Comparison Between a Standard and SalivaDirect RNA Extraction Protocol for Molecular Diagnosis of SARS-CoV-2 Using Nasopharyngeal Swab and Saliva Clinical Samples

Flores, Sofía N. Rodríguez; Rodríguez-Martínez, Luis Mario; Reyes-Berrones, Bernardita L.; Fernández‐Santos, Nadia A.; Sierra-Moncada, Elthon J.; Rodríguez‐Pérez, Mario A.

doi:10.3389/fbioe.2021.638902

Cited by 16 publications

(20 citation statements)

References 29 publications

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“…Testing for SARS-CoV-2 in saliva mitigates many of the challenges associated with NPS sampling (Tan et al, 2021;Vaz et al, 2020;Wyllie et al, 2020). Although various different protocols for SARS-CoV-2 testing in saliva have been proposed, including colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) and lateral flow assays (Faustini et al, 2020;Lalli et al, 2021), RT-qPCR is the most common used modality (Caulley et al, 2021;Migueres et al, 2020;Teo et al, 2021) with a reported sensitivity between ~ 69 to 100% (Azzi et al, 2020;Kojima et al, 2020;Pasomsub et al, 2021;Skolimowska et al, 2020;.…”

Section: Amendments From Version 1 Introductionmentioning

confidence: 99%

Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

et al. 2021

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Introduction: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited. The aim of our study was to assess SalivaDirect as an alternative method for COVID-19 testing. Methods: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings, respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using RdRp and N1 gene targets in NPS and saliva, respectively. Results: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833–0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample (p=0.860). A highly significant correlation (r = 0.475, p<0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens. Conclusions: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Accurate and less invasive saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.

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Section: Amendments From Version 1 Introductionmentioning

confidence: 99%

Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

et al. 2021

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“…Our results are consistent with the original publication of the SalivaDirect method, where the positive agreement was 94% in the hospitalised cohort, and sensitivity and specificity of saliva versus NPS in 3779 asymptomatic individuals were 89.5% and >99.9%, respectively ( Vogels et al , 2021 ). A separate study reported a sensitivity of 88.2% of saliva samples assessed with SalivaDirect when compared to matching NPS samples taken from 30 COVID-19-positive individuals ( Rodríguez Flores et al , 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…Initial studies using SalivaDirect reported a significant positive agreement (94%) between paired saliva and NPS samples obtained from a hospital cohort of 37 asymptomatic HCP and 30 COVID-19-positive inpatients ( Vogels et al , 2021 ). In another study, matched saliva and NPS samples obtained from 30 individuals with COVID-19 illustrated a 88.2% concordance when using the SalivaDirect protocol ( Rodríguez Flores et al , 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

et al. 2021

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Introduction: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited. The aim of our study was to to assess SalivaDirect as an alternative method for COVID-19 testing. Methods: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings, respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using RdRP and N1 gene targets in NPS and saliva, respectively. Results: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833–0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample (p=0.860). A highly significant correlation (r = 0.475, p<0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens. Conclusions: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Accurate and less invasive saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.

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“…The LumiraDx test is a microfluidic immunofluorescence assay for qualitative detection of antigen in nasal specimens [19–24]. SalivaDirect is a dual-plexed RT-PCR method for SARS-CoV-2 detection from minimally processed saliva [25,26].…”

Section: Methodsmentioning

confidence: 99%

Screening for SARS-CoV-2 in close contacts of individuals with confirmed infection: performance and operational considerations

Zobrist

Oliveira-Silva²,

Vieira³

et al. 2022

Preprint

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Background. Point-of-care and decentralized testing for SARS-CoV-2 is critical to inform public health responses. Performance evaluations in priority use cases such as contact tracing can highlight trade-offs in test selection and testing strategies. Methods. A prospective diagnostic accuracy study was conducted among close contacts of COVID-19 cases in Brazil. Two anterior nares swabs (ANS), a nasopharyngeal swab (NPS), and saliva were collected at all visits. Vaccination history and symptoms were assessed. Household contacts were followed longitudinally. Three rapid antigen tests and one molecular method were evaluated for usability and performance against reference RT-PCR on NPS. Results. Fifty index cases and 214 contacts (64 household) were enrolled. Sixty-five contacts were RT-PCR positive during at least one visit. Vaccination did not influence viral load. Gamma variants were most prevalent; Delta emerged increasingly during implementation. Overall sensitivity of evaluated tests ranged from 33% to 76%. Performance was higher among symptomatic cases and cases with Ct<34 and lower among oligo/asymptomatic cases. Assuming a 24-hour time-to-result for RT-PCR, the cumulative sensitivity of an ANS rapid antigen test was >70% and almost 90% after four days. Conclusions. The near immediate time-to-result for antigen tests significantly offsets lower analytical sensitivity in settings where RT-PCR results are delayed or unavailable.

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Comparison Between a Standard and SalivaDirect RNA Extraction Protocol for Molecular Diagnosis of SARS-CoV-2 Using Nasopharyngeal Swab and Saliva Clinical Samples

Cited by 16 publications

References 29 publications

Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

Screening for SARS-CoV-2 in close contacts of individuals with confirmed infection: performance and operational considerations

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