Saliva as an alternate specimen source for the diagnosis of coronavirus disease 2019 in symptomatic patients using cepheid xpert xpress SARS-CoV-2

Abstract

Background: Rapid and accurate SARS-CoV-2 diagnostic testing is essential for controlling the ongoing coronavirus disease 2019 (COVID-19) pandemic. The current gold standard for COVID-19 diagnosis is real-time reverse transcription-polymerase chain reaction (RT-PCR) detection of SARS-CoV-2 from nasopharyngeal swab (NPS) specimens. The objective of this study is to assess saliva specimens for the diagnosis of COVID-19 using the GeneXpert® Xpress SARS-CoV-2 assay. Materials and Methods: In June 2020, we prospectively simultaneously collected saliva samples and a standard NPS from 60 patients meeting case definition of COVID-19 in the Emergency Department and from inpatients in Rashid Hospital at Dubai Health Authority during the outbreak of COVID-19. Real-time RT-PCR using the Cepheid Xpert Xpress SARS-CoV-2 was performed, and the results of the two specimens were compared. Results: A total of 60 paired NPS and saliva specimens were tested. An analysis of the agreement between the two specimens demonstrated a 97% observed agreement. 30/28 samples were positive in saliva when compared to the NPS, resulting in a positive percent agreement of 93%. 30/32 samples had a negative saliva and NPS. Two samples demonstrated detectable levels of SARS-CoV-2 nucleic acid in the saliva, but the NPS was negative, resulting in a negative percent agreement of 94%. Conclusion: Our data showed that saliva is an acceptable sensitive and specific alternative source for detecting SARS-CoV-2 nucleic acid and the use of saliva samples is safer and more convenient for the patient. NPS sampling inconsistency may be one of the potential issues for false-negative results.