Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva

Iwasaki, Shinya; Fujisawa, Shinichi; Nakakubo, Sho; Kamada, Keisuke; Yamashita, Yu; Fukumoto, Tatsuya; Sato, Kaori; Oguri, Satoshi; Taki, Keisuke; Senjo, Hajime; Sato, Junichi; Hayasaka, Kasumi; Konno, Satoshi; Nishida, Mutsumi; Teshima, Takanori

doi:10.1016/j.jinf.2020.05.071

Cited by 235 publications

(245 citation statements)

References 7 publications

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“…In contrast, studies have shown that while live virus can no longer be cultured from patients 10 days after symptom onset, 42 NP swabs continue to be positive after a patient is in the convalescent phase and no longer infectious. 13 As such, it is quite possible that differences observed in studies comparing SARS-CoV-2 levels in saliva and NP swabs are real, and not an artifact of different testing sensitivities; while in general concordance between the NP swab and saliva testing has been high in other studies (87%, 40 Our preliminary assessment of clinical samples is very promising, especially given that these samples were not collected and processed under the optimized protocol (they were collected before our discovery of the benefits of TBE buffer and Tween 20); with these samples TE buffer was added to the sample, and they were frozen for over a week before processing. However, even under this non-optimized workflow we were able to identify all 9 NP swab positives with duplicate runs of the samples.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, a number of recent reports have detailed the detection of SARS-CoV-2 in saliva through the workflow in Figure 1B, including a report showing higher viral loads in saliva when compared to matched NP swabs from the same patients. 12 Importantly, saliva (expelled in aerosols and droplets) may be a significant factor in personto-person transmission of SARS-CoV-2, 10 and it has been suggested that NP swab tests remain positive long after patients are infectious (potentially due to detection of inactive virus or remnants of viral RNA in the NP cavity), 13 whereas SARS-CoV-2 viral loads in saliva are highest during the first week of infection, when a person is most infectious. These data suggest that viral loads in saliva may be a good reflection of the transmission potential of patients infected SARS-CoV-2.…”

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confidence: 99%

“…These data suggest that viral loads in saliva may be a good reflection of the transmission potential of patients infected SARS-CoV-2. [13][14][15] While we are unaware of direct SARS-CoV-2 detection from saliva that bypasses RNA isolation/purification, there are several reports of detection from swab/VTM that bypasses RNA isolation/purification (Figure 1C). [16][17][18][19][20][21][22][23] With the ultimate goal of providing convenient, scalable, and costeffective molecular diagnostic testing for >10,000 individuals per day using a single COVID-19 testing center, here we report the discovery of a sensitive saliva-based detection method for SARS-CoV-2 that bypasses RNA isolation/purification (Figure 1D).…”

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confidence: 99%

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Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction

Rañoa

Holland

Alnaji

et al. 2020

Preprint

123

178

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Convenient, repeatable, large-scale molecular testing for SARS-CoV-2 would be a key weapon to help control the COVID-19 pandemic. Unfortunately, standard SARS-CoV-2 testing protocols are invasive and rely on numerous items that can be subject to supply chain bottlenecks, and as such are not suitable for frequent repeat testing. Specifically, personal protective equipment (PPE), nasopharyngeal (NP) swabs, the associated viral transport media (VTM), and kits for RNA isolation and purification have all been in short supply at various times during the COVID-19 pandemic. Moreover, SARS-CoV-2 is spread through droplets and aerosols transmitted through person-to-person contact, and thus saliva may be a relevant medium for diagnosing SARS-CoV-2 infection status. Here we describe a saliva-based testing method that bypasses the need for RNA isolation/purification. In experiments with inactivated SARS-CoV-2 virus spiked into saliva, this method has a limit of detection of 500-1000 viral particles per mL, rivalling the standard NP swab method, and initial studies also show excellent performance with 100 clinical samples. This saliva-based process is operationally simple, utilizes readily available materials, and can be easily implemented by existing testing sites, thus allowing for high-throughput, rapid, and repeat testing of large populations. Graphical Abstract3 BackgroundThe slow roll-out and inconsistent availability of diagnostic testing for SARS-CoV-2 has hobbled efforts to control the COVID-19 pandemic in many countries. Testing protocols based on the use of nasopharyngeal (NP) swabs as the collection agent, placed in a tube containing viral transport media (VTM), followed by RNA isolation/purification and subsequent analysis by RT-qPCR is currently the most common method ( Figure 1A). 1,2 While some variant of this process has been implemented worldwide, there are multiple challenges with this workflow. Sample collection using NP swabs requires healthcare workers wearing personal protective equipment (PPE) to collect samples, the swabs can be uncomfortable for the patients during collection, and the swabs and the associated VTM have been in short supply at many times and in most locations. In addition, RNA isolation/purification is another significant bottleneck, both in the time and labor required for this process, and in the availability of the equipment and reagents. All of these components also add to the cost of the testing process.There is emerging consensus that widespread, frequently repeated testing is necessary for a safer return to activities that are important for society. Given the data suggesting that SARS-CoV-2 can be spread by pre-symptomatic/asymptomatic carriers, 3-6 localized outbreaks could be dramatically reduced or prevented if individuals shedding SARS-CoV-2 could be readily identified and isolated. For example, imagine a testing bubble placed over a group that desires face-to-face interaction -employees of a company, members of a sports team, extended family networks, etc. If all members of...

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction

Rañoa

Holland

Alnaji

et al. 2020

Preprint

123

178

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“…In the following weeks, other studies investigated the role of saliva as a diagnostic tool by also recruiting symptomatic patients with a milder form of the disease ( Becker et al 2020 ; Caulley et al. 2020 ; Iwasaki et al 2020 ; Jamal et al 2020 ; Kim, Lee, et al 2020 ; McCormick-Baw et al 2020 ; Migueres et al. 2020 ; Nagura-Ikeda et al 2020 ; Pasomsub et al 2020 ; Williams et al 2020 ; Wyllie et al 2020 ).…”

Section: The Detection Of Sars-cov-2 In Salivamentioning

confidence: 99%

Diagnostic Salivary Tests for SARS-CoV-2

et al. 2020

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The diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection relies on the detection of viral RNA by real-time reverse transcription polymerase chain reaction (rRT-PCR) performed with respiratory specimens, especially nasopharyngeal swabs. However, this procedure requires specialized medical personnel, centralized laboratory facilities, and time to provide results (from several hours up to 1 d). In addition, there is a non-negligible risk of viral transmission for the operator who performs the procedure. For these reasons, several studies have suggested the use of other body fluids, including saliva, for the detection of SARS-CoV-2. The use of saliva as a diagnostic specimen has numerous advantages: it is easily self-collected by the patient with almost no discomfort, it does not require specialized health care personnel for its management, and it reduces the risks for the operator. In the past few months, several scientific papers, media, and companies have announced the development of new salivary tests to detect SARS-CoV-2 infection. Posterior oropharyngeal saliva should be distinguished from oral saliva, since the former is a part of respiratory secretions, while the latter is produced by the salivary glands, which are outside the respiratory tract. Saliva can be analyzed through standard (rRT-PCR) or rapid molecular biology tests (direct rRT-PCR without extraction), although, in a hospital setting, these procedures may be performed only in addition to nasopharyngeal swabs to minimize the incidence of false-negative results. Conversely, the promising role of saliva in the diagnosis of SARS-CoV-2 infection is highlighted by the emergence of point-of-care technologies and, most important, point-of-need devices. Indeed, these devices can be directly used in workplaces, airports, schools, cinemas, and shopping centers. An example is the recently described Rapid Salivary Test, an antigen test based on the lateral flow assay, which detects the presence of the virus by identifying the spike protein in the saliva within a few minutes.

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“…The WHO currently recommends RT-PCR testing using nasopharyngeal (NPS) and oropharyngeal swabs (OPS) as gold standard for SARS-CoV-2 diagnosis and for monitoring viral load [ 4 , 5 ]. OF has been suggested as an alternate clinical sample, easy and safer to collect, minimizing exposure of healthcare workers and could be useful for making a diagnosis and measuring SARS-CoV-2 viral load and viral shedding during the course of the illness and convalescence [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. To et al, demonstrated that SARS-CoV-2 was present in OF specimen of 11 out of 12 patients, with viral load being higher during the first week after symptoms onset and declining thereafter, being detectable until 25 days after symptoms onset (DSO) [ 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay

Bordi

Sberna

Lalle

et al. 2020

Viruses

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Background: RT-PCR on nasopharyngeal (NPS)/oropharyngeal swabs is the gold standard for diagnosis of SARS-CoV-2 infection and viral load monitoring. Oral fluid (OF) is an alternate clinical sample, easy and safer to collect and could be useful for COVID-19 diagnosis, monitoring viral load and shedding. Methods: Optimal assay conditions and analytical sensitivity were established for the commercial Simplexa™ COVID-19 Direct assay adapted to OF matrix. The assay was used to test 337 OF and NPS specimens collected in parallel from 164 hospitalized patients; 50 bronchoalveolar lavage (BAL) specimens from a subgroup of severe COVID-19 cases were also analysed. Results: Using Simplexa™ COVID-19 Direct on OF matrix, 100% analytical detection down to 1 TCID50/mL (corresponding to 4 × 103 copies (cp)/mL) was observed. No crossreaction with other viruses transmitted through the respiratory toute was observed. Parallel testing of 337 OF and NPS samples showed highly concordant results (κ = 0.831; 95 % CI = 0.771–0.891), and high correlation of Ct values (r = 0.921; p < 0.0001). High concordance and elevated correlation was observed also between OF and BAL. Prolonged viral RNA shedding was observed up to 100 days from symptoms onset (DSO), with 32% and 29% positivity observed in OF and NPS samples, respectively, collected between 60 and 100 DSO. Conclusions: Simplexa™ COVID-19 Direct assays on OF have high sensitivity and specificity to detect SARS-CoV-2 RNA and provide an alternative to NPS for diagnosis and monitoring SARS-CoV-2 shedding.

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Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva

Cited by 235 publications

References 7 publications

Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction

Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction

Diagnostic Salivary Tests for SARS-CoV-2

Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay

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