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Rational use of SARS-CoV-2 polymerase chain reaction tests within institutions caring for the vulnerable.

ABSTRACT: Institutions such as hospitals and nursing or long-stay residential homes accommodate individuals at considerable risk of mortality should they acquire SARS-CoV-2 infection. In these settings, polymerase chain reaction tests play a central role in infection prevention and control. Here, we argue that both false negative and false positive tests are possible and that careful consideration of the prior probability of infection and of test characteristics are needed to prevent harm. We outline evidence suggesting that regular systematic testing of asymptomatic and pre-symptomatic individuals could play an important role in reducing transmission of SARS-CoV-2 within institutions. We discuss how such a programme might be organised, arguing that frequent testing and rapid reporting of results are particularly important. We highlight studies demonstrating that polymerase chain reaction testing of pooled samples can be undertaken with acceptable loss of sensitivity, and advocate such an approach where test capacity is limited. We provide an approach to calculating the most efficient pool size. Given the current limitations of tests for SARS-CoV-2 infection, physical distancing and meticulous infection prevention and control will remain essential in institutions caring for vulnerable people.

SUBMITTER: Yates TA

PROVIDER: S-EPMC7489272 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Rational use of SARS-CoV-2 polymerase chain reaction tests within institutions caring for the vulnerable.

Yates Tom A TA Cooke Graham S GS MacPherson Peter P

F1000Research 20200702

Institutions such as hospitals and nursing or long-stay residential homes accommodate individuals at considerable risk of mortality should they acquire SARS-CoV-2 infection. In these settings, polymerase chain reaction tests play a central role in infection prevention and control. Here, we argue that both false negative and false positive tests are possible and that careful consideration of the prior probability of infection and of test characteristics are needed to prevent harm. We outline evid ...[more]

PMID: 32968484

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Project description:BACKGROUND:Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on reverse transcriptase polymerase chain reaction (RT-PCR) are being used to rule out infection among high-risk persons, such as exposed inpatients and health care workers. It is critical to understand how the predictive value of the test varies with time from exposure and symptom onset to avoid being falsely reassured by negative test results. OBJECTIVE:To estimate the false-negative rate by day since infection. DESIGN:Literature review and pooled analysis. SETTING:7 previously published studies providing data on RT-PCR performance by time since symptom onset or SARS-CoV-2 exposure using samples from the upper respiratory tract (n = 1330). PATIENTS:A mix of inpatients and outpatients with SARS-CoV-2 infection. MEASUREMENTS:A Bayesian hierarchical model was fitted to estimate the false-negative rate by day since exposure and symptom onset. RESULTS:Over the 4 days of infection before the typical time of symptom onset (day 5), the probability of a false-negative result in an infected person decreases from 100% (95% CI, 100% to 100%) on day 1 to 67% (CI, 27% to 94%) on day 4. On the day of symptom onset, the median false-negative rate was 38% (CI, 18% to 65%). This decreased to 20% (CI, 12% to 30%) on day 8 (3 days after symptom onset) then began to increase again, from 21% (CI, 13% to 31%) on day 9 to 66% (CI, 54% to 77%) on day 21. LIMITATION:Imprecise estimates due to heterogeneity in the design of studies on which results were based. CONCLUSION:Care must be taken in interpreting RT-PCR tests for SARS-CoV-2 infection-particularly early in the course of infection-when using these results as a basis for removing precautions intended to prevent onward transmission. If clinical suspicion is high, infection should not be ruled out on the basis of RT-PCR alone, and the clinical and epidemiologic situation should be carefully considered. PRIMARY FUNDING SOURCE:National Institute of Allergy and Infectious Diseases, Johns Hopkins Health System, and U.S. Centers for Disease Control and Prevention.

Project description:BackgroundTesting, traceability, and isolation actions are a central strategy defined by the World Health Organization to contain the COVID-19 pandemic. In this sense, the countries have had difficulties in counting the number of people infected with SARS-CoV-2. Errors in reporting results are a common factor, as well as the lack of interoperability between laboratories and governments. Approaches aimed at sending spreadsheets via email expose patients' privacy and have increased the probability of errors due to retyping, which generates a delay in the notification of results.ObjectiveThis study aims to design and develop an interoperable platform to report polymerase chain reaction (PCR) SARS-CoV-2 tests from laboratories to the Chilean government.MethodsThe methodology to design and develop the interoperable platform was comprised of six well-structured stages: (1) creation of a minimum data set for PCR SARS-CoV-2 tests, (2) modeling processes and end points where institutions interchange information, (3) standards and interoperability design, (4) software development, (5) software testing, and (6) software implementation.ResultsThe interoperable Fast Healthcare Interoperability Resources (FHIR) platform to report PCR SARS-CoV-2 tests from laboratories to the Chilean government was successfully implemented. The platform was designed, developed, tested, and implemented following a structured methodology. The platform's performance to 1000 requests resulted in a response time of 240 milliseconds, throughput of 28.3 requests per second, and process management time of 131 milliseconds. The security was assured through a private network exclusive to the Ministry of Health to ensure confidentiality and integrity. The authorization and authentication of laboratories were implemented with a JavaScript Object Notation Web Token. All the PCR SARS-CoV-2 tests were accessible through an application programming interface gateway with valid credentials and the right access control list.ConclusionsThe platform was implemented and is currently being used by UC Christus Laboratory. The platform is secure. It was tested adequately for confidentiality, secure authorization, authentication, and message integrity. This platform simplifies the reporting of PCR SARS-CoV-2 tests and reduces the time and probability of mistakes in counting positive cases. The interoperable solution with FHIR is working successfully and is open for the community, laboratories, and any institution that needs to report PCR SARS-CoV-2 tests.

Project description:Background and aimDifferent polymerase chain reaction (PCR) techniques have and are still being used for the direct detection of Brucella DNA in serum samples of different animal species and humans without being validated or properly validated, resulting in discrepancies. Thus, this study aimed to evaluate the diagnostic performance of the TaqMan Real-Time-PCR (RT-PCR) targeting the bcsp31 gene versus conventional PCR for the accurate diagnosis of brucellosis at the genus level in cattle sera.Materials and methodsOne hundred and eighty-four serum samples were collected from bacteriologically positive and negative cows with ages ranging from 1 to 5 years old at some infected private farms in the Nile Delta under quarantine measures as well as brucellosis free farms. These samples were classified into four groups after serological diagnosis and investigated by TaqMan RT-PCR and conventional PCR targeting the IS711 gene for Brucella DNA detection. The diagnostic performance characteristics of both PCR techniques were estimated considering the bacteriological results as a gold standard.ResultsTaqMan RT-PCR revealed superiority over conventional PCR; it was able to detect Brucella DNA in 95% (67/70) and 89% (25/28) of the cattle sera samples belonging to Group 1 (serologically and bacteriologically positive) and Group 2 (serologically negative but bacteriologically positive), respectively. On evaluating the diagnostic performance, TaqMan RT-PCR showed superior diagnostic sensitivity (93.9%), diagnostic specificity (88.4%), performance index (182.3), almost perfect kappa agreement (0.825±0.042), strong positive correlation (r=0.826), high accuracy based on the receiver operating characteristic (ROC) curve, and area under the ROC curve (0.911) at p<0.05 and CI of 95%.ConclusionA cattle serum sample is not the metric of choice for targeting Brucella genomic DNA by conventional PCR. The time-saving and rapid TaqMan RT-PCR method revealed a better diagnostic performance in the detection of Brucella DNA in cattle sera. Such performance offered by TaqMan RT-PCR may be considered a step toward the possibility of using such technology in the direct differentiation between Brucella-infected and -vaccinated cattle immunized by smooth vaccines from cattle sera using primers specific for such vaccines.

Dataset Information

Rational use of SARS-CoV-2 polymerase chain reaction tests within institutions caring for the vulnerable.

Publications

Rational use of SARS-CoV-2 polymerase chain reaction tests within institutions caring for the vulnerable.

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