A Pooled RT-PCR Testing Strategy for More Efficient Covid-19 Pandemic Management

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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Application of a Serial Antigen Based Testing Strategy for SARS-CoV-2 and Student Adherence in a University Setting, Wisconsin — October–November 2020

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab472 ◽

2021 ◽

Author(s):

John Paul Bigouette ◽

Laura Ford ◽

Ian Pray ◽

Kimberly Langolf ◽

Juliana Kahrs ◽

...

Keyword(s):

Male Students ◽

Test Results ◽

Antigen Test ◽

Testing Strategy ◽

Rt Pcr ◽

Testing Strategies ◽

Serial Testing ◽

Polymerase Chain ◽

Antigen Tests ◽

University Setting

Abstract Background Serial SARS-CoV-2 testing has been implemented at institutions of higher education (IHEs) and other settings. Testing strategies can include algorithms specifying confirmatory reverse transcription polymerase chain reaction (RT-PCR) testing after an antigen test. It is unknown how testing strategies perform detecting SARS-CoV-2, including individual adherence to serial testing requirements. Methods Student serial testing adherence was defined as completing ≥80% of weekly tests from October 5–November 14, 2020 and evaluated using logistic regression. Medical records were reviewed for all positive antigen test encounters and 10% of daily negative antigen test encounters during October 19–November 30, 2020. Results were used to estimate the proportion of individuals requiring only antigen tests, requiring and completing RT-PCR testing, and associated costs of tests. Results Two-thirds (66.5%; 1,166/1,754) of eligible on-campus students adhered to weekly testing; female students were more adherent (adjusted odds ratio [aOR]:2.07, 95% CI:1.66–2.59) than male students. Of all antigen test encounters, 11.5% (1,409/12,305) reported >1 COVID-19 symptoms. Of non-COVID-19 exposed antigen test encounters, 88% (10,386/11,769) did not require confirmatory RT-PCR testing. Only 28% (390/1,387) of testing encounters had an associated recommended confirmatory RT-PCR test performed. We estimated the testing strategy captured 61% (235/389) of predicted RT-PCR positive specimens. Conclusions At this IHE, most students voluntarily adhered to serial testing. The majority of antigen test results did not require confirmatory RT-PCR testing, but when required, most students did not obtain it. Including strategies to increase the proportion of individuals obtaining indicated confirmatory testing might improve the testing program’s performance.

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EXPRESS: Performance characteristics of five SARS-CoV-2 serological assays: clinical utility in healthcare workers

Annals of Clinical Biochemistry International Journal of Laboratory Medicine ◽

10.1177/00045632211012728 ◽

2021 ◽

pp. 000456322110127

Author(s):

Emma Heffernan ◽

Lisa Kennedy ◽

Margaret Hannan ◽

Navneet Ramlaul ◽

Stephanie Denieffe ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Acute Infection ◽

Elisa Assay ◽

Testing Strategy ◽

Rt Pcr ◽

Important Indicator ◽

Study Objective ◽

Previous Infection ◽

Asymptomatic Individuals ◽

Prior Infection

Study Objective: SARS-CoV-2 which causes Coronavirus disease (COVID-19) continues to cause significant morbidity and mortality. The diagnosis of acute infection relies on RT-PCR based viral detection. The objective of this study was to evaluate the optimal serological testing strategy for anti-SARS-CoV-2 antibodies which provides an important indicator of prior infection and potential short-term immunity. Methods: The sensitivity and specificity of four different ELISA assays (Euroimmun IgG, Euroimmun NCP-IgG, Fortress and DIAsource) and one CLIA assay (Roche ELECSYS) were evaluated in 423 samples; 137 patients with confirmed RT-PCR COVID-19 infection (true positives), and 100 pre-pandemic samples collected prior to October 2019 (true negatives). A further 186 samples were collected from healthcare staff and analysed by all five assays. Results: The Fortress ELISA assay demonstrated the highest sensitivity and specificity followed by the Roche ECLIA assay. The highest overall sensitivity came from the assays that measured total antibody (IgM-IgG combined) and the three assays that performed the best (Fortress, Roche, Euroimmun IgG) all have different antigens as their target proteins which suggests that antigen target does not affect assay performance. In mildly symptomatic participants with either a negative RT-PCR or no RT-PCR performed, 16.76% had detectable antibodies suggesting previous infection. Conclusions: We recommend a combined testing strategy utilising assays with different antigenic targets using the fully automated Roche ECLIA assay and confirming discordant samples with the Fortress Total Antibody ELISA assay. This study provides an important indicator of prior infection in symptomatic and asymptomatic individuals.

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Flu Viral Multiplex Testing and its Implication for COVID-19 Testing

New Emirates Medical Journal ◽

10.2174/0250688201999200908150437 ◽

2020 ◽

Vol 01 ◽

Author(s):

Aaron Han ◽

Janet Hicban

Keyword(s):

Viral Agent ◽

Testing Strategy ◽

Rt Pcr ◽

Chain Reaction ◽

Parallel Testing ◽

Appropriate Treatment ◽

Simultaneous Testing ◽

Polymerase Chain ◽

The Impact ◽

Rule Out

Background: The diagnosis of viral causes for flu-like syndromes have been positively impacted by the availability of molecular assays. In recent years, syndromic multiplex panels have been able to give rapid turn-around-times and highly accurate results. We examine the use of this test during the first four months of 2020 during the COVID-19 pandemic. Methods: Retrospective review of 2145 patient results from multiplex syndromic flu panel using Biofire RP2 was performed. Cases in which parallel testing for COVID-19 by real-time polymerase chain reaction (RT-PCR) was compared. Results: 53% of the patients tested identified a viral agent. 13% of the positive cases were coinfection with more than a single virus. The most frequently detect virus(es) were rhinovirus/enterovirus, followed by coronaviruses (non-MERS, non COVID-19). One hundred patients had simultaneous testing for COVID-19. Seventeen (17%) had positive COVID-19 by RT-PCR. Three of these patients had coinfection with rhinovirus/enterovirus and COVID-19. The negative predictive value for COVID-19 based on a positive non-COVID agent was 95% in our sample. Conclusions: Viral syndromic panels are useful for rapid detection and appropriate treatment of patients. Our results suggest coinfection is infrequent, and we discuss the impact of COVID-19 on patient testing strategy. The use of multiplex panels is useful to provide accurate diagnosis and rule out important pathogens that have different treatment approaches.

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Predictors of characteristics associated with negative SARS-CoV-2 PCR test despite proven disease and association with treatment and outcomes. The COVID-19 RT-PCR Study.

10.1101/2020.09.14.20194001 ◽

2020 ◽

Author(s):

Jean Baptiste Lascarrou ◽

Gwenhael Colin ◽

Aurelie Le Thuaut ◽

Nicolas Serck ◽

Mickael Ohana ◽

...

Keyword(s):

False Negative ◽

Final Diagnosis ◽

Case Control ◽

Hospital Length ◽

Testing Strategy ◽

Rt Pcr ◽

Chain Reaction ◽

Polymerase Chain ◽

And Control ◽

Pcr Test

Background: Reverse transcriptase-polymerase chain reaction (RT PCR) testing is an important tool for the diagnosis of coronavirus disease 2019 (COVID19). However, performance concerns have recently emerged, especially about its sensitivity.. We hypothesized that clinical, biological and radiological characteristics of patients with false negative first RT-PCR testing, despite final diagnosis of COVID19, might differ from patients with positive first RT PCR. Methods: Case / control, multicenter study in which COVID19 patients with negative first RT PCR testing were matched to patients with positive first RT PCR on age, gender and initial admission unit (ward or intensive care). Results: Between March 30, and June 22, 2020, 80 cases and 80 controls were included. Neither proportion of death at hospital discharge, nor duration of hospital length stay differed between case and control patients (P=0.80 and P=0.54, respectively). In multivariate analysis, headache (adjusted OR: 0.07 [0.01 ; 0.49]; P=0.007) and fatigue/malaise (aOR: 0.16 [0.03 ; 0.81]; P=0.027) were associated with lower risk of false negative, whereas platelets > 207.103.mm-3 (aOR: 3.81 [1.10 ; 13.16]; P=0.034) and CRP > 79.8 mg.L-1 (aOR: 4.00 [1.21 ; 13.19]; P=0.023) were associated with higher risk of false negative. Interpretation: Patients with suspected COVID19 and higher inflammatory biological signs expected higher risk of false negative RT PCR testing. Strategy of serial RT PCR testings must be rigorously evaluated before adoption by clinicians.

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Testing of Healthcare Workers Exposed to COVID19 with Rapid Antigen Detection

10.1101/2020.08.12.20172726 ◽

2020 ◽

Author(s):

Victor Herrera ◽

Vincent Hsu ◽

Ademola Adewale ◽

Timothy Hendrix ◽

Lee Johnson ◽

...

Keyword(s):

Healthcare Workers ◽

Cost Effective ◽

Antigen Detection ◽

Testing Strategy ◽

Rt Pcr ◽

Asymptomatic Individuals ◽

Antigen Testing

There is a need to develop safe and cost-effective ways to test healthcare workers for COVID19. Here we describe a rapid antigen testing strategy in a cohort of 497 Healthcare workers exposed to SARS-CoV-2 that can be applied by systems facing a surge of COVID19 cases, increased exposures in their workforce and limited RT-PCR availability. Our findings support an expanded use for antigen testing beyond its current indication and highlights the importance of further studying this modality for the diagnosis of COVID19 on asymptomatic individuals.

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Detection of Nucleic Acids in Cells or Tissue Sections Using In situ Polymerase Chain Reaction (PCR)

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100162545 ◽

1996 ◽

Vol 54 ◽

pp. 16-17

Author(s):

J. R. Hully ◽

K. R. Luehrsen ◽

K. Aoyagi ◽

C. Shoemaker ◽

R. Abramson

Keyword(s):

Nucleic Acids ◽

Viral Infections ◽

Anatomical Location ◽

Rt Pcr ◽

Reverse Transcription Pcr ◽

Cellular Source ◽

Gene Transcripts ◽

Initial Description ◽

In Cells

The development of PCR technology has greatly accelerated medical research at the genetic and molecular levels. Until recently, the inherent sensitivity of this technique has been limited to isolated preparations of nucleic acids which lack or at best have limited morphological information. With the obvious exception of cell lines, traditional PCR or reverse transcription-PCR (RT-PCR) cannot identify the cellular source of the amplified product. In contrast, in situ hybridization (ISH) by definition, defines the anatomical location of a gene and/or it’s product. However, this technique lacks the sensitivity of PCR and cannot routinely detect less than 10 to 20 copies per cell. Consequently, the localization of rare transcripts, latent viral infections, foreign or altered genes cannot be identified by this technique. In situ PCR or in situ RT-PCR is a combination of the two techniques, exploiting the sensitivity of PCR and the anatomical definition provided by ISH. Since it’s initial description considerable advances have been made in the application of in situ PCR, improvements in protocols, and the development of hardware dedicated to in situ PCR using conventional microscope slides. Our understanding of the importance of viral latency or viral burden in regards to HIV, HPV, and KSHV infections has benefited from this technique, enabling detection of single viral copies in cells or tissue otherwise thought to be normal. Clearly, this technique will be useful tool in pathobiology especially carcinogenesis, gene therapy and manipulations, the study of rare gene transcripts, and forensics.

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