Posterior Oropharyngeal Saliva for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Abstract

Background: The coronavirus disease 2019 (COVID-19) pandemic has put tremendous pressure on the healthcare system worldwide. Diagnostic testing remained one of the limiting factors for early identification and isolation of infected patients. This study aimed to evaluate posterior oropharyngeal saliva (POPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection among patients with confirmed or suspected COVID-19.

Methods: The laboratory information system was searched retrospectively for all respiratory specimens and POPS requested for SARS-CoV-2 RNA detection between 1 February 2020 and 15 April 2020. The agreement and diagnostic performance of POPS against NPsp were evaluated.

Results: A total of 13772 specimens were identified during the study period, including 2130 POPS and 8438 nasopharyngeal specimens (NPsp). Two hundred and twenty-nine same-day POPS-NPsp paired were identified with POPS and NPsp positivity of 61.5% (95% confidence interval [CI] 55.1-67.6%) and 53.3% (95% CI 46.8-59.6%). The overall, negative and positive percent agreement were 76.0% (95% CI 70.2-80.9%), 65.4% (95% CI 55.5-74.2%), 85.2% (95% CI 77.4-90.8%). Better positive percent agreement was observed in POPS-NPsp obtained within 7 days (96.6%, 95% CI 87.3-99.4%) compared with after 7 days of symptom onset (75.0%, 95% CI 61.4-85.2%). Among the 104 positive pairs, the mean difference in Cp value was 0.26 (range: 12.63 to -14.74), with an overall higher Cp value in NPsp (Pearson coefficient 0.579). No significant temporal variation was noted between the 2 specimen types.

Conclusions: POPS is an acceptable alternative specimen to nasopharyngeal specimen for the detection of SARS-CoV-2.

Keywords: COVID-19; mass screening; pandemic; saliva; severe acute respiratory syndrome coronavirus 2.

Figure 1.

Breakdown of respiratory specimens received during the study period. Between 1 February 2020 and 15 April 2020, a total of 13772 specimens for SARS-CoV-2 testing were received from inpatients in the Kowloon Central Cluster, as well as ambulatory patients and asymptomatic patients from different surveillance programs and clinical settings. Subgroup head-to-head comparison of posterior oropharyngeal saliva with nasopharyngeal specimens were performed on the 229 posterior oropharyngeal saliva when concurrent nasopharyngeal specimen taken on the same day from the same patient. Abbreviations: COVID-19, coronavirus disease 2019; NPA, nasopharyngeal aspirates; NPA/T: nasopharyngeal aspirate pooled with throat swab; NPS, nasopharyngeal swabs; NPS/T: nasopharyngeal swab pooled with throat swab; POPS, posterior oropharyngeal saliva; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 2.

Percent agreement of the 229 posterior oropharyngeal saliva-nasopharyngeal pair. Overall negative and positive percent agreement of the 229 pairs and positive percent agreement of the symptomatic patients according to symptom onset with the corresponding 95% confidence interval. Abbreviations: NPA, negative percent agreement; OPA, overall percent agreement; PPA, positive percent agreement.

Figure 3.

Comparison of Cp values of same-day posterior oropharyngeal saliva-nasopharyngeal specimen pairs. Cp values from 104 posterior oropharyngeal saliva and nasopharyngeal specimen pairs collected from 43 patients with detectable SARS-CoV-2 were included for comparison (Pearson correlation coefficient: 0.579). Abbreviation: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 4.

Longitudinal SARS-CoV-2 RNA test results from the 44 patients with confirmed COVID-19. Forty-four symptomatic COVID-19 patients were included with SARS-CoV-2 RNA results from posterior oropharyngeal saliva and nasopharyngeal specimens during their stay in the airborne infection isolation facilities in the hospitals of the Kowloon Central Cluster, with the day of symptom onset being day 0 on the chart. Only days where both posterior oropharyngeal saliva and nasopharyngeal specimen types were obtained were included on the diagram. Asymptomatic COVID-19 patients with paired POPS-NPsp specimens were not included in this figure. Abbreviations: COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.