key: cord-0707492-scn86ale authors: Migueres, M.; Vellas, C.; Abravanel, F.; Da Silva, I.; Dimeglio, C.; Ferrer, V.; Raymond, S.; Mansuy, JM.; Izopet, J. title: Testing individual and pooled saliva samples for sars-cov-2 nucleic acid: a prospective study date: 2021-07-15 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2021.115478 sha: 307b0b34447a4baf3b2ffbc2e29a877ee2b5015d doc_id: 707492 cord_uid: scn86ale Control of the rapid spread of the SARS-CoV-2 virus requires efficient testing. We collected paired nasopharyngeal swab (NPs) and saliva samples from 303 subjects (52.8% symptomatic) at a drive-through testing center; 18% of whom tested positive. The NPs, salivas and five saliva pools were tested for SARS-CoV-2 RNA using the Aptima™ assay and a laboratory-developed test (LDT) on the Panther-Fusion™ Hologic® platform. The saliva sensitivity was 80% (LDT) and 87.5% (Aptima™) whereas that of NPs was 96.4% in both assays. The pooled saliva sensitivity of 72.7% (LDT) and 75% (Aptima™) was not significantly different of that of individual saliva testing. Saliva specimens appear to be suitable for sensitive non-invasive assays to detect SARS-CoV-2 nucleic acid; pooling them for a single test will improve laboratory throughput. Saliva sampling is non-invasive, painless and much more acceptable. It does not use 85 swabs, and patients can easily collect their own samples, so reducing crowding at testing sites. 86 However, the results of studies that used saliva samples for SARS-CoV-2 diagnosis have 87 been variable. Some reported that saliva samples were inappropriate (4-6), while others found 88 them acceptable or even provided greater sensitivity (7-13). These differences could be due 89 to the sampling protocol used (saline gargle and spit, posterior oral saliva, crude saliva, oral 90 swabs) or the individuals tested (hospitalized patients or health-care workers in most cases). Few studies assessed the performance of saliva samples for SARS-CoV-2 testing according to 92 the time from symptom onset, or in asymptomatic non-hospitalized individuals (10,14-16). In 93 addition, little is known of the suitability of pooled saliva samples for increasing laboratory 94 throughput, which optimizes reagent use and reduces cost. This prospective study of outpatients examined SARS-CoV-2 detection in individual 96 and pooled saliva specimens, and NP swabs. SARS-CoV-2 RNA was detected using two Patients who came to the Toulouse University Hospital drive-through testing center 27 104 -29 October 2020 during the second epidemic wave in France were enrolled prospectively. They were informed of and consented to the test before they provided a saliva specimen plus 106 a NP swab sample. The saliva samples were self-collected under the supervision of a health 107 care worker (HCW) and the NPs was collected by a HCW following CDC specimen 108 collection guidelines (17) . (Table 5) . The literature on the sensitivity of tests on saliva has not produced unanimous results. Reported sensitivities range from 46 to 100% (4,5,7,9-14,16,21-29). We find overall 217 sensitivities of 80.0% using our LDT and 87.5% with the Aptima assay, indicating that testing 218 saliva is acceptable for SARS-CoV-2 diagnosis in outpatients, which is consistent with the 219 findings of a recent meta-analysis (30). The published discrepancies could be due to 220 differences between the populations studied, the time of sampling and the patients' virus load, 221 the saliva collection method, or even the amplification assay used. While some studies found 222 higher virus loads in saliva than in NPs (7) (10), we and others find higher Ct values in saliva, 223 indicating lower virus loads in saliva (5, 9, 12, 13) . This could be due to differences in the 224 saliva collection method. A recent meta-analysis reported that tests using posterior 225 oropharyngeal saliva samples were more sensitive than samples obtained by the swill-and-spit 226 method (30). 227 We tested saliva samples provided by subjects, both symptomatic and asymptomatic, 228 who came to a drive-through testing center during the second epidemic wave in France, 229 unlike the majority of studies which were done on inpatients or asymptomatic individuals. We We observed a slight loss of sensitivity with saliva samples compared to NPS. Whereas this slight loss can be unimportant if prevalence is 0.1% (few missed cases per 1000 246 tested) it can be very important if prevalence is 10% (many missed cases per 1000 tested). However we think, given our results, that these missed cases with saliva samples, are less 248 likely to participate to the viral spread of the SARS-CoV-2 due to their low viral loads. Moreover, any risk that this sampling is less sensitive than NPs sampling is offset by the In conclusion, we believe that the good sensitivity of saliva-based tests for SARS-CoV-2 291 nucleic acid indicates that this medium is a desirable non-invasive way of obtaining samples 292 15 that is well accepted by patients and allows repeated testing. Pools of five saliva samples 293 appear to be suitable for mass screening. Hologic provided the molecular reagents for SARS-CoV-2 detection. The English text was edited by Dr Owen Parkes. 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