Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection

• Published in: Scientific reports Vol. 11; no. 1; pp. 3134 - 8
• Main Authors: Teo, Alvin Kuo Jing, Choudhury, Yukti, Tan, Iain Beehuat, Cher, Chae Yin, Chew, Shi Hao, Wan, Zi Yi, Cheng, Lionel Tim Ee, Oon, Lynette Lin Ean, Tan, Min Han, Chan, Kian Sing, Hsu, Li Yang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 04.02.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 692/699/255/2514; 692/700/139; Adult; Asymptomatic; Cohort Studies; Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 diagnostic tests; COVID-19 Nucleic Acid Testing; Diagnosis; Female; Genomes; Humanities and Social Sciences; Humans; Infections; Male; Migrant workers; multidisciplinary; Nasal Mucosa - virology; Nasopharynx - virology; Next-generation sequencing; Phylogenetics; Phylogeny; Polymerase chain reaction; RNA, Viral - isolation & purification; Saliva; Saliva - virology; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Science; Science (multidisciplinary); Sensitivity analysis; Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Singapore - epidemiology; Specimen Handling; Singapore
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-82787-z

We aimed to test the sensitivity of naso-oropharyngeal saliva and self-administered nasal (SN) swab compared to nasopharyngeal (NP) swab for COVID-19 testing in a large cohort of migrant workers in Singapore. We also tested the utility of next-generation sequencing (NGS) for diagnosis of COVID-19. Saliva, NP and SN swabs were collected from subjects who presented with acute respiratory infection, their asymptomatic roommates, and prior confirmed cases who were undergoing isolation at a community care facility in June 2020. All samples were tested using RT-PCR. SARS-CoV-2 amplicon-based NGS with phylogenetic analysis was done for 30 samples. We recruited 200 subjects, of which 91 and 46 were tested twice and thrice respectively. In total, 62.0%, 44.5%, and 37.7% of saliva, NP and SN samples were positive. Cycle threshold (Ct) values were lower during the earlier period of infection across all sample types. The percentage of test-positive saliva was higher than NP and SN swabs. We found a strong correlation between viral genome coverage by NGS and Ct values for SARS-CoV-2. Phylogenetic analyses revealed Clade O and lineage B.6 known to be circulating in Singapore. We found saliva to be a sensitive and viable sample for COVID-19 diagnosis.