Natural spring water gargle samples as an alternative to nasopharyngeal swabs for SARS-CoV-2 detection using a laboratory-developed test

Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle

Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.

Verification of the efficiency of saline gargle sampling for detection of the Omicron variant of SARS-CoV-2, a pilot study

A saline gargle (SG) has proven to be an efficient method of sampling to detect SARS-CoV-2. The aim of this pilot study was to verify the efficiency of SG sampling in detecting the Omicron variant of SARS-CoV-2. Subjects were a total of 68 patients with COVID-19 (Omicron variant), and 167 pairs of samples were collected. A conventional oropharyngeal swab (OPS) was obtained and SG sampling was performed immediately afterward; both were subjected to RT-qPCR. A subgroup analysis of symptomatic and asymptomatic patients was performed. Results revealed no significant differences in the distribution of patients and cycle threshold (CT) values between the SG and OPS in overall data and data on days 1-3, 4-7, and 8-14. The subgroup analysis revealed no significant differences between the SG and OPS results in symptomatic patients. In asymptomatic patients, the CT values for the SG were significantly lower than those for the OPS, implying that SG sampling had better sensitivity in the context of the Omicron variant. These data indicate that the SG had satisfactory efficiency (vs. the OPS). An SG is a simple and less invasive method of sampling that is suited to mass, frequent, and repeated sampling to detect SARS-CoV-2.

Evaluation of Real-life Use of Point-of-care Rapid Antigen Testing for SARS-CoV-2 in Schools (EPOCRATES): a cohort study

BACKGROUND

SARS-CoV-2 transmission has an impact on education. In this study, we assessed the performance of rapid antigen detection tests (RADTs) versus polymerase chain reaction (PCR) for the diagnosis of SARS-CoV-2 infection in school settings, and RADT use for monitoring exposed contacts.

METHODS

In this real-world, prospective observational cohort study, high-school students and staff were recruited from 2 high schools in Montréal, Canada, and followed from Jan. 25 to June 10, 2021. Twenty-five percent of asymptomatic participants were tested weekly by RADT (nasal) and PCR (gargle). Class contacts of cases were tested. Symptomatic participants were tested by RADT (nasal) and PCR (nasal and gargle). The number of cases and outbreaks were compared with those of other high schools in the same area.

RESULTS

Overall, 2099 students and 286 school staff members consented to participate. The overall specificity of RADTs varied from 99.8% to 100%, with a lower sensitivity, varying from 28.6% in asymptomatic to 83.3% in symptomatic participants. Secondary cases were identified in 10 of 35 classes. Returning students to school after a 7-day quarantine, with a negative PCR result on days 6-7 after exposure, did not lead to subsequent outbreaks. Of cases for whom the source was known, 37 of 51 (72.5%) were secondary to household transmission, 13 (25.5%) to intraschool transmission, and 1 to community contacts between students in the same school.

INTERPRETATION

Rapid antigen detection tests did not perform well compared with PCR in asymptomatic individuals. Reinforcing policies for symptom screening when entering schools and testing symptomatic individuals with RADTs on the spot may avoid subsequent substantial exposures in class. Preprint: medRxiv - doi.org/10.1101/2021.10.13.21264960.

Evaluation of water gargle samples for SARS-CoV-2 detection using Abbott ID NOW COVID-19 assay

The Abbott ID NOW™ COVID‐19 assay has been shown as a reliable and sensitive alternative to reverse transcription‐polymerase chain reaction (RT‐PCR) testing from nasopharyngeal or nasal samples in symptomatic patients. Water gargle is an acceptable noninvasive alternative specimen for severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) detection by RT‐PCR. The objective of this study was to evaluate the performance of water gargle samples for the detection of SARS‐CoV‐2 using the ID NOW. Residual gargle samples were randomly selected among positive standard of care (SOC)‐nucleic acid amplification test (NAAT) samples. For testing on ID NOW, the manufacturer's instructions were followed, except for the specimen addition step: 500 µl of the gargle specimen was added to the blue sample receiver with a pipette and gently mixed. Among the 202 positive samples by SOC‐NAAT, 185 were positive by ID NOW (positive percent agreement [PPA]) = 91.6% (95% confidence interval [CI]: 86.9−95.0). For the 17 discordant samples, cycle threshold (C_t) values were all ≥31.0. The PPA was significantly lower among asymptomatic patients (84.4%; 95% CI: 73.2−92.3) versus symptomatic patients (95.2%; 95% CI: 89.8−98.2). The performance of the ID NOW for the detection of SARS‐CoV‐2 infection on gargle samples is excellent when C_t values are <31.0 and for patients that have COVID‐19 compatible symptoms.

The PRONTO study: Clinical performance of ID NOW in individuals with compatible SARS-CoV-2 symptoms in walk-in centres-accelerated turnaround time for contact tracing

Background

This PRONTO study investigated the clinical performance of the Abbott ID NOW^TM (IDN) COVID-19 diagnostic assay used at point of care and its impact on turnaround time for divulgation of test results.

Methods

Prospective study conducted from December 2020 to February 2021 in acute symptomatic participants presenting in three walk-in centres in the province of Québec.

Results

Valid paired samples were obtained from 2,372 participants. A positive result on either the IDN or the standard-of-care nucleic acid amplification test (SOC-NAAT) was obtained in 423 participants (prevalence of 17.8%). Overall sensitivity of IDN and SOC-NAAT were 96.4% (95% CI: 94.2-98.0%) and 99.1% (95% CI: 97.6-99.8), respectively; negative predictive values were 99.2% (95% CI: 98.7-99.6%) and 99.8% (95% CI: 99.5-100%), respectively. Turnaround time for positive results was significantly faster on IDN.

Conclusion

In our experience, IDN use in symptomatic individuals in walk-in centres is a reliable sensitive alternative to SOC-NAAT without the need for subsequent confirmation of negative results. Such deployment can accelerate contact tracing, reduce the burden on laboratories and increase access to testing.