SARS-CoV-2 detection in setting of viral swab scarcity: are MRSA swabs and viral swabs equivalent?

Abstract: Background: The global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown. Methods: We compared simultaneous nasal MRSA swabs (COPAN ESwabs 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress SARS-CoV-2 assay. Results: Of the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs 480C and the viral swabs in 78 (96.3%). Conclusion: We found a high rate of concordance in test results between COPAN ESwabs 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs 480C to help in the diagnosis of COVID-19.


Introduction:
As early as December 2019, a cluster of patients with pneumonia of unknown etiology was identified in Wuhan, China (1) and shortly thereafter, the causative agent was identified as a novel betacoronavirus, the severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) (2). The spectrum of disease severity ranges from asymptomatic disease to severe pulmonary disease including acute respiratory distress syndrome, multisystem organ failure, and death. Genetic sequencing performed early in the course of the outbreak led to the development of diagnostic testing.
With testing, SARS-CoV-2 was noted to be responsible for a global pandemic, and as of April 27, 2020, a total of nearly 3 million cases worldwide have been diagnosed, and at least 207,000 have died from COVID-19 (coronavirus disease 2019) (3). Many experts have advocated for widespread testing. Due to the rapidity of and extensive spread of the infection however, many countries, including the United States, were ill-prepared to employ widespread testing as an effective public health tool (4). Limitations related to the availability of testing were complex, and occurred on many levels: first, various assays had to be developed and deployed, second, physical testing sites (including drive-through) had to be operationalized, and lastly supplies of ancillary equipment had to be obtained. Key to ancillary equipment was adequate and sustained supply of viral sample collection kits. Many healthcare systems that have overcome the first two of these barriers have been faced with unexpected shortages of swabs and transport media, compounded by slow or non-existent replacements and unreliable supply chains.
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The copyright holder for this preprint (which this version posted May 8, 2020. . As with creative interventions to re-purpose personal protective equipment (PPE), healthcare systems have looked for ways to overcome barriers to testing. Interim guidelines issued by the CDC on April 14, 2020 clarified the allowance of other swab types with guidance on specimen collection and transport. In these guidelines, both FDA and CDC allowed for expansion of the specimen types and swab/transport media to accommodate demand for more testing. While nasopharyngeal specimens obtained with a "mini-tip" viral swab and transported in viral transport medium is still the preferred choice for initial testing, acceptable alternatives include nasopharyngeal aspirates and nasal washes as well as swabs of oropharynx, anterior nares, and nasal mid-turbinates. The latter two are only appropriate in symptomatic patients and both nares must be sampled. The anterior nares specimen should be collected using a spun polyester or flocked COPAN ESwabs® used for MRSA detection. These interim guidelines allow for anterior nares and mid-turbinate specimens to be transported in viral transport medium, Amies transport medium, or sterile saline. There is no data, however on the effect on diagnostic accuracy of SARS-CoV-2 tests based on these variable swabs and transport media used for specimen collection from sites other than the nasopharynx.
Given the wide availability of specimen collection kits used for MRSA testing in our facility, we sought to determine whether nasal MRSA swabs (flocked polyester COPAN ESwab® 480C) and their transport medium (1mL of liquid Amies medium) can be used to detect SARS-CoV-2 when viral swabs are not available. We therefore sought to assess the concordance between the test results using these two different collection kits. This of paramount importance at this critical time.

Methods:
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This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. presenting to a pre-scheduled "drive-through" outpatient testing center, its emergency department, as well as the inpatient and medical intensive care COVID-19 units over a four-day period. Hospitalized inpatients on the inpatient unit and medical intensive care unit had been initially diagnosed with SARS-CoV-2 from one day to 24 days prior to re-testing.
Each patient underwent concomitant testing with both a "viral swab" in Becton, Dickinson and Company H192(07) flexible fine-tip flocked nasopharyngeal swab, with 3 mL of Universal Viral Transport medium (Becton Dickinson H192(07) and an "MRSA swab" COPAN ESwab ® 480C with a flocked polyester nasal swab in 1mL of liquid Amies solution. Trained nurses or physicians collected the specimens. The viral swab specimens were nasopharyngeal. Each MRSA swab specimen was collected by accessing a single nare, and extending the swab as far into the mid-turbinate area as the thickness of the swab would allow. After collection, specimens were stored at room temperature until received by the lab and subsequently at -20 degrees Celsius.
We found that the COPAN ESwab® was not compatible with the Roche Cobas 6800 machine due to the high concentration of mucus and particulate matter that is incompatible with that instrument's sampling apparatus. We therefore tested both samples on the Simplexa ® COVID-19 Direct Kit (DiaSorin). When the MRSA and viral swabs were discordant, the viral swab was run on the Xpert® Xpress SARS-CoV-2 (Cepheid). The protocol was considered a quality improvement project and granted exemption by the VA Connecticut Research Office and deemed that review by the VA Connecticut Investigational Review Board or R&D Committee was not needed since the objective was optimization of testing supplies.. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which this version posted May 8, 2020. . https://doi.org/10.1101/2020.05.04.20084657 doi: medRxiv preprint 3 mL). At a minimum, we can conclude that the COPAN ESwab® with liquid Amies transport medium appears as sensitive for detecting SARS-CoV-2 RNA as the viral swab in UTM.
There are several limitations to our study. Our sample size is small and needs to be confirmed in future larger studies. Furthermore, we used two proprietary testing formulations.
Whether this is generalizable to other formulations of viral and non-viral sampling systems is not known. Ideally, we would have liked to test each sample on multiple platforms looking for concordance between several testing modalities, as it is conceivable that inhibitory substances may be present in nasal materials or different transport media. However, due to the ongoing relative shortage of available reagents, we could not justify this for this quality improvement project. Additionally, while our study was conducted only in Veterans, we do not believe there should be a difference in test results between Veterans and non-Veterans for the positive or negative predictive value of testing for SARS-CoV-2 infection.
In addition to its tremendous physical and emotional toll, infection caused by SARS-CoV-2 has stressed supply chains. While some may have used typical MRSA swabs when there have been shortages of viral swabs, heretofore there has been little evidence of their testing characteristics. We found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and swabs in viral media. Clinicians and laboratories should feel better informed and assured that using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19 is acceptable in resource-limited settings.
for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.