key: cord-0709037-c6psmshz
authors: Leung, Eddie Chi‐man; Chow, Viola Chi‐ying; Lee, May Kin‐ping; Lai, Raymond Wai‐man
title: Deep throat saliva as an alternative diagnostic specimen type for the detection of SARS‐CoV‐2
date: 2020-07-14
journal: J Med Virol
DOI: 10.1002/jmv.26258
sha: 39e6c7732642d79926385828525800fade085ed0
doc_id: 709037
cord_uid: c6psmshz

Nasopharyngeal swabs (NPS) are widely accepted as specimens for the detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in the current pandemic of coronavirus disease 2019. However, the collection procedures for NPS specimens causes sneezing and coughing in most patients, which generate droplets or aerosol particles that are hazardous to the healthcare workers collecting these specimens. In this study, 95 patient‐matched paired deep throat saliva (DTS) and NPS specimens from 62 patients were analyzed. Samples were tested for SARS‐CoV‐2 by reverse‐transcription polymerase chain reaction (RT‐PCR). The rates of detection for DTS (53.7%) and NPS (47.4%) samples were comparable (P = .13). It is important to note that the patients should be clearly instructed or supervised during DTS collection. In conclusion, SARS‐CoV‐2 detection by RT‐PCR was equivalent in DTS and NPS specimens.

Hospital in Hong Kong. To collect DTS samples, patients were provided clear instructions to collect saliva from the deep throat (posterior oropharyngeal) in a sterile sputum container. 8 In-house prepared viral transport medium (2 mL) was added in the laboratory for sample processing. NPS samples were collected by the nursing staff using flocked swabs in a container with 3 ml viral transport medium. Collected specimens were sent to the laboratory immediately for SARS-CoV-2 RT-PCR testing.

An RT-PCR assay using the lightMix Modular SARS-CoV (COVID19) E-gene detection kit (TIB Molbiol, Berlin, Germany), which target a 78 base pair fragment from a conserved region in the E gene of SARS CoV-1, SARS CoV-2, and the bat-associated SARS-related virus (Sarbecovirus), was used as a screening assay. Briefly, nucleic acid extraction was performed using the MagMAX (Applied Biosystems, Foster city) and a viral RNA isolation kit (Applied Biosystems), and 50 µL of viral RNA was obtained from every 200 µL sample. A 20 µL reaction mix containing 5 µL of 4X TaqMan fast (Applied Biosystems), 0.5 µL primer-probe mix, 4.5 µL Nuclease-free water, and 10 µL nucleic acid was prepared. RT-PCR was conducted using the ABI 7900 real-time PCR system (Applied Biosystems) under the following conditions: 5 minutes at 55°C, 20 seconds at 95°C, 40 cycles of 3 seconds at 95°C, and 30 seconds at 60°C. The samples that tested positive for SARS-CoV-2 were sent to the Public Health Laboratory Service Branch in Hong Kong for confirmation, where they used a different RT-PCR assay that targeted a SARS-CoV-2 specific RdRp gene region.

The SARS-CoV-2 detection rates for DTS and NPS were compared by Pearson's χ 2 test. Analysis of correlation agreement methods, such as percent agreement and κ statistic, were used to determine the comparability of the two sampling methods. Statistical analyses were 

Nasopharyngeal specimens, either from nasopharyngeal aspirates (NPA) or NPS, are the recommended specimen type for the detection of respiratory viruses. 11 The NPS is also the most common validated specimen type for a majority of the commercially available respiratory virus detection kits. Thus, NPA or NPS is also the recommended specimen type for SARS-CoV-2 detection. Given the invasive nature of the procedures used to obtain NPA, NPS specimens were the specimen of choice for SARS-CoV-2 detection. The collection of NPS, although less invasive than NPA, may cause 

This study showed that the overall performance of DTS was equivalent to that of the NPS, as specimens used in the detection of SARS-CoV-2 by RT-PCR assay.

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The authors declare that there are no conflict of interests.

Dr. Eddie Leung carried out the experiments, performed the analysis and drafted the manuscript. Dr. Viola Chow and Dr. May Lee contributed to the interpretation of the results. Dr. Raymond Lai conceptualized and supervised the project. All authors discussed the results and contributed to the final manuscript.

Eddie Chi-man Leung http://orcid.org/0000-0002-5036-1707