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COVID-19 laboratory testing issues and capacities as we transition to surveillance testing and contact tracing

      As of May 19, 2020, 11,834,508 COVID-19 tests have been performed in the US resulting in 1,523,534 (12.9%) confirmed cases [

      COVID-19 map. Johns Hopkins Coronavirus Resource Center. https://coronavirus.jhu.edu/map.html. Published January 22, 2020. Accessed May 19th, 2020.

      ]. The actual number of infected Americans is much larger. Antibody seroprevalence testing in Los Angeles County , California, estimates those infected around 4.65% implying actual infection is about 43-fold larger than confirmed cases [
      • Sood N.
      • Simon P.
      • Ebner P.
      • et al.
      Seroprevalence of SARS-CoV-2-Specific Antibodies Among Adults in Los Angeles County, California, on April 10-11, 2020.
      ]. Another study concluded that undiagnosed COVID cases represent the infection source of 79% of documented cases [
      • Cheng M.P.
      • Papenburg J.
      • Desjardins M.
      • et al.
      Diagnostic testing for severe acute respiratory syndrome–related coronavirus-2: a narrative review.
      ]. Accurate testing will be crucial to controlling and understanding this pandemic. Estimation relies on testing kit accuracy (sensitivity/specificity). Low sensitivity will underestimate disease prevalence, while low specificity will overestimate [
      • Sood N.
      • Simon P.
      • Ebner P.
      • et al.
      Seroprevalence of SARS-CoV-2-Specific Antibodies Among Adults in Los Angeles County, California, on April 10-11, 2020.
      ].
      Testing comes in two broad types, testing for nasopharyngeal viral RNA and serologic testing for antibodies, which occur in response to the disease. RNA testing is done with polymerase chain reaction (PCR) is cost-effective, easy to perform, and now available [

      Walensky RP, del Rio C. From mitigation to containment of the COVID-19 pandemic: putting the SARS-CoV-2 genie back in the bottle. JAMA. Published online April 17, 2020. https://doi.org/10.1001/jama.2020.6572. [Accessed May 19th, 2020].

      ]. However, the PCR test has accuracy issues. Sensitivity of FDA-approved viral RNA tests range from 63%–95% (Table 1) [
      • Wang W.
      • Xu Y.
      • Gao R.
      • et al.
      Detection of SARS-CoV-2 in different types of clinical specimens.
      ,

      Smart detect SARS-CoV-2 rRT-PCR kit. InBios. https://inbios.com/smart-detecttm-sars-cov-2-rrt-pcr-kit/. Accessed May 19th, 2020.

      ,

      COVID-19 RT-digital PCR detection kit. Gnomegen. https://www.fda.gov/media/136738/download. Accessed May 19th, 2020.

      ,

      QIAstat-Dx respiratory SARS-CoV-2 panel instructions for use (handbook). Qiagen. https://www.fda.gov/media/136571/download. Accessed May 19th, 2020.

      ]. Sensitivity of RNA tests is dependent on the site of specimen collection. Sensitivity was highest in bronchioalveolar lavage (93%), then sputum (73%), nasal swab (63%), feces (29%) and blood (1%) [
      • Wang W.
      • Xu Y.
      • Gao R.
      • et al.
      Detection of SARS-CoV-2 in different types of clinical specimens.
      ]. Another study found that patients with pneumonia often have negative nasopharyngeal samples, but positive lower airway samples [
      • Patel R.
      • Babady E.
      • Theel E.S.
      • et al.
      Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: value of diagnostic testing for SARS-CoV-2/COVID-19.
      ]. The sensitivity of PCR tests have been estimated at 71%, resulting in ~30% of infected patients having a negative finding. Another drawback is the presence of viral RNA does not mean the virus is live, therefore, detection does not necessarily mean the virus can be transmitted [
      • Patel R.
      • Babady E.
      • Theel E.S.
      • et al.
      Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: value of diagnostic testing for SARS-CoV-2/COVID-19.
      ]. RNA-based tests are limited to the setting of acute illness. Saliva-based tests offer promising results as a non-invasive and non-aerosol generating method of specimen collection [
      • Pasomsub E.
      • Watcharananan S.P.
      • Boonyawat K.
      • et al.
      Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease-2019 (COVID-19): a cross-sectional study.
      ]. Compared to nasopharyngeal tests, saliva specimens have high sensitivity (84.2% [
      • Pasomsub E.
      • Watcharananan S.P.
      • Boonyawat K.
      • et al.
      Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease-2019 (COVID-19): a cross-sectional study.
      ]) and can be self-administered [
      • Pasomsub E.
      • Watcharananan S.P.
      • Boonyawat K.
      • et al.
      Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease-2019 (COVID-19): a cross-sectional study.
      ]. Another study reported that SARS-CoV-2 viral load in posterior oropharyngeal saliva samples was higher at initial presentation of COVID-19 symptomatic patients, increased with age, presence of comorbidities, and severity of the COVID-19 disease [
      • Kelvin Kai-Wang To
      • Tak-Yin Tsang Owen
      • Leung Wai-Shing
      • et al.
      Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.
      ]. Reduced variability in samples taken from self-administered tests is helpful for mass testing because it preserves collection reliability and allows patients to send in their own samples from the comfort of their home.
      Table 1Overview of COVID-19 FDA approved/non-FDA approved diagnostic tests.
      COVID-19 diagnostic tests
      Authors/companyCountryType of testSensitivity & specificityDevelopment phase
      Tests approved for use in the United States
      Cellex Inc.US/ChinaRapid Diagnostic TestSensitivity: 93.8%

      Specificity: 95.6%
      Approved by FDA for EUA; CE approval
      Diasorin Inc.USAELISASensitivity: 90–97%

      Specificity: 98%
      Approved by FDA for EUA
      Bio-RadUSAModified ELISASensitivity: 98%

      Specificity: 99%
      Received EUA
      RocheUS/SwitzerlandElectro-chemiluminescence immunoassay (ECLIA)Sensitivity: 65–100%

      Specificity: 99.81%
      Received EUA, available for purchase by healthcare professionals and researchers.
      Euroimmun AGGermanyELISASensitivity: 61.1–90%

      Specificity:100%
      Received EUA, available for purchase by healthcare professionals and researchers.
      DiacartaUSQuantifier SARS-CoV-2 Multiplex Test KitSensitivity: 95%

      Specificity: 100%
      EUA
      InBiosUSSmart Detec SARS-CoV-2 rRT-PCR KitSensitivity: 100%

      Specificity: 96.7%
      EUA
      GnomeganUSCOVID-19 RT-Digital PCR Detection KitSensitivity: 100%

      Specificity: 100%
      EUA
      Simplexa COVID-19 DirectUSCOVID-19 RT-Digital PCR Detection KitSensitivity: 100%

      Specificity: 100%
      EUA
      QIASTAT-DXUSCOVID-19 RT-Digital PCR Detection KitSensitivity: 85.1–98.1

      Specificity: 99.2–100
      EUA
      Tests approved for diagnostic use in other countries
      Aytu Biosciences/Orient Gene BiotechUS/ChinaRDT, solid phase immunochromatographic assaySensitivity: 87.9% (IgM) and 97.2% (IgG)

      Specificity: 100% for IgM and IgG
      CE approved, used in China in clinical settings, awaiting FDA approval
      ScanWell Health/INNOVITAUS/ChinaProprietarySensitivity: 87.3%

      Specificity: 100%
      Cleared by China's National Medical Products Administration (NMPA), and pending approval by US FDA
      QuotientSwitzerlandMIRA - Multiplexed Immuno-Refractive AssaySensitivity: 100%

      Specificity: 99.8%
      Currently available in Europe
      Liming BioChinaRDT (colloidal gold lateral flow assay)Sensitivity: 62% (IgM)

      Specificity: 100% (IgM)
      CE/IVD
      Tests in development
      Broughton et al. (Mammoth Biosciences)USCRISPR-based lateral flow assaySensitivity: 90%

      Specificity: 100%
      Pre-clinical
      United Biomedical (UBI)/c19USProprietarySensitivity: 100%

      Specificity: 100%
      In testing in San Miguel, CO
      Coris BioconceptBelgiumDipstick (lateral flow assay)Sensitivity: 60%

      Specificity: 99%
      Clinically testing
      Ma et al.ChinaChemiluminescent immunoassaySensitivity: 98.6%

      Specificity: 92.3–99.8%
      Pre-clinical
      The second type of test is serologic, which detects immunoglobulins (IgG and IgM) specific for SARS-CoV-2 and provides an estimation of population virus exposure [

      Walensky RP, del Rio C. From mitigation to containment of the COVID-19 pandemic: putting the SARS-CoV-2 genie back in the bottle. JAMA. Published online April 17, 2020. https://doi.org/10.1001/jama.2020.6572. [Accessed May 19th, 2020].

      ]. One drawback of serologic testing is the lag period between symptoms and antibody formation-one analysis found patients do not begin to seroconvert until 11–12 days post-symptom onset [

      Abbasi J. The promise and peril of antibody testing for COVID-19. JAMA. Published online April 17, 2020. https://doi.org/10.1001/jama.2020.6170. [Accessed May 19th, 2020].

      ].The sensitivity and specificity of FDA-approved serologic tests ranges from 61.1%–98% and 90%–100% [

      Serology-based tests for COVID-19. Johns Hopkins – Center for Health Security. https://www.centerforhealthsecurity.org/resources/COVID-19/serology/Serology-based-tests-for-COVID-19.html. Accessed May 19th, 2020.

      ]. Many FDA-approved serologic tests have high sensitivity and specificity. For example, Cellex Inc. developed a rapid diagnostic test with 93.8% sensitivity and 95.6% specificity. Bio-Rad manufactured an ELISA test with sensitivity and specificity of 98% and 99%, respectively (Table 1) [

      Serology-based tests for COVID-19. Johns Hopkins – Center for Health Security. https://www.centerforhealthsecurity.org/resources/COVID-19/serology/Serology-based-tests-for-COVID-19.html. Accessed May 19th, 2020.

      ].
      There are also clinical associations with confirmed COVID-19 patients. An analysis of 119 patients with COVID-19 at from Wuhan University revealed an association with low urine specific gravity and increased pH [
      • Liu R.
      • Ma Q.
      • Han H.
      • et al.
      The value of urine biochemical parameters in the prediction of the severity of coronavirus disease 2019.
      ]. In addition, the urine glucose and proteinuria correlated with severe/critical cases compared to mild/moderate [

      Walensky RP, del Rio C. From mitigation to containment of the COVID-19 pandemic: putting the SARS-CoV-2 genie back in the bottle. JAMA. Published online April 17, 2020. https://doi.org/10.1001/jama.2020.6572. [Accessed May 19th, 2020].

      ]. The results imply that certain urinalysis profiles can be used to predict the severity of disease and possibly testing of asymptomatic patients that could be quarantined until a definitive test can be completed [
      • Liu R.
      • Ma Q.
      • Han H.
      • et al.
      The value of urine biochemical parameters in the prediction of the severity of coronavirus disease 2019.
      ].
      To address the development of a reliable test, the Department of Health & Human Services (HHS) provided funding for the development of Simplexa COVID-19 Direct Assay and to QIAGEN to accelerate development of their RPS2 test [

      HHS funds development of COVID-19 diagnostic tests. U.S. Department of Health & Human Services. https://www.hhs.gov/about/news/2020/03/13/hhs-funds-development-covid-19-diagnostic-tests.html. Published March 13th, 2020. Accessed April 20th, 2020.

      ]. Additionally, HHS is purchasing the ID NOW COVID-19 rapid point-of-care test (Abbott Diagnostics Scarborough Inc.) for public health labs (Table 1) [

      HHS supports state, territorial and tribal public health labs with COVID-19 rapid point-of-care test. https://www.hhs.gov/about/news/2020/04/06/hhs-supports-state-territorial-and-tribal-public-health-labs-with-covid-19-rapid-point-of-care-test.html. Published April 6th, 2020. Accessed April 20th, 2020.

      ]. The FDA is issuing Emergency Use Authorizations to expedite distribution [

      Coronavirus disease 2019 (COVID-19) – laboratory capacity. Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/php/open-america/laboratory.html. Accessed April 20th, 2020.

      ]. States have differing amounts of laboratories authorized for testing (Fig. 1). The targeted distribution of tests to areas of high density (Fig. 1–black diamonds) is paramount to ensure that resources are not undersupplied.
      Fig. 1
      Fig. 1COVID-19 laboratory facilities across the United States (US). Areas of the US with a high density of testing centers are labeled with a diamond, whereas areas with a low density of testing centers are marked by asterisks.
      *Source: COVID-19 Testing Sites Locator. Arcgis. https://www.arcgis.com/apps/webappviewer/index.html?id=2ec47819f57c40598a4eaf45bf9e0d16
      The road back to normalcy is contingent on accurate tests, allowing suppression of spread. When a localized outbreak occurs, it will be important to have reliable testing methods to promptly contain it. Random serologic testing can be used to surveil populations at high-risk for an outbreak. PCR tests can be used to assess those with active infection who may be asymptomatic.
      Targeted distribution of tests needs to be to areas where COVID is more prevalent and where people are at higher risk. In addition to distribution, the quality of the tests requires improvement. Many prospective tests in development report promising results in under 60 min, such as Mammoth Bioscience's CRISPR-based lateral flow assay (sensitivity:90%, specificity:100%) and United Biomedical's kit (sensitivity:100%, specificity:100%) (Table 1) [

      Serology-based tests for COVID-19. Johns Hopkins – Center for Health Security. https://www.centerforhealthsecurity.org/resources/COVID-19/serology/Serology-based-tests-for-COVID-19.html. Accessed May 19th, 2020.

      ,

      Broughton JP, Deng X, Yu G, et al. CRISPR-Cas12-based detection of SARS-CoV-2 [published online ahead of print, 2020 Apr 16]. Nat Biotechnol 2020; https://doi.org/10.1038/s41587-020-0513-4. https://doi.org/10.1038/s41587-020-0513-4. [Accessed May 19th, 2020].

      ].
      In the present era, technology allows diagnostics to be readily available. Understanding the current disease state in communities' plays a role in the acceptance of control measures that require individual actions. Now is the time to ensure systematic and coordinated efforts between the clinical, commercial and public sectors to leverage the power of testing to address the pandemic at our door.

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      4. COVID-19 RT-digital PCR detection kit. Gnomegen. https://www.fda.gov/media/136738/download. Accessed May 19th, 2020.

      5. QIAstat-Dx respiratory SARS-CoV-2 panel instructions for use (handbook). Qiagen. https://www.fda.gov/media/136571/download. Accessed May 19th, 2020.

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      7. Serology-based tests for COVID-19. Johns Hopkins – Center for Health Security. https://www.centerforhealthsecurity.org/resources/COVID-19/serology/Serology-based-tests-for-COVID-19.html. Accessed May 19th, 2020.

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      9. HHS supports state, territorial and tribal public health labs with COVID-19 rapid point-of-care test. https://www.hhs.gov/about/news/2020/04/06/hhs-supports-state-territorial-and-tribal-public-health-labs-with-covid-19-rapid-point-of-care-test.html. Published April 6th, 2020. Accessed April 20th, 2020.

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      11. Broughton JP, Deng X, Yu G, et al. CRISPR-Cas12-based detection of SARS-CoV-2 [published online ahead of print, 2020 Apr 16]. Nat Biotechnol 2020; https://doi.org/10.1038/s41587-020-0513-4. https://doi.org/10.1038/s41587-020-0513-4. [Accessed May 19th, 2020].