Highlights We assess the performance of the LUMIPULSE antigen test compared to RT-qPCR The antigen level was significantly higher in PCR-positive samples than in negative samples The antigen test determined all samples (>100 viral copies) to be positive Likewise, it determined 85% of samples (>10 viral copies) to be positive The kinetics of viral loads and antigen levels showed a similar declining trend

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Background Reverse-transcription PCR (RT-PCR) is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. Previously, we demonstrated the accuracy of the quantitative LUMIPULSE SARS-CoV-2 antigen test using samples collected retrospectively. Here, the antigen test was clinically validated using prospective samples. Methods A total of 1,033 nasopharyngeal swab samples were collected 1,033 individuals and an additional 275 follow-up samples were collected from 43 patients who later tested positive for COVID-19. All 1,308 samples were subjected to quantitative RT-PCR (RT-qPCR) and the LUMIPULSE antigen test. Antibody response was investigated for patients with discordant results to clarify whether seroconversion had occurred. Results RT-qPCR identified 990 samples as negative and 43 as positive, while the antigen test identified 992 as negative, 37 as positive, and 4 as inconclusive. The overall concordance rate was 99.7% (1,026/1,029). The sensitivity, specificity, positive predictive value and negative predictive value of the antigen test were 92.5% (37/40), 100% (989/989), 100% (37/37) and of 99.7% (989/992), respectively, after excluding the four inconclusive results. The kappa coefficient was 0.960 (95% confidence interval, 0.892‐0.960), suggesting excellent agreement between the two tests. The seropositive in five out of the seven patients with discordant results suggested that the discrepancy was caused by samples collected during the late phase of infection. Using the follow-up samples, we observed a correlation between the antigen level and the viral load or threshold cycle (Ct) value. The concordance rate between these test results tended to be high among samples collected up to 9 days after symptom onset but this gradually decreased thereafter. Conclusions This prospective study demonstrated that the LUMIPULSE antigen test is a highly accurate diagnostic for SARS-CoV-2.

Severe acute respiratory coronavirus 2 (SARS-CoV-2) testing reagents are expected to become scarce worldwide. However, little is known regarding whether pooling of samples accurately detects SARS-CoV-2. To validate the feasibility of pooling samples, serial dilution analysis and spike-in experiments were conducted using synthetic DNA and nucleic acids extracted from SARS-CoV-2-positive and -negative patients. Furthermore, we studied 1000 individuals, 667 of whom were “healthy” individuals (195 healthcare workers and 472 hospitalized patients with disorders other than COVID-19 infection), and 333 infection-suspected patients with cough and fever. Serial dilution analysis showed a limit of detection of around 10–100 viral genome copies according to the protocol of the National Institute of Infectious Diseases, Japan. Spike-in experiments demonstrated that RT-qPCR detected positive signals in pooled samples with SARS-CoV-2-negative and -positive patients at 5-, 10-, 20-fold dilutions. By screening with this pooling strategy, by the end of April 2020 there were 12 SARS-CoV-2-positive patients in 333 infection-suspected patients (3.6%) and zero in 667 “healthy” controls. We obtained these results with a total of 538 runs using the pooling strategy, compared with 1000 standard runs. In a prospective study, we successfully detected SARS-CoV-2 using 10- to 20-fold diluted samples of nasopharyngeal swabs from eighteen COVID-19 patients with wide ranges of viral load. Pooling sample is feasible for conserving test reagents and detecting SARS-CoV-2 in clinical settings. This strategy will help us to research the prevalence infected individuals and provide infected-status information to prevent the spread of the virus and nosocomial transmission.

Various diagnostic tests utilizing different principles are currently under development for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, these tests can occasionally produce discrepant results, causing confusion in their interpretation. Here, we evaluated the performance and features of three diagnostic assays: quantitative reverse transcription polymerase chain reaction (RT-qPCR), FilmArray Respiratory Panel (RP) v2.1, and the LUMIPULSE antigen test. Twenty-seven serial nasopharyngeal swabs were collected from a prolonged viral shedding patient who had been hospitalized for 51 days. We examined the SARS-CoV-2 detection rates of the three tests. The overall agreement rate was 81% between RT-qPCR and FilmArray RP v2.1, 63% between the antigen test and FilmArray RP v2.1, and 59% between the antigen test and RT-qPCR. We obtained concordant results in samples with high viral loads (low threshold cycle values) by all three tests. RT-qPCR and FilmArray RP v2.1 accurately detected SARS-CoV-2 at the early to intermediate phases of infection, but the results varied at the late phase. The antigen test also produced a positive result at the early phase but varied at the intermediate phase and consistently produced negative results at late phase of infection. These results demonstrated FilmArray RP v2.1 could detect SARS-CoV-2 with accuracy comparable to RT-qPCR. Further, there were discrepant results using different types of diagnostic tests during the clinical course of prolonged viral shedding patient. We provided insights into how to utilize different types of kits to assess and manage SARS-CoV-2 infections.