Saliva as a Potential Clinical Specimen for Diagnosis of SARS-CoV-2

Background: There is no sign of stopping the spread of corona virus disease- 2019 (COVID-19) pandemic since it has started in December 2019. Rapid and early detection is extremely crucial to slow down the quick spread of the virus and break the human transmission chain. There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of severe acute respiratory syndrome coronavirus- 2 (SARS-CoV-2). We aimed to analyse the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS-CoV-2.Methods: A total number of 74 patients were enrolled for this study. We analysed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We used real time quantitative polymerase chain reaction (RT-qPCR), gene sequencing for the detection and determination SARS-CoV-2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We use Bland-Altman model to identify the agreement between two specimens.Findings: This study shows a lower cycle threshold (CT) mean value for the detection of SARS-CoV-2 ORF1 gene (mean 27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (mean 28.24; 95% CI, 26.62 to 29.85) specimen although the difference is statistically non-significant (p>0.05). Bland-Altman analysis produces relatively smaller bias and high agreement between these two clinical specimens. Phylogenetic analysis with the RdRp and Spike gene confirmed the presence of SARS-CoV-2 in the saliva samples.Interpretation: In conclusion, our study highlights that saliva represents a promising tool in COVID-19 diagnosis and the collection method would reduce the exposure risk of frontline health workers which is one of major concerns in primary healthcare settings.Funding Statement: ICMR for provided financial grants for this study.Declaration of Interests: The authors declare that they have no competing interests.Ethics Approval Statement: The study was approved by Institutional Ethics Committee and written informed consent was obtained from the study subjects.