key: cord-0893878-10cvnnpx
authors: Hanson, K. E.; Barker, A. P.; Hillyard, D.; Gilmore, N.; Barrett, J. W.; Orlandi, R. R.; Shakir, S. M.
title: Self-Collected Anterior Nasal and Saliva Specimens versus Healthcare Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2
date: 2020-07-19
journal: nan
DOI: 10.1101/2020.07.17.20155754
sha: 5e9685e872eeebc63e24c57eb619e587b3cebf0b
doc_id: 893878
cord_uid: 10cvnnpx

We prospectively compared healthcare worker-collected nasopharyngeal swabs (NPS) to self-collected anterior nasal swabs (ANS) and straight saliva for the diagnosis of COVID-19 in 354 patients. The positive percent agreement between NPS and ANS or saliva was 86.3% (95% CI: 76.7-92.9) and 93.8% (95% CI: 86.0-97.9), respectively. Negative percent agreement was 99.6% (95% CI: 98-100) for NPS vs. ANS and 97.8% (95% CI: 95.3 - 99.2) for NPS vs. saliva. NPS (n=80) and saliva (n=81) detected more cases than ANS (n=70), but no single specimen type detected all SARS-CoV2 infections.

We prospectively compared healthcare worker-collected nasopharyngeal swabs (NPS) to self-21 collected anterior nasal swabs (ANS) and straight saliva for the diagnosis of The positive percent agreement between NPS and ANS or saliva was 86.3% (95% CI: 76.7-92.9) and 23 93.8% (95% CI: 86.0-97.9), respectively. Negative percent agreement was 99.6% (95% CI: 98-100) for 24 NPS vs. ANS and 97.8% (95% CI: 95.3 -99.2) for NPS vs. saliva. NPS (n=80) and saliva (n=81) detected 25 more cases than ANS (n=70), but no single specimen type detected all SARS-CoV2 infections. 26 27 Introduction: Rapid and accurate diagnostic tests are essential for controlling the SARS-CoV-2 pandemic. 28

The Centers for Disease Control (CDC) currently recommends collecting and testing an upper respiratory 29 tract specimen for initial SARS-CoV-2 diagnostic testing (1), but the most sensitive specimen type has not 30 been defined. Nasopharyngeal swabs (NPS) have historically been considered the reference method for 31 respiratory virus detection. In addition, anterior nasal swabs (ANS) are used routinely for influenza 32 nucleic acid amplification testing (NAAT). Recurrent shortages of swabs and personal protective 33 equipment (PPE), however, have prompted evaluation of alternatives to NPS including the use of patient 34 self-collected ANS and saliva. 35

The advantages of ANS and saliva are the minimally invasive nature of sampling and potential for 36 patient self-collection, which may reduce healthcare worker exposure to infectious aerosols. Saliva also 37 has the added benefit being a "swab-free" specimen type known to contain high concentrations of 38 SARS-CoV-2 RNA (2-4). Surprisingly few studies have assessed the performance of self-collected ANS for 39 SARS-CoV-2 testing (5, 6). Small sample sizes and use of selected cases limits the available evidence for 40 ANS. More performance data exists for saliva (7), but published studies vary substantially in the way the 41 specimens were obtained. Many saliva protocols require patients to cough before pooling saliva in their 42 mouth (2, 3, 8) , entail avoidance of food, water, or tooth brushing prior to testing (9), and/or rely on 43 . 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 July 19, 2020. supply shortages, and may not be compatible with all NAAT chemistries. Larger studies that compare 47 the performance of self-collected ANS and "straight" saliva to NPS for SARS-CoV-2 detection are needed. 48 Therefore, we performed a prospective comparative study to evaluate the performance of self-collected 49 ANS and saliva versus healthcare provider-collected NPS for SARS-CoV-2 diagnostic testing. 50 51

Study Subjects-Adult patients presenting to a drive-thru test center with symptoms suggestive of 53 COVID-19 were includes. After obtaining consent, subjects were instructed to swab both nostrils, pool 54 saliva in their mouth, and then repeatedly spit a minimum of 1 mL saliva into a sterile tube in the 55 presence of a healthcare worker. The NPS was collected last in the sampling sequence. The University of 56 Utah Institutional Review Board approved all study procedures. 57

Specimen collection -Flocked mini-tip and foam swabs (Puritan Medical Products) were used for 58 the nasopharyngeal and nasal collections. Swabs placed in 3 mL of sterile saline and straight saliva were 59 transported to the clinical laboratory at 4 ○ C. Saliva was diluted 1:1 in ARUP Laboratories universal 60 transport media™ (UTM) prior to testing. 61 SARS-CoV-2 detection -All specimens were analyzed using the Hologic Aptima SARS-CoV-2 62 transcription mediated amplification (TMA) test (Hologic Inc.). Discrepant NAAT results across 63 specimens collected from the same patient triggered repeat testing using the Hologic Panther Fusion 64 (Hologic Inc.), a PCR-based platform, to assess crossing thresholds (Cts) as a surrogate measure of RNA 65 concentration. Cts of ≤ 42 by PCR are considered positive. 66 . 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 July 19, 2020. 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 July 19, 2020. Given that all participants had a strong clinical suspicion for COVID-19, and molecular testing in general 105 has very high specificity, it is likely that the NPS or saliva positive only specimens are true positives; but 106 the lack of an accepted external reference standard precludes calculations of clinical sensitivity and 107 specificity. Even though there was excellent qualitative agreement across specimen types, relying on 108 ANS alone could have missed infection in 10 to 11 patients compared with NPS or saliva, respectively. 109

Missed COVID-19 cases have major clinical implications affecting isolation decisions for symptomatic 110 patients and are a lost opportunity for contact tracing. 111 . 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 July 19, 2020. . https://doi.org/10. 1101 No single sample type detected all potential cases and discrepant results were not always 112 explained by high Ct values (i.e. low RNA concentrations near the limit of detection of the test). There 113 are several potential explanations for "false negative" results. First, inadequate swab collection 114 technique is possible. We did not include a host genomic marker to assure presence of respiratory 115 epithelial cells on the swab, nor did we compare self-collection to healthcare provider-collected ANS. 116

Previous respiratory virus studies, however, suggest that self-collected is equivalent to provider-117 collected ANS (11). Additionally, the level of viral replication in the nasopharynx or posterior 118 oropharynx/salivary glands may vary over the course of infection. We did not collect information on the 119 duration or type of symptoms at the time of specimen collection, which is an additional limitation of the 120 study. Lastly, in an attempt to exclude RNA degradation in straight saliva as a potential explanation for 121 "false negatives", we performed stability studies at ambient and refrigerated temperatures for up to 5 122 days and saw no reduced TMA or PCR signal (data not shown). 123

In conclusion, NPS and saliva were superior to ANS alone for the detection of SARS-CoV-2 in 124 symptomatic patients. These observations, along with other recent reports (9, 12), suggest that 125 straight saliva is an acceptable specimen type for symptomatic patients especially if swab or PPE 126 supplies are limited. However, not all patients could provide adequate volume and saliva is a complex 127 matrix that requires clinical laboratories to validate this specimen type on their respective NAAT 128

platforms. An increased indeterminate or invalid rate (3.3% for saliva vs. 0% for swabs in saline) was 129 observed using the Hologic Panther despite a 1:1 dilution in UTM. This could be related to issues of 130 sample viscosity affecting the automated pipetting and/or internal control inhibition. We did not test 131 whether an additional dilution step would reduce the invalid rate without loss of sensitivity. 132

Combination testing with simultaneous sample collection from multiple anatomic sites may increase 133 SARS-CoV-2 detection rates slightly, but multisite testing could be impractical given current swab and 134 reagent shortages. Requiring two separate NAAT reactions would also increase costs. 135 . 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 July 19, 2020. 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 July 19, 2020. . https://doi.org/10. 1101 

Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens 154 for COVID-19

Consistent detection of 2019 novel coronavirus in saliva

Temporal profiles of viral load in posterior oropharyngeal 162 saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational 163 cohort study

Clinical 165 Significance of a High SARS-CoV-2 Viral Load in the Saliva

Assessment of Sensitivity and Specificity of Patient-Collected Lower Nasal Specimens for 168 Sudden Acute Respiratory Syndrome Coronavirus 2 Testing

Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity 172 to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection

Syed Faraz Moin, Muhammad Sohail Zafar

Saliva as a non-invasive sample for the detection of SARS-CoV-2: a systematic 176 review

2020. 178 Evaluating the use of posterior oropharyngeal saliva in a point-of-care assay for the detection of 179 SARS-CoV-2

Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 190 patients than nasopharyngeal swabs

Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19

Equivalence of self-and staff-197 collected nasal swabs for the detection of viral respiratory pathogens

Saliva as a non-invasive 199 specimen for detection of SARS-CoV-2