Data from: Detection of silent SARS-CoV-2 infection (S1 File)
Sugawa, Satoshi (2022), Data from: Detection of silent SARS-CoV-2 infection (S1 File), Dryad, Dataset, https://doi.org/10.5061/dryad.kwh70rz5r
Background: To control COVID-19 pandemic is of critical importance to the global public health. To capture the prevalence in an accurate and timely manner and to understand the mode of nosocomial infection are essential for its preventive measure.
Methods: We recruited 685 healthcare workers (HCW’s) at Tokyo Shinagawa Hospital prior to the vaccination with COVID-19 vaccine. Sera of the subjects were tested by assays for the titer of IgG against S protein’s receptor binding domain (IgG (RBD)) or IgG against nucleocapsid protein (IgG (N)) of SARS-CoV-2. Together with PCR data, the positive rates by these methods were evaluated.
Results: Overall positive rates among HCW’s by PCR, IgG (RBD), IgG (N) with a cut-off of 1.4 S/C (IgG (N)1.4), and IgG (N) with a cut-off of 0.2 S/C (IgG (N)0.2) were 3.5%, 9.5%, 6.1%, and 27.7%, respectively. Positive rates of HCW’s working in COVID-19 ward were significantly higher than those of HCW’s working in non-COVID-19 ward by all the four methods. Concordances of IgG (RBD), IgG (N)1.4, and IgG (N)0.2 against PCR were 97.1%, 71.4%, and 88.6%, respectively. By subtracting the positive rates of PCR from that of IgG (RBD), the rate of overall silent infection and that of HCW’s in COVID-19 ward were estimated to be 6.0% and 21.1%, respectively.
Conclusions: For the prevention of nosocomial infection of SARS-CoV-2, identification of silent infection is essential. For the detection of ongoing infection, periodical screening with IgG (RBD) in addition to PCR would be an effective measure. For the surveillance of morbidity in the population, on the other hand, IgG (N)0.2 could be the most reliable indicator among the three serological tests.
This study was conducted at Tokyo Shinagawa Hospital. The study protocol conformed to the ethical guidelines of the 1975 Declaration of Helsinki and was approved by the Ethics Committee at Tokyo Shinagawa Hospital (approval no. 20-A-34) prior to the start of the study. 685 HCW’s at Tokyo Shinagawa Hospital were included in this study after obtaining written informed consent. Sera were obtained from the subjects for the test of IgG against S protein’s receptor binding domain (IgG (RBD)) and IgG against nucleocapsid protein (IgG (N)) of SARS-CoV-2. None of them had been vaccinated with COVID-19 vaccine prior to the specimen collection. Subject information including age, sex, height, weight, job category in the hospital, history of SARS-CoV-2 infection diagnosed by PCR, and co-morbidity were obtained and anonymized before analyses.
Tokyo Shinagawa Hospital started accommodating COVID-19 patients in March 2020. All the HCW’s were provided with full personal protective equipment (PPE). Especially, all frontline HCW’s wore long-sleeved gowns, N95 respirators, gloves, goggles or face shields when treating patients. SARS-CoV-2 testing by PCR was promptly carried out for HCW’s who showed symptoms suggestive of COVID-19 including fever, dry cough, respiratory distress, loss of smell, or dysgeusia.
Clinical and laboratory tests
Sera from the subjects were drawn during March and April 2021 and were tested with IgG (RBD) and IgG (N) assays. The titer of IgG (RBD) was measured by an ARCHITECT SARS-CoV-2 IgG II Quant assay on Architect i2000 CS5100 (Abbott Laboratories, Abbott Park, IL, USA) and that of IgG (N) was measured by an ARCHITECT SARS-CoV-2 IgG assay on Architect i2000 CS5100 (Abbott Laboratories, Abbott Park, IL, USA). According to the package insert of IgG (RBD) assay, the cut-off index is 50.0 AU/mL and lowest concentration at which CV% is within 20% is 7.8 AU/mL. Narasimhan et al. reported that the specificity of the IgG (RBD) assay was 100% while sensitivity of the IgG (RBD) exceeded 96% after 15 days from symptom onset by applying the cut-off of 50.0 AU/mL . According to the package insert of IgG (N) assay, the cut-off index is 1.4 S/C and CV% at a mean index of 0.04 S/C of 50 negative controls is 5.9%. According to a report by Bryan et al., sensitivity and specificity of the IgG (N) assay assessed with series of specimens from 125 patients were both 100% after 17 days from symptom onset with the cut-off of 1.4 S/C . In addition to this cut-off, we used 0.2 S/C as one of the candidate cut-offs for the long-term assessment of the history of SARS-CoV-2 infection by referring to the preceding literatures [7, 8, 9, 10].
PCR was performed on QuantStudio™ 5 Real-Time PCR System (Thermo Fisher SCIENTIFIC, Waltham, MA, USA) which targets N1 and N2 regions of SARS-CoV-2. The PCR result was defined as positive when cycle threshold (Ct) was equal to or less than 40. Nasopharyngeal swabs for the PCR were collected by nurses who had ample experience of routine swab collections from fever outpatients and hospitalized patients.
We used JMP 15.1.0 (SAS Institute Inc., Cary, NC, USA) for Pearson’s chi-square test in Table 3 in which antibody titers below the cut-off were categorized as “0” while those equal to or above the cut-off were categorized as “1”. P-value of <0.01 was considered significant.
|0 = no, 1 = yes|
|NA: not applicable|