SARS-CoV-2 molecular testing for the diagnosis of COVID-19: One test does not fit all

Evaluation of a new point-of-care quantitative reverse transcription polymerase chain test for detecting severe acute respiratory syndrome coronavirus 2

Background

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection is rapidly spreading worldwide, and the resultant disease, coronavirus disease (COVID‐19), has become a global pandemic. Although there are multiple methods for detecting SARS‐CoV‐2, there are some issues with such tests, including long processing time, expense, low sensitivity, complexity, risk of contamination, and user friendly. This study evaluated the reproducibility and usability of a new point‐of‐care test (POCT) using real‐time quantitative reverse transcription polymerase chain reaction (qRT‐PCR) for detecting SARS‐CoV‐2.

Methods

Samples from 96 patients with suspected SARS‐CoV‐2 infection were assessed using the real‐time qRT‐PCR‐based POCT and the conventional real‐time qRT‐PCR method based on the Japanese National Institute of Infectious Diseases guidelines (registration number: jRCT1032200025).

Results

The real‐time qRT‐PCR‐based POCT had a positive agreement rate of 90.0% (18/20), a negative agreement rate of 100% (76/76), and a total agreement rate of 97.9% (94/96), and the significantly high score of questionnaire survey (total score p < 0.0001). In the two cases in which real‐time qRT‐PCR‐based POCT results did not match conventional real‐time qRT‐PCR test results, the SARS‐CoV‐2 RNA copy numbers were 8.0 copies per test in one case and below the detection limit in the other case when quantified using conventional real‐time qRT‐PCR. All patients could be triaged within 1 day using the real‐time qRT‐PCR‐based POCT without invalid reports.

Conclusions

The real‐time qRT‐PCR‐based POCT not only had high reproducibility and useability but also allowed rapid patient triage. Therefore, it may be helpful in clinical settings.

Validation of saliva sampling as an alternative to oro-nasopharyngeal swab for detection of SARS-CoV-2 using unextracted rRT-PCR with the Allplex 2019-nCoV assay

Introduction. The current severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) pandemic has stressed the global supply chain for specialized equipment, including flocked swabs.Hypothesis. Saliva could be a potential alternative specimen source for diagnosis of SARS-CoV-2 infection by reverse-transcriptase PCR (RT-PCR).Aim. To compare the detection efficiency of SARS-CoV-2 RNA in saliva and oro-nasopharyngeal swab (ONPS) specimens.Methodology. Patients recruited from hospital provided paired saliva and ONPS specimens. We performed manual or automated RT-PCR with prior proteinase K treatment without RNA extraction using the Seegene Allplex 2019 nCoV assay.Results. Of the 773 specimen pairs, 165 (21.3 %) had at least one positive sample. Additionally, 138 specimens tested positive by both sampling methods. Fifteen and 12 cases were detected only by nasopharyngeal swab and saliva, respectively. The sensitivity of ONPS (153/165; 92.7 %; 95 % CI: 88.8-96.7) was similar to that of saliva (150/165; 90.9 %; 95 % CI: 86.5-95.3; P=0.5). In patients with symptoms for ≤ 10 days, the sensitivity of ONPS (118/126; 93.7 %; 95 % CI: 89.4-97.9) was similar to that of saliva (122/126; 96.8 %; 95 % CI: 93.8-99.9 %; P=0.9). However, the sensitivity of ONPS (20/22; 95.2 %; 95 % CI: 86.1-100) was higher than that of saliva (16/22; 71.4 %; 95 % CI: 52.1-90.8) in patients with symptoms for more than 10 days.Conclusions. Saliva sampling is an acceptable alternative to ONPS for diagnosing SARS-CoV-2 infection in symptomatic individuals displaying symptoms for ≤ 10 days. These results reinforce the need to expand the use of saliva samples, which are self-collected and do not require swabs.

Practical challenges to the clinical implementation of saliva for SARS-CoV-2 detection

Due to global shortages of flocked nasopharyngeal swabs and appropriate viral transport media during the COVID-19 pandemic, alternate diagnostic specimens for SARS-CoV-2 detection are sought. The accuracy and feasibility of saliva samples collected and transported without specialized collection devices or media were evaluated. Saliva demonstrated good concordance with paired nasopharyngeal swabs for SARS-CoV-2 detection in 67/74 cases (90.5%), though barriers to saliva collection were observed in long-term care residents and outbreak settings. SARS-CoV-2 RNA was stable in human saliva at room temperature for up to 48 h after initial specimen collection, informing appropriate transport time and conditions.