CMS Guidance for Laboratories during COVID-19 Emergency

CMS is committed to taking critical steps to ensure America’s clinical laboratories are prepared to respond to the threat of 2019 Novel Coronavirus (COVID-19) and other respiratory illnesses to ensure reliable testing as well as ensuring patient health and safety. CMS is issuing this guidance to laboratory surveyors to provide important guidance to surveyors and laboratories during the COVID-19 public health emergency, such as:

  • CMS’ Exercise of enforcement discretion to ensure pathologists may review pathology slides remotely if certain defined conditions are met,
  • Ensuring that laboratories located in the United States wishing to perform COVID-19 testing that applies for CLIA certification are able to begin testing as quickly as possible during the public health emergency,
  • Highlighting that laboratories within a hospital/University Hospital Campus may hold a single certificate for the laboratory sites within the same physical location or street address,
  • Offering enforcement discretion as to Proficiency Testing (PT) During the duration of the Public Health Emergency,
  • Addressing alternate Specimen Collection Devices, and
  • Addressing Laboratory Developed Tests

CLIA program and an 1135 waiver

The CLIA program is unable to approve section 1135 waiver requests with respect to waivers of CLIA program requirements. Section 1135 waiver authority is only applicable to specified programs (or penalties) authorized by the Social Security Act (SSA). The CLIA program does not fall into this category of programs. CMS does not have the authority to grant waivers or exceptions that are not established in statute or regulation.

Laboratories and temporary testing sites

CMS will allow laboratories to utilize temporary testing sites for remote review and reporting of laboratory data/slides/images as long as specific criteria are met. As long as the facility has the appropriate CLIA certificates and follows applicable CLIA regulations, state regulations, and guidelines, the laboratory may perform testing in the parking lot or any other designated overflow location in its facility. QSOG memo: Clinical Laboratory Improvement Amendments (CLIA) Laboratory Guidance During COVID-19 Public Health Emergency

Proficiency Testing (PT)

If the laboratory is performing testing and providing patient results, PT is still required and must be performed, as required by the CLIA regulations. Furthermore, the following may be of note:

  • Only CMS may exercise enforcement discretion as to CLIA- requirements like PT. Unless CMS has given the directive, a PT program may not permit a laboratory to opt-out of participating in a PT event while continuing to test patient specimens for reasons such as emerging public health outbreaks like seasonal influenza epidemic.
  • A PT program must immediately notify CMS, Accreditation Organizations (AO), Exempt States (ES), and laboratories if they need to postpone, suspend, or cancel an event.
  • Laboratories will not be penalized for lack of PT results if PT is postponed, suspended, or canceled with CMS’s approval. However, laboratories should consider performing their own self-assessment in such a scenario to ensure reliable results.
  • Laboratories should document any notification from a PT program regarding postponement, suspension or cancelation of a PT event.
  • The laboratory must document on the PT result sheet that a test is not currently being performed if testing is temporarily suspended for a specific test due to staffing shortage, supply shortage, or reagent shortage.
  • The inspecting agency and PT program must be notified within the timeframe of submitting PT results if a laboratory will not be submitting results due to a temporary suspension of its performing a specific test. Such notice must include the reason for that temporary suspension.

Using alternate specimen collection devices

During this public health emergency, with the exceptions outlined in the QSOG memo, CLIA regulations remain applicable. CLIA regulations are not prescriptive about the type of transport device, specimen collection swabs, and viral transport media (VTM) that laboratories use. CMS CLIA only requires that the laboratory follow manufacturer’s instructions. If a laboratory modifies the manufacturer’s instructions, the laboratory must establish performance specifications and validate the assay prior to performing patient testing. CLIA is not prescriptive as to how the study is performed; the Laboratory Director is responsible for defining the validation parameters. Please refer to the FDA COVID-19 Diagnostic Test Guidance FAQs for further information.

During the public health emergency, according to the 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, and the laboratory agrees to FDA sharing that information for use by other laboratories, FDA posts this information on its website so other laboratories can refer to the validation for their testing, without conducting their own bridging study for the same modification. For additional information regarding FDA’s policy for modifications refer to the FDA COVID-19 Guidance.

In instances where the FDA has indicated that certain alternate collection devices and specimen transport media could be used, the CLIA laboratory director will need to decide if subsequent validation studies are needed before tests are performed. Additionally, the CDC has posted a new standard operating procedure (SOP) for laboratories to create their own VTM in accordance with CDC’s protocol.

Performing COVID-19 testing

While the CLIA program is a Federal program, it contracts with State Agencies to carry out certain oversight and recording functions of the CLIA program. The State Agency in the state where the laboratory is located can answer your questions and will process your application. Some states also have laboratory licensing laws separate from the CLIA regulations; laboratories in such states must meet the CLIA requirements and the state requirements.

If you would like to apply for a CLIA certificate, please submit your application form (CMS-116, CLIA Application Form) to the state (SA Contacts) where the laboratory is located. CMS wants to ensure that laboratories located in the United States applying for a CLIA certificate are able to begin testing for COVID-19 as quickly as possible. Once the laboratory has identified a qualified laboratory director and has provided all required information on the CMS-116 application, a CLIA number will be assigned. Once the CLIA number has been assigned, the laboratory can begin testing as long as applicable CLIA requirements have been met (e.g…, establishing performance specifications).

Payment Information for COVID-19 testing

Payment Information for COVID-19 testing is available at Medicare COVID-19 Testing Fact Sheet and new Medicare FAQs found here. Additional inquiries can be submitted at