RT-PCR results during early SARS-CoV-2 infection course require cautious interpretation

1. The interpretation of reverse transcriptase polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was shown to require caution particularly early in the course of infection.

2. RT-PCR results, alone, were shown not to be sufficient to rule out infection when the clinical suspicion was high.

Evidence Rating Level: 2 (Good)

Study Rundown: Reverse transcriptase polymerase chain reaction tests are being used to “rule out” SARS-CoV-2 infection among high-risk people such as inpatients and health care workers. Therefore, it is important to determine the variation of the test predictive values with time from exposure and symptom onset to avoid false-negative tests rates. As such, this study estimated the false-negative rate per day since infection. A literature review and pooled analysis was conducted on seven previously published studies. The pooled analysis applied a Bayesian hierarchical model to estimate the false-negative rate by day since exposure and symptom onset. The study determined caution must be exercised when interpreting RT-PCR test results for SARS-CoV-2 infection during the early course of the infection. Furthermore, the test results, alone, should never supersede high clinical suspicion of infection. This literature review and pooled analysis was limited by the heterogeneity in the study designs of the individual published studies. The heterogeneity resulted in the imprecise estimates during the pooled analysis causing the potential loss of data and incomplete understanding of the false-negative rates of RT-PCR tests. Another limitation of the study is the Bayesian hierarchical model was only applicable for a one-time exposure, which does not account for the continual exposures present in a hospital setting. Nonetheless, this study was strengthened by the pooled analysis of seven different studies to determine the false-negative rate of RT-PCR for SARS-CoV-2 infections. For physicians, these findings highlighted the importance of using RT-PCR test results as a tool in determining SARS-CoV-2 infections along with clinical acuity.

Click to read the study in Annals of Internal Medicine

Relevant Reading: Diagnostic Performance of CT and Reverse Transcriptase-Polymerase Chain Reaction for Coronavirus Disease 2019: A Meta-Analysis

In-Depth [systematic review and meta-analysis]: This literature review analyzed data from seven previous studies on RT-PCR performance for SARS-CoV-2 infections. The seven studies had a combined study population enrolled of 1330 people. Inclusion criteria for the studies in the literature review included: use of an RT-PCR-based test; sample collection from upper respiratory tract; and reporting of time since symptom onset or exposure. The exclusion criteria for studies in the literature review included unclear definition of time between testing and symptom onset or exposure. Confirmed cases were defined as at least one positive RT-PCR test result. The statistical analysis consisted of the data being fit to a Bayesian hierarchical logistic regression model to test sensitivity. The model assumed exposure occurred five days before symptom onset. From the sensitivity, the false-negative rate was calculated for each day after exposure. The primary outcome was the false-negative rate of the RT-PCR test for each day after the initial exposure, which was known as day 0. The false-negative rate in an infected person over the four days prior to symptom onset decreased from 100% (95% confidence interval [CI], 100% to 100%) on day 1 to 67% (95% CI, 27% to 94%) on day 4. The day of symptom onset, day 5, the false-negative rate was 38% (95% CI, 18% to 65%). The rate continued to decrease after symptom onset until day 8 with a false-negative rate of 20% (95% CI, 12% to 30%). Beginning on day 9, the false-negative rate increased to 21% (95% CI, 13% to 31%) to 66% (95% CI, 54% to 77%) on day 21. Translating these results indicated a negative result on day 3 would reduce the relative probability a patient was infected by 3% (95% CI, 0% to 47%). Furthermore, RT-PCR tests conducted on the first day of symptom onset were more informative as the relative probability of a patient being infected was reduced by 60% (95% CI, 33% to 80%). Taken together, the RT-PCR results must be cautiously incorporated into the clinical decisions of SARS-CoV-2 patients, particularly early in the infection course.

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