The basics of COVID-19 testing and associated codes

April 27th, 2020 / By Bobbie Starkey, Colleen Deighan, RHIA

Testing for COVID-19 continues to be a major concern in the fight to bring the virus under control. Today we are going to talk about the CPT and HCPCS codes that are being released at a fast and furious pace as new testing capabilities are emerging. It is not an easy task to keep up with all the new tests and associated codes. Our goal is to help you by explaining the types of COVID-19 tests available today as well as the associated codes.

Tests for COVID-19 virus detection

Microbiology tests are performed for the purpose of detecting the presence of an infectious agent known as an antigen. The test is accomplished by amplified probe technique. The specimen, typically collected via nasal or nasopharyngeal swab, is treated to isolate the nucleic acid (DNA, RNA) and eliminate substances that inhibit amplification. The nucleic acid is amplified using specific primers for COVID-19 sequences.

We have been hearing about high throughput testing in the news. We mention this now because high throughput testing is used in the detection of the COVID-19 virus. High throughput technology uses a platform that employs automated processing of more than two hundred specimens a day. High throughput machines are sophisticated pieces of equipment that are operated by highly skilled laboratory technicians.

Tests for COVID-19 virus antibody detection

Immunology/Serologic tests  are qualitative or semi-quantitative immunoassays for the detection of antibodies to infectious agents. Immunoassays may be qualitative (i.e., positive or negative for the presence of antibodies) or quantitative (measures the amount of antibodies present in the blood.) These tests identify two types of antibodies:

  • IgM, a transient antibody the body makes soon after infection for about two  weeks before the levels in the blood drop.
  • IgG, a subsequent antibody that the body makes more slowly (within approximately four weeks) but which usually last longer in blood.

There are two different methods of performing these tests:

Single step method: the patient’s blood is added to a reagent well that has been coated with anti-human monoclonal IgM and IgG antibodies. A specimen diluent is added. After the patient specimen and the reagent react with the test area the result is read optically as a yes/no for the presence of antibodies. This is a rapid-testing methodology and is used for point of care testing.

Multi-step method: A sample of the patient’s serum is diluted and an aliquot is placed in a multi- well plate, incubated and then washed. Anti- human IgG and IgM antibodies are added to the sample plate and incubated. Then a chromogenic substrate is added, incubated and read on a microtiter plate reader. This lab technique is known as the Elisa method.

Now that we have talked about the basic types of tests and methodologies for performing them, let’s discuss the coding of them.

Antigen detection testing

On March 13, 2020 the American Medical Association (AMA) published CPT® Assistant Special Edition, volume 30, 2020, in which they announced the creation of a unique Current Procedural Terminology (CPT) code that would allow providers to code and bill for COVID-19 testing. This CPT code, 87635, described below,  is to be used to help efficiently report (bill) as well as track testing services related to COVID-19. The code effective date is March 13, 2020 for use as the industry standard for the reporting of tests for the novel coronavirus across the nation’s healthcare system.  Laboratories can also use this CPT code to bill Medicare if the laboratory uses the method specified by CPT 87635. 

87635 – Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique

Additional guidance on the use of this code is provided by the AMA. CPT Assistant also provides a description of the new CPT code along with a clinical example and FAQs for use of the code.  

On March 5, 2020, CMS created a second Healthcare Common Procedure Coding System (HCPCS) code to report COVID-19 testing. Developed in February, HCPCS code U0001 is to be reported for tests performed by the Centers for Disease Control and Prevention (CDC) for COVID-19. The newly created HCPCS code U0002 is to be reported for non-CDC lab tests for SARS-CoV-2/2019-nCoV (COVID-19). The new code U0002 became effective on April 1, 2020 and was made retroactive to February 1, 2020.  It is important that these two codes are assigned appropriately to meet the needs of the CDC for tracking the specific testing performed.

Some of the guidelines for use of the new COVID-19 codes are documented in the Medicare COVID-19 Fact Sheet. Healthcare providers using the CDC 2019 Novel Coronavirus Real Time RT-PCR Diagnostic Test Panel may bill for that test using the newly created HCPCS code (U0001). HCPCS code (U0002) 2019-nCoV Coronavirus, SARS-CoV-2/2019-nCoV (COVID-19), any technique, multiple types or subtypes (includes all targets), non-CDC can also be used by laboratories and healthcare facilities. Both codes can be used to bill Medicare as well as by other health insurers that choose to utilize and accept the codes. CMS recommends contacting your Medicare Administrative Contractor (MAC) to determine if they have any additional payment guidance regarding these codes.

Regarding high-throughput testing, on April 14, 2020 CMS published a ruling, CMS-2020-01-R, introducing new HCPCS codes U0003 and U0004 as described below. 

U0003 –  Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique, making use of high throughput technologies as described by CMS-2020-01-R.

U0004 –  2019-nCoV Coronavirus, SARS-CoV-2/2019-nCoV (COVID-19), any technique, multiple types or subtypes (includes all targets), non-CDC, making use of high throughput technologies as described by CMS-2020-01-R.

The ruling states that Clinical Diagnostic Laboratory Tests (CDLTs) that utilize high throughput technologies administered on or after March 18, 2020 for the detection of SARS–CoV–2 or the diagnosis of the virus that causes COVID-19, and are a type of CDLT currently paid for under Medicare Part B using CPT code 87635 or U0002, such tests, as identified using U0003 or U0004 as appropriate, shall be paid for at the rate of $100. It also notes that payment for all other CDLTs will remain at the current level.

U0003 should be used to identify tests that would otherwise be reported by CPT code 87635 but were performed with the high throughput technologies. 

U0004 would be used to identify tests that would otherwise by reported by HCPCS code U0002 but were performed with the high throughput technologies. Neither U0003 nor U0004 should be used for tests performed for the purpose of  detecting COVID-19 antibodies.

Antibody detection testing

On April 10, 2020 the AMA published a CPT Assistant Special Edition, April Update, in which they revised one CPT code and created two new CPT codes (as seen below) for reporting serologic laboratory testing for COVID-19, which allows for the reporting and tracking of antibody testing. These code changes/additions became effective April 10, 2020.

(revised) 86318 – Immunoassay for infectious agent antibody(ies), qualitative or semiquantitative, single step method (eg, reagent strip)

(new) 86328 –  severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19])

(new) 86769 – Antibody; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19])

These serology codes are used to identify the presence of antibodies to the SARS-CoV-2 virus in serum.  These codes differ from CPT 87635 which is used to test respiratory specimens in which DNA/RNA is analyzed and used to detect the actual presence of the virus. The April issue of CPT Assistant Special Edition provides descriptions of the new/revised codes along with clinical examples and FAQs for use of the code and appropriate use of modifiers

All these codes can be reported by laboratories or physicians for the testing for COVID-19 and reporting is dependent on the method of testing being utilized.

We will continue to provide updates regarding the CPT and HCPCS codes for laboratory testing of COVID-19 as they become available. Due to the fluidity of the situation, we encourage our readers to be diligent in keeping abreast of this subject utilizing CMS, CDC, AMA, AHIMA and other trusted resources.

Bobbie Starkey, RHIT, CCS-P, is an outpatient expert and consultant with 3M Health Information Systems.

Colleen Deighan, RHIA, CCS, CCDS-O, is a consultant with 3M Health Information Systems.

Sue Belley, RHIA is a clinical content development manager with the consulting services business of 3M Health Information Systems.

Beth Eichorst is a project manager with 3M Health Information Systems.


During a pandemic, healthcare information is gathered, studied, and published rapidly by scientists, epidemiologists and public health experts without the usual processes of review. Our understanding is rapidly evolving and what we understand today will change over time. Definitive studies will be published long after the fact. 3M Inside Angle bloggers share our thoughts and expertise based on currently available information.