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Nucleic acid amplification tests (NAATs) play a pivotal role in clinical laboratories for diagnosing COVID-19. This study aimed to elucidate the accuracy of these tests. In 2021, an external quality assessment of NAATs for SARS-CoV-2 was conducted in 47 laboratories in Tokyo, Japan. In open testing, where the laboratories knew that the samples were intended for the survey, a simulated nasopharyngeal swab suspension sample was used, featuring a positive sample A with a viral concentration of 50 copies/μL, positive sample B with 5 copies/μL, and a negative sample. Laboratories employing real-time RT-PCR were required to report cycle threshold (Ct) values. In blind testing, where the samples were processed as normal test samples, a positive sample C with 50 copies/μL was prepared using a simulated saliva sample. Of the 47 laboratories, 41 were engaged in open testing. For sample A, all 41 laboratories yielded positive results, whereas for sample B, 36 laboratories reported positive results, 3 laboratories reported "test decision pending", 1 laboratory reported "suspected positive", and 1 laboratory did not respond. All 41 laboratories correctly identified the negative samples as negative. The mean Ct values were 32.2 for sample A and 35.2 for sample B. In the blind test, six laboratories received samples. Sample C was identified as positive by five laboratories and negative by one laboratory. The nature of the specimen, specifically the saliva, may have influenced the blind test outcomes. The identified issues must be meticulously investigated and rectified to ensure accurate results. [ABSTRACT FROM AUTHOR]

Junna Oba,1 Masako Toriya,2 Yoshifumi Uwamino,3 Koichi Matsuo4 1Department of Extended Intelligence for Medicine, the Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan; 2Global Research Institute, Keio University, Tokyo, Japan; 3Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan; 4Collaborative Research Resources, Keio University School of Medicine, Tokyo, JapanCorrespondence: Masako Toriya, Global Research Institute, Keio University, 2-15-45 Mita, Minato-ku, Tokyo, 108-8345, Japan, Tel +81-3-5427-1379, Fax +81-3-5427-1703, Email masako.toriya@keio.jpBackground: During the COVID-19 pandemic, there was an increasing need to expand diagnostic testing in hospitals. At Keio University Hospital (KUH), clinical staff were concerned that the demand for PCR testing might exceed the capacity of the Clinical Laboratory. In response, basic researchers at Keio University School of Medicine (KUSM) set out to build a new, collaborative, PCR testing system. To be authorized to perform such diagnostic PCR testing, KUSM registered its core laboratory as an external clinical laboratory (ECL).Methods: In the pandemic, there was a pressure to build the PCR system quickly. Speed required discussions that developed a shared understanding of the unprecedented, new KUH/KUSM PCR system. To design, construct, and archive the new PCR testing system, we used a systems engineering (SE) approach. This included diagram visualization of functional flows and application of the Unified Architecture Framework (UAF), both of which are often used in system building. We considered daily demand for PCR testing at KUH and KUSM, and daily COVID-19 infections in Japan.Results: We operated the collaborative PCR testing system from August 2020 to June 2022. Given public health insurance reimbursement policies, KUH focused on individuals with suspicious symptoms, while the ECL at KUSM screened samples from asymptomatic individuals. KUSM performed about half as many tests as KUH. Interviewing KUH staff revealed that diagrams helped promote a better understanding of the KUH/KUSM PCR testing system.Conclusion: When designing temporary systems that may be repurposed in the future, we suggest using an SE approach with diagrams and UAF perspectives. This approach will enable stakeholders to understand what is being proposed to be built, and facilitate achieving an informed consensus on the proposed system. We suggest that SE approaches should be widely used in projects that involve building and operating complex, collaborative systems, and documenting the process. Keywords: COVID-19, PCR test, clinical laboratory, systems engineering, diagram, temporary system

Abstract Background In 2022/2023, Influenza A and Respiratory Syncytial Virus (RSV) reappeared in hospitalized patients, which was in parallel to ongoing SARS-CoV-2 infections. The aim of our study was to compare the characteristics and outcomes of these infections during the same time. Methods We included patients of all ages with a positive polymerase chain reaction (PCR) test for Influenza A/B, RSV, or SARS-CoV-2 virus hospitalized in the neurological, internal or paediatric units of the RoMed Hospital Rosenheim, Germany, between October 1st 2022 and February 28th 2023. Results A total of 906 patients were included (45.6% female; median age 68.0 years; 21.9% Influenza A, 48.2% SARS-CoV-2, 28.3% RSV). Influenza B (0.2%) and co-infections (1.5%) played a minor role. In patients aged ≥ 18 years (n = 637, 71%), Influenza A, SARS-CoV-2 and RSV groups differed in age (median 72, 79, 76 years, respectively; p

Background: In 2022/2023, Influenza A and Respiratory Syncytial Virus (RSV) reappeared in hospitalized patients, which was in parallel to ongoing SARS-CoV-2 infections. The aim of our study was to compare the characteristics and outcomes of these infections during the same time. Methods: We included patients of all ages with a positive polymerase chain reaction (PCR) test for Influenza A/B, RSV, or SARS-CoV-2 virus hospitalized in the neurological, internal or paediatric units of the RoMed Hospital Rosenheim, Germany, between October 1st 2022 and February 28th 2023. Results: A total of 906 patients were included (45.6% female; median age 68.0 years; 21.9% Influenza A, 48.2% SARS-CoV-2, 28.3% RSV). Influenza B (0.2%) and co-infections (1.5%) played a minor role. In patients aged ≥ 18 years (n = 637, 71%), Influenza A, SARS-CoV-2 and RSV groups differed in age (median 72, 79, 76 years, respectively; p < 0.001). Comorbidities, particularly asthma and COPD, were most prevalent for RSV. 103 patients were admitted to the intensive care unit (ICU) (16.3% Influenza A, 15.3% SARS-CoV-2, 19.2% RSV; p = 0.649), 56 died (6.8% Influenza A, 9% SARS-CoV-2, 11.1% RSV; p = 0.496). RSV showed the highest frequencies of low-flow oxygen supplementation for admission and stay. Differences in the length of stay were minor (median 7 days). Conversely, in patients aged < 18 years (n = 261, 28,8%), 19.5%, 17.6% and 60.2% were in the Influenza A, SARS-CoV-2 and RSV groups, respectively; 0.4% showed Influenza B and 2.3% co-infections. 17 patients were admitted to ICU (3.9% Influenza A, 9.6% RSV, 0% SARS-CoV-2); none died. RSV showed the highest frequencies of high- and low-flow oxygen supplementation, SARS-CoV-2 the lowest. Conclusion: When comparing infections with Influenza, SARS-CoV-2 and RSV in the winter 2022/2023 in hospitalized adult patients, rates of ICU admission and mortality were similar. RSV showed the highest frequencies of obstructive airway diseases, and of oxygen supplementation. The latter was also true in children/adolescents, in whom RSV dominated. Thus, in the situation of declining importance of SARS-CoV-2, RSV showed a disease burden that was relatively higher than that from Influenza and SARS-CoV-2 across ages, and this might be relevant for the seasons coming. [ABSTRACT FROM AUTHOR]

Roommates of unrecognized nosocomial methicillin-resistant Staphylococcus aureus (MRSA) cases are at a higher acquisition risk; however, optimal surveillance strategies are unknown. Using simulation, we analyzed surveillance testing and isolation strategies for MRSA among exposed hospital roommates. We compared isolating exposed roommates until conventional culture testing on day 6 and a nasal polymerase chain reaction test on day 3 (PCR3) with/without day 0 culture testing (Cult0). The model represents MRSA transmission in medium-sized hospitals using data and recommends best practices from the literature and Ontario community hospitals. Cult0 + PCR3 incurred a slightly lower number of MRSA colonizations and 38.9% lower annual cost in the base case compared to Cult0 + culture testing on day 6 because the reduced isolation cost compensated for the increased testing cost. The reduction in MRSA colonizations was due to a 54.5% drop in MRSA transmissions during isolation as PCR3 reduced the exposure of MRSA-free roommates to new MRSA carriers. Removing the day 0 culture test from Cult0 + PCR3 increased total cost, the number of MRSA colonization, and missed cases by $1,631, 4.3%, and 50.9%, respectively. Improvements were higher under aggressive MRSA transmission scenarios. Adopting direct nasal polymerase chain reaction testing for determining post-exposure MRSA status reduces transmission risk and costs. Day 0 culture would still be beneficial. • Exposed roommates of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) cases are at high acquisition risk. • We analyzed MRSA surveillance and isolation strategies among exposed roommates. • We developed a computer simulation model to mimic transmission and progression. • Using nasal polymerase chain reaction testing for MRSA surveillance reduces transmission risk and costs. • Day 0 culture test on top of day 3 polymerase chain reaction test is beneficial for MRSA surveillance. [ABSTRACT FROM AUTHOR]

Introduction: To date various oral manifestations in patients with coronavirus disease 2019 (COVID-19) have been reported. Objectives: In the present study, we investigated the relationship between Polymerase Chain Reaction (PCR) positivity and oral signs in patients with suspected COVID-19. Methods: A total of 383 patients who presented to the emergency department for the first time with any symptoms associated with COVID-19 were included in the study. Oral examinations were performed and the findings, PCR status, and thorax computerized tomography (CT) reports were recorded. Results: Oral mucosa was involved in 246 (64.2%) patients. 175 (78,4%) of patients with COVID-19 confirmed the diagnosis with PCR test or CT results had oral manifestation. Dry mouth, microvesicles on the tonsils or pharynx, and petechiae in the oropharynx were significantly higher in patients with positive PCR tests (P = 0.001, P < 0.001, P < 0.001, respectively). The ratio of intact oral mucosa was statistically significantly higher in patients with negative PCR tests compared to those with positive PCR tests (P < 0.001). Microvesicles on the tonsils or pharynx were most associated with PCR positivity in patients without lung involvement (P < 0.001). Dry mouth, erythema of the tonsils and pharynx, petechiae in the oropharynx, and primary/secondary herpes infection are more related to PCR positivity in patients without lung involvement (P < 0.05). Lung involvement in patients with PCR positivity is related to only cheilitis (P = 0.034). Conclusions: Our study revealed that especially microvesicles, petechiae, erythema on the tonsils or pharynx, and some other oral lesions such as dry mouth, oral aphthae, and primary/secondary herpes infection are associated with PCR positivity.

Wafa Elhag,1,2 Bahaeldin K Elamin,1,3 Ebtehal Idris,4 Azza Elsheikh,1 Khaled Ghaleb,4 Ibtihal Fallatah,5 Doaa Hassan,5 Mahmoud Elkhalifa,5 Ehssan Moglad,6 Ali Eleragi1 1Department of Basic Medical Sciences (Microbiology Unit), College of Medicine, University of Bisha, Bisha, Saudi Arabia; 2Microbiology Department, Faculty of Medical Laboratory Sciences, Al Neelain University, Khartoum, Sudan; 3Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan; 4Medical Laboratories Department, College of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia; 5Laboratory and ICU (Medical Department) King Abdullah Hospital-Bisha, Bisha, Saudi Arabia; 6Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi ArabiaCorrespondence: Wafa Elhag, Department of Basic Medical Sciences (Microbiology Unit), College of Medicine, University of Bisha, P.O.Box 1290, Bisha, 61922, Saudi Arabia, Email welhag@ub.edu.saBackground: Understanding COVID-19’s onset and clinical effects requires knowing host immune responses.Objective: To investigate the presence of IgM, IgG, and cytokine levels (IL-2 and IL-6) in individuals with COVID-19 who have had their diagnosis confirmed by PCR.Methods: This cross-sectional research included 70 adult ICU patients from King Abdullah Hospital in Bisha, Saudi Arabia. Subjects gave two blood samples. After hospital release, only 21 patients provided the second sample. Each patient provided a sample upon admission. Quantitative ELISAs evaluated IL-2, IL-6, and SARS-CoV-2-specific IgM and IgG antibodies.Results: All patients were critically ill and unvaccinated against COVID-19. 46 (65.7%) of the patients were male, and their age range was 33– 98 years (with a mean age of 66.5); 24.3%) were 51– 61 years old. IgG was positive in all patients, although IgM predominated in 57/70 (81.4%) (6– 1200 IU/mL). Total data analysis yielded these results. IL-6 was calculated at 10– 1900 ng/mL, whereas IL-2 was 4– 280. Discharged hospital patients had a statistically significant increase in IgM and IgG (P = 0.01, 0.004) but a statistically insignificant decline in IL-6 and IL-2 (P = 0.761, 0.071). Low IgM levels increased hospital stays. The study found lengthier hospital stays with higher IgG levels.Conclusion: The identification of IgM and IgG antibodies, greater IL-6 levels, and lower IL-2 levels can help diagnose and monitor COVID-19 infection.Keywords: COVID-19 patients, antibodies, cytokines levels, PCR test, ELISA, Saudi Arabia

Multiple outbreaks of fatal infectious diseases throughout history have intensified the need for early diagnostic methods to efficiently control their spread. Polymerase chain reaction (PCR)-based diagnosis is a sensitive, accurate, and effective method for detecting infections. However, conventional PCR-based diagnosis is slow and consumes large amounts of energy, primarily because of bulky, power-consuming thermal cyclers. Herein, we review recently published PCR-based diagnostic methods, in which plasmonic light-to-heat conversion-based thermal cyclers replace conventional ones. First, we explain the structures of recently developed rapid plasmonic-based thermal cyclers and review the various materials used. Next, we review the fabrication methods used in recent developments in rapid plasmonic thermal cyclers. Then, we discuss sustainable methods that have been and can be implemented to develop a rapid plasmonic thermal cycler. With this review, the requirements for developing a plasmonic-based sustainable PCR with high speed, accuracy, and sensitivity can be understood to contain future pandemics.

Objective: This study was designed to determine the reasons for vaccine rejection in patients who applied for the coronavirus disease-2019 (COVID-19) polymerase chain reaction (PCR) test but did not receive the vaccine. Methods: The study was conducted prospectively in the emergency department of a tertiary hospital between 31.01.2022 and 31.05.2022. 1000 patients who applied for the COVID-19 PCR test and refused to be vaccinated were included. The COVID-19 status of the participants, reasons for their application, number of PCR tests, methods of obtaining information about the vaccine, and reasons for the rejection of the vaccine were questioned. Results: 54.6% of the participants were male and 45.4% were female. 60.7% of the patients applied for testing due to symptoms, 25.4% due to contact with people with symptoms, and 23.9% due to travel. 43.3% of the cases had COVID-19 infection; 53.6% of them had tested an average of 2-5 times in the last year. Most of the information about the vaccine was taken from social media, television, medical publications, and people around, respectively. Of the participants, 62.0% believed that COVID-19 vaccines had side effects, 47.3% believed that it had no protection, and 30.9% believed that there was not enough study on the subject. As the age grew, the rate of learning information from social media increased. Conclusions: The most common reasons for COVID-19 vaccine rejection were vaccine side effects, doubtful vaccine protection, and concerns about the lack of sufficient studies on the vaccine. The higher the education level, the higher the vaccine rejection rate. [ABSTRACT FROM AUTHOR]

Purpose: To investigate the perception of SARS-CoV-2 detection methods, information sources, and opinions on appropriate behavior after receiving negative or positive test results. Methods: In a questionnaire-based, cross-sectional study conducted between September 1 and November 17, 2021, epidemiological, behavioral, and COVID-19-related data were acquired from the public in Munich, Germany. Results: Most of the 1388 participants obtained information from online media (82.8%) as well as state and federal authorities (80.3%). 93.4% believed in the accuracy of SARS-CoV-2 PCR testing and 41.2% in the accuracy of rapid antigen tests (RATs). However, RATs were preferred for testing (59.1%) over PCR (51.1%). 24.0% of all individuals were willing to ignore hygiene measures and 76.9% were less afraid of SARS-CoV-2 transmission after receiving a negative PCR test (5.9% and 48.8% in case of a negative RAT). 28.8% reported not to self-isolate after receiving a positive RAT. Multivariate analyses revealed that non-vaccinated individuals relied less on information from governmental authorities (p = 0.0004) and more on social media (p = 0.0216), disbelieved in the accuracy of the PCR test (p ≤ 0.0001) while displaying strong preference towards using RATs (p ≤ 0.0001), were more willing to abandon pandemic-related hygiene measures (p ≤ 0.0001), less afraid of transmitting SARS-CoV-2 after a negative RAT (p ≤ 0.0001), and less likely to isolate after a positive RAT (p ≤ 0.0001). Conclusion: Insights into preferred information sources as well as perception, preferences, and behavior related to SARS-CoV-2 testing and hygiene measures are key to refining public health information and surveillance campaigns. Non-vaccinated individuals' divergent believes and behaviors possibly increase their COVID-19 risk. [ABSTRACT FROM AUTHOR]

This study aimed to determine the effectiveness of stress balls and relaxation exercises in relieving PCR test-induced fear and pain in adolescents. A randomized controlled experimental study with a parallel-group design was conducted. The sample size was determined by G*Power analysis, and 32 adolescents were included in each group accordingly. The data were collected using the Adolescent and Parent Information Form, The Children's Fear Scale, and The Wong-Baker Faces Pain Scale. Descriptive statistics, t -test, paired t-test, ANOVA, and Tukey's forward analysis were used to analyze the data. The mean age was 14.93 ± 2.07 years for the adolescents, 43.58 ± 4.50 years for the mothers, and 48.25 ± 4.92 years for the fathers. Adolescents were stratified according to age, gender, and fear of invasive procedures, and homogeneity was ensured in their distribution to the groups. The pre-procedural level of fear was moderate in each group with no significant difference (p > 0.05). However, a significant difference was found between the groups in terms of both post-procedure levels of fear and pain. The pre-procedural fear of the adolescents in the control group (3.91 ± 0.29) did not change much after the procedure (3.91 ± 0.30), while there was a decrease in the other groups. The least post-procedure fear (0.09 ± 0.29) and pain (0.44 ± 0.67) were found to be in the relaxation exercise group. Relaxation exercise is the most effective method to reduce fear and pain during the PCR procedure. It is recommended to use it during the PCR procedure for being easily accessible, applicable, and cost-effective. Clinical Trials ID: NCT05250544. • To reduce the negative effects of the PCR test in adolescents, it is important to use attracting attention methods. • Stress ball and relaxation exercises were found to be effective in reducing the pain and fear levels of adolescents. • It is recommended that in-service training should be planned for health professionals to use the methods. • It is recommended to spread the use of these non-invasive nursing interventions in PCR testing in health institutions. [ABSTRACT FROM AUTHOR]

Introduction: The aim of the present study is to investigate the baseline predictive factors of prolonged hospital stay and to compare the patient characteristics according to polymerase chain reaction (PCR) positivity. Methods: Between March 11 and June 1, 2020, 234 patients hospitalized in a non-intensive care unit clinic with a diagnosis of COVID-19 were included retrospectively. The duration of hospitalization were classified as =7 days and >7 days. Furthermore, according to real-time PCR (RT-PCR) of nasopharyngeal swab positivity, patients were divided into two Groups. Results: Of all the 234 patients, the mean age was 54±13 and 167 (71%) was male. Thirty-six (36%) were PCR positive (+) at the first swab samples. Hospital stay was longer than 7 days in 122 (52%) of the patients. Ten patients (4.3%) died within 60-days. PCR-positive cases had lower baseline leukocytes (p=0.002), C-reactive protein (p=0.001) values, whereas hemoglobin (p=0.001) and albumin levels (p<0.0001) were detected in PCR-positive patients. While demographics and mortality were similar, hospital stay longer than 7 days were detected in a higher rate in PCR-positive patients (p=0.025). The analysis on hospital stay proved that, apart from PCR positivity rate, baseline aspartate aminotransferase (AST) level prolongs hospital stay in COVID-19 patients. Discussion and Conclusion: This study demonstrates significant differences in patients with and without PCR positivity. Higher baseline AST levels and first PCR positivity prolongs hospital stay. Studies including larger patient groups would be better determine and enhance in this regard. [ABSTRACT FROM AUTHOR]

Abstract Background Since social distancing during the COVID-19-pandemic had a profound impact on professional life, this study investigated the effect of PCR testing on on-site work. Methods PCR screening, antibody testing, and questionnaires offered to 4,890 working adults in Lower Saxony were accompanied by data collection on demographics, family status, comorbidities, social situation, health-related behavior, and the number of work-related contacts. Relative risks (RR) with 95 % confidence intervals were estimated for the associations between regular PCR testing and other work and health-related variables, respectively, and working on-site. Analyses were stratified by the suitability of work tasks for mobile office. Results Between April 2020 and February 2021, 1,643 employees underwent PCR testing. Whether mobile working was possible strongly influenced the work behavior. Persons whose work was suitable for mobile office (mobile workers) had a lower probability of working on-site than persons whose work was not suitable for mobile office (RR = 0.09 (95 % CI: 0.07 – 0.12)). In mobile workers, regular PCR-testing was slightly associated with working on-site (RR = 1.19 (0.66; 2.14)). In those whose working place was unsuitable for mobile office, the corresponding RR was 0.94 (0.80; 1.09). Compared to persons without chronic diseases, chronically ill persons worked less often on-site if their workplace was suitable for mobile office (RR = 0.73 (0.40; 1.33)), but even more often if their workplace was not suitable for mobile office (RR = 1.17 (1.04; 1.33)). Conclusion If work was suitable for mobile office, regular PCR-testing did not have a strong effect on presence at the work site. Trial registration An ethics vote of the responsible medical association (Lower Saxony, Germany) retrospectively approved the evaluation of the collected subject data in a pseudonymized form in the context of medical studies (No. Bo/30/2020; Bo/31/2020; Bo/32/2020).

Introduction: The lack of information about the impact of Covid-19 on pregnancy and the increased side-effects of the disease for pregnant mothers and fetuses showed the importance of investigating its impact on pregnancy and neonate. The present study was performed with aim to investigate the impact of positive test result of PCR on the weight and Apgar scores of infants. Methods: In this analytical study (retrospective cohort), sampling was conducted by examining the files of 98 pregnant women who gave birth between April 2020 and September 2021 using the apple system which were covered by health care centers located in Isfahan province. The information obtained from the comparison of two groups of mothers based on the results of the PCR test was analyzed by SPSS software (version 18) and Independent t-test. P

We present an unusual case of a previously healthy 74-year-old man who presented with diffuse weakness, severe myalgias, petechial palmar rash and hypotension, but without fever, altered mental status, nuchal rigidity or headache, who was ultimately found through PCR testing to have meningococcal meningitis.

Abstract Background RSV-incidence estimates obtained from routinely-collected healthcare data (e.g., MarketScan) are commonly adjusted for under-reporting using test positivity reported in national Surveillance Systems (NREVSS). However, NREVSS lacks detail on patient-level characteristics and the validity of applying a single positivity estimate across diverse patient groups is uncertain. We aimed to describe testing practices and test positivity across subgroups of private health insurance enrollees in the US and illustrate the possible magnitude of misclassification when using NREVSS to correct for RSV under ascertainment. Methods Using billing records, we determined distributions of RSV-test claims and test positivity among a national sample of private insurance enrollees. Tests were considered positive if they coincided with an RSV-diagnosis. We illustrated the influence of positivity variation across sub-populations when accounting for untested acute respiratory infections. Results Most tests were for children (age 0–4: 65.8%) and outpatient encounters (78.3%). Test positivity varied across age (0–4: 19.8%, 5–17: 1.8%, adults: 0.7%), regions (7.6–16.1%), settings (inpatient 4.7%, outpatient 14.2%), and test indication (5.0–35.9%). When compared to age, setting or indication-specific positivity, bias due to using NREVSS positivity to correct for untested ARIs ranged from − 76% to 3556%. Conclusions RSV-test positivity depends on the characteristics of patients for whom those tests were ordered. NREVSS-based correction for RSV-under-ascertainment underestimates the true incidence among children and overestimate rates among adults. Demographic-specific detail on testing practice and positivity can improve the accuracy of RSV-incidence estimates.

Abstract Background COVID-19 has caused over 305 million infections and nearly 5.5 million deaths globally. With complete eradication unlikely, organizations will need to evaluate their risk and the benefits of mitigation strategies, including the effects of regular asymptomatic testing. We developed a web application and R package that provides estimates and visualizations to aid the assessment of organizational infection risk and testing benefits to facilitate decision-making, which combines internal and community information with malleable assumptions. Results Our web application, covidscreen, presents estimated values of risk metrics in an intuitive graphical format. It shows the current expected number of active, primarily community-acquired infections among employees in an organization. It calculates and explains the absolute and relative risk reduction of an intervention, relative to the baseline scenario, and shows the value of testing vaccinated and unvaccinated employees. In addition, the web interface allows users to profile risk over a chosen range of input values. The performance and output are illustrated using simulations and a real-world example from the employee testing program of a pediatric oncology specialty hospital. Conclusions As the COVID-19 pandemic continues to evolve, covidscreen can assist organizations in making informed decisions about whether to incorporate covid test based screening as part of their on-campus risk-mitigation strategy. The web application, R package, and source code are freely available online (see “Availability of data and materials”).

Background: Since social distancing during the COVID-19-pandemic had a profound impact on professional life, this study investigated the effect of PCR testing on on-site work. Methods: PCR screening, antibody testing, and questionnaires offered to 4,890 working adults in Lower Saxony were accompanied by data collection on demographics, family status, comorbidities, social situation, health-related behavior, and the number of work-related contacts. Relative risks (RR) with 95 % confidence intervals were estimated for the associations between regular PCR testing and other work and health-related variables, respectively, and working on-site. Analyses were stratified by the suitability of work tasks for mobile office. Results: Between April 2020 and February 2021, 1,643 employees underwent PCR testing. Whether mobile working was possible strongly influenced the work behavior. Persons whose work was suitable for mobile office (mobile workers) had a lower probability of working on-site than persons whose work was not suitable for mobile office (RR = 0.09 (95 % CI: 0.07 – 0.12)). In mobile workers, regular PCR-testing was slightly associated with working on-site (RR = 1.19 (0.66; 2.14)). In those whose working place was unsuitable for mobile office, the corresponding RR was 0.94 (0.80; 1.09). Compared to persons without chronic diseases, chronically ill persons worked less often on-site if their workplace was suitable for mobile office (RR = 0.73 (0.40; 1.33)), but even more often if their workplace was not suitable for mobile office (RR = 1.17 (1.04; 1.33)). Conclusion: If work was suitable for mobile office, regular PCR-testing did not have a strong effect on presence at the work site. Trial registration: An ethics vote of the responsible medical association (Lower Saxony, Germany) retrospectively approved the evaluation of the collected subject data in a pseudonymized form in the context of medical studies (No. Bo/30/2020; Bo/31/2020; Bo/32/2020). [ABSTRACT FROM AUTHOR]

Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has necessitated novel testing strategies, including the use of rapid antigen tests (RATs). The widespread distribution of RATs to the public prompted Peterborough Public Health to launch a pilot RAT self-report tool to assess its utility in COVID-19 surveillance. The objective of this study is to investigate the utility of RAT using correlations between RAT self-report results and other indicators of COVID-19. Methods: We investigated the association between RAT results, PCR test results and wastewater levels of nmN1N2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes (to infer COVID-19 levels) using Pearson's correlation coefficient. Percent positivity and count of positive tests for RATs and polymerase chain reaction (PCR) tests were analyzed. Results: The PCR percent positivity and wastewater were weakly correlated (r=0.33, p=0.022), as were RAT percent positivity and wastewater nmN1N2 levels (r=0.33, p=0.002). The RAT percent positivity and PCR percent positivity were not significantly correlated (r=-0.035, p=0.75). Count of positive RATs and count of positive PCR tests were moderately correlated (r=0.59, p<0.001). Wastewater nmN1N2 levels were not significantly correlated with either count of positive RATs (r=0.019, p=0.864) or count of positive PCR tests (r=0.004, p=0.971). Conclusion: Our results support the use of RAT self-reporting as a low-cost simple adjunctive COVID-19 surveillance tool, and suggest that its utility is greatest when considering an absolute count of positive RATs rather than percent positivity due to reporting bias towards positive tests. These results can help inform COVID-19 surveillance strategies of local public health units and encourage the use of a RAT self-report tool. [ABSTRACT FROM AUTHOR]

Abstract Background Point-of-care (POC) polymerase chain reaction (PCR) tests have the ability to improve testing efficiency in the Coronavirus disease 2019 (COVID-19) pandemic. However, real-world data on POC tests is scarce. Objective To evaluate the efficiency of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) POC test in a clinical setting and examine the prognostic value of cycle threshold (CT) on admission on the length of hospital stay (LOS) in COVID-19 patients. Methods Patients hospitalised between January and May 2021 were included in this prospective cohort study. Patients’ nasopharyngeal swabs were tested for SARS-CoV-2 with Allplex™2019-nCoV (Seegene Inc.) real-time (RT) PCR assay as gold standard as well as a novel POC test (Bosch Vivalytic SARS-CoV-2 [Bosch]) and the SARS-CoV-2 Rapid Antigen Test (Roche) accordingly. Clinical sensitivity and specificity as well as inter- and intra-assay variability were analyzed. Results 120 patients met the inclusion criteria with 46 (38%) having a definite COVID-19 diagnosis by RT-PCR. Bosch Vivalytic SARS-CoV-2 POC had a sensitivity of 88% and specificity of 96%. The inter- and intra- assay variability was below 15%. The CT value at baseline was lower in patients with LOS ≥ 10 days when compared to patients with LOS

ABSTRACT: Aims: The objective of the present study was to investigate the presence of SARS-CoV-2 in aerosol and COVID-19 contamination distance asssociated with ultrasonic scaling and tooth preparation. Methods: Twenty-four patients with COVID-19 were included in this study. Removal of supragingival plaque with ultrasonic instruments for 10 minutes and high-speed air-turbine using for the simulation of cutting the maxillary right canine tooth with a round diamond bur for 5 minutes were performed. Patients were randomly assigned to 2 groups: In group A, medium-volume suction was used during treatment. In group B, high-volume suction with an aerosol cannula was added to medium-volume suction. Prior to treatment, 5 glass petri dishes containing viral transport medium were placed in the operating room. After treatment, petri dishes were immediately delivered to a microbiology laboratory for real-time polymerase chain reaction (RT-PCR) analysis. Results: RT-PCR test results were negative for all specimens in group B. However, 5 positive test results for COVID-19 were detected in group A specimens. Conclusions: Suction with an aerosol cannula is very important to prevent COVID-19 viral contamination via aerosol. In addition, a high-volume suction capacity (air volume) of 150 mm Hg or 325 L/min is sufficient for elimination of viral contamination. Thus, high-volume suction should be used during dental treatments in COVID-19 patients.

Objective: We evaluated PCR negativity in oropharyngeal and nasopharyngeal secretions of COVID-19 patients at the end of hydroxychloroquine and/or favipiravir treatments. Methods: Study inclusion criteria were being hospitalized, being older than 18 years, PCR positivity in oropharyngeal and nasopharyngeal secretions and being tested for SARS CoV-2-RNA PCR after treatment. Initially hydroxychloroquine treatment (group 1) was administered to the patients according to COVID-19 guide of Health Ministry. Favipiravir (group 2) alone or in combination with hydroxychloroquine (group 3) was administered to patients who were unresponsive to hydroxychloroquine or had severe pneumonia or were admitted to intensive care unit. Control respiratory specimens were taken no earlier than 24 hours, after the end of therapy. Repeated tests with 24-48-hour intervals were performed in patients with still positive PCR test results. The detection of SARS CoV-2-RNA was made by real-time PCR. Results: The study group included 492 patients who received treatment. Mean duration of symptoms was similar among three groups. PCR negativity rate was 52.8% in the specimens taken 24 hours after the end of treatment. PCR negativity rates was 27.9% (200/492) in 48 hours after the end of treatment, %13.8 (123/492) in 72nd hour and %3.8 (80/492) in 96th hour. The ratios of PCR negativity for all specimen days were similar in three groups. There was no statistically significant difference between the groups for time to PCR negativity from the date of positivity and after the end of treatment. We determined that early or late treatment did not make a difference in terms PCR negativity time. Conclusion: No difference was found in terms of the ratios of PCR negativity or time for negativity in oropharyngeal and/or nasopharyngeal specimens taken after the end of treatment in COVID-19 patients receiving hydroxychloroquine and/or favipiravir treatment. [ABSTRACT FROM AUTHOR]

Copyright of Balkan & Near Eastern Journal of Social Sciences (BNEJSS) is the property of Balkan & Near Eastern Journal of Social Sciences (BNEJSS) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Medizinische Klinik: Intensivmedizin & Notfallmedizin is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective. Examine clinical manifestations, PCR test results, and visit outcomes in patients in COVID-outpatient clinics. Method. The survey was performed using the questionnaire, in February 2021. in patients in four COVID-outpatient clinics in Belgrade and one in Subotica. We got the data about their jobs, gender, age, present symptoms and comorbidities, PCR-testing, and visit outcomes. The data were processed using the software statistical package SPSS 17. Statistical significance was defined for level p

Polymerase chain reaction (PCR) for the detection of nucleic acids is the gold standard test for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is the probability of false-negative results with this test, which poses a threat to public health. Here, we highlight some important factors that should be considered for reducing the false-negative results of the SARS-CoV-2 PCR test. Copyright © 2022 Sabzevari and Nikbakht. Published by Global Health and Education Projects, Inc. This is an open-access article distributed under the terms of the Creative Commons Attribution License CC BY 4.0.

Background: RSV-incidence estimates obtained from routinely-collected healthcare data (e.g., MarketScan) are commonly adjusted for under-reporting using test positivity reported in national Surveillance Systems (NREVSS). However, NREVSS lacks detail on patient-level characteristics and the validity of applying a single positivity estimate across diverse patient groups is uncertain. We aimed to describe testing practices and test positivity across subgroups of private health insurance enrollees in the US and illustrate the possible magnitude of misclassification when using NREVSS to correct for RSV under ascertainment.Methods: Using billing records, we determined distributions of RSV-test claims and test positivity among a national sample of private insurance enrollees. Tests were considered positive if they coincided with an RSV-diagnosis. We illustrated the influence of positivity variation across sub-populations when accounting for untested acute respiratory infections.Results: Most tests were for children (age 0-4: 65.8%) and outpatient encounters (78.3%). Test positivity varied across age (0-4: 19.8%, 5-17: 1.8%, adults: 0.7%), regions (7.6-16.1%), settings (inpatient 4.7%, outpatient 14.2%), and test indication (5.0-35.9%). When compared to age, setting or indication-specific positivity, bias due to using NREVSS positivity to correct for untested ARIs ranged from - 76% to 3556%.Conclusions: RSV-test positivity depends on the characteristics of patients for whom those tests were ordered. NREVSS-based correction for RSV-under-ascertainment underestimates the true incidence among children and overestimate rates among adults. Demographic-specific detail on testing practice and positivity can improve the accuracy of RSV-incidence estimates. [ABSTRACT FROM AUTHOR]

Background: COVID-19 has caused over 305 million infections and nearly 5.5 million deaths globally. With complete eradication unlikely, organizations will need to evaluate their risk and the benefits of mitigation strategies, including the effects of regular asymptomatic testing. We developed a web application and R package that provides estimates and visualizations to aid the assessment of organizational infection risk and testing benefits to facilitate decision-making, which combines internal and community information with malleable assumptions.Results: Our web application, covidscreen, presents estimated values of risk metrics in an intuitive graphical format. It shows the current expected number of active, primarily community-acquired infections among employees in an organization. It calculates and explains the absolute and relative risk reduction of an intervention, relative to the baseline scenario, and shows the value of testing vaccinated and unvaccinated employees. In addition, the web interface allows users to profile risk over a chosen range of input values. The performance and output are illustrated using simulations and a real-world example from the employee testing program of a pediatric oncology specialty hospital.Conclusions: As the COVID-19 pandemic continues to evolve, covidscreen can assist organizations in making informed decisions about whether to incorporate covid test based screening as part of their on-campus risk-mitigation strategy. The web application, R package, and source code are freely available online (see "Availability of data and materials"). [ABSTRACT FROM AUTHOR]

This document is a letter to the editor of the Medeniyet Medical Journal, responding to a study titled "Factors in Vaccine Refusal by Patients Applying for COVID-19 PCR Test." The authors express gratitude for the criticisms and congratulate the author for their scientific courage. The study aimed to determine the reasons for vaccine refusal among patients who applied for a COVID-19 PCR test but did not receive the vaccine. The study focused on analyzing the answers of participants who refused vaccination and did not compare the benefits of the vaccine or include participants who agreed to be vaccinated. The authors acknowledge the limitations of their study and welcome further criticism and discussion. [Extracted from the article]

COVID-19 modified the healthcare system. Nasal-pharyngeal swab (NPS), with real-time reverse transcriptase-polymerase (PCR), is the gold standard for the diagnosis; however, there are difficulties related to the procedure that may postpone it. The study aims to evaluate whether other elements than the PCR-NPS are reliable and confirm the diagnosis of COVID-19. This is a cross-sectional study on data from the Lung Unit of Pavia (confirmed) and at the Emergency Unit of Palermo (suspected). COVID-19 was confirmed by positive NPS, suspected tested negative. We compared clinical, laboratory and radiological variables and performed Logistic regression to estimate which variables increased the risk of COVID-19. The derived ROC-AUCcurve, assessed the accuracy of the model to distinguish between COVID-19 suspected and confirmed. We selected 50 confirmed and 103 suspected cases. High Reactive C-Protein (OR: 1.02; CI95%: 0.11–1.02), suggestive CT-images (OR: 11.43; CI95%: 3.01–43.3), dyspnea (OR: 10.48; CI95%: 2.08–52.7) and respiratory failure (OR: 5.84; CI95%: 1.73–19.75) increased the risk of COVID-19, whereas pleural effusion decreased the risk (OR: 0.15; CI95%: 0.04–0.63). ROC confirmed the discriminative role of these variables between suspected and confirmed COVID-19 (AUC 0.91). Clinical, laboratory and imaging features predict the diagnosis of COVID-19, independently from the NPS result. [ABSTRACT FROM AUTHOR]

Background: Point-of-care (POC) polymerase chain reaction (PCR) tests have the ability to improve testing efficiency in the Coronavirus disease 2019 (COVID-19) pandemic. However, real-world data on POC tests is scarce.Objective: To evaluate the efficiency of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) POC test in a clinical setting and examine the prognostic value of cycle threshold (CT) on admission on the length of hospital stay (LOS) in COVID-19 patients.Methods: Patients hospitalised between January and May 2021 were included in this prospective cohort study. Patients' nasopharyngeal swabs were tested for SARS-CoV-2 with Allplex™2019-nCoV (Seegene Inc.) real-time (RT) PCR assay as gold standard as well as a novel POC test (Bosch Vivalytic SARS-CoV-2 [Bosch]) and the SARS-CoV-2 Rapid Antigen Test (Roche) accordingly. Clinical sensitivity and specificity as well as inter- and intra-assay variability were analyzed.Results: 120 patients met the inclusion criteria with 46 (38%) having a definite COVID-19 diagnosis by RT-PCR. Bosch Vivalytic SARS-CoV-2 POC had a sensitivity of 88% and specificity of 96%. The inter- and intra- assay variability was below 15%. The CT value at baseline was lower in patients with LOS ≥ 10 days when compared to patients with LOS < 10 days (27.82 (± 4.648) vs. 36.2 (25.9-39.18); p = 0.0191). There was a negative correlation of CT at admission and LOS (r[44]s = - 0.31; p = 0.038) but only age was associated with the probability of an increased LOS in a multiple logistic regression analysis (OR 1.105 [95% CI, 1.03-1.19]; p = 0.006).Conclusion: Our data indicate that POC testing with Bosch Vivalytic SARS-CoV-2 is a valid strategy to identify COVID-19 patients and decrease turnaround time to definite COVID-19 diagnosis. Also, our data suggest that age at admission possibly with CT value as a combined parameter could be a promising tool for risk assessment of increased length of hospital stay and severity of disease in COVID-19 patients. [ABSTRACT FROM AUTHOR]

Abstract Background During the spike of COVID-19 pandemic in Kazakhstan (June-2020), multiple SARS-CoV-2 PCR-test negative pneumonia cases with higher mortality were reported by media. We aimed to study the epidemiologic characteristics of hospitalized PCR-test positive and negative patients with analysis of in-hospital and post-hospital mortality. We also compare the respiratory disease characteristics between 2019 and 2020. Methods The study population consist of 17,691 (March–July-2020) and 4600 (March–July-2019) hospitalized patients with respiratory diseases (including COVID-19). The incidence rate, case-fatality rate and survival analysis for overall mortality (in-hospital and post-hospital) were assessed. Results The incidence and mortality rates for respiratory diseases were 4-fold and 11-fold higher in 2020 compared to 2019 (877.5 vs 228.2 and 11.2 vs 1.2 per 100,000 respectively). The PCR-positive cases (compared to PCR-negative) had 2-fold higher risk of overall mortality. We observed 24% higher risk of death in males compared to females and in older patients compared to younger ones. Patients residing in rural areas had 66% higher risk of death compared to city residents and being treated in a provisional hospital was associated with 1.9-fold increased mortality compared to those who were treated in infectious disease hospitals. Conclusion This is the first study from the Central Asia and Eurasia regions, evaluating the mortality of SARS-CoV-2 PCR-positive and PCR-negative respiratory system diseases during the peak of COVID-19 pandemic. We describe a higher mortality rate for PCR-test positive cases compared to PCR-test negative cases, for males compared to females, for elder patients compared to younger ones and for patients living in rural areas compared to city residents.

The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place within the context of the world-wide SARS-CoV-2 crisis. Here, for the first time in history, laboratory test results have a dramatic impact on political decisions. Therefore, transparent, comprehensible, and reliable data is mandatory. It is in the nature of wet lab tests that their quality and outcome are influenced by multiple factors reducing their performance by handling procedures, underlying test protocols, and analytical reagents. These limitations in sensitivity and specificity have to be taken into account when calculating the real test results. As a resolution method, we have developed a Bayesian calculator, the Bayes Lines Tool (BLT), for analyzing disease prevalence, test sensitivity, test specificity, and, therefore, true positive, false positive, true negative, and false negative numbers from official test outcome reports. The calculator performs a simple SQL (Structured Query Language) query and can easily be implemented on any system supporting SQL. We provide an example of influenza test results from California, USA, as well as two examples of SARS-CoV-2 test results from official government reports from The Netherlands and Germany-Bavaria, to illustrate the possible parameter space of prevalence, sensitivity, and specificity consistent with the observed data. Finally, we discuss this tool’s multiple applications, including its putative importance for informing policy decisions.

Abstract Our work highlights patients at risk of prolonged viral shedding in COVID‐19 and its implications for isolation strategies and explores possible solution by PCR‐CT value testing (cycle threshold value). We also review the impact of HIV on COVID‐19.

Objective: This study aims to investigate the relationship between prothrombin time (PT), activated partial thromboplastin time (aPTT), INR (International Normalized Ratio), and Ddimer levels, platelet (PLT) levels at hospital admission, and positivity or negativity of Polymerase Chain Reaction (PCR) test results in patients with suspected coronavirus disease-19 (COVID-19) followed at COVID-19 services. Methods: This study was performed on 238 patients with the prediagnosis of COVID-19, all patients are hospitalised in Samsun city at our hospital between 11 March 2020-30 May 2020. According to COVID-19 PCR test results, PCR test negative 119 individua and PCR test positive 119 patients were included in the study. PT, aPTT, D-dimer, INR, and PLT levels were examined. Results: While PCR test negative individuals had a mean PT value of 11.46±0.86 sec, PCR test positive patients had a mean PT value of 12.97±3.65 sec (p<0.001). There was no significant difference in mean aPTT values of PCR test positive and negative patients. Whereas INR, D-dimer increased significantly in PCR test positive patients. PLT value decreased from a mean value of 266.75±71.36*109/L in PCR test negative patients to 241.18±96.64*109/L in PCR test positive patients (p=0.002). Conclusions: In our study, it was found that in patients who were admitted to hospital with COVID-19 suspicion and followed up in COVID-19 services, PT, D-dimer, INR, PLT values were important in detecting coagulopathy and thrombocytopenia in the group who were PCR positivity. [ABSTRACT FROM AUTHOR]

Background: Pain is a common complaint in COVID-19 disease. Neurotrophic features of the COVID virus are reported. Neuropathic pain is seen during many viral infections and observed during the COVID-19 pandemic part of the clinical presentations. Objective: The aim of this is to evaluate neuroptic pain as presenting symptom in COVID-19 patients. Materials and Methods: In this cross-sectional descriptive study, adult patients (18 years and older) who applied to the COVID Outpatient Clinic completed the demographic data form and the neuropathic pain questionnaire. The patients were divided into positive and negative according to the PCR test results and the presence of neuropathic pain was compared. Results: In total, 440 participants included in the study. Among 301 who stated to had any complaints, 197 (65.4%) had pain. The intensity of their pain was 5.8 ± 2.4 (0 – no pain and 10 – the most severe pain of life). Neuropathic pain component was present in 29.2% of the patients. Among the first admissions, neuropathic pain component was observed significantly higher in those with positive PCR test (55.0%) than negative ones (23.8%), and the Odd's ratio was calculated as 3.911. Conclusions: COVID-19 virus is thought to have neuroinvasion and neurotropic effects. In this study, neuropathic pain specifically was evaluated in COVID-19 patients, and the frequency of neuropathic pain was significantly higher in PCR confirmed COVID-19 patients at the onset of the disease. [ABSTRACT FROM AUTHOR]

Background: Nasopharyngeal (NP) and oropharyngeal (OP) swab sampling for coronavirus disease 2019 (COVID-19) diagnosis may lead to release of particles of varying sizes and increase the exposure risk for health care workers (HCWs). However, there is limited evidence for effective methods to reduce occupational exposure from NP and OP swab sampling. This study aimed to reduce droplet-forming responses (DFRs) and the related exposure risk of NP and OP swab sampling by administering 10% lidocaine spray (LS) to the NP and OP areas prior to conducting swab tests. Methods: This quasi-experimental study was conducted with 100 patients who presented to our tertiary care hospital with symptoms of COVID-19 between December 1 and 15, 2020. First, NP and OP swabbings were performed on each patient. Thereafter, LS was applied to the OP and NP regions, and the swab samples were taken once again. Frequency of DFRs and real-time polymerase chain reaction (RT-PCR) test results before and after LS application were recorded for comparison. In addition, the cycle threshold (Ct) was used as a proxy indicator for SARS-CoV-2 viral load in COVID-19 positive cases. Findings: Significant differences in OP DFR frequencies before and after LS intervention were found (37% and 9%, respectively), as well as before and after NP DFR (31% and 18%, respectively). The mean Ct values for the positive samples did not differ before and after applying LS. Conclusion: Our results suggest that applying LS to the OP and NP area prior to swab testing reduces DFR frequencies without affecting (RT-PCR) test results for SARS-CoV-2 and may increase patient and practitioner comfort. [ABSTRACT FROM AUTHOR]

This work has aimed to create a PCR test to identify avian and mammalian DNA in meat products. The test is based on phylogenetic analysis of 18S ribosomal RNA (rRNA) of four major groups of Tetrapod: Amphibia, Reptilia, Mammalia, and Aves. 18S rDNA complete coding sequences from GenBank have been used for phylogenetic analysis by the Maximum Likelihood method. The alignment of these 18S rDNA sequences has been used for PCR primers modeling. We have received the following PCR fragment for these primers: for birds – 97 base pairs (bp), and for mammals − 134 bp. The difference between them in 37 bp is sufficient for separating these fragments in standard agarose gel. We have tested this PCR to identify avian or mammalian DNA in sausage products and confirmed the suitability of this test for avian (chicken) and mammalian (sheep, cows) meat identification and meat identification in sausage products.

The rapid spread of highly transmissible respiratory infections in carceral settings occurs due to their conglomerate nature. The COVID-19 pandemic has resulted in large outbreaks in jails and prisons in many settings. Herein, we describe an outbreak of SARS-CoV2 infection in a prison in Alicante, Spain. Prior to January 2021, testing for coronavirus infection was not widely available in jails and prisons nationwide. Offering of testing services in Spanish carceral facilities, coincided with the deployment of COVID-19 vaccination in the larger community. However, COVID-19 vaccine role out of incarcerated individuals occurred later during the deployment plan. With the identification of the initial cases of this outbreak, two units of the facility were assigned for population management: one for inmates with confirmed infection by positive PCR detection of SARS-COV-2 infection in nasopharyngeal swabs. Inmates with confirmed exposure and thus considered close contacts were place in a second isolation unit. Functional quarantine was employed in some instances. A reactive testing strategy was instituted at baseline, and at 7 and 14 days of nasopharyngeal specimens by PCR. A total of 1,097 nasopharyngeal specimens were obtained for PCR testing during the outbreak, which lasted a total of 80 days between the index case the end of medical isolation of the last case. A total of 103 COVID-19 cases were identified during the outbreak. Of these, three inmates developed severe manifestations requiring hospitalization, and one died. Were identified, among which there were three hospitalized and one deceased. Among cases and confirmed contacts, we conducted close clinical monitoring, symptom screening, and daily temperature checks. The implementation of these interventions along with early medical isolation of cases, quarantining of contacts, and interval testing to detect presymptomatic or asymptomatic cases were instrumental in containing this outbreak.

The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place within the context of the world-wide SARS-CoV-2 crisis. Here, for the first time in history, laboratory test results have a dramatic impact on political decisions. Therefore, transparent, comprehensible, and reliable data is mandatory. It is in the nature of wet lab tests that their quality and outcome are influenced by multiple factors reducing their performance by handling procedures, underlying test protocols, and analytical reagents. These limitations in sensitivity and specificity have to be taken into account when calculating the real test results. As a resolution method, we have developed a Bayesian calculator, the Bayes Lines Tool (BLT), for analyzing disease prevalence, test sensitivity, test specificity, and, therefore, true positive, false positive, true negative, and false negative numbers from official test outcome reports. The calculator performs a simple SQL (Structured Query Language) query and can easily be implemented on any system supporting SQL. We provide an example of influenza test results from California, USA, as well as two examples of SARS-CoV-2 test results from official government reports from The Netherlands and Germany-Bavaria, to illustrate the possible parameter space of prevalence, sensitivity, and specificity consistent with the observed data. Finally, we discuss this tool’s multiple applications, including its putative importance for informing policy decisions.

Copyright of Rheuma Plus is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

OBJECTIVE: People experiencing homelessness have peculiar characteristics that make them more vulnerable to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transmission and to more serious forms of Coronavirus Disease 19 (COVID-19). The aim of this study was to evaluate the prevalence of SARS-CoV-2 infection in the homeless population assisted by the primary care services of the Eleemosynaria Apostolica, Vatican City. PATIENTS AND METHODS: Persons experiencing homelessness and the volunteers assisting them were tested for COVID-19 through PCR and antigen rapid test between October 1st, 2020, and June 5th, 2021, in the clinical facilities of the Eleemosynaria Apostolica. RESULTS: A total of 1665 subjects from 96 different countries in five continents were included in the study; age range was 1-90 years. Overall, 2315 COVID-19 tests through nasopharyngeal swab were performed; 1052 Polymerase Chain Reaction (PCR) tests and 1263 antigen rapid tests. Nearly 40% of the subjects underwent both tests (n=650, 39.04%), 402 were tested with PCR test only (24.14%) and 613 with antigen test only (36.8%). PCR tests were negative in 966 cases and positive in 86 (8.17%), while antigen tests were negative in 1205 cases and positive in 58 (4.59%). The number of positive cases varied over time, with a drastic increase during the winter months of 2020 and a progressive decrease over 2021. Among positive cases, 24.41% were symptomatic; symptoms included fever, breathing difficulties, anosmia/hyposmia, cough, headache, and diarrhea. CONCLUSIONS: This study reported an overall prevalence of SARS-CoV-2 infection in our sample slightly above 8%. Additional data on viral genome through sequencing of SARS-CoV-2 in positive cases are of utmost importance to help identify variants and implement specific infection control measures. [ABSTRACT FROM AUTHOR]

Background: COVID-19 has spread worldwide since its emergence in 2019. In contrast to many other countries with epidemics, Japan differed in that it avoided lockdowns and instead asked people for self-control. A travel campaign was conducted with a sizable budget, but the number of PCR tests was severely limited. These choices may have influenced the course of the epidemic. Methods: The increase or decrease in the classes of SARS-CoV-2 variants was estimated by analyzing the published sequences with an objective multivariate analysis. This approach observes the samples in multiple directions, digesting complex differences into simpler forms. The results were compared over time with the number of confirmed cases, PCR tests, and overseas visitors. The kinetics of infection were analyzed using the logarithmic growth rate. Results: The declared states of emergency failed to alter the movement of the growth rate. Three epidemic peaks were caused by domestically mutated variants. In other countries, there are few cases in which multiple variants have peaked. However, due to the relaxation of immigration restrictions, several infective variants have been imported from abroad and are currently competing for expansion, creating the fourth peak. By April 2021, these foreign variants exceeded 80%. The chaotic situation in Japan will continue for some time, in part because no effort has been made to identify asymptomatic carriers, and details of the vaccination program are undecided. [ABSTRACT FROM AUTHOR]

The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place within the context of the world-wide SARS-CoV-2 crisis. Here, for the first time in history, laboratory test results have a dramatic impact on political decisions. Therefore, transparent, comprehensible, and reliable data is mandatory. It is in the nature of wet lab tests that their quality and outcome are influenced by multiple factors reducing their performance by handling procedures, underlying test protocols, and analytical reagents. These limitations in sensitivity and specificity have to be taken into account when calculating the real test results. As a resolution method, we have developed a Bayesian calculator, the Bayes Lines Tool (BLT), for analyzing disease prevalence, test sensitivity, test specificity, and, therefore, true positive, false positive, true negative, and false negative numbers from official test outcome reports. The calculator performs a simple SQL (Structured Query Language) query and can easily be implemented on any system supporting SQL. We provide an example of influenza test results from California, USA, as well as two examples of SARS-CoV-2 test results from official government reports from The Netherlands and Germany-Bavaria, to illustrate the possible parameter space of prevalence, sensitivity, and specificity consistent with the observed data. Finally, we discuss this tool’s multiple applications, including its putative importance for informing policy decisions.

The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place within the context of the world-wide SARS-CoV-2 crisis. Here, for the first time in history, laboratory test results have a dramatic impact on political decisions. Therefore, transparent, comprehensible, and reliable data is mandatory. It is in the nature of wet lab tests that their quality and outcome are influenced by multiple factors reducing their performance by handling procedures, underlying test protocols, and analytical reagents. These limitations in sensitivity and specificity have to be taken into account when calculating the real test results. As a resolution method, we have developed a Bayesian calculator, the Bayes Lines Tool (BLT), for analyzing disease prevalence, test sensitivity, test specificity, and, therefore, true positive, false positive, true negative, and false negative numbers from official test outcome reports. The calculator performs a simple SQL (Structured Query Language) query and can easily be implemented on any system supporting SQL. We provide an example of influenza test results from California, USA, as well as two examples of SARS-CoV-2 test results from official government reports from The Netherlands and Germany-Bavaria, to illustrate the possible parameter space of prevalence, sensitivity, and specificity consistent with the observed data. Finally, we discuss this tool’s multiple applications, including its putative importance for informing policy decisions.