Performance of nasopharyngeal swab and saliva in detecting Delta and Omicron SARS‐CoV‐2 variants

Abstract

A prospective cohort study was conducted during the Delta and Omicron severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) epidemic waves from paired nasopharyngeal swab (NPS or NP swab) and saliva samples taken from 624 participants.The study aimed to assess if any differences among participants from both waves could be observed and if any difference in molecular diagnostic performance could be observed among the two sample types. Samples were transported immediately to the laboratory to ensure the highest possible sample quality without any freezing and thawing steps before processing. Nucleic acids from saliva and NPS were prospectively extracted and SARS-CoV-2 was detected using a real-time reverse-transcription polymerase chain reaction. All observed results were statistically analyzed. Although the results obtained with NP and saliva agreed overall, higher viral loads were observed in NP swabs regardless of the day of specimen collection in both SARS-CoV-2 epidemic waves. No significant difference could be observed between the two epidemic waves characterized by Delta or Omicron SARS-CoV-2. To note, Delta infection resulted in higher viral loads both in NP and saliva and more symptoms, including rhinorrhea, cough, and dyspnea, whereas Omicron wave patients more frequently reported sore throat. An increase in the mean log RNA of SARS-CoV-2 was observed with the number of expressed symptoms in both waves, however, the difference was not significant. Data confirmed that results from saliva were concordant with those from NP swabs, although saliva proved to be a challenging sample with frequent inhibitions that required substantial retesting.

Role of population and test characteristics in antigen-based SARS-CoV-2 diagnosis, Czechia, August to November 2021

“…This is consistent with the technical report of the European Centre for Disease Prevention and Control, which states that the suitability of saliva sampling for rapid antigen tests is not supported by the available data and that nasopharyngeal sampling remains the gold standard [26]. Saliva sample type also had low sensitivity in some clinical and analytical studies [1,2], and the average viral load in saliva was reported to be lower than for nasopharyngeal swabs [27].…”

Validation of RT-qPCR test for SARS-CoV-2 in saliva specimens

“…[47] Therefore, we did not assess the performance of saliva testing in presence of more transmissible but milder variants. [48] However, saliva testing performance seems similar in the presence of Delta and Omicron SARS-CoV-2 variants. In spite of the potential usefulness of saliva tests, our findings cannot be directly extrapolated to other populations.…”

Direct comparison of clinical diagnostic sensitivity of saliva from buccal swabs versus combined oro-/nasopharyngeal swabs in the detection of SARS-CoV-2 B.1.1.529 Omicron

“…In this study, we observed reduced clinical diagnostic sensitivity of saliva collected by buccal swabs in comparison to matched combined oro-/nasopharyngeal swabs in the detection of Omicron (BA.1 and BA.2). Serval studies on the sensitivity of saliva versus respiratory tract specimens for the detection of SARS-CoV-2, including Omicron, have been conducted, leading to mixed and in parts contradictory results [5][6][7][8][11][12][13]. In this study, samples were collected from hospitalized, symptomatic individuals who had previously been confirmed to be SARS-CoV-2 positive, resulting in sample collection at median six days after initial symptom onset.…”