key: cord-0785203-ygg1u4i7 authors: Gertler, M.; Krause, E.; van Loon, W.; Krug, N.; Kausch, F.; Rohardt, C.; Roessig, H.; Michel, J.; Nitsche, A.; Mall, M. A.; Nikolai, O.; Hommes, F.; Burock, S.; Lindner, A. K.; Mockenhaupt, F. P.; Pison, U.; Seybold, J. title: Self-collected oral, nasal and saliva samples yield sensitivity comparable to professional-collected oro-nasopharyngeal swabs in SARS-CoV-2 diagnosis date: 2021-04-20 journal: nan DOI: 10.1101/2021.04.13.21255345 sha: 67bc1513f680928ee39fbe01780f7eb064a6a784 doc_id: 785203 cord_uid: ygg1u4i7 Introduction: Containment of the COVID-19 pandemic requires broad-scale testing. Laboratory capacities for real-time-PCR were increased, and are complemented by Ag-tests. However, sample-collection still requires qualified personnel and protective equipement, may produce transmission to others during conduct and travel, and is perceived uncomfortable. We tested sensitivity of three simplified self-sampling techniques compared to professional-collected combined oro-nasopharyngeal samples (cOP/NP). Methods: From 62 symptomatic COVID-19 outpatients, we obtained simultaneously three self- and one professional-collected sample after initial confirmation in a testing centre: (i) combination swab (tongue, cheek, both nasal vestibula, MS, (ii) saliva sponge combined with both nasal vestibula, SN, and (iii) gargled tap water, GW, (iv) professionally-collected cOP/NP (standard). We compared the results of SARS-CoV-2 PCR-assays detecting E-gene and ORF1ab for the different sample types and performed bivariate statistical analysis to determine the variables reducing sensitivity of the self-collecting procedures. Results: SARS-CoV-2 RNA was detected in all 62 professionally-collected cOP/NP. MS and SN samples showed a sensitivity of 95.2% (95%CI 86.5-99.0) and GW samples of 88.7% (78.1-95.3). Compared to the median ct-values of cOP/NP samples for E-gene (20.7) and ORF1ab (20.2) these were higher for MS (22.6 and 21.8), SN (23.3 and 22.3), and for GW (30.3 and 29.8). For MS and SN samples but not for GW specimens, false negativity in bivariate analysis was associated with non-German mother-tongue, number of sampling errors, and with symptom duration. For symptom duration of [≤]8 days, test sensitivity for SN samples was 98.2% (95%CI 90.4-100.0) and for MS 96.4% (95%CI 87.7-99.6) and drops after day 8 below 90%. Discussion: The study is limited to sensitivity of self-collection in symptomatic patients. Still, in this group, self-collected oral/nasal/saliva samples are reliable alternatives to professional-collected cOP/NP samples, if symptom duration does not exceed eight days and operational errors are minimized. Self-sampling could contribute to up-scaling of safe and efficient testing. Wong, 2020). Moroever, (oro-)nasopharyngeal sampling is being perceived as 82 uncomfortable, and possibly deterring, by many patients. Simplified sampling 83 techniques may help overcoming these limitations. Reliable self-collecting 84 procedures could be home-based and thus, contribute to reduced virus transmission 85 due to more rapid diagnosis and reduced mobility of potentially contagious persons. 86 Self-collected samples from the oral cavitiy, e.g. saliva or from the nasal vestibule 87 (anterior nasal cavitiy) are therefore being investigated as non-invasive, more 88 comfortable and less resource-intensive alternatives and show variable 89 additional verbal instructions or intervention, and performance and irregularities were 124 documented by the study team. The three procedures of self-collection included (i) 125 MS (multi-swab): a combination swab from the tongue, the inner cheek and both 126 nasal vestibules (insertion 2-3 cm, twisting 4x), (ii) SN (saliva-nasal): insalivating of 127 the swab for 10-15 sec. before swabing both nasal vestibules (insertion 2-3 cm, 128 twisting 4x), and (iii) GW (gargle water): collection of 10 ml of gargled tap water into a 129 plastic container (Sarsted R , L494-9). Swabs used were nylon-flocked applicators with 130 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted April 20, 2021. ; Probit analysis revealed the limit of detection for the quadruplex PCR under the 150 above described conditions as 28.7 genome copies for the E-Gene assay and 32.0 151 genome copies for the ORF1ab assay. Tests with signals that crossed the detection 152 threshold were considered positive. All samples were measured on the day of 153 collection by using 140 µl aliquots for RNA extraction, respectively. 154 155 Descriptive statistics used proportions, means + standard deviation (SD), or medians 157 with interquartile ranges (IQR), as applicable. Categorial variables were compared by 158 two-tailed Fisher´s exact test, numeric variables by a Mann Whitney U-test, and 159 paired numeric data by a Wilcoxon Signed Rank test. Sensitivity and 95% confidence 160 interval (CI) were calculated for each sampling method. In three (4.8%) MS and SN samples as well as in seven (11.3%) GW specimens, 204 none of the two SARS-CoV-2 genes were detected. These false negative results 205 were associated with high ct-values, i.e. low viral loads, in the corresponding 206 professional-collected swab (Table 2) . For MS and SN samples, but not for GW 207 specimens, false negativity was also associated with a non-German mother-tongue, 208 the number of sampling procedure mistakes, and as a trend, with symptom duration. 209 In a binomial logistic regression model fit on our data, for every day of symptom 210 duration, the odds for a positive test decreased by 40% (OR, 0.6; 95%CI, 0.4-0.9; 211 P=0.01, for both MS and SN samples). Following the model, sensitivity (as compared 212 to oro-nasopharyngeal swabs) dropped below 90% for symptom duration longer than 213 eight days. In addition, when only assessing patients with a symptom duration of less 214 Our findings indicate that self-collected samples provide only slightly reduced 219 sensitivity in the detection of SARS-CoV-2 by RT-PCR as compared to professional-220 collected oro-nasopharyngeal samples. This is particularly true for sample collection 221 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. procedures were associated with procedural errors and reduced German language 247 competence (written instructions in German). This shows an even higher potential for 248 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted April 20, 2021. ; https://doi.org/10.1101/2021.04.13.21255345 doi: medRxiv preprint sample self-collection when pictorial illustrations are offered, and in different 249 Supervision and support of self-collection procedures may be provided directly by 251 personnel through a window or via video consultation. Such would not require 252 personal protective equipment and still reduce transmission risks at testing sites. 253 With respect to the slightly reduced sensitivity of self-collected samples (MS and SN) 254 in this study, it needs to be taken into account that oro-nasopharyngeal swabbing 255 was performed by very experienced medical professionals. In a scenario of massive 256 up-scale of testing by public health systems this may not be the case, potentially 257 shrinking the sensitivity differences between professional and self-collection of 258 samples. This has particular significance for a central component of pandemic 259 response globally, i.e., repetitive testing of groups, e.g., school attendees or 260 employees as claimed also by the WHO (World Health Organization, 2021) . For that, 261 testing including sample-collection needs to be simplified, non-invasive to prevent 262 refusal, efficient and safe. In this regard, we provide further evidence that (home) 263 sample self-collection may help to reduce test restraints, transmission risks as well 264 as human and material resources. This data refers only to self-collecting for RT-PCR 265 and not to self-collecting for rapid-tests. However the results may support the 266 reliability of self-testing based on rapid tests as public-health tool which is currently 267 becomming the most frequent test-method in the reality. 268 A limitation of our study is that only symptomatic patients were included. While there 269 is no reason to believe that self-collection does not work in asymptomatic individuals, 270 findings with respect to, e.g., symptom duration are not transferrable. Our study 271 among SARS-CoV-2 positive patients could not produce specificity data. However, 272 since specificity is predominantely determined by the diagnostic assay applied, we 273 assume that this parameter is comparable for the sampling method. Moreover, 274 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted April 20, 2021. ; https://doi.org/10.1101/2021.04.13.21255345 doi: medRxiv preprint . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted April 20, 2021. ; https://doi.org/10.1101/2021.04.13.21255345 doi: medRxiv preprint . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted April 20, 2021. ; https://doi.org/10.1101/2021.04.13.21255345 doi: medRxiv preprint Interim Guidelines for Collecting and Handling of Clinical 343 Specimens for COVID-19 Testing nCoV/lab/guidelines-clinical-specimens.html#handling-specimens-safely Detection of 2019 novel 346 coronavirus (2019-nCoV) by real-time RT-PCR Performance of 348 saliva specimens for the molecular detection of SARS-CoV-2 in the community setting: does sample 349 collection method matter Samples as an Alternative to Healthcare Worker Collected Nasopharyngeal Swabs for COVID-19 Time PCR Assay for the Simultaneous Detection and Quantification of Botulinum Neurotoxin-355 Producing Clostridia in Food and Clinical Samples Nasal Swab Specimens Demonstrate Comparable Sensitivity to Clinician-Collected Nasopharyngeal 359 Swab Specimens for the Detection of SARS-CoV-2. 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