key: cord-0777995-v6k9ifzi authors: Kojima, N; Turner, F; Slepnev, V; Bacelar, A; Deming, L; Kodeboyina, S; Klausner, J D title: Self-Collected Oral Fluid and Nasal Swab Specimens Demonstrate Comparable Sensitivity to Clinician-Collected Nasopharyngeal Swab Specimens for the Detection of SARS-CoV-2 date: 2020-10-19 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1589 sha: 006e5efdad9eb4268729d9c0727dfbb9d8f7c93e doc_id: 777995 cord_uid: v6k9ifzi We compared self-collected oral fluid swab specimens with and without clinician supervision, clinician-supervised self-collected mid-turbinate (nasal) swab specimens, and clinician-collected nasopharyngeal swab specimens for the detection of SARS-CoV-2. Supervised oral fluid and nasal swab specimens performed similarly to clinician-collected nasopharyngeal swab specimens. No sample type could detect SARS-CoV-2 infections amongst all positive participants. A c c e p t e d M a n u s c r i p t The 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, was first detected in Wuhan, China in late 2019 [1] . On 20 January 2020, the first case of COVID-19 was reported in the United States [2] . After more than 118,000 cases were detected in 114 countries with over 4,000 deaths, the World Health Organization declared COVID-19 pandemic [3] . The ideal specimen for the detection of SARS-CoV-2 is unknown. Currently, trained health care professionals and specialized collection devices are recommended for the collection of nasopharyngeal swab specimens [4] . This requires staffing of health care workers, who could be performing other duties, and the use of personal protective equipment (PPE), during a severe shortage. Additionally, patients report discomfort during nasopharyngeal swab specimen collection, which may deter patients from being tested [5] . The use of midturbinate (nasal) swab and oral fluid specimens could potentially greatly increase health worker safety and the number of persons tested. We recruited participants recently tested for SARS-CoV-2 to assess differences in specimen types and collection methods for SARS-CoV-2 testing. We recruited participants that recently tested for SARS-CoV-2 at a CLIA-certified, highcomplexity laboratory. The patient population and recruitment methods are described below. We recruited non-hospitalized persons tested for SARS-CoV-2 in Los Angeles County, California, that included symptomatic adults older than age 65, those with a chronic disease, first responders, and law enforcement officers that may have been exposed to SARS-CoV-2. We aimed to recruit 30 persons that tested negative for SARS-CoV-2 and 30 persons that A c c e p t e d M a n u s c r i p t tested positive. Participants were contacted via telephone or email and provided with details of the study. Participants were given a study information sheet and gave verbal informed consent. We obtained unsupervised self-collected oral fluid swab specimens, clinician-supervised self-collected oral fluid swab specimens, clinician-supervised self-collected mid-turbinate (nasal) swab specimens, and clinician-collected posterior nasopharyngeal swab specimens. For the unsupervised self-collected oral fluid swab specimens, we provided written instructions with the testing kit, which included a sterile swab and a tube with an RNA preservative media (DNA/RNA Shield™ solution, Zymo Research Corp., Irvine, CA, USA). Participants were instructed to cough deeply three to five times collecting any phlegm or secretions in their mouth, rub the swab on both cheeks, above and below the tongue, both gums, and on the hard palate for a total of 20 seconds to ensure the swab was saturated with oral fluid. Following that, participants were instructed to place the swab into the tube, secure the lid, invert the tube three to five times, and place the capped tube into a collection bag. Unsupervised specimen collection was observed by a clinician but from a greater distance than the supervised collections, and the clinician did not provide any feedback to the participant. For the clinician-supervised self-collected oral fluid swab specimens, the same instructions were provided and a clinician provided real time feedback. Without clinician feedback, some unsupervised patients did not cough before self-collecting their sample. For the clinician-supervised self-collected nasal swab specimen, a kit was provided that included a flocked swab (Copan Diagnostics, Murrieta, CA, USA) and the same collection A c c e p t e d M a n u s c r i p t media as described above The participant was verbally instructed to insert the swab into one nostril to the depth of three to four cm, rotate the swab for five to ten seconds, place the swab into the collection tube, invert the tube three to five times, and place the capped tube into a collection bag. Posterior nasopharyngeal swab specimens were collected by a clinician with the recommended medical technique using nasopharyngeal swabs (Becton Dickinson and Company, Franklin Lakes, NJ, USA) [6] . We collected samples in private areas of participant homes. We collected symptom data immediately prior to sampling. Sampling methods are detailed above. For each patient, all samples were collected within a 30-minute window. Samples were transported to the laboratory at ambient temperature for testing on the day of collection. We processed samples from the specimen collection tubes. We lysed and extracted RNA from samples (RNA purification kit, Norgen Biotek Corp., Thorold, ON, Canada) using an automated instrument (Resolvex A200, Tecan Group Ltd., Zürich, Switzerland) on a 96-well plate. We used a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay that utilized a single color TaqMan probe with a modified version of the qualitative detection of SARS-CoV-2 (N1, N2 primer/probe assay) designed and validated by the Centers for Disease Control and Prevention (CDC) (Integrated DNA Technologies, Coralville, IA, USA) [7] . We recorded cycle threshold values for tests. We detected human Ribonuclease P RNA with an additional single color TaqMan assay, in a parallel reaction using an aliquot of the extracted participant specimen to serve as a control for specimen extraction, specimen adequacy, and RT-PCR inhibition. We ran samples on an RT-qPCR The Institutional Review Board of the University of California Los Angeles reviewed and approved the study (reference number 20-000545). We recruited 45 participants. The median age of study participants was 42 years Table. Overall, we collected 180 specimens from 45 participants. Of those specimens, one specimen was lost and two specimens had insufficient sample for laboratory analysis. Therefore, 177 specimens yielded results (Figure) We found that clinician-supervised self-collected specimens for SARS-CoV-2 detection were feasible. No single specimen type identified all participants with COVID-19. The performance of clinician-supervised self-collected oral fluid and nasal swab specimens was similar to clinician-collected nasopharyngeal swab specimens. Unsupervised self-collected oral fluid swab specimens performed worse in this study sample. The CDC currently recommends the use of nasopharyngeal or oropharyngeal swab specimens either collected by a health care worker or self-collected mid-turbinate or anterior nares samples in symptomatic patients in a health care setting, including a supervised drivethrough setting, if nasopharyngeal swab specimens are not available [4] . Prior studies reported that SARS-CoV-2 detection was similar among oral fluid and mid-turbinate specimens when compared to nasopharyngeal swabs specimens [8, 9] . It was found in one of those studies that multiple anatomic site testing may improve the sensitivity and reduce false-negative test results. A c c e p t e d M a n u s c r i p t There is an urgent need to validate reliable specimen collection methods for the detection of SARS-CoV-2 to increase access to safe and easy testing. Our findings support that cliniciancollected posterior nasopharyngeal swab specimens has a similar testing sensitivity to clinician-supervised self-collected oral fluid and clinician-supervised self-collected nasal swab specimens for the detection of SARS-CoV-2. Further research on other supervised means of collection, such as video-based instructions or observation and feedback via telehealth, is warranted. In our sample, there were 6 cases of COVID-19 detected among oral fluid swab specimens, which were not detected in clinician-collected nasopharyngeal swab specimens. It is possible that the detection of SARS-CoV-2 may differ at anatomic sites based on the timing of infection [10, 11] . There were also 3 cases of COVID-19 detected among nasopharyngeal specimens not detected in oral fluid swab specimens. That suggests that testing any single anatomic site may miss some cases of COVID-19, which is consistent with a prior study [12] . We did not find significant differences in cycle threshold values between groups. Prior studies have found that oral fluid provides a similar sensitivity to nasopharyngeal swabs [13] [14] [15] [16] , particularly when combined with coughing before specimen collection to provide an upper respiratory tract sample. We found that unsupervised self-collected oral fluid swab specimens detected SARS-CoV-2 in fewer patients than other specimen types, and this discrepancy was unexpected. We observed that without feedback, some unsupervised participants did not cough before selfcollecting their sample. A pre-printed study reported that after bronchoalveolar lavage fluid, which is not feasible in the outpatient setting, sputum samples showed the highest positive rate in all stages following a SARS-CoV-2 infection, followed by nasal swabs [17] . Coughing was included as part of this specimen collection protocol and may provide a sputum A c c e p t e d M a n u s c r i p t specimen in the oral fluid specimen in addition to saliva. Laboratory studies and a case series have indicated that oral fluid collected after a participant coughs are reliable specimens [13, 15] . This study suggests that coughing may be a critical step when collecting oral fluid swab specimens for the detection of SARS-CoV-2. Our report has several strengths. We were able to perform self-collected specimen collection for COVID-19 testing. We studied multiple sample types and collection methods, including unsupervised self-collected specimens and clinician-supervised self-collected specimens. Clinician-collected nasopharyngeal specimens were collected in all patients for comparison. All samples were tested at a CLIA-certified, high-complexity laboratory with a validated FDAauthorized COVID-19 assay. However, our study had a limited sample size due to the current shortage of testing supplies. Our study was not designed to detect statistical differences between specimen types or collection methods. Given the urgency of obtaining results, recruitment took place over a short period. Supervised self-collected oral fluid and nasal swab specimens performed similarly to clinician-collected nasopharyngeal swab specimens for the detection of SARS-CoV-2. No sample type captured all infections. Supervised self-collected methods were feasible and could enable widespread access to testing by removing the need for a healthcare professional to collect each sample, reducing potential exposure for healthcare professionals and reducing the amount of PPE used for testing. A c c e p t e d M a n u s c r i p t Declarations A Novel Coronavirus Emerging in China -Key Questions for Impact Assessment First Case of 2019 Novel Coronavirus in the United States World Health Organization. WHO Director-General's opening remarks at the media briefing on COVID-19 -11 Centers for Disease Control and Prevention Accuracy and Discomfort of Different Types of Intranasal Specimen Collection Methods for Molecular Influenza Testing in Emergency Department Patients H1N1 influenza A disease--information for health professionals CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel In Detection of SARS-CoV-2 in Different Types of Clinical Specimens Swabs Collected by Patients or Health Care Workers for SARS-CoV-2 Testing Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study Virological assessment of hospitalized patients with COVID-2019 Identification of respiratory viruses in adults: nasopharyngeal versus oropharyngeal sampling Improved molecular diagnosis of COVID-19 by the novel, highly sensitive and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain reaction assay validated in vitro and with clinical specimens Escalating infection control response to the rapidly evolving epidemiology of the Coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in Hong Kong Consistent detection of 2019 novel coronavirus in saliva Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study The authors want to acknowledge the staff of University of California Los Angeles, TKSL, Curative Inc. and Korva-Labs Inc. F.T. and V.S. developed a viral assay for the detection of SARS-CoV-2. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or UCGHI. A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t M a n u s c r i p t A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p tA c c e p t e d M a n u s c r i p t