Accuracy of saliva and nasopharyngeal sampling for detection of SARS-CoV-2 in community screening: a multicentric cohort study

Kernéis, Solen; Elie, Caroline; Fourgeaud, Jacques; Choupeaux, Laure; Delarue, Séverine; Alby, Marie-Laure; Quentin, P.; Pavie, Juliette; Brazille, Patricia; Néré, Marie-Laure; Minier, Marine; Gabassi, Audrey; Gibaud, Aurélien; Gauthier, Sébastien A.; Leroy, C.; Voirin-Mathieu, Etienne; Poyart, Claire; Vidaud, Michel; Parfait, Béatrice; Delaugerre, Constance; Tréluyer, Jean‐Marc; LeGoff, Jérôme

doi:10.1007/s10096-021-04327-x

Cited by 17 publications

(20 citation statements)

References 36 publications

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“…Ag-RDT screening is widely used in healthcare settings, but there is limited empirical evidence demonstrating efficacy for SARS-CoV-2 transmission prevention. 17 Despite a range of studies reporting efficacy for case identification, 18–20 interventional trials are needed to understand impacts on nosocomial spread. Our comparison of apparent and real screening efficiency demonstrates why case identification may be a poor proxy measure for actual health and economic benefit.…”

Section: Discussionmentioning

confidence: 99%

Rapid antigen testing as a reactive response to surges in nosocomial SARS-CoV-2 outbreak risk

Duval

Zahar

et al. 2021

Preprint

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Background: Surges in community SARS-CoV-2 incidence increase risk of importation and subsequent transmission in healthcare facilities. Antigen rapid diagnostic testing (Ag-RDT) is widely used for population screening, but its health and economic benefits as a reactive intervention in healthcare settings are unclear. Methods: We used stochastic, individual-based modelling to simulate SARS-CoV-2 transmission in a long-term care facility with varying COVID-19 containment measures in place (social distancing, face masks, vaccination). In contrast to routine symptomatic testing using reverse-transcriptase polymerase chain reaction (RT-PCR), we evaluated the efficacy and health-economic efficiency of single or repeated population-wide Ag-RDT screening interventions implemented in response to surges in nosocomial outbreak risk. Results: Depending on the baseline containment measures in place, nosocomial SARS-CoV-2 incidence was reduced by up to 40-47% (range of means) with routine RT-PCR testing, 59-63% with the addition of a timely round of Ag-RDT screening, and 69-75% with well-timed two-round screening. For the latter, a delay of 4 to 5 days between the first and second rounds was optimal for transmission prevention. Efficacy varied depending on test sensitivity, subpopulations targeted, and SARS-CoV-2 incidence in the community. Efficiency, however, varied primarily depending on the other containment measures in place: surveillance costs for a combined strategy of routine RT-PCR testing and reactive Ag-RDT screening ranged from a mean €420-€10,260/infection averted across scenarios (default unit costs: €5/Ag-RDT test, €50/RT-PCR test). Interpretation: Reactive Ag-RDT screening complements routine RT-PCR testing, and systematic two-round screening helps overcome limited, time-varying diagnostic sensitivity. Health-economic gains scale significantly with underlying nosocomial outbreak risk.

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Section: Discussionmentioning

confidence: 99%

Rapid antigen testing as a reactive response to surges in nosocomial SARS-CoV-2 outbreak risk

Duval

Zahar

et al. 2021

Preprint

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“…All samples were stored until they were to be sniffed by the dogs in a minus 20°C freezer and were never manipulated without disposable surgical gloves to prevent contamination. Nasopharyngeal samples (NPS) were collected by a trained nurse, and participants were asked to self-collect the saliva sample after swishing saliva in their mouths for 30 seconds [6].…”

Section: Methodsmentioning

confidence: 99%

“…SARS CoV-2 RNA amplification was performed using the TaqPath(tm) COVID-19 CE IVD RT PCR Kit (Thermo Fisher Scientific, Coutaboeuf, France). This technique provides results expressed as a cycle threshold (Ct) for each gene target (ORF1ab, N and S genes) [6].…”

Section: Methodsmentioning

confidence: 99%

“…Informed consent was obtained from all subjects. Eligible persons received detailed oral and written information [6]. Participants were prospectively enrolled if they were not opposed to participating in the study.…”

Section: Recruitment Of Participantsmentioning

confidence: 99%

“…SARS CoV-2 RNA amplification was performed using the TaqPath™ COVID-19 CE IVD RT PCR Kit (Thermo Fisher Scientific, Coutaboeuf, France). This technique provides results expressed as a cycle threshold (Ct) for each gene target (ORF1ab, N and S genes)[6].Detection of other pathogens in saliva The detection of other viruses (adenovirus, coronaviruses (229E, HKU1, NL63, and OC43), human metapneumovirus A and B, influenza , influenza A H1, influenza A H3, influenza A H1N1/2009, influenza B, parainfluenza viruses (1, 2, 3, and 4), rhinovirus/enterovirus, respiratory syncytial virus A and B) and intracellular bacteria (Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae) was performed in saliva samples with the multiplex test QIAstat-Dx® Respiratory SARS-CoV-2 Panel QIAStat (Qiagen, Courtaboeuf, France). Briefly, 100 μL of saliva was mixed with 400 µL of NeuMoDx Viral Lysis Buffer (NeuMoDx Molecular, Inc., Ann Arbor, MI).…”

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confidence: 99%

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Diagnostic Accuracy of Non-Invasive Detection of Sars-Cov-2 Infection by Canine Olfaction

Grandjean

Elie

Gallet

et al. 2022

Preprint

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BACKGROUND Throughout the COVID-19 pandemic, testing individuals remains a key action. One approach to rapid testing is to consider the olfactory capacities of trained detection dogs. METHODS Prospective cohort study in two community COVID-19 screening centers. Two nasopharyngeal swabs (NPS), one saliva and one sweat samples were simultaneously collected. The dog handlers (and the dogs) were blinded with regards to the Covid status. The diagnostic accuracy of non-invasive detection of SARS-CoV-2 infection by canine olfaction was assessed as compared to nasopharyngeal RT-PCR as the reference standard, saliva RT-PCR and nasopharyngeal antigen testing. RESULTS 335 ambulatory adults (143 symptomatic and 192 asymptomatic) were included. Overall, 109/335 participants tested positive on nasopharyngeal RT-PCR either in symptomatic (78/143) or in asymptomatic participants (31/192). The overall sensitivity of canine detection was 97% (95% CI, 92 to 99) and even reached 100% (95% CI, 89 to 100) in asymptomatic individuals compared to NPS RT-PCR. The specificity was 91% (95% CI, 72 to 91), reaching 94% (95% CI, 90 to 97) for asymptomatic individuals. The sensitivity of canine detection was higher than that of nasopharyngeal antigen testing (97% CI: 91 to 99 versus 84% CI: 74 to 90, p=0.006), but the specificity was lower (90% CI: 84 to 95 versus 97% CI: 93 to 99, p=0.016). CONCLUSIONS Non-invasive detection of SARS-CoV-2 infection by canine olfaction could be one alternative to NPS RT-PCR when it is necessary to obtain a result very quickly according to the same indications as antigenic tests in the context of mass screening.

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The effect of sample site and collection procedure on identification of SARS-CoV-2 infection

Davenport,

Arevalo-Rodriguez,

Mateos-Haro

et al. 2024

Cochrane Database of Systematic Reviews

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Background Sample collection is a key driver of accuracy in the diagnosis of SARS‐CoV‐2 infection. Viral load may vary at different anatomical sampling sites and accuracy may be compromised by difficulties obtaining specimens and the expertise of the person taking the sample. It is important to optimise sampling accuracy within cost, safety and accessibility constraints. Objectives To compare the sensitivity of different sampling collection sites and methods for the detection of current SARS‐CoV‐2 infection with any molecular or antigen‐based test. Search methods Electronic searches of the Cochrane COVID‐19 Study Register and the COVID‐19 Living Evidence Database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on 22 February 2022. We included independent evaluations from national reference laboratories, FIND and the Diagnostics Global Health website. We did not apply language restrictions. Selection criteria We included studies of symptomatic or asymptomatic people with suspected SARS‐CoV‐2 infection undergoing testing. We included studies of any design that compared results from different sample types (anatomical location, operator, collection device) collected from the same participant within a 24‐hour period. Data collection and analysis Within a sample pair, we defined a reference sample and an index sample collected from the same participant within the same clinical encounter (within 24 hours). Where the sample comparison was different anatomical sites, the reference standard was defined as a nasopharyngeal or combined naso/oropharyngeal sample collected into the same sample container and the index sample as the alternative anatomical site. Where the sample comparison was concerned with differences in the sample collection method from the same site, we defined the reference sample as that closest to standard practice for that sample type. Where the sample pair comparison was concerned with differences in personnel collecting the sample, the more skilled or experienced operator was considered the reference sample. Two review authors independently assessed the risk of bias and applicability concerns using the QUADAS‐2 and QUADAS‐C checklists, tailored to this review. We present estimates of the difference in the sensitivity (reference sample (%) minus index sample sensitivity (%)) in a pair and as an average across studies for each index sampling method using forest plots and tables. We examined heterogeneity between studies according to population (age, symptom status) and index sample (time post‐symptom onset, operator expertise, use of transport medium) characteristics. Main results This review includes 106 studies reporting 154 evaluations and 60,523 sample pair comparisons, of which 11,045 had SARS‐CoV‐2 infection....

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Accuracy of saliva and nasopharyngeal sampling for detection of SARS-CoV-2 in community screening: a multicentric cohort study

Cited by 17 publications

References 36 publications

Rapid antigen testing as a reactive response to surges in nosocomial SARS-CoV-2 outbreak risk

Rapid antigen testing as a reactive response to surges in nosocomial SARS-CoV-2 outbreak risk

Diagnostic Accuracy of Non-Invasive Detection of Sars-Cov-2 Infection by Canine Olfaction

The effect of sample site and collection procedure on identification of SARS-CoV-2 infection

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