Characteristics of Inpatients with False-Negative SARS-CoV-2 PCR Test Results

Background: At our institution, the concern for false-negative nasopharyngeal testing for SARS-CoV-2 at the onset of illness led to a general policy of retesting inpatients at 48 hours. For such patients, 2 negative SARS-CoV-2 PCR test results were required prior to discontinuation of COVID-19 control precautions. To assess the utility of routine repeat testing We analyzed patients presenting to our hospital who initially tested negative for SARS-CoV-2 but were found to be positive on repeated testing. Methods: All inpatients with symptoms concerning for COVID-19 were tested via nasopharyngeal sample for SARS-CoV-2 by PCR on admission. Patients with continued symptoms and no alternative diagnosis were retested 48 hours later. Testing was performed using either the Roche cobas SARS-CoV-2 RT-PCR assay or the Cepheid Xpert Xpress SARS-CoV-2 test. Between March 17, 2020, and May 10, 2020, we retrospectively analyzed data from patients with false-negative SARS-CoV-2 PCR test results who were subsequently confirmed positive 48 hours later. We evaluated demographic information, days since symptom onset, symptomatology, chest imaging, vital sign trends, and the overall clinical course of each patient. Results: During the study period, 14,683 tests were performed, almost half (n = 7,124) were performed through the ED and in the inpatient setting. Of 2,283 patients who tested positive for SARS-CoV-2, only 19 (0.01%) initially tested negative. Patients with initial false-negative test results presented with symptoms that ranged from fever and dyspnea to fatigue and vomiting. Notably, few patients presented “early” in their disease (median, 6 days; range, 0–10 days). However, patients with initial false-negative PCR test results did seem to have consistent imaging findings, specifically bilateral bibasilar ground glass opacities on chest radiograph or computed tomography scan. Conclusions: Among inpatients with COVID-19, we found a very low rate of initial false-negative SARS-CoV-2 PCR test results, which were not consistently related to premature testing. We also identified common radiographic findings among patients with initially false-negative test results, which could be useful in triaging patients who may merit retesting. Based on these data, we revised our existing clearance criteria to allow for single-test removal of COVID-19 precautions. Evaluating subsequent reduction in unnecessary testing is difficult given changing community prevalence, increased census, and increased opening to elective procedures. However, given the significant percentage of ED and inpatient testing, removal of repeated testing has likely resulted in a reduction of several thousand unnecessary COVID-19 tests monthly.Funding: NoDisclosures: None

Clinical characteristics of hospitalized patients with false-negative severe acute respiratory coronavirus virus 2 (SARS-CoV-2) test results

Objective: To determine clinical characteristics associated with false-negative severe acute respiratory coronavirus virus 2 (SARS-CoV-2) test results to help inform coronavirus disease 2019 (COVID-19) testing practices in the inpatient setting. Design: A retrospective observational cohort study. Setting: Tertiary-care facility. Patients: All patients 2 years of age and older tested for SARS-CoV-2 between March 14, 2020, and April 30, 2020, who had at least 2 SARS-CoV-2 reverse-transcriptase polymerase chain reaction tests within 7 days. Methods: The primary outcome measure was a false-negative testing episode, which we defined as an initial negative test followed by a positive test within the subsequent 7 days. Data collected included symptoms, demographics, comorbidities, vital signs, labs, and imaging studies. Logistic regression was used to model associations between clinical variables and false-negative SARS-CoV-2 test results. Results: Of the 1,009 SARS-CoV-2 test results included in the analysis, 4.0% were false-negative results. In multivariable regression analysis, compared with true-negative test results, false-negative test results were associated with anosmia or ageusia (adjusted odds ratio [aOR], 8.4; 95% confidence interval [CI], 1.4–50.5; P = .02), having had a COVID-19–positive contact (aOR, 10.5; 95% CI, 4.3–25.4; P < .0001), and having an elevated lactate dehydrogenase level (aOR, 3.3; 95% CI, 1.2–9.3; P = .03). Demographics, symptom duration, other laboratory values, and abnormal chest imaging were not significantly associated with false-negative test results in our multivariable analysis. Conclusions: Clinical features can help predict which patients are more likely to have false-negative SARS-CoV-2 test results.

Predictors of negative first SARS-CoV-2 RT-PCR despite final diagnosis of COVID-19 and association with outcome

Reverse transcriptase-polymerase chain reaction (RT-PCR) testing is an important tool for diagnosing coronavirus disease 2019 (COVID-19). However, performance concerns have emerged recently, notably regarding sensitivity. We hypothesized that the clinical, biological, and radiological characteristics of patients with a false-negative first RT-PCR test and a final diagnosis of COVID-19 might differ from those of patients with a positive first RT-PCR test. We conducted a multicenter matched case–control study in COVID-19 patients. Patients with a negative first RT-PCR test were matched to patients with a positive first RT-PCR test on age, sex, and initial admission unit (ward or intensive care). We included 80 cases and 80 controls between March 30, and June 22, 2020. Neither mortality at hospital discharge nor hospital stay length differed between the two groups (P = 0.80 and P = 0.54, respectively). By multivariate analysis, two factors were independently associated with a lower risk of a first false-negative test, namely, headache (adjusted OR [aOR], 0.07; 95% confidence interval [95% CI], 0.01–0.49]; P = 0.007) and fatigue/malaise (aOR, 0.16; 95% CI, 0.03–0.81; P = 0.027); two other factors were independently associated with a higher risk of a first false-negative test, namely, platelets > 207·103 mm−3 (aOR, 3.81; 95% CI, 1.10–13.16]; P = 0.034) and C-reactive protein > 79.8 mg·L−1 (aOR, 4.00; 95% CI, 1.21–13.19; P = 0.023). Patients with suspected COVID-19 whose laboratory tests indicating marked inflammation were at higher risk of a first false-negative RT-PCR test. Strategies involving serial RT-PCR testing must be rigorously evaluated.

Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR

Background Reverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives are possible depending on swab type and time since symptom onset. Aim To determine how the probability of obtaining a false-negative test in infected patients is affected by time since symptom onset and swab type. Methods We used generalised additive mixed models to analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once. Results The probability of a positive test decreased with time since symptom onset, with oropharyngeal (OP) samples less likely to yield a positive result than nasopharyngeal (NP) samples. The probability of incorrectly identifying an uninfected individual due to a false-negative test was considerably reduced if negative tests were repeated 24 hours later. For a small false-positive test probability (<0.5%), the true number of infected individuals was larger than the number of positive tests. For a higher false-positive test probability, the true number of infected individuals was smaller than the number of positive tests. Conclusion NP samples are more sensitive than OP samples. The later an infected individual is tested after symptom onset, the less likely they are to test positive. This has implications for identifying infected patients, contact tracing and discharging convalescing patients who are potentially still infectious.

An epidemic CC1-MRSA-IV clone yields false-negative test results in molecular MRSA identification assays: a note of caution, Austria, Germany, Ireland, 2020

We investigated why a clinical meticillin-resistant Staphylococcus aureus (MRSA) isolate yielded false-negative results with some commercial PCR tests for MRSA detection. We found that an epidemic European CC1-MRSA-IV clone generally exhibits this behaviour. The failure of the assays was attributable to a large insertion in the orfX/SCCmec integration site. To ensure the reliability of molecular MRSA tests, it is vital to monitor emergence of new SCCmec types and junction sites.

Multicentre comparison of quantitative PCR-based assays to detect SARS-CoV-2, Germany, March 2020

Containment strategies and clinical management of coronavirus disease (COVID-19) patients during the current pandemic depend on reliable diagnostic PCR assays for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we compare 11 different RT-PCR test systems used in seven diagnostic laboratories in Germany in March 2020. While most assays performed well, we identified detection problems in a commonly used assay that may have resulted in false-negative test results during the first weeks of the pandemic.

Chronic and Early Antiretroviral Therapy Impact Human Immunodeficiency Virus (HIV) Serological Assay Sensitivity, Leading to More False-Negative Test Results in HIV Diagnosis

This retrospective study evaluated the reactivity of 3 human immunodeficiency virus (HIV) confirmatory assays (INNO-LIA, Geenius, and MP) and 7 HIV rapid tests on samples from 2 different study populations in Belgium. For the early-treated cohort (83 HIV-1 adult patients treated within 3 months after infection), HIV-1 diagnosis was not obtained in at least 1 confirmatory assay in 12.0% (10/83) and in an HIV rapid test in 31.3% (26/83). Confirmation assay sensitivities ranged from 87.5% to 95.2%, whereas rapid test assay sensitivities ranged from 75.9% to 100%. The time to treatment initiation or the length of time on treatment did not have a statistical influence on the probability to obtain a false-negative test result. The fastest reversion was demonstrated after 4 months of treatment. Among the long-term treated cohort (390 HIV-1 patients with ≥ 9 years of undetectable viral load), false-negative test results were found in at least 1 HIV confirmatory assay for 2.1% (8/390) of the patients and in a HIV rapid test for 4.9% (19/390). Confirmation assay sensitivities ranged from 98.1% to 99.5%, whereas rapid test sensitivities ranged from 96.2% to 100%. Longer treatment increased nonreactivity of the HIV rapid tests (P = .033). Undetectable viral load decreases the sensitivities of HIV diagnostic tests, and further monitoring of the performance of serological assays is advised.

An epidemic CC1-MRSA-IV clone yields false negative test results in molecular MRSA identification assays: a note of caution

ABSTRACTBackgroundA variety of rapid molecular PCR tests has been developed and commercialised that interrogate the junction site between the staphylococcal core genome, and the mobile genetic element (SCCmec) which harbours the gene responsible for methicillin-/beta-lactam-resistance.AimThe purpose of the present study was to investigate why a clinical MRSA isolate yielded false negative test results with widely used, commercial orfX/SCCmec junction site PCR tests.MethodsA collection of isolates that belonged to the same epidemic strain as the index isolate were investigated with commercial MRSA assays and all isolates were sequenced in order to explain this observation.ResultsIt was found that isolates of the epidemic “European CC1-MRSA-IV” clone, which likely originated in South-Eastern Europe and subsequently spread to Western Europe, generally exhibit this behaviour. The failure of the assays was attributable to a characteristic large insertion in the orfX/SCCmec integration site presumably targeted by such tests. In contrast to MW2 (GenBank BA000033.2, a CC1 “USA400” strain which also harbours SCCmec IVa), the European CC1 clone harbours an insertion of ca. 5,350 nucleotides adjacent to orfX. This sequence starts with a novel SCC terminal sequence alternate to dcs and encodes six different hypothetical proteins (E7MHX1, ydiL2, C5QAP8, A8YYX4, npd-SCC, H4AYD7; nucleotide positions 280,690–286,024 of GenBank RBVO000005.1). An SCCmec element with the same insertion was previously found in a Staphylococcus epidermidis isolate (GenBank MH188467.1) suggesting transfer between staphylococcal species.ConclusionIn order to ensure the reliability of molecular MRSA tests, it is vital to monitor the emergence of new SCCmec junction sites, not only in Staphylococcus aureus but also in coagulase-negative staphylococci.

COVID-19 Testing: Challenges, Limitations and Suggestions for Improvement

Reliable methods to confirm the diagnosis of COVID-19 are essential to the successful management and containment of the virus. Current diagnostic options are limited in type, supply, and reliability. This article explores the controversial unreliability of existing diagnostic methods and maintains that more reliable diagnostic methods, combinations, and sequencing are necessary to effectively assist in reducing the occurrence of discharge of the patient on false negative test results. This reduction would in effect reduce transmission of the disease.