scholarly journals Dynamical Pool-Size Optimization for the SARS-CoV-2 PCR Test

2021 ◽  
Author(s):  
Juri Smirnov ◽  
Thomas Fenner
Keyword(s):  
Risk Assessment ◽  
Pool Size ◽  
Size Optimization ◽  
Rt Pcr ◽  
Efficiency Loss ◽  
Test Strategy ◽  
Highly Effective ◽  
Pcr Test ◽  
Risk Assessment Scheme

In this work, we put forward a novel test strategy, that allows to significantly increase the test capacity for SARS-CoV-2. The test strategy is based on an a priory risk assessment scheme, that allows to dynamically find and adapt an optimal clustering size of test pools. We, furthermore, suggest a method to overcome the efficiency loss of test clustering by avoiding concentration losses in the test samples. We validated our method with several thousand probe pools performing RT-PCR tests, and found it highly effective.

scholarly journals The performance of the SARS-CoV-2 RT-PCR test as a tool for detecting SARS-CoV-2 infection in the population. A survey of routine laboratory RT-PCR test results from the region of Muenster, Germany

2021 ◽  
Author(s):  
Andreas Stang ◽  
Johannes Robers ◽  
Birte Schonert ◽  
Karl-Heinz Joeckel ◽  
Angela Spelsberg ◽  
...  
Keyword(s):  
The Elderly ◽  
Population Based ◽  
Test Results ◽  
Rt Pcr ◽  
Test Strategy ◽  
National Test ◽  
Roche Diagnostics ◽  
Regional Hospitals ◽  
Test Result ◽  
Pcr Test

Objectives: To evaluate the population-based performance of the SARS-CoV-2 RT-PCR test as a tool for detecting SARS-CoV-2 infection during the pandemic in 2020. Methods: We analysed SARS-CoV-2 RT-PCR results of 162,457 people living in Muenster, Germany screened at nursing homes, testing sites, at schools, regional hospitals, and by general practitioners. All PCRs were done with the same cobas SARS-CoV-2 RT-PCR system (Roche Diagnostics). We stratified positive RT-PCR results by cycle threshold (Ct) values, periods of the national test strategy, age, sex, and symptoms. Results: Among 162,457 individuals, 4164 (2.6%) had a positive RT-PCR test result, defined as Ct<40. Depending on the national test strategy, higher positive rates were associated with testing predominantly symptomatic people. Children (0-9 years) and older adults (70+ years). Only 40.6% of test positives showed low Ct values < 25 (potentially infectious). The percentage of Ct values below 25 was lower among children (0-9), adolescents (10-19), and among the elderly (70+ years). Conclusions: RT-PCR testing as a tool for mass screening should not be used alone as a base for pandemic decision making including measures such as quarantine, isolation, and lockdown.

scholarly journals Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 730
Author(s):  
Magda Rybicka ◽  
Ewa Miłosz ◽  
Krzysztof Piotr Bielawski
Keyword(s):  
Mass Spectrometry ◽  
Gold Standard ◽  
Viral Genome ◽  
False Negative ◽  
Rt Pcr ◽  
Rna Detection ◽  
Maldi Tof ◽  
Negative Results ◽  
False Negative Results ◽  
Pcr Test

At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome.

scholarly journals The role of CT imaging for management of COVID-19 in epidemic area: early experience from a University Hospital

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Vikram rao Bollineni ◽  
Koenraad Hans Nieboer ◽  
Seema Döring ◽  
Nico Buls ◽  
Johan de Mey
Keyword(s):  
Ct Scan ◽  
Predictive Value ◽  
Ct Imaging ◽  
Chest Ct ◽  
University Hospital ◽  
Rt Pcr ◽  
Ct Findings ◽  
Epidemic Area ◽  
Chest Ct Scan ◽  
Pcr Test

Abstract Background To evaluate the clinical value of the chest CT scan compared to the reference standard real-time polymerase chain reaction (RT-PCR) in COVID-19 patients. Methods From March 29th to April 15th of 2020, a total of 240 patients with respiratory distress underwent both a low-dose chest CT scan and RT-PCR tests. The performance of chest CT in diagnosing COVID-19 was assessed with reference to the RT-PCR result. Two board-certified radiologists (mean 24 years of experience chest CT), blinded for the RT-PCR result, reviewed all scans and decided positive or negative chest CT findings by consensus. Results Out of 240 patients, 60% (144/240) had positive RT-PCR results and 89% (213/240) had a positive chest CT scans. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of chest CT in suggesting COVID-19 were 100% (95% CI: 97–100%, 144/240), 28% (95% CI: 19–38%, 27/240), 68% (95% CI: 65–70%) and 100%, respectively. The diagnostic accuracy of the chest CT suggesting COVID-19 was 71% (95% CI: 65–77%). Thirty-three patients with positive chest CT scan and negative RT-PCR test at baseline underwent repeat RT-PCR assay. In this subgroup, 21.2% (7/33) cases became RT-PCR positive. Conclusion Chest CT imaging has high sensitivity and high NPV for diagnosing COVID-19 and can be considered as an alternative primary screening tool for COVID-19 in epidemic areas. In addition, a negative RT-PCR test, but positive CT findings can still be suggestive of COVID-19 infection.

scholarly journals Delayed pulmonary embolism after COVID-19 pneumonia: a case report

2020 ◽  
Author(s):  
Mohamad Kanso ◽  
Thomas Cardi ◽  
Halim Marzak ◽  
Alexandre Schatz ◽  
Loïc Faucher ◽  
...  
Keyword(s):  
Risk Factors ◽  
Intensive Care Unit ◽  
Pulmonary Embolism ◽  
Acute Pulmonary Embolism ◽  
Index Hospitalization ◽  
Rt Pcr ◽  
Moderate Severity ◽  
Respiratory Status ◽  
Case Summary ◽  
Pcr Test

Abstract Background  Since the onset of the COVID-19 pandemic, several cardiovascular manifestations have been described. Among them, venous thromboembolism (VTE) seems to be one of the most frequent, particularly in intensive care unit patients. We report two cases of COVID-19 patients developing acute pulmonary embolism (PE) after discharge from a first hospitalization for pneumonia of moderate severity. Case summary  Two patients with positive RT-PCR test were initially hospitalized for non-severe COVID-19. Both received standard thromboprophylaxis during the index hospitalization and had no strong predisposing risk factors for VTE. Few days after discharge, they were both readmitted for worsening dyspnoea due to PE. One patient was positive for lupus anticoagulant. Discussion  Worsening respiratory status in COVID-19 patients must encourage physicians to search for PE since SARS-CoV-2 infection may act as a precipitant risk factor for VTE. Patients may thus require more aggressive and longer thromboprophylaxis after COVID-19 related hospitalization.

Death and COVID-19 Anxiety in Home-Quarantined Individuals Aged 65 and Over During the Pandemic

2021 ◽  
pp. 003022282110598
Author(s):  
Hümeyra Aslaner ◽  
Betül Özen ◽  
Zeliha K. Erten ◽  
Mebrure Beyza Gökçek
Keyword(s):  
Polymerase Chain Reaction ◽  
Death Anxiety ◽  
Short Form ◽  
Anxiety Score ◽  
Test Results ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Test Result ◽  
Pcr Test

Urgent measures were taken for those at the age of 65 and over who were at the risk group all over the world due to the COVID-19 pandemic. It is known that many individuals at the age of 65 and over have experienced anxiety due to the uncertainties. This study aimed to determine the anxiety and death anxiety in individuals aged 65 and over who were isolation at home due to being diagnosed with COVID-19 or being in contact during the pandemic process. The study is descriptive and cross-sectional. It was performed with 656 home-quarantined individuals aged between 65–80 years with positive or negative real-time polymerase chain reaction (RT-PCR) test result. A form including questions about the death anxiety and the Coronavirus Anxiety Scale Short Form prepared by the researchers were administered to the individuals by phone call. Of the participants, 49.5% were male. Median COVID-19 anxiety score was 4 (0–18). Anxiety scores of the male and female participants were similar. Participants with negative polymerase chain reaction (PCR) results and those with death anxiety had higher COVID anxiety scores. Death anxiety has increased by 1.661 times in male gender, 1.983 times in RT-PCR positivity and 0.146 times in the presence of symptoms. Individuals with positive COVID-19 test results or those aged 65 and over who had death anxiety and negative COVID-19 test result but who were in home-isolation due to being a contact had higher anxiety score. For this reason, those with death anxiety can be supported in line with their religious beliefs to reduce anxiety. Those with negative PCR test results in quarantine can be adequately informed about the COVID-19.

Accuracy of Computed Tomography for Detection of COVID-19 among Suspected Patients

2021 ◽  
Vol 15 (9) ◽  
pp. 2474-2476
Author(s):  
Maham Munir Awan ◽  
Afshan Noreen ◽  
Farah Kalsoom ◽  
Muhammad Tahir ◽  
Umaima Majeed ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Predictive Value ◽  
Gold Standard ◽  
Radiology Department ◽  
True Positive ◽  
Test Results ◽  
Rt Pcr ◽  
Radiological Society ◽  
Medical University ◽  
Pcr Test

Objective: To determine the accuracy of CT chest in diagnosis of COVID-19 taking RT-PCR-testing as gold standard. Materials and Methods: A total of 150 patients of suspicion of COVID-19 who were referred for CT Chest in Radiology Department of Nishtar Medical University Multan from June-2020 to May-2021 were included. In all patients, two RT-PCR test results were obtained with 7 days of admission in hospital. Presence of any of these positive was labelled as COVID-19 infection. CT chest was performed in all patients within 2 days of admission in hospital using 128 slices CT scan machine. The diagnosis of COVID-19 infection was made according to the recommendations by Radiological Society of North America (RSNA) protocol. Results: Mean age was 51.3±14.7 years. 78 (52%) patients were male and 72 (48%) patients were female. RTPCR test was positive in 89 (59.3%) patients. While the CT chest findings were suggestive of COVID-19 infection in 130 (86.7%) patients. The sensitivity of CT chest was 95.5%, specificity 26.2%, PPV wad 65.4% and NPV was 80.0%. Conclusion: CT chest has a very good sensitivity for detection of COVID-19, it can be used as a rapid diagnostic tool especially in areas of pandemic. However, the specificity of CT chest is low, that can limit its use in low COVID-19 affected areas. Keywords: COVID-19, Computed tomography, False Positive, True Positive, Positive Predictive Value, Negative Predictive Value.

DIAGNOSTIC ROLE OF CHEST CT USING CO-RADS CATEGORIZATION IN SARS-COV-2 INFECTION WITH EMPHASIS ON IMPACT OF CT IN PATIENTS WITH DELAYED OR NEGATIVE INITIAL RTPCR TEST

2021 ◽  
pp. 51-52
Author(s):  
Tharani Putta ◽  
Kaushik Deconda
Keyword(s):  
Diagnostic Performance ◽  
Virus Disease ◽  
Vital Role ◽  
Chest Ct ◽  
Lung Involvement ◽  
Test Results ◽  
Rt Pcr ◽  
Diagnostic Role ◽  
Pcr Test

BACKGROUND AND OBJECTIVE: Role of chest CT in diagnosis of corona virus disease 2019 (COVID-19) has been controversial. The purpose of this study is to evaluate the diagnostic performance of chest CT when utilizing COVID-19 Reporting and Data System (CO-RADS). METHODOLOGY: Retrospective study including consecutive patients with positive SARS-CoV-2 RT-PCR test (initial or repeat test) and chest CT done in our institute between June and September 2020. Spectrum of CT ndings, CO-RADS score and 25 point CT severity score (CTSS) were recorded. RESULTS: A total of 300 consecutive patients with SARS-CoV-2 infection were included in the analysis. Out of the 168 patients who underwent CT prior to positive RT-PCR result, 125 (74.4%) had CO-RADS 3, 4 or 5 score on chest CT. 32 study patients (10.6%) had initial negative RT-PCR of which 24 (75%) had CO-RADS 4 or 5 score. Of the total patients with CO-RADS 3 to 5 score (227), 20 (8.8%) had severe lung involvement (CTSS 18-25), 83 (36.6%) had moderate lung involvement (CTSS 8-17) and 124 (54.6%) had mild lung involvement (CTSS 1-7). The mean CTSS was 7.9 with mean lobar score being higher in lower lobes (RLL=1.82, LLL=1.78) compared to the upper and middle lobes (RUL=1.61, RML=1.19, LUL=1.53). CONCLUSION:CT using CO-RADS scoring system has good diagnostic performance. In addition to assessing disease severity, it plays a vital role in triage of patients with suspected COVID-19 especially when there is limited availability of SARS-CoV-2 RT-PCR tests, delay in RT-PCR test results or in negative RT-PCR cases when there is high index of clinical suspicion.

scholarly journals Assessment of the National Test Strategy on the Development of the COVID-19 Pandemic in Denmark

Epidemiologia ◽  
2021 ◽  
Vol 2 (4) ◽  
pp. 540-552
Author(s):  
Peter Kamp Busk ◽  
Thomas Birk Kristiansen ◽  
Allan Engsig-Karup
Keyword(s):  
Educational Institutions ◽  
Free Access ◽  
Testing Strategy ◽  
Rt Pcr ◽  
Test Strategy ◽  
Testing Frequency ◽  
National Test ◽  
The Relationship ◽  
Antigen Testing

During the COVID-19 pandemic, Denmark has pursued a mass testing strategy culminating in the testing of 12.167 individuals per 100,000 inhabitants per day during the spring of 2021. The strategy included free access to COVID-19 testing, and since 2021, compulsory documentation for negative tests or vaccination has been required for access to workplace, educational institutions, restaurants, and many other places. Testing and subsequent isolation if testing was positive were voluntary. The present study provides an analysis of whether testing frequency in Denmark showed any correlation to hospitalizations throughout the relevant stages of the pandemic. Mass testing was found not to correlate significantly with the number of hospitalizations during the pandemic. Interestingly, during the highest level of testing in spring 2021 the fraction of positive tests increased slightly; thus, the Danish mass testing strategy, at its best, failed to reduce the prevalence of COVID-19. Furthermore, the relationship between positives in antigen testing and in rt-PCR testing indicated that many patients were not tested early in their infection when the risk of transmission was at the highest. In conclusion, the Danish mass testing strategy for COVID-19 does not appear to have a detectable correlation to the number of hospitalizations due to COVID-19.

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