Coronavirus

Frequently Asked Questions about Coronavirus (COVID-19) for Laboratories

Accessing Laboratory TestingPublic health laboratories can access test kits and extraction materials for SARS-CoV-2 testing through the International Reagent Resource (IRR)external icon. The IRR supports state and local public health laboratories, as well as other qualified laboratories participating in public health surveillance and studies. CDC’s real-time reverse transcription polymerase chain reaction (RT-PCR) test to detect…

Accessing Laboratory Testing

Public health laboratories can access test kits and extraction materials for SARS-CoV-2 testing through the International Reagent Resource (IRR)external icon. The IRR supports state and local public health laboratories, as well as other qualified laboratories participating in public health surveillance and studies.

CDC’s real-time reverse transcription polymerase chain reaction (RT-PCR) test to detect SARS-CoV-2 in upper and lower respiratory specimens received an Emergency Use Authorization (EUA) from FDA on February 4, 2020, and is distributed by IRR. CDC’s new multiplex assay, which detects influenza A, influenza B, and SARS-CoV-2 simultaneously, received an EUA from FDA on July 2, 2020, and is also being distributed through IRR. IRR also provides several additional commercially produced assays that have received an EUA from FDA to detect SARS-CoV-2 viral RNA in respiratory samples.

Clinical and commercial laboratories conducting SARS-CoV-2 viral testing can acquire test reagents from commercial reagent manufacturers that have received EUA from FDA. Commercial labs can get reagents for CDC’s 2019-nCoV Real-Time RT-PCR from qualified sources listed in the instructions for useexternal icon. A list of commercially available reagents for use with the multiplex assay is not currently available. However, CDC has shared the primers and probes sequences, so other laboratories and companies may manufacture their own reagents. Genomic RNA material for validation purposes can be obtained from BEI Resources as indicated below (in Test Developers FAQs).

According to FDA, when one entity establishes equivalent performance between parallel testing of the same specimens with the new and original components (including viral transport media [VTM]), and FDA’s review of the validation data indicates that it could be applicable to modifications of other tests with an authorized EUA, FDA will post this information on its website so that other laboratories can refer to the validation for their testing. Then, other laboratories do not need to conduct their own bridging study for the same modification. For additional information regarding FDA’s policy for modification, see FDA’s frequently asked questionsexternal icon website.

The US Department of Health and Human Services (HHS) is directly managing allocation of swabs and media, including viral transport medium (VTM), based on state and territory testing plans that were submitted in response to the Coronavirus Aid, Relief, and Economic Security (CARES) Act requirements. Allocations were predetermined to maximize state and territory testing using a data-driven algorithm based on population, high incidence areas, and COVID-19 Task Force’s directives. Currently, HHS is distributing the following swabs: nasopharyngeal (NP), nasal, foam, and poly swabs. HHS is distributing the following media: saline, phosphate buffered saline solution (PBS), and VTM. For specific swab or medium requests, delivery site changes, or other related requests, contact COVID19TestSupplies@hhs.gov.

Public health and clinical laboratories can also produce their own VTM if it is unavailable for purchase. In response to VTM shortages, CDC posted a standard operating procedurepdf icon for the preparation of VTM. Saline is also an acceptable transport medium for some COVID-19 viral assays, including the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panelpdf icon. Check the Instructions for Useexternal icon to see which transport medium is acceptable.

CMS has indicated that it will allow laboratories to use temporary testing sites for remote review and reporting of laboratory data, slides, and images if specific criteria are met. Please refer to this CMS Memorandumexternal icon for additional information.

On June 12, 2020, the U.S. Food and Drug Administration approved an amendmentexternal icon to this test’s Emergency Use Authorization to allow state public health laboratories and others the flexibility to use the following alternatives:

  1. A new authorized extraction method performed with the Roche MagNA Pure 24.
  2. Additional extraction reagent options with the already-authorized extraction instruments from Roche and QIAGEN.
  3. Heat treatment to replace the extraction method. However, heat treatment is recommended only if insufficient extraction reagents are available to extract every upper respiratory clinical specimen received, since this method could potentially reduce test sensitivity. Please note: Laboratories using heat treatment will still need extraction reagents on hand to aid in resolution of any inconclusive or invalid test results obtained for heat-treated specimens and to test lower respiratory specimens.

Additionally, FDA approved an amendmentexternal icon on July 13, 2020, to add the Promega Maxwell® RSC 48 as an authorized extraction instrument for use with the CDC 2019-nCoV rRT-PCR Diagnostic Panel.

Testing Strategies for SARS-CoV-2

Diagnostic testing for SARS-CoV-2 is intended to identify current infection at the individual level and is performed when a person has signs or symptoms consistent with COVID-19, or when a person is asymptomatic but has recent known or suspected exposure to SARS-CoV-2.

Screening testing for SARS-CoV-2 is intended to identify infected persons who are asymptomatic and without known or suspected exposure to SARS-CoV-2. Screening testing is performed to identify persons who may be contagious so that measures can be taken to prevent further transmission.

Any laboratory or testing site that performs diagnostic or screening testing must have a Clinical Laboratory Improvement Amendments (CLIA) certificate and meet all requirements to perform testing. For more information, see the Centers for Medicare & Medicaid Services (CMS) summary of the CLIA regulationspdf iconexternal icon. Assays and test systems used for COVID-19 diagnostic or screening testing must have received an Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) or be offered under the policies in FDA’s Policy for COVID-19 Testsexternal icon.

See CDC’s Overview of Testing for SARS-CoV-2, and FDA’s FAQs on Testing for SARS-CoV-2external icon.

No. Both diagnostic testing results and screening testing results are reported to the persons whose specimens were tested and/or to their healthcare provider or employer.

In addition, both diagnostic testing results and screening testing results (positive and negative) must be reported to the local, state, tribal, or territory health department in accordance with Public Law 116-136, § 18115(a), the Coronavirus Aid, Relief, and Economic Security (CARES) Act. On June 4, 2020, the Department of Health and Human Services published guidance on COVID-19 Pandemic Response, Laboratory Data Reporting: CARES Act Section 18115pdf iconexternal icon that specifies what additional data laboratories and testing sites should collect and electronically report, in addition to COVID-19 diagnostic or screening test results.

Screening testing for SARS-CoV-2 is intended to identify infected persons who are asymptomatic and without known or suspected exposure to SARS-CoV-2. Screening testing is performed to identify persons who may be contagious so that measures can be taken to prevent further transmission.

Public health surveillance is the ongoing, systematic collection, analysis, and interpretation of health-related data essential to planning, implementation, and evaluation of public health practice. See CDC’s Introduction to Public Health Surveillance.

Surveillance testing for SARS-CoV-2 is intended to monitor community- or population-level outbreak of disease, or to characterize the incidence and prevalence of disease. Surveillance testing is performed on de-identified specimens, and thus results are not linked to individuals. Surveillance testing cannot be used for individual decision-making.

Any laboratory or testing site that performs screening testing must have a Clinical Laboratory Improvement Amendments (CLIA) certificate and meet all requirements to perform testing. For more information, see the Centers for Medicare & Medicaid Services (CMS) summary of the CLIA regulationspdf iconexternal icon. Assays and test systems used for COVID-19 screening testing must have received an Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) or be offered under the policies in FDA’s Policy for COVID-19 Testsexternal icon.

Laboratories that conduct surveillance testing for SARS-CoV-2 are not obligated to comply with the FDA and CLIA requirements for diagnostic and screening testing.

See CDC’s Overview of Testing for SARS-CoV-2, and FDA’s FAQs on Testing for SARS-CoV-2external icon.

Yes. Screening results are a specific person’s test results, whereas surveillance results are reported in aggregate, or as de-identified individual reports.

Screening testing results are reported to the persons whose specimens were tested or to their healthcare provider or employer. In addition, screening testing results (positive and negative) must be reported to the local, state, tribal, or territory health department.

By contrast, surveillance testing results cannot be reported to the persons whose specimens have been tested, nor to their healthcare provider or employer. Surveillance testing results also should not be officially reported to the local, state, tribal, or territory health department as diagnostic or screening test results. If a local, state, tribal, or territory health department, or another institution, requests access to the results of surveillance testing for SARS-CoV-2, those results may only be reported in aggregate to the requesting institution, and a statement should be included that indicates the data are surveillance testing results that do not represent COVID-19 diagnostic or screening test results.

General Guidance and Regulatory Requirements

FDA has authorized EUAs for both viral and antibody tests for COVID-19. Viral (nucleic acid and antigen) tests are used to diagnose the presence of SARS-CoV-2 infections. In contrast, antibody tests can detect IgG, IgA, and IgM antibodies from an immune response to SARS-CoV-2.

Whenever possible, laboratories should rely on viral tests to diagnose the presence of SARS-CoV-2 infections. However, a negative result from viral testing does not rule out COVID-19.

Most of the PCR-based tests that use two or more targets are likely to have high specificity (few false positives). However, there is some variation in the stated sensitivity of the different assays, and sensitivity is highly dependent on the stage of the disease. For this reason, negative results should always be interpreted in the context of the exposure history and symptoms of the patient.

Results from antibody testing should not be used to diagnose or exclude SARS-CoV-2 infections or to inform infection status. Negative results from antibody testing do not rule out SARS-CoV-2 infections, particularly for those individuals who have been exposed to the virus and are still within the estimated incubation period. Until the performance characteristics of antibody tests have been evaluated, it is possible that positive results from such testing may be due to past or present infections with a coronavirus other than SARS-CoV-2.

If a laboratory initially uses antibody testing for diagnostic purposes, follow-up testing using a viral test should be performed. Read more:

Before conducting SARS-CoV-2 viral testing, a laboratory must be CLIA-certified and meet applicable regulatory requirements. The Centers for Medicare and Medicaid Services (CMS) does not have the authority to grant waivers of exceptions that are not established in a statute or regulation. For additional information, please refer to the  FAQs on the CMS website: CMS Coronavirus Informationexternal icon.

Tests for SARS-CoV-2 that are offered prior to or without an EUA have not been reviewed by FDA, are not FDA-authorized, and have not received a CLIA categorizationexternal icon. Thus, those tests are considered high complexity by default until they receive an EUA or other FDA review that indicates they may be performed as moderate complexity or waived tests. For more information, visit FDA COVID-19 Resourcesexternal icon, and navigate to the section titled “General FAQs.”

When the FDA grants an EUA for a point-of-care test, that test is deemed to be CLIA-waived. For the duration of the national emergency declaration for COVID-19, such tests can be performed in any CLIA-certified patient care setting with a certificate of waiver.

The federal CLIA program contracts with states to carry out certain oversight and recording functions of the CLIA program. The state in which the laboratory is located processes applications for CLIA certificates. After the laboratory has identified a qualified and certified laboratory directorexternal icon and has provided all required information on the CMS-116 application, a CLIA number will be assigned and the laboratory can begin testing if applicable CLIA requirements have been met. For additional information, please refer to the FAQs on the CMS website: CMS Coronavirus Informationexternal icon.

Yes. If a laboratory conducts surveillance testing on a specimen without a unique identifier and the results of that testing are not returned to the individual, or to the individual’s healthcare provider, employer, etc., that laboratory does not need a CLIA certificate. Surveillance testing results may be returned in aggregate to the institution that requested the study. In such cases, surveillance testing may indicate the need to conduct additional and perhaps more targeted diagnostic testing or screening at the individual level in a CLIA-certified laboratory to improve population or setting-specific health. If at any time a facility conducting surveillance testing intends to report a patient-specific testing result, it must first obtain a CLIA certificate and meet all CLIA requirements to perform that testing.

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