with results of real-time reverse-transcription polymerase chain reaction (RT-PCR) and rapid antigen (RAG) COVID-19 testing methods. The review aims to systematically evaluate the strengths and weaknesses of utilizing trained scent dogs in COVID-19 screening. At the time of submission of our earlier review paper in August 2021, we found only four peer-reviewed COVID-19 scent dog papers: three clinical research studies and one preprint perspective paper. In March and April 2023, the first author conducted new literature searches of the MEDLINE/PubMed, Google Scholar, and Cochrane Library websites. Again, the keyword phrases utilized for the searches included "COVID detection dogs," "COVID scent dogs," and "COVID sniffer dogs." The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2020 Checklist was followed to ensure that our review adhered to evidence-based guidelines for reporting. Utilizing the results of the reviewed papers, we compiled statistics to intercompare and summarize basic information concerning the scent dogs and their training, the populations of the study participants, the types of sampling methods, the comparative tests utilized, and the effectiveness of the scent dog screening. A total of 8,043 references were identified through our literature search. After removal of duplicates, there were 7,843 references that were screened. Of these, 100 were considered for full-text eligibility, 43 were included for qualitative synthesis, and 29 were utilized for quantitative analysis. The most relevant peer-reviewed COVID-19 scent dog references were identified and categorized. Utilizing all of the scent dog results provided for this review, we found that 92.3 % of the studies reached sensitivities exceeding 80 and 32.0 % of the studies exceeding specificities of 97 %. However, 84.0 % of the studies reported specificities above 90 %. Highlights demonstrating the effectiveness of the scent dogs include: (1) samples of breath, saliva, trachea-bronchial secretions and urine as well as face masks and articles of clothing can be utilized; (2) trained COVID-19 scent dogs can detect presymptomatic and asymptomatic patients; (3) scent dogs can detect new SARS-CoV-2 variants and Long COVID-19; and (4) scent dogs can differentiate SARS-CoV-2 infections from infections with other novel respiratory viruses. The effectiveness of the trained scent dog method is comparable to or in some cases superior to the real-time RT-PCR test and the RAG test. Trained scent dogs can be effectively utilized to provide quick (seconds to minutes), nonintrusive, and accurate results in public settings and thus reduce the spread of the COVID-19 virus or other viruses. Finally, scent dog research as described in this paper can serve to increase the medical community's and public's knowledge and acceptance of medical scent dogs as major contributors to global efforts to fight diseases.

PERFORMANCE OF RAPID ANTIGEN TEST IN COMPARISON TO REAL-TIME RT-PCR IN DIAGNOSIS OF COVID-19 INFECTION: A SHORT STUDY

Objective: The global pandemic of Coronavirus Disease 2019 (COVID-19) is still spreading. Because of this, it is urgently necessary to develop quick, easy, and accurate assays to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. For the purpose of diagnosing COVID-19 cases, the quick SARS-CoV-2 antigen detection test’s performance attributes should be assessed and contrasted with the gold standard real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. Methods: A retrospective analysis was done during January to May, 2022 at IPGME&amp;R and SSKM Hospital, Kolkata, India. 2842 paired samples were taken from all patients reporting to the hospital for Rapid Antigen Test (RAT) and RT-PCR. The sensitivity and specificity were calculated to evaluate the performance of the RAT. Results: Of 2842 samples, 229 (8%) were positive, and 2613 (92%) were negative for SARS-CoV-2 RNA by real-time RT-PCR assay. The rapid SARS-CoV-2 antigen detection test’s sensitivity and specificity were 77.29% (177 out of 229) and 99.54% (2601 out of 2613), respectively. Positive predictive value was 93.65% and negative predictive value was 93% with the Ct value ≤35 of real-time RT-PCR result. Conclusion: RAT-positive samples are also positive by real-time RT-PCR test though RAT-negative patient with symptom, should further test for real-time RT-PCR as sensitivity is bit low particularly in symptomatic patient respect to real-time RT-PCR result. Hence, we can conclude that specificity- and sensitivity-wise real-time RT-PCR method is best, but during pandemic/outbreak situation, RAT is good alternative for fast screening and point-of-care test of COVID-19 detection.

Association of Serum Ferritin With Severity of Disease in Real-Time Reverse Transcription-Polymerase Chain Reaction Negative COVID-19 Patients.

Coronavirus disease 2019 (COVID-19) is still causing disastrous effects in various parts of the world through recurring waves. Real-time reverse transcription polymerase chain reaction (RT-PCR)-negative COVID-19 is particularly challenging as these patients are less likely to receive treatment and more likely to progress to severe disease. Thus, it is imperative to find markers that can predict the severity of disease at an early stage. The objective of the present study was to analyze the association of ferritin levels with severe disease in RT-PCR-negative COVID-19 patients. A prospective cross-sectional analytical study was conducted in adults with COVID-19 pneumonia with a negative RT-PCR test from October 2020 to September 2021. Hematologic, biochemical, and inflammatory parameters were investigated within 24 h of hospitalization. Demographic, clinical, and laboratory findings were compared between patients with and without severe disease. A total of 220 patients were included. The mean age of the study participants was 47.3 ± 14.2 years, and 55.5% (n=122) were male. C-reactive protein, D-dimer, and ferritin levels were significantly higher in patients with severe disease (p<0.01). Receiver operating characteristic curve analyses were performed, and ferritin was found as significant predictor of severe disease (area under the curve=0.642, p<0.001). Early analysis of ferritin can predict the severity of disease in COVID-19 patients, irrespective of the RT-PCR status.

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 of COVID-19 Infection With Incident Diabetes

SARS-CoV-2 infection may lead to acute and chronic sequelae. Emerging evidence suggests a higher risk of diabetes after infection, but population-based evidence is still sparse. To evaluate the association between COVID-19 infection, including severity of infection, and risk of diabetes. This population-based cohort study was conducted in British Columbia, Canada, from January 1, 2020, to December 31, 2021, using the British Columbia COVID-19 Cohort, a surveillance platform that integrates COVID-19 data with population-based registries and administrative data sets. Individuals tested for SARS-CoV-2 by real-time reverse transcription-polymerase chain reaction (RT-PCR) were included. Those who tested positive for SARS-CoV-2 (ie, those who were exposed) were matched on sex, age, and collection date of RT-PCR test at a 1:4 ratio to those who tested negative (ie, those who were unexposed). Analysis was conducted January 14, 2022, to January 19, 2023. SARS-CoV-2 infection. The primary outcome was incident diabetes (insulin dependent or not insulin dependent) identified more than 30 days after the specimen collection date for the SARS-CoV-2 test with a validated algorithm based on medical visits, hospitalization records, chronic disease registry, and prescription drugs for diabetes management. Multivariable Cox proportional hazard modeling was performed to evaluate the association between SARS-CoV-2 infection and diabetes risk. Stratified analyses were performed to assess the interaction of SARS-CoV-2 infection with diabetes risk by sex, age, and vaccination status. Among 629 935 individuals (median [IQR] age, 32 [25.0-42.0] years; 322 565 females [51.2%]) tested for SARS-CoV-2 in the analytic sample, 125 987 individuals were exposed and 503 948 individuals were unexposed. During the median (IQR) follow-up of 257 (102-356) days, events of incident diabetes were observed among 608 individuals who were exposed (0.5%) and 1864 individuals who were not exposed (0.4%). The incident diabetes rate per 100 000 person-years was significantly higher in the exposed vs nonexposed group (672.2 incidents; 95% CI, 618.7-725.6 incidents vs 508.7 incidents; 95% CI, 485.6-531.8 incidents; P < .001). The risk of incident diabetes was also higher in the exposed group (hazard ratio [HR], 1.17; 95% CI, 1.06-1.28) and among males (adjusted HR, 1.22; 95% CI, 1.06-1.40). The risk of diabetes was higher among people with severe disease vs those without COVID-19, including individuals admitted to the intensive care unit (HR, 3.29; 95% CI, 1.98-5.48) or hospital (HR, 2.42; 95% CI, 1.87-3.15). The fraction of incident diabetes cases attributable to SARS-CoV-2 infection was 3.41% (95% CI, 1.20%-5.61%) overall and 4.75% (95% CI, 1.30%-8.20%) among males. In this cohort study, SARS-CoV-2 infection was associated with a higher risk of diabetes and may have contributed to a 3% to 5% excess burden of diabetes at a population level.

High positive rate after consecutive negative tests of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a global public health event since 2019. Real-time reverse transcription polymerase chain reaction (RT-PCR) assays of upper respiratory tract specimens were used as the most common method for confirmation of SARS-CoV-2. Patients diagnosed with coronavirus disease 2019 and hospitalized in Cancer Center of Wuhan Union Hospital were retrospectively enrolled. Epidemiological, clinical, and laboratory records were analyzed with highlights on the pattern of results of repeated RT-PCR tests. Nine hundred eighty-four patients admitted to hospital between February 13, 2020 to March 10, 2020 were enrolled. The median age was 62.0 years (interquartile range 49.0-68.0) and 44.5% was male. Three thousand-three hundred eleven specimens were collected for RT-PCR tests with a median of 3 tests (interquartile range 2.0-4.0) per patient. Three hundred sixty-two (36.8%) patients showed positive records from repeated RT-PCR tests. For the 362 confirmed patients, 147 cases received further RT-PCR tests after 2 consecutive negative records of SARS-CoV-2 and 38 (26%) of them obtained a positive result. Ten (23%) of 43 patients showed positive results after 3 consecutive negative tests and 4 (24%) of 17 patients were positive after 4 negative tests. Consecutive negative RT-PCR tests with respiratory specimens could not guarantee a viral clearance.

Performance of a SARS-CoV-2 RT-PCR Assay with Non-Traditional Specimen Types

During the first two years of the coronavirus disease 2019 (COVID-19) pandemic, nasopharyngeal (NP) specimens were the gold standard for clinical diagnostic testing. As information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the pandemic continued to be shared, it was clear that the virus could be detected in other specimen types during an active infection. The University of Louisville Infectious Diseases Laboratory accepted non-traditional specimen types, most without a paired, positive NP result, for research purposes only to support local epidemiology efforts. A real-time reverse transcription-polymerase chain reaction (RT-PCR) assay originally validated for NP specimens was used for non-traditional specimen types using a variety of specimen preparation methods. Limit of detection (LOD) studies allowed for direct comparison between NP, sputum, and breast milk specimen types. The primary aim of the study was to determine whether SARS-CoV-2 RNA could be detected in different human specimen types. The results showed that the non-traditional specimens were not inherently inhibitory since SARS-CoV-2 RNA was detected in 36 (14.5%) out of 249 non-traditional specimens, and the limit of detection for SARS-CoV-2 in breast milk and sputum was the same as for NP specimens. SARS-CoV-2 was not detected in 15 breast milk specimens from mothers with positive SARS-CoV-2 NP results. In addition, a direct comparison study showed that NP specimens performed better than paired nasal specimens. In conclusion, by analyzing real-time RT-PCR test results for these non-traditional specimen types, two benefits were realized. Health care providers gained additional epidemiologic information (since information was not to be used for managing or treating patients), and the laboratory gathered important information about specimen types for which complete method validation studies could be pursued in the future.

Adaptation of the Sars-Cov-2 Screening and Testing Strategy in Pregnant Women during the Second Wave of the Covid-19 Pandemic

Background: Approaches to SARS-CoV-2 screening and testing of pregnant women vary among different obstetrics units and are usually tailored to the current epidemiological situation. Dramatic increase in the SARS-CoV-2 incidence in autumn 2020 prompted our hospital to adapt its protocol for SARS-CoV-2 screening and testing of pregnant women at admission. Methods: To assess the usefulness of the updated SARS-CoV-2 screen-and-test approach, we retrospectively reviewed the Ljubljana Maternity Hospital database and searched for pregnant women admitted to the hospital between 27 October 2020 and 28 February 2021. SARS-CoV-2 real-time reverse-transcription polymerase chain reaction (RT-PCR) and Rapid Antigen Test (RAT) results were retrieved from the database. Results: During the four-month period analysed, 2,552 hospitalizations and 5,516 outpatient visits occurred at our hospital. Records for nasopharyngeal swab testing using SARS-CoV-2 RAT were available for 1,836 questionnaire screen-negative women admitted for delivery, planned procedure or hospitalization, of which 26 (1.4%) tested RAT positive. Subsequent RT-PCR testing identified presence of SARS-CoV-2 RNA in 20/26 (76.9%) and RAT false-positive results in 6/26 (23.1%) cases. Conclusions: During the peak of the COVID-19 pandemic in Slovenia, the updated screen-and-test approach using RAT with subsequent RT-PCR confirmation identified 1.1% of screen-negative pregnant women to be infected with SARS-CoV-2 at admission. Our experience may help efficient adaptation of screen-and-test approaches in obstetric units facing a surge in SARS-CoV-2 cases.

The Relationship Between Population-Level SARS-CoV-2 Cycle Threshold Values and Trend of COVID-19 Infection: Longitudinal Study.

The distribution of population-level real-time reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold (Ct) values as a proxy of viral load may be a useful indicator for predicting COVID-19 dynamics. The aim of this study was to determine the relationship between the daily trend of average Ct values and COVID-19 dynamics, calculated as the daily number of hospitalized patients with COVID-19, daily number of new positive tests, daily number of COVID-19 deaths, and number of hospitalized patients with COVID-19 by age. We further sought to determine the lag between these data series. The samples included in this study were collected from March 21, 2021, to December 1, 2021. Daily Ct values of all patients who were referred to the Molecular Diagnostic Laboratory of Iran University of Medical Sciences in Tehran, Iran, for RT-PCR tests were recorded. The daily number of positive tests and the number of hospitalized patients by age group were extracted from the COVID-19 patient information registration system in Tehran province, Iran. An autoregressive integrated moving average (ARIMA) model was constructed for the time series of variables. Cross-correlation analysis was then performed to determine the best lag and correlations between the average daily Ct value and other COVID-19 dynamics-related variables. Finally, the best-selected lag of Ct identified through cross-correlation was incorporated as a covariate into the autoregressive integrated moving average with exogenous variables (ARIMAX) model to calculate the coefficients. Daily average Ct values showed a significant negative correlation (23-day time delay) with the daily number of newly hospitalized patients (P=.02), 30-day time delay with the daily number of new positive tests (P=.02), and daily number of COVID-19 deaths (P=.02). The daily average Ct value with a 30-day delay could impact the daily number of positive tests for COVID-19 (β=-16.87, P<.001) and the daily number of deaths from COVID-19 (β=-1.52, P=.03). There was a significant association between Ct lag (23 days) and the number of COVID-19 hospitalizations (β=-24.12, P=.005). Cross-correlation analysis showed significant time delays in the average Ct values and daily hospitalized patients between 18-59 years (23-day time delay, P=.02) and in patients over 60 years old (23-day time delay, P<.001). No statistically significant relation was detected in the number of daily hospitalized patients under 5 years old (9-day time delay, P=.27) and aged 5-17 years (13-day time delay, P=.39). It is important for surveillance of COVID-19 to find a good indicator that can predict epidemic surges in the community. Our results suggest that the average daily Ct value with a 30-day delay can predict increases in the number of positive confirmed COVID-19 cases, which may be a useful indicator for the health system.

The effect of inflammatory markers on the CORADS degree and the effects of treatments on RT-PCR test results in COVID-19

&lt;b&gt;Objective:&lt;/b&gt; There is still no diagnosis method with high sensitivity and specificity for COVID-19. Patient complaints, real-time reverse transcription-polymerase chain reaction (RT-PCR), inflammatory markers, clinical prognosis, and the degree of involvement in the chest CT, if necessary are evaluated in an effort to make a diagnosis. Delays in diagnosis have led to a rapid spread of the disease. This study aims to evaluate the effectiveness of the inflammatory markers and to determine the follow-up process of the patients by assessing the impact of the treatments administered on RT-PCR test results.&lt;br /&gt; &lt;b&gt;Material and methods: &lt;/b&gt;Files of 150 patients monitored in the wards with suspected COVID-19 are analyzed retrospectively. Patients were selected among those who underwent laboratory tests, RT-PCR testing and Thoracic CT within the first 24 hours of admission. Patients were divided into 5 groups based on the severity of involvement in Thoracic CT. Inflammatory markers were compared among the groups. Impact of the administered treatments on follow-up RT-PCR test results was evaluated.&lt;br /&gt; &lt;b&gt;Results: &lt;/b&gt;Studied inflammatory markers were in normal ranges and similar across all CORADS groups. Only the C-Reactive Protein (CRP) and Ferritin levels were showing an increase in accordance with CORADS severity. Mean time to testing negative on RT-PCR was 10 days across all treatment groups. Times to testing negative among patients receiving other treatments were similar.&lt;br /&gt; &lt;b&gt;Conclusion: &lt;/b&gt;Among the inflammatory markers, CRP and Ferritin values are correlated with CORADS severity. Administered COVID-19 treatments have similar impact on RT-PCR test results.

Automated diagnosis of COVID-19 using radiological modalities and Artificial Intelligence functionalities: A retrospective study based on chest HRCT database

Background and Objective:The spread of coronavirus has been challenging for the healthcare system’s proper management and diagnosis during the rapid spread and control of the infection. Real-time reverse transcription-polymerase chain reaction (RT-PCR), though considered the standard testing measure, has low sensitivity and is time-consuming, which restricts the fast screening of individuals. Therefore, computer tomography (CT) is used to complement the traditional approaches and provide fast and effective screening over other diagnostic methods. This work aims to appraise the importance of chest CT findings of COVID-19 and post-COVID in the diagnosis and prognosis of infected patients and to explore the ways and means to integrate CT findings for the development of advanced Artificial Intelligence (AI) tool-based predictive diagnostic techniques. Methods:The retrospective study includes a 188 patient database with COVID-19 infection confirmed by RT-PCR testing, including post-COVID patients. Patients underwent chest high-resolution computer tomography (HRCT), where the images were evaluated for common COVID-19 findings and involvement of the lung and its lobes based on the coverage region. The radiological modalities analyzed in this study may help the researchers in generating a predictive model based on AI tools for further classification with a high degree of reliability. Results:Mild to moderate ground glass opacities (GGO) with or without consolidation, crazy paving patterns, and halo signs were common COVID-19 related findings. A CT score is assigned to every patient based on the severity of lung lobe involvement. Conclusion:Typical multifocal, bilateral, and peripheral distributions of GGO are the main characteristics related to COVID-19 pneumonia. Chest HRCT can be considered a standard method for timely and efficient assessment of disease progression and management severity. With its fusion with AI tools, chest HRCT can be used as a one-stop platform for radiological investigation and automated diagnosis system.

Sex Differences in the Relation between Comorbidities and Prognosis in Hospitalized Patients with COVID-19.

Purpose There is a lack of information of the difference in sex-aggregated prevalence of comorbid noncommunicable disease (NCD) in patients hospitalized with COVID-19 in Iran. This study aimed to evaluate sex differences in the relation between medical comorbidities and subsequent death in patients hospitalized with COVID-19. Methods All subsequently hospitalized patients with a diagnosis of moderate to severe COVID-19 since February 19th to June 14th, 2020, in Isfahan, Iran, were recruited in the ongoing I-CORE Registry. Real-time reverse-transcription polymerase chain reaction (RT-PCR) testing was done upon admission. Data on preexisting comorbid NCDs including hypertension, coronary heart disease (CHD), diabetes mellitus (DM), cancers, chronic renal disease (CRD), and chronic respiratory disease were collected through self-reported questionnaires. Results Overall, 12,620 individuals were enrolled in this registry of which 4,356 were positive for the COVID-19 RT-PCR test. In the whole population, in women, DM, hypertension, and CHD, and in men, DM, CHD, and hypertension were, respectively, the most frequent comorbidities. The frequency of at least one NCD did not differ between men and women, but a greater proportion of women had two or more NCDs. Increasing the number of comorbidities was associated with higher death frequency and mortality risk in the unadjusted model but remained no longer significant after adjustment for age. There was no statistically significant difference in this regard between men and women. Conclusion Overall, we found that DM, hypertension, and CHD were the most frequent comorbidities. Although comorbidities were more frequent among women, mortality risk did not significantly differ between men and women.

Monitoring of aquatic birds and surveillance of avian influenza and Newcastle disease of waterfowls at the National Park of Urmia Lake

BackgroundUrmia lake, as a national park, is one of the most valuable aquatic ecosystems in the Middle East and quatitative and qualitative changes in Urmia lake water have a great impact on its ecological performance and in the region.ObjectivesThis project was designed to study the effects of the extent of Urmia lake water surface area on the area size and on the number of aquatic birds of the six selected habitats in 2011–2019. The presence of avian influenza (AI) and Newcastle disease (ND) viruses in migratory aquatic birds together with their impacts on poultry farms as well as on rural birds was also under surveillance in 2018–2019.MethodsChanges of Urmia lake and its impacts on area size of the six selected birds habitats were monitored by GIS. The small monitoring program with circular plot point counts was used for counting of the number of birds of the six selected habitats. At least, 100 samples (oropharyngeal and cloacal swabs) were collected. each sample was placed in a sterile plastic tube containg transport media and assigned with an number and store untill used. Reverse transcription‐polymerase chain reaction (RT‐PCR) and real‐time RT‐PCR test were used for detection of AI and ND viruses in the samples.ResultsThe results revealed that changes in the water surface area of Urmia lake had a gsignificat impacts on area size and the number of aquatic birds of the six selected habitats. The surveillance results showed that 5% of the samples were AIV positvie while 25% of the samples were pasitive for NDV including 20% for non‐virulent NDV (lNDV) and 5% for virulent NDV (vNDV) strains.ConclusionThis study showed that fluctuation of Urmia lake's water surface area influenced (p < 0.05) the area size of the six selected aquatic birds' habitats and had a great impacts on the number of the migratory birds. Detection of AIV and vNDV emphesises that the seasonal migratory waterfowls spread AI and vND viruses to the ponds and estuaries as well as to the rural birds and industrialised poultry units around the Urmia lake. Potential public health treats were also discussed.

PB2281: HOW TO AVOID FALSE-NEGATIVE AND FALSE-POSITIVE COVID-19 PCR TESTING

Background: Since early 2020 the most demanded molecular genetic test is real-time reverse transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2. However, up to 40% of test results for COVID-19 in the presence of clinical manifestations of the disease might be negative. A false-negative analysis means untimely treatment of the patient and the possible spread of infection from a non-isolated person. Despite the fact that there are many highly sensitive RT-PCR test systems for COVID-19 on the market, the search for new reliable approaches to increase the robustness of testing is still relevant. Aims: To develop a PCR testing approach featured to minimize the risk of the false-negative results and to increase assay sensitivity and specificity by the use of multiple targets. Methods: A cotton swab taken from the nasopharynx was placed in an Eppendorf tube with 300 μl of phosphate-buffered saline. The resulting suspension (100 μl) was taken for RNA isolation using the Riboprep Amplisens kit (InterlabService, Russia). Primer sequences for RT-PCR are shown in Table 1. Results: The reason for a false-negative result might originate from any stage of the analysis: poor-quality or empty swab, poor RNA isolation, inactivation of reverse transcriptase or Taq polymerase in the test. To control the entire process usually control DNA or an RNA-containing virus (eg bacteriophage MS-2) is added to the sample before RNA isolation. This is sufficient to control RNA isolation, reverse transcription, and PCR amplification. However, improper swab application, handling, transporting, or even attempts to falsify the sample, cannot be excluded this way. Here we propose to include primers for the detection of human ABL1 gene RNA to control swab quality and integrity. Designed primers work with the cDNA of the ABL1 gene, not genomic DNA. Therefore achieved ABL1 gene amplification ensures that enough material containing host RNA was taken by the swab, RNA was nicely isolated, reverse transcribed, and PCR-amplified. For SARS-CoV-2 detection, we propose to use primers targeted to the conserved region of the nucleocapsid gene and the less conserved region of the spike gene (currently specific for the Omicron strain). The simultaneous appearance of three signals corresponding to the nucleocapsid, spike, and ABL1 gene indicates infection with the Omicron strain. The amplification of ABL1 gene and nucleocapsid only indicate other than Omicron infection. The appearance of ABL1 amplification only indicates a true negative result for SARS-CoV-2. All other variants are null and void. Image:Summary/Conclusion: A system has been developed for multiplex PCR diagnostics of SARS-CoV-2, which makes it possible to eliminate errors leading to false-negative and false-positive results at all stages of analysis. This is accomplished by the presence of specific primers for human RNA, controlling proper swab application, handling, and all the stages of RT-PCR. Targeting diverse regions of SARS-CoV-2 increases the reliability of the results and makes it possible to identify the virus strain.