key: cord-0930153-msmc0yd2 authors: Hart, B.; Tu, Y.-P.; Jennings, R.; Verma, P.; Padgett, L.; Rains, D.; Vojta, D.; Berke, E. title: A comparison of health care worker-collected foam and polyester nasal swabs in convalescent COVID-19 patients date: 2020-05-01 journal: nan DOI: 10.1101/2020.04.28.20083055 sha: 8bdfa4c0edee1d8c41fb8e5dabd173ad59bdafeb doc_id: 930153 cord_uid: msmc0yd2 Background: The exponential growth of COVID-19 cases and testing has created supply shortages at various points in the testing workflow. As of April 15, 2020 FDA recommendations only allowed for the use of nasopharyngeal, flocked mid turbinate, or foam nasal swabs, all of which are in very low supply. Polyester swabs are more readily available and mass producible. We compare the performance of polyester and foam swabs stored in different transport media. Methods: Both polyester and foam nasal swabs were collected from convalescent COVID-19 patients at a single visit. Using the foam nasal swabs as the comparator, sensitivity of the polyester swabs in each media were calculated, three by three tables were constructed to measure concordance, and cycle threshold (Ct) values were compared. Findings: 126 visits had polyester and foam swabs stored in viral transport media (VTM), 51 had polyester and foam swabs stored in saline, and 63 had a foam swab in VTM and a polyester swab stored in a dry tube. Using nasal foam swabs as a comparator, polyester nasal swabs had a sensitivity of 86*5% when both samples were stored in VTM, 86*7% when both samples were stored in saline, and 72*4% when the polyester swab was stored dry and the foam swab was stored in VTM. Polyester and foam Ct values from the same visit were correlated, but polyester swabs showed decreased performance for cases with a viral load near the detection threshold and higher Ct values on average. Interpretation: Polyester nasal swabs showed a reduction in performance from foam nasal swabs, but may still provide a viable sample collection method given the current supply shortages and public health emergency. We compare the performance of polyester and foam swabs stored in different transport media. Interpretation: Polyester nasal swabs showed a reduction in performance from foam nasal 36 swabs, but may still provide a viable sample collection method given the current supply 37 shortages and public health emergency. . 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 May 1, 2020. . https://doi.org/10.1101/2020.04.28.20083055 doi: medRxiv preprint Funding: Laboratory testing was conducted with financial support from Thermo Fisher 39 Scientific. . 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 May 1, 2020. and nylon flocked swabs are not as readily available or mass produced as polyester swabs 8 . Additionally, swabs are typically stored and transported in VTM under refrigeration at or below 59 4°C. With VTM and swab supplies running low, and difficulties in obtaining sufficient 60 refrigeration space for the massive number of samples arriving at the labs to be tested, testing 61 requirements must be reevaluated to see if they can be safely altered 9, 10 . Recent work has shown 62 that saline may be a suitable replacement for VTM 11 . Since these findings were released, the Food 63 . 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 May 1, 2020. . https://doi.org/10.1101/2020.04.28.20083055 doi: medRxiv preprint and Drug Administration (FDA) has updated their testing recommendations to allow for a wider 64 variety of substances to be used for viral transport and stabilization and allow for self-collected 65 foam nasal swabs when VTM and NP swabs are not available 12 . To address the dwindling supply of recommended swabs, we compared the relative performance 67 of polyester and foam nasal swabs for detecting SARS-CoV-2, stored and transported either in 68 VTM, saline, or in a dry tube. 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 May 1, 2020. . https://doi.org/10.1101/2020.04.28.20083055 doi: medRxiv preprint low platelet and low white blood cell counts, or acute facial trauma were excluded from the 86 study. Health care workers used a written consent form to explain the study and give eligible 87 patients the opportunity to decline. This study protocol was deemed to be part of a minimal risk swabs stored in VTM were refrigerated and sent to a reference laboratory for immediate testing, 97 while the dry polyester swab was stored without refrigeration for four days prior to testing. Due 98 to participant testing constraints, the polyester swab to be stored in a dry tube was not collected 99 from all patients. These swabs will be referred to as the foam, VTM polyester, and dry polyester 100 swabs. Patients in the second cohort were also convalescing from COVID-19. They were recruited 102 immediately after their initial positive test result for SARS-CoV-2. During a single visit 103 (between two and seven days after initial diagnosis), these patients were swabbed twice: once 104 with a polyester swab and once with a foam swab. The order of sample collection was 105 randomized in the same manner as in the first cohort. Both samples were refrigerated at 4°C after 106 storage and tested in a reference laboratory as soon as possible. . 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 May 1, 2020. Ct adjustment and F is the fold increase in volume. 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. The copyright holder for this preprint this version posted May 1, 2020. Polyester nasal swabs detected four fewer positive cases than foam swabs and had an estimated 149 sensitivity (95% confidence interval) of 86•5% (77•3% -95•8%) when stored in VTM (Table 1) . 150 Additionally, there were eight visits with an inconclusive VTM foam swab and a negative VTM 151 polyester swab, but no visits with an inconclusive VTM polyester swab and a negative VTM 152 foam swab. In saline, the polyester swabs detected two fewer positive cases and had an estimated 153 . 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 May 1, 2020. (Table 3) . 156 Correlations between foam and polyester Ct values were highest in the saline samples, followed . 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 May 1, 2020. The comparison of polyester and foam swabs did not differ between saline and VTM storage. should not be ruled out entirely based on this study 14 . The current study has several limitations. All participants were convalescing COVID-19 patients, 198 and the time from first symptoms and first diagnosis to test date varied from test to test. As 199 . 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 May 1, 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. The copyright holder for this preprint this version posted May 1, 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. The copyright holder for this preprint this version posted May 1, 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. The copyright holder for this preprint this version posted May 1, 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. The copyright holder for this preprint this version posted May 1, 2020. . https://doi.org/10.1101/2020.04.28.20083055 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 May 1, 2020. . https://doi.org/10.1101/2020.04.28.20083055 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 May 1, 2020. . https://doi.org/10.1101/2020.04.28.20083055 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 May 1, 2020. . https://doi.org/10.1101/2020.04.28.20083055 doi: medRxiv preprint COVID-19) in the US Doctors and Govenors Vie for Masks in 252 Cloak-and Dagger Deals A joint statement by the Association of State and Territorial Health Officials, Association 255 of Public Health Laboratories, and Council of State and Territorial Epidemiologists COVID-19 Testing Needs to Be Limited to Priority Groups Until Sufficient Testing 257 Supplies and Personal Protective Equipment is Available Nationwide. Association of 258 State and Territorial Health Officials Berke 260 EM. Patient-collected tongue, nasal, and mid-turbinate swabs for SARS-CoV-2 yield 261 equivalent sensitivity to health care worker collected nasopharyngeal swabs. medRxiv Self-collected mid-turbinate swabs for the detection of respiratory viruses in 265 adults with acute respiratory illnesses Effectiveness of patient-collected 268 swabs for influenza testing International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity Testing Swabs Run In Short Supply As Makers Try To Speed 271 Up Production. NPR Viral Transport Medium (VTM) Supplies Needed. American Academy of Dermatology US virus testing faces new headwind: Lab supply shortages. The Associated 276 Press Evaluation of saline, phosphate buffered saline and 279 minimum essential medium as potential alternatives to viral transport media for SARS-280 CoV-2 testing 12. FAQs on Diagnostic Testing for SARS-CoV-2. The Food and Drug Administration Self-collection 287 of foam nasal swabs for respiratory virus detection by PCR among immunocompetent 288 subjects and hematopoietic cell transplant recipients Virological assessment of hospitalized 292 patients with COVID-2019 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 May 1, 2020. . https://doi.org/10.1101/2020.04.28.20083055 doi: medRxiv preprint