Patient samples
The research related to human use has been complied with all the relevant national regulations, institutional policies and in accordance the tenets of the Helsinki Declaration, and has been approved by the authors’ institutional review board at Juntendo University Hospital, Tokyo, Japan (IRB #20-036) and Kobe City Medical Center General Hospital, Hyogo, Japan (IRB #zn200615). This study used an opt-out consent method. Therefore, written informed consent was not required.
Classification of disease severity was determined according to the Clinical Spectrum of SARS-CoV-2 Infection (https://www.covid19treatmentguidelines.nih.gov/overview/clinical-spectrum/). To determine the relationship between photo counts and viral loads, a total of 84 nasopharyngeal swabs were collected from 17 patients at Kobe City Medical Center General Hospital and 67 commercially available samples (Cantor Bioconnect, Santee, CA, USA; validation dataset). For clinical performance analysis, a total of 115 nasopharyngeal swabs were collected from 115 patients at Juntendo University Hospital (test dataset).
SARS-CoV-2 RT-qPCR
Viral RNAs were extracted using QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany). RT-qPCR was performed following the protocol developed by the National Institute of Infectious Diseases of Japan. The primer/probe set (N2) was designed based on the N sequence of SARS-CoV-2 RNA (NC_045512.2) [24]. The primer/probe sequences were as following: forward primer (5′-AAATTTTGGGGACCAGGAAC-3′), reverse primer (5′-TGGCAGCTGTGTAGGTCAAC-3′), and TaqMan probe (5′-FAM-ATGTCGCGCATTGGCATGGA-BHQ-3′). The expected amplicon size was 158 bp. QuantiTect Probe RT-PCR Kit (Qiagen, Germantown, MD, USA) and Applied Biosystems 7500 Fast Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA) were used. The Ct values were assessed using the protocol developed by the National Institute of Infectious Diseases (version 2.9.1) [24]. The association between absolute viral copy numbers (viral loads) and Ct values was determined using SARS-CoV-2 Positive Control RNA (JP-NN2-PC, Nihon Gene Research Laboratories, Miyagi, Japan).
Recombinant antigen production
For antigen cross-reactivity tests, nucleocapsid antigens derived from the other coronaviruses and influenza viruses were prepared. The recombinant nucleocapsid proteins were produced based on the following sequences: SARS-CoV (YP_009825061), Middle East respiratory syndrome-related coronavirus (MERS-CoV; YP_009047211), human coronavirus HKU1 HCoV-HKU1 (YP_173242), HCoV-OC43 (YP_009555245), HCoV-NL63 (YP_003771), and HCoV-229E (NP_073556). Each recombinant protein was prepared according to previously described methods [25].
Western blot
The detection of SARS-CoV-2 antigens by SARS-CoV antibodies was confirmed via western blot analysis using the previously produced anti-N capsid SARS-CoV antibodies [25]. Histidine (His)-tagged SARS-CoV-2 N proteins (10 ng) were loaded on NEXT Page II gel (5–20% gradient; Gellex, Tokyo, Japan) and electrophoresis was performed using iBind Western Device (Thermo Fisher Scientific). Two lots each of anti-SARS-CoV antibodies (0.5 μg/mL) and horseradish peroxidase (HRP)-conjugated anti-His antibodies (Penta-His Antibody; Cat. No. 34660, Qiagen) were used as primary antibodies. Anti-IgG antibodies (Medical & Biological Laboratories, Nagoya, Japan) were used as the secondary antibodies. Immobilon Western HRP substrate (Millipore, Burlington, MA, USA) was used for chemiluminescent detection.
HISCL SARS-CoV-2 Antigen assay kit
Previously produced monoclonal antibodies against the SARS-CoV N proteins [25] were used to probe the SARS-CoV-2 N proteins (ACROBiosystems, Newark, DE, USA). The HISCL SARS-CoV-2 Antigen assay kit is a chemiluminescent enzyme immunoassay that uses a HISCL automatic immunoassay analyzer (Sysmex, Kobe, Japan).
Figure 1 presents a schematic illustration of the procedure: (1) the samples were incubated with biotinylated SARS-CoV-2 antibodies at 42 ℃ for 3 min; (2) the mixtures were incubated with streptavidin-bonded magnetic particles at 42 ℃ for 2 min; (3) after protein separation and washing, alkaline phosphatase (ALP)-bound SARS-CoV-2 antibodies were added and the mixtures were incubated at 42 ℃ for 3 min; (4) after magnetic separation and washing again, the chemiluminescent substrates were added and the mixtures were incubated at 42°C for 5.5 min; and (5) chemiluminescence signals (CDP-Star, C0712, Sigma-Aldrich, St. Louis, MO, USA) were measured using the photo counter of HISCL-800 (Sysmex, Kobe, Japan). The level of SARS-CoV-2 Ag was indicated as cut-off index (COI), calculated by the difference in the luminescence intensities in the buffers with and without the SARS-CoV-2 antigens.
Human sample collection
Human samples were obtained using nasopharyngeal cotton swabs following the standard method [26]. The swabs were immersed in 0.5 mL phosphate-buffered saline or viral transfer medium (Lampire Biological Laboratories, Pipersville, PA, USA). The suspensions were frozen at -80 ℃ until antigen tests were performed. Highly viscous samples were centrifuged (2,000 × g for 5 minutes), and the supernatants were used for subsequent analyses.
Reproducibility
Within-run and between-run reproducibility were determined by running the buffers with and without SARS-CoV-2 antigens. The recombinant human antigen for SARS-CoV-2 was purchased from ACRO Biosystems (Beijing, China). To test reproducibility, buffers containing SARS-CoV-2 antigens (positive control) and those without antigens (negative control) were prepared. To test between-run reproducibility, both negative and positive controls were tested twice per day each for five consecutive days.
Cross-reaction
Cross-reactions were checked using measuring buffers containing various recombinant viral antigens: human SARS-CoV, MERS-CoV, HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, influenza virus H1N1, influenza virus H3N2, and influenza virus B. Inactivated influenza viruses were purchased from Advanced Biotechnologies (Eldersburg, MD, USA). The antigens of SARS-CoV, MERS-CoV, HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 were prepared according to a previous established protocol [25]. HISCL SARS-CoV-2 Antigen assays were carried out following the manufacturer’s instructions.
Statistical analyses
Statistical analyses were performed in Excel (Microsoft, Redmond, WA, USA). Receiver operating characteristic (ROC) curve analyses were conducted using GraphPad Prism (GraphPad Software, San Diego, USA) to evaluate the assay performance and visualize the curves. The areas under the ROC curves (AUCs), sensitivity, and specificity were calculated.