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

Li Yang Hsu, Alvin Kuo Jing Teo, Yukti Choudhury, Iain Tan, Chae Yin Cher, Shi Hao Chew, Zi Yi Wan, Lionel Tim Ee Cheng, Lynette Oon, Min Han Tan, Kian Sing Chan

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Received date: 23rd September 2020

Objectives: This study 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 used next-generation sequencing (NGS) for confirmatory detection of low-level SARS-CoV-2 signal and to establish phylogeny for tested samples. Methods: NP and SN swabs, and saliva samples were collected from subjects from a purpose-built dormitory who presented with symptoms of acute respiratory infection, their roommates who were asymptomatic, 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 was done for 30 samples and phylogenetic analysis was performed to identify lineages based on sequence variants. Results: We recruited 200 subjects, of which 91 and 46 were tested twice and thrice respectively, resulting in 337 sets of tests. In total, 44.5%, 37.7%, and 62.0% of NP, SN, and saliva 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 collected within week 1 and 2 of illness. We found a strong correlation between viral genome coverage by NGS and Ct values for SARS-CoV-2. Phylogenetic analyses showed Clade O and lineage B.6 known to be circulating in Singapore. Conclusion: We found saliva to be a sensitive and viable sample for COVID-19 diagnosis. NGS workflow provided confirmatory support of SARS-CoV-2 RT-PCR detection at low levels.

Read in full at medRxiv.

This is an abstract of a preprint hosted on a preprint server, which is currently undergoing peer review at Scientific Reports. The findings have yet to be thoroughly evaluated, nor has a decision on ultimate publication been made. Therefore, the results reported should not be considered conclusive, and these findings should not be used to inform clinical practice, or public health policy, or be promoted as verified information.

Scientific Reports

Nature Research, Springer Nature