COVID 19 Testing - Guide for Physicians

Updated: 7/28/20

Information on coronavirus testing options and availability is changing rapidly. Tests and specimen collection components remain in short supply and are being directed to areas of greatest need. 

To date, no coronvirus tests have been approved by the FDA. But tests are available under Emergency Use Authorization (EUA)(, which means the FDA has not thoroughly vetted these tests to grant full approval. There is limited information on the efficacy (sensitivity and specificity); a low threshold of detection studies are needed to achieve FDA EUA status. Laboratories developing coronvirus tests may begin patient testing while their assays are under FDA review. Additionally, there are tests being marketed to physicians that do not have EUA status.

Who Should be Tested for COVID-19?

Family physicians should use their best clinical judgement to determine who should be tested. The CDC recommends giving testing priority( to:

  • Hospitalized patients
  • Health care facility workers, workers in congregate living settings, and first responders with symptoms
  • Residents in long-term care facilities or other congregate living settings, including correctional and detention facilities and shelters, with symptoms

Persons identified by public health officials or clinicians as high priority include:

  • Persons with symptoms of a possible infection with COVID-19, including fever, cough, shortness of breath, chills, muscle pain, new loss of taste or smell, vomiting or diarrhea, and/or sore throat.
  • Persons without symptoms who come from racial and ethnic minority groups disproportionately affected by adverse COVID-19 outcomes. This currently includes African Americans, Hispanics and Latinos, some American Indian tribes (e.g., Navajo Nation).
  • Persons without symptoms who are prioritized by health departments or clinicians, including but not limited to: public health monitoring, sentinel surveillance, presence of underlying medical condition or disability, residency in a congregate housing setting such as a homeless shelter or long term care facility, or screening of other asymptomatic individuals according to state and local plans.

CME COVID-19 Testing Course

The “COVID-19 Testing: Fundamental and Application to Practice” self-study session offers a look at testing options, testing procedures, and access to testing. View the full Pandemic Self-Study Package for additional sessions. 

COVID-19 Testing Access
and Availability

The number and types of available tests vary widely based on geographic region and health care facility. If a patient is suspected of having COVID-19 and tests aren't available, clinicians should work with local and state public health offices to determine where and how patients can access coronavirus tests in the community.

General population screening is not currently being offered routinely due to limits on available tests. Testing is currently based on prioritization, as outlined above, and adapted by state and local health departments to respond to rapidly changing local circumstances. As states reopen and increase their testing capacity, this may change.

Overview of Available Coronavirus Tests

Two different types of testing are currently available:

  1. Molecular (Reverse Transcriptase-Polymerase Chain Reaction or
  2. Serological (antibody detection)

Three CLIA certification complexity classifications can be given to a diagnostic test that is EUA designated.

  1. High Complexity – These labs have the most stringent regulations regarding testing personnel and testing.
  2. Moderate Complexity – These labs are more stringent than waived or provider-performed microscopy (PPM) labs but less stringent than high complexity labs.
  3. Waived – These labs can perform point of care testing and personnel regulations are not as stringent.

To use for testing patients, you must have a valid CLIA certificate for your practice that matches your normal testing practices. Review a complete list of FDA authorized EUA tests( as well as their CLIA classification. 

COVID-19 Contact Tracing Guidance for Family Medicine

Contact tracing is a core disease control measure employed by local and state health departments. This guidance from the AAFP outlines contact tracing basics for COVID-19 and how it will impact family medicine practices.

Types of COVID-19 Tests Available

Serological (Antibody) Testing

Tests detect the presence of IgM and IgG antibodies against SARS-CoV-2, the virus that causes COVID-19.

  • Currently, there are several test kits granted emergency use authorization( (EUA) by the FDA. Only High and Moderate complexity labs are allowed to run these tests. The FDA has now reviewed tests previously granted EUA and identified those that are of low clinical utility. The FDA has issued a list of those tests in a June 24, 2020 letter( to clinicians and consumers. 
  • The CDC has recently developed its own serologic test that will be used to validate tests from commercial entities and perform surveillance.
  • These tests are NOT diagnostic tests and should not be used as such. There is a high potential for false negatives and false positives with these tests. 
  • These tests are to be used to show past or present infections, but there is not enough evidence to support that the presence of IgG antibodies to COVID-19 provide short- or long-term immunity to illness, nor whether it reduces the risk of viral shedding in infected individuals.
  • These tests are to be used to show past or present infections, but do not confirm the patient has immunity. Some of the tests are not specific enough for COVID-19 infections and will show antibodies for past infections with other coronaviruses. Read the package insert before purchasing.

Approach any coronavirus test kit being marketed to you with caution during this emergency and rapid test deployment. Physicians should be wary of tests from unfamiliar sources.

IgM antibodies are the first to appear and are indicative of a new infection. But it can take days to weeks for these to appear; false negatives can be an issue. False positives are also a concern as there may be cross-reactivity with other coronaviruses. IgG antibodies usually takes at least 4 weeks to appear. These usually show if someone had a past infection but may not be a confirmation of immunity, as they do not measure the effectiveness of a memory response to reinfection. Scientists do not know how SARS-CoV-2 antibodies stay within the body after the infection has cleared.


Molecular Testing (RT-PCR)

Tests used for diagnostic purposes; use reverse transcriptase to create and amplify DNA from SARS-CoV-2 RNA.

  • There are now a few molecular tests that are have been classified as waived( and can be done as a point of care test. These can be found on the FDA website and are indicated with a “W”. The molecular test is much more specific but false negatives do occur. Use clinical judgement and continue to treat the patient as positive if symptomatic or if there was a known exposure.
  • While these tests can detect viral RNA/DNA, they do not distinguish between replicating virus (infectious) and remnants of viral RNA/DNA.

The CDC has developed patient fact sheets( and health care worker fact sheets( the available molecular tests.

Antigen Testing

Currently, there is only one antigen test( given EUA by the FDA. This test detects viral proteins in the nasal cavity. Only high and moderate complexity laboratories can run this test. While the antigen test can be completed in minutes, it is not as sensitive as the PCR tests and may not detect all active infections (false negative).

Point of Care COVID-19 Testing

Rapid COVID-19 tests and those that can provide results for patients in the physician’s office (point of care) are appearing on the market. The AAFP supports point of care testing that is accurate and reliable, and encourages physicians to stay informed about the tests offered for COVID-19 as the accuracy and reliability varies.

There are multiple tests that have been granted EUA for use in CLIA-specified laboratories. Three tests are now available for use in family physician offices as outlined above.

At Home COVID-19 Testing

Only one molecular test( has received EUA from the FDA, but is currently being prioritized for healthcare workers. Additionally, it is not available in all states. The test kit, which includes nasal swab and saline for self-collection, can be ordered online. Samples must be returned the same day. 

There are concerns that swab samples are difficult to obtain and can reduce the sensitivity and specificity of the test if not collected optimally. 

SARS-CoV2 Proficiency Tests Available from AAFP Program

SARS-CoV2 Viral Detection: Compatible with molecular methods (Available October 2020)

  • Module #959 | $294
  • 2 specimens, 3 times per year

SARS-CoV2 Serology Antibody Detection: IgM and IgG antibodies for SARS-CoV2 (Available October 2020)

  • Module #927 | $294
  • 2 specimens, 3 times per year

COVID-19 Specimen Collection—Biohazard and
PPE Considerations

Collection of Diagnostic Respiratory Specimens

Proper collection of specimens is the most important step in the laboratory diagnosis of infectious disease. A specimen that is not collected correctly may lead to false negative test results. The CDC listed the following specimens acceptable for diagnostic testing( for SARS-CoV-2.

  1. Nasopharyngeal (NP) collected by Healthcare Professional
  2. Oropharyngeal (OP) collected by Healthcare Professional
  3. Nasal Mid-turbinate collected by Healthcare Professional or supervised onsite self-collection (using flocked tapered swab)
  4. Anterior nares collected by Healthcare Professional or self-collection onsite or home (using flocked tapered swab)
  5. Nasopharyngeal wash/aspirate or nasal wash/aspirate (NW) collected by Healthcare Professional

All swab specimens should be placed immediately in a sterile transport tube containing viral transport medium, Amies transport medium or sterile saline, unless using a POC test system which analyzes specimen directly.

  • When collecting diagnostic respiratory specimens( (e.g., nasopharyngeal swab) from a patient with possible COVID-19, the following should occur:
  • Specimen collection should be performed in a normal examination room with the door closed, if possible.
  • Healthcare Professional collecting the sample should wear an N95, eye protection, gloves, and a gown.
  • Healthcare Professionals assisting but not directly involved in the collection (such as self-collection) and able to maintain 6 feet from the patient should wear face mask, eye protection, gloves and gown.
  • If N95 are not readily available wear facemask. N95 may be prioritized for other procedures at higher risk for producing infectious aerosols (e.g., intubation), instead of for collecting nasopharyngeal swabs.
  • The number of Healthcare Professionals present during the procedure should be limited to only those essential for patient care and procedure support. Visitors should not be present for specimen collection.
  • Clean and disinfect procedure room surfaces promptly. 

Testing Diagnostic Specimens, including Point of Care specimens

For handling and testing clinical specimens, use standard precautions( to provide a barrier between the specimen and HCP during specimen manipulation. Required PPE includes:

  • eye protection &/or splash guard
  • gloves
  • laboratory coats or gowns.
  • do not wear lab coat or gown outside of testing area.
  • hand hygiene

Employers should select appropriate PPE and provide it to HCP in accordance with OSHA PPE standards (29 CFR 1910 Subpart I)( HCP must receive training on and demonstrate an understanding of:

  • when to use PPE
  • what PPE is necessary
  • how to properly don, use, and doff PPE in a manner to prevent self-contamination
  • how to properly dispose of or disinfect and maintain PPE
  • the limitations of PPE.

Any reusable PPE must be properly cleaned, decontaminated, and maintained after and between uses. Facilities should have policies and procedures describing a recommended sequence for safely donning and doffing PPE. 

Transporting or shipping specimens

If you are sending specimens directly to CDC or state health laboratory, check with your local health department for guidance on transporting and shipping of infectious substances. Most health departments have processes established to ship specimens to state labs or CDC. Suspected COVID-19 specimens must be transported according to International Air Transport Association (IATA) guidelines for infectious substances, category B.

Packaging must contain three components

  1. Primary receptacle
  2. Secondary packaging
  3. Rigid outer packaging, labeled with UN3373 label. See CDC packaging schema diagram( and IATA packing instructions 650 for UN 3373(

Click on “Infectious substances” and download packing instructions. The Requisition for submitting specimens to CDC for lab testing( form must be completed electronically to use the drop downs. Review guidance for completing the form(

Testing Data Reporting Deadline: August 1

Reporting of data elements must be reported no later than August 1, 2020. Reporting should occur within 24 hours of results being known. 

CMS/CLIA Laboratory Guidance for COVID-19 Testing

ALERT: Becton Dickinson (BD) Max System has found to produce false positive SARS-CoV2 results. View the FDA's statement( to health care professionals. (7/10/20)

Laboratories need a CLIA certificate to perform COVID-19 testing. Under CLIA, laboratories are prohibited from testing human specimens for the purpose of diagnosis, prevention, treatment, or health assessment without a valid CLIA certificate. To become CLIA-certified, laboratories must comply with the accuracy, quality, and reliability requirements as dictated by the statute.

The purpose of these requirements is to ensure that the information that patients or their clinicians receive from a clinical laboratory is accurate and reliable test results. No requirements are being waived in response to COVID-19. However, to expedite access to testing( CLIA is allowing for testing to begin once a CLIA number has been assigned as opposed to laboratories waiting for a hard copy paper certificate to come in the mail. 

CMS has provided updated guidance on available tests( and the level of lab required for testing.

Reporting COVID-19 Testing

On June 4, 2020, the U.S. Department of Health and Human Services (HHS) announced new guidance( for reporting COVID-19 testing. This guidance is pursuant to the CARES Act and impacts all laboratories that are performing or analyzing tests intended to detect SARS-CoV-2 or diagnose possible cases of COVID-19. The goal of this new guidance is to standardize the required reporting information to better monitor disease incidence and trends. Laboratories are now required to report the results from each test to the HHS Secretary of the via existing public health channels to ensure rapid initiation of case investigations. 

For detailed information, see Data Reporting Deadline side bar or the following resources:

Important Alert for Laboratories Performing COVID-19 Testing

CDC and FDA release Lab Alert: PrimeStore® Molecular Transport Medium (MTM) – an approved transport media for COVID-19 diagnostic swab samples – contains guanidine thiocyanate, which produces a chemical reaction releasing cyanide gas when exposed to bleach (sodium hypochlorite).

The PrimeStore MTM transport media being provided by state health departments is labeled at the bulk box level, but individual vials lack labels and therefore should be handled with caution. Do not use PrimeStore MTM with platforms that include a disinfecting step that uses bleach

For detailed information, see the side bar or the following resources:

Coding and Billing for COVID-19 Testing

The Centers for Medicare & Medicaid Services and the American Medical Association’s Current Procedural Terminology Editorial Panel are creating relevant codes to keep up with the evolving coronavirus testing environment.

The COVID-19 codes are generalized to capture any technique or target. However, determining the correct code for test procedures can be confusing. This quick reference guide can help you determine the correct code for the test procedure. You can also use the AMA CPT Guidance(