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

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

Scientific Reports volume 11, Article number: 3134 (2021) 

Published: 04 February 2021

Acute coronavirus disease 2019 (COVID-19) is primarily diagnosed via reverse transcription-polymerase chain reaction (RT-PCR) detection of viral genetic material. However, considering the three primary modes of transmission of SARS-Cov-2 i.e., contact, droplet and aerosol routes, various types of samples have been suggested for the purpose of detection⁴. In Singapore and several other countries, nasopharyngeal (NP) swabs are the principal means for collecting specimens for testing^5,6. However, the collection procedure for NP swabs can cause discomfort and require trained healthcare staff to perform.

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.

Saliva and self-administered nasal (SN) swabs are, in many ways, ideal specimens for COVID-19 screening. Both can be collected safely without the need for trained staff. The utility of saliva for COVID-19 testing has been tested in multiple territories and countries^{7,8,9,10,11,12,13,14,15}. The majority of current published studies involve relatively small numbers of subjects. A meta-analysis suggests that saliva is at best slightly less sensitive or similar to other specimens, including NP swabs¹⁶. However, one caveat relates to how saliva is collected—saliva is a complex bio-mixture which can consist of salivary gland secretion, gingival crevicular fluid, sputum and/or mucosal transudate, in varying proportions depending on collection method. Some studies tested only secretions from the mouth^11,12, others explicitly tested “posterior oropharyngeal” or “deep throat” saliva with secretions from the oropharynx^7,8,9,10, while the rest were unspecified^13,14,15,16.

We aimed to test the sensitivity of “naso-oropharyngeal” saliva and SN swabs compared to NP swabs in a large cohort of migrant workers in Singapore using RT-PCR testing. We additionally used direct-from-RNA amplicon-based next-generation sequencing (NGS) for confirmatory detection of low-level SARS-CoV-2 signal and to establish phylogeny for tested samples.

Discussion

Our study is concordant with multiple published works supporting saliva as an alternative sample for COVID-19 screening and diagnosis^{7,8,9,10,11,12,13,14,15}, and one of a minority where saliva was shown to be more sensitive than the corresponding NP swab^8,9,13, although the results by Leung et al. (53.7% saliva vs. 47.4% NP swab, 95 subjects) were not statistically different⁸. Several reasons may account for this difference in the studies, including enrichment from nasal and oropharyngeal secretions, where the viral load is potentially higher^8,9, or a higher volume of samples collection, where approximately 10 mL of saliva was collected for testing¹³. Steps were taken to minimize biases and errors—NP swabs performed by trained healthcare staff, environmental testing of CAP-accredited laboratory (no evidence of contamination), conduction of tests for most of the samples in the same laboratory, and pre-processing of saliva samples with dithiothreitol before RNA extraction to resolve the issues of saliva specimen viscosity, which can lead to false negatives.

Interestingly but perhaps unsurprisingly, the use of different RT-PCR kits in the present study resulted in different test-positive rates in saliva, suggesting that this can potentially be an important consideration for clinical laboratories, where more sensitive laboratory protocols should be deployed for clinical diagnosis as opposed to mass screening for low-prevalence populations. More validation would be required to confirm this finding.

SN swabs, however, appeared less sensitive compared to both saliva and NP swabs for the diagnosis of COVID-19. Although it was convenient, less time-consuming to perform relative to saliva collection, and caused less discomfort compared to NP swabs, the markedly lower sensitivity should preclude its use where other sample types can be collected.

In our study, NGS provided efficient whole-genome profiling of SARS-CoV-2 for phylogenetic analysis directly from the clinical samples without culture. NGS detection sensitivity was excellent with a threshold of 1.7% genome coverage or 5 amplicons targets, confirming all CDC-LDT positives tested. Other groups have reported highly sensitive performance for NGS with limits of detection ranging between a threshold of 5% genome coverage or 84 genome-equivalents per mL²¹, or at least 5 SARS-CoV-2 targets for detection²². The phylogeny results were consistent with the virus belonging to a viral type (Clade O, lineage B.6) known to be circulating in the geographical regions of Singapore and India.

There are several limitations to our work. Firstly, the study population was confined to young and middle-aged men who were either asymptomatic or had mild disease. The results cannot be extrapolated to other populations (e.g., paediatric), where there is a clear need for alternate sample types to NP swabs. Secondly, we did not extend the follow-up testing sufficiently to determine when saliva viral shedding stopped for the majority of subjects, although this has been explored in other studies^7,10. Thirdly, we did not test for the difference, if any, between saliva obtained from naso-oropharyngeal or the mouth alone, although it is biologically plausible that the latter would result in lower sensitivity for COVID-19 diagnosis¹⁶.

In conclusion, our study adds to the body of evidence supporting saliva as a sensitive and less intrusive sample for COVID-19 diagnosis and further defines the role of naso-oropharyngeal secretions and the impact of different RT-PCR kits in increasing the sensitivity of testing. In our study, SN swabs were inferior to both saliva and NP swabs. Our study also provides evidence to support NGS in challenging samples for sensitive COVID-19 molecular diagnosis. Such an NGS workflow can also provide direct-from-sample phylogenetic analysis for public health decision-making, such as contact tracing.