Prospective Evaluation of SARS-CoV-2 Rapid Antigen Test for Screening of Asymptomatic Caregivers.

BACKGROUND: This study aimed to assess clinical performance of a rapid antigen test (RAT) for screening asymptomatic patients during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron outbreak. METHODS: RAT with the routine real-time reverse transcription-polymerase chain reaction (rRT-PCR) using the same nasopharyngeal swab in universal transport medium was performed for rapid screening of asymptomatic caregivers of emergent patients from March to April 2022 in a tertiary-care hospital in Korea. Clinical performance of RAT compared to that analyzed by rRT-PCR was evaluated. RESULTS: A total of 900 caregivers were enrolled in this study, of which 14 (1.6%) were RAT-positive and 44 (5.0%) were positive for rRT-PCR. Overall sensitivity and specificity of RAT were 31.8% and 100.0%, respectively. CONCLUSIONS: Caution must be taken when using RAT as a screening test for asymptomatic caregivers as this may lead to outbreaks among high-risk patients.

Evaluation of the cobas Liat detection test for SARS-CoV-2 and influenza viruses following the emergence of the SARS-CoV-2 Omicron variant.

OBJECTIVES: This study assessed the clinical performance of the cobas Liat SARS­CoV­2 & Influenza A/B assay (LiatCOVID/flu) for the detection of both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses during the SARS-CoV-2 Omicron outbreak. METHODS: Residual nasopharyngeal swab samples (NPS) previously tested with cobas SARS-CoV-2 & Influenza A/B for SARS-CoV-2 and with the Allplex Respiratory Panel 1 for influenza viruses were collected. All samples were submitted to the LiatCOVID/flu assay. RESULTS: A total of 1147 samples were collected comprising 167 SARS-CoV-2-positive, 556 SARS-CoV-2-negative, 224 influenza-positive, and 200 influenza-negative cases. The positive percent agreement (PPA)/negative percent agreement (NPA) of LiatCOVID/flu for SARS-CoV-2 and influenza viruses compared to the previously tested methods were 100% of 100% and 99.6% of 100%, respectively. CONCLUSIONS: The LiatCOVID/flu assay shows an acceptable performance in the detection of SARS-CoV-2 and influenza viruses using NPS samples.

Patterns of Possible False-Positive Results for Three Commercial Real-Time PCR Kits for SARS-CoV-2.

BACKGROUND: We retrospectively examined all initial positive SARS-CoV-2 test results using three real-time PCR tests from patients without a history of COVID-19 collected from September to October 2021 at a university-affiliated hospital. METHODS: We defined a possible false-positive (PFP) case as a positive case that showed negative results upon per-forming a confirmatory test on the same specimen. Positivity% and PFP% were defined as the number of first positive and the number of PFP cases divided by the total test numbers, respectively. RESULTS: The positivity%/PFP% values were 0.76%/0.10%, 0.29%/0.02%, and 0.21%/0.03% for the Xpert, Allplex, and cobas tests, respectively. Six (75%) cobas PFP cases were RdRp-only positive. All PFP cases analyzed by Xpert except one had cycle threshold values ≥ 40. Contamination during extraction was suspected in five of the 10 PFP cases analyzed by Allplex, which requires a separate extraction step. CONCLUSIONS: Care must be taken when analyzing first-positive cases as these may be false-positive signals.

Evaluation of Intra- and Interlaboratory Variations in SARS-CoV-2 Real-Time RT-PCR Through Nationwide Proficiency Testing.

OBJECTIVE: This study aimed to examine the intra- and interlaboratory variations of cycle threshold (Ct) values using the nationwide proficiency testing for SARS-CoV-2. METHODS: Triplicated strong-positive contrived samples duplicated weak-positive contrived samples, and 2 negative samples were transported to participating laboratories in October 2021. RESULTS: A total of 232 laboratories responded. All except 4 laboratories correctly answered. Six false-negative results, including 2 false-negatives with Ct values beyond the threshold and 1 clerical error, were noted from weak-positive samples. Intralaboratory variations of Ct values of weak-positive and strong-positive samples were not acceptable (Ct > 1.66) in 17 and 7 laboratories, respectively. High interlaboratory variations of Ct values (up to 7 cycles) for the 2 commonly used polymerase chain reaction (PCR) reagents were observed. CONCLUSION: The overall qualitative performance was acceptable; intralaboratory variation was acceptable. However, interlaboratory variations of Ct values were remarkable even when the same PCR reagents were used.

Epidemiologic Linkage of COVID-19 Outbreaks at Two University-affiliated Hospitals in the Seoul Metropolitan Area in March 2020.

BACKGROUND: Coronavirus disease 2019 (COVID-19) outbreaks emerged at two university-affiliated hospitals in Seoul (hospital A) and Uijeongbu City (hospital S) in the metropolitan Seoul area in March 2020. The aim of this study was to investigate epidemiological links between the outbreaks using whole genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: Fifteen patients were enrolled in the study, including four non-outbreak (A1-A4) and three outbreak cases (A5-A7) in hospital A and eight cases (S1-S8) in hospital S. Patients' hospital stays, COVID-19 symptoms, and transfer history were reviewed. RNA samples were submitted for WGS and genome-wide single nucleotide variants and phylogenetic relationships were analyzed. RESULTS: The index patient (A5) in hospital A was transferred from hospital S on 26 March. Patients A6 and A7 were the family caregiver and sister, respectively, of the patient who shared a room with A5 for 4 days. Prior to transfer, A5 was at the next bed to S8 in the emergency room on 25 March. Patient S6, a professional caregiver, took care of the patient in the room next to S8's room for 5 days until 22 March and then S5 for another 3 days. WGS revealed that SARS-CoV-2 in A2, A3, and A4 belong to clades V/B.2, S/A, and G/B.1, respectively, whereas that of A5-A7 and S1-S5 are of the V/B.2.1 clade and closely clustered. In particular, SARS-CoV-2 in patients A5 and S5 showed perfect identity. CONCLUSION: WGS is a useful tool to understand epidemiology of SARS-CoV-2. It is the first study to elucidate the role of patient transfer and caregivers as links of nosocomial outbreaks of COVID-19 in multiple hospitals.

Evaluation of Four Commercial Kits for SARS-CoV-2 Real-Time Reverse-Transcription Polymerase Chain Reaction Approved by Emergency-Use-Authorization in Korea.

SARS-CoV-2 real-time reverse-transcription PCR (rRT-PCR) is the most effective testing system currently available to counter COVID-19 epidemics when potent treatments and vaccines are unavailable. Therefore, four SARS-CoV-2 rRT-PCR kits have been approved by the emergency-use-authorization (EUA) without clinical validation in Korea until March 15, 2020. This study evaluated the analytical and clinical performance of these kits. Allplex 2019-nCoV Real-time PCR (Seegene, Seoul, Korea), PowerChek 2019-nCoV (KogeneBiotech, Seoul), Real-Q 2019-nCoV Real-Time Detection (BioSewoom, Seoul), and StandardM nCoV Detection (SD BIOSENSOR, Osong, Korea) were evaluated. The limit of detection (LODs) of Allplex, PowerChek, and Real-Q was determined by testing the transcribed RNA of SARS-CoV-2 E and the RNA of SARS-CoV Frankfurt1. A total of 27 consecutive samples comprising 13 sputum, 12 nasopharyngeal swab (NPS), 1 urine and 1 stool sample were collected from 2 COVID-19 patients for sensitivity analysis. Precision was assessed via daily tests of positive and negative controls in each kit for 5 d. Reproducibility was examined by repeating 21 samples and 10-fold dilutions of 14 samples in pairs using Allplex. Specificity was evaluated with 24 other respiratory virus-positive samples. LOD of Allplex, PowerChek, and Real-Q were 153.9, 84.1, and 80.6 copies/mL, respectively. The degrees of association between Cts and log viral concentrations by Allplex and PowerChek was expressed as y = -3.319 log (x) + 42.039 (R = 0.96) and y = -3.392 log(x) + 43.113 (R = 0.98), respectively. One or more of the 4 kits detected 20 out of 27 clinical samples positive. Of the 20 positive samples, the detection rates of positives for Allplex, PowerChek, Real-Q, and StandardM were 90.0, 82.3, 75.0, and 100.0%, respectively, but those of PowerChek and Real-Q would be 100% if out-of-cutoff Cts were counted as positives. Precision was 100%. Interpretation of Allplex results was reproducible when Ct of E ≤33. All 4 kits showed no cross-reactivity with other respiratory viruses. Performance of the 4 kits indicated the suitability of these for diagnosis and follow-up testing of COVID-19. Laboratory doctors who initially implement these EUA kits must be able to interpret quality control parameters.