Update: Establishing a COVID-19 Diagnostic Lab

Recent updates issued by the CDC affect COVID-19 diagnostics labs

Tracy Wieder, MBA
Mar 01, 2022 | 5 min read

Two years into the COVID-19 pandemic, COVID-19 testing is still in high-demand, leading to the opening of many new clinical diagnostic laboratory facilities to analyze patient samples for COVID-19. In early 2020, many articles outlined how to set up a COVID-19 diagnostic lab. But things have changed since the pandemic began. 

This article will review the basics needed to establish a COVID-19 diagnostic laboratory and highlight recent updates issued by the U.S. CDC that affect COVID-19 diagnostics labs. 

Major equipment

Setting up a COVID-19 diagnostic laboratory requires a basic virology laboratory setup in terms of equipment and supplies. See the below table for average equipment costs that can be used for budgeting when buying equipment. Keep in mind, you may be able to negotiate lower prices depending on your location:

item

size

Cost

Type II-A2 biosafety cabinet with base4 ft$7,500
-80C freezer with racks*500 box capacity$16,000
-20C biomedical freezer, manual thaw*#13 cu ft$8,000
Pharmaceutical refrigerator24 cu ft$6,000
Reverse transcriptase polymerase chain reaction (RT-PCR) machine96 x 0.1 mL tubes, 12 x 8-tube strips, 1 x 96-well plate$25,000
Centrifuge with sealed rotorsTable-top, refrigerated$9,000
*Any equipment that is used to store patient samples (or vaccines) must have attached chart recorders to verify that the freezer is operating in the proper range at all times. 
#-20 freezers should be purchased as manual thaw units, not auto-thaw or “frost-free” units because these units periodically warm up enough to avoid ice accumulation and do not provide a stable environment for the storage of samples or reagents. 
NOTE: There are currently long lead times when purchasing some centrifuges. However, the supply chain delays in shipping -80 and -20 freezers have been resolved.

Reagents and supplies

Primers, probes, and reagents for RT-PCR
Positive control for real-time RT-PCR is an in vitro transcribed RNA derived from strain BetaCoV_Wuhan_WIV04_2019 (EPI_ISL_402124)
Lab coats
Lab chairs
Basic lab consumables including gloves, masks, Kimwipes, pipet tips, centrifuge tubes, hand soap, paper towels, disposable bench covers, bleach, glass disposal boxes, biohazardous disposal boxes, autoclave tape, and office supplies
Supplies to disinfect the lab benches and equipment must meet the EPA’s criteria for use against SARS-CoV-2 to disinfect surfaces
Personal protective equipment (PPE) (i.e., face shields, goggles, N95 respirators, disposable gowns, and gloves)

Regulations

  • Certification and oversight of clinical laboratory testing is detailed in the law cited as CLIA '88 (Clinical Laboratory Improvement Amendments). All labs intending to run COVID-19 diagnostic testing should be very well versed in the contents of these laws and must be CLIA certified. 
  • ISO 15189:2012 is an international regulatory standard that details the quality and competence requirements for clinical laboratories. In the United States, ISO 15189:2012 accreditation is voluntary but whether a COVID-19 diagnostics lab has this accreditation or not, every COVID-19 diagnostic lab should be familiar with these standards.
  • All patients and their samples are covered by The Health Insurance Portability and Accountability ACT (HIPAA) Privacy Rule. All samples need to be deidentified and if informed consent forms were collected from patients by the diagnostic lab, these need to be kept by the diagnostic laboratory. 
  • The CDC recently updated its Interim Guidance for Antigen Testing for SARS-CoV-2 on January 20, 2022, providing guidelines detailing what information must be included on an antigen test result. 

Per CDC guidelines, a test result must be in the form of written documentation (paper or digital copy). The documentation must include the following:

  • Type of test, indicating whether it is a NAAT (nucleic acid amplification test) or antigen test
  • Entity issuing the result (e.g., laboratory, health care entity, or telehealth service)
  • Sample collection date
  • Information that identifies the person (full name plus at least one other identifier such as date of birth or passport number)
  • Test result

Testing protocols

The FDA regulates the tests that are approved to be used for COVID-19 diagnostic testing. This website lists which diagnostic tests are presently cleared for usage, and provides fact sheets for health care providers and patients, as well as other vital information for diagnostic laboratories performing COVID-19 diagnostic testing. The World Health Organization (WHO) published an RT-PCR protocol for the detection of SARS-CoV-2 on their website.

Lab safety in a COVID-19 diagnostics lab

In January 2022, the CDC updated their Guidance for General Laboratory Safety Practices during the COVID-19 Pandemic to align with CDC recommendations for people who are up to date with their vaccines:

Face masks

Staff who are up-to-date with their vaccines: Staff who are up to date with their vaccines should wear a well-fitting mask when in an area of substantial or high transmission of COVID-19. This helps protect staff from SARS-CoV-2 variants and prevents spreading it to others.
Staff who are unvaccinated or not up-to-date with their vaccines: The CDC recommends staff who are unvaccinated or not up-to-date with their vaccines to wear a well-fitting mask and physically distance, especially when indoors around people who don’t live in their household. This includes office spaces, computer workstations, and break rooms. In general, employees who are not up-to-date with their vaccines should wear a well-fitting mask in laboratory spaces that do not have requirements for respiratory PPE and where other physical distancing measures are difficult to maintain.
Any face mask worn inside a laboratory area where personnel work with potentially infectious material should subsequently not be worn outside of that laboratory area. Laboratory PPE is considered a critical supply, and employees should refrain from removing any PPE from the laboratory for general use.
Face masks are not intended to protect those who wear them from any biological or chemical agent handled in the laboratory and are not considered laboratory PPE.
All staff should follow established PPE requirements for working in laboratory spaces.
Staff should wash their hands before putting on face masks and minimize mask removal while in the clinical laboratory. Depending on the facility’s design or configuration, additional physical barriers, such as a face shield, plexiglass, partition, or plastic barriers, may be needed to achieve physical distancing goals in settings with unvaccinated staff or staff who are not up-to-date with their vaccines.


For more safety measures for avoiding laboratory inquired infections, read our latest article.

Helpful resources

The CDC’s Division of Laboratory Systems holds regular calls with clinical laboratories to discuss the nation’s clinical laboratory response to COVID-19. Clinical Laboratory COVID-19 Response Calls are held every other Monday at 3:00pm ET and transcripts of the calls are posted online after each call.