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COVID-19 Coding

Last updated 9/18/2020

This CMS Fact Sheet and this FAQ provides detailed information about Medicare Fee-for-Service billing, cost-sharing waivers, and more for various healthcare settings, including physician offices, RHCs, FQHCs, hospital in- and outpatient settings, and telehealth.

ICD 10 Codes

Code only confirmed diagnosis as documented by the clinician, documentation of a positive test result, or a presumptive positive test result.

U07.1 - ​2019-nCoV acute respiratory disease.  Effective April 1, 2020, the CDC has issued a new ICD10CM emergency code.  

If the clinician document “suspected,” “possible,” “probable,” or “inconclusive, assign a code explaining the reason for the encounter.

Z20.828 - ​Contact with and suspected exposure to other viral communicable diseases (actual exposure).

Z03.818​ - Encounter for observation for suspected exposure to other biological agents ruled out (possible exposure, but ruled out after evaluation).

Z11.59​ - Encounter for screening for other viral diseases (for asymptomatic individuals being screened for COVID-19, have no know exposure to the virus, and test results are either unknown or negative).

Sequencing:  U07.1 should be the primary diagnosis, followed by appropriate codes for associated manifestations:

  • J12.89 (other viral pneumonia)
  • J20.8 (acute bronchitis due to other specified organisms)
  • J22 (unspecified acute lower respiratory infection NOS)
  • J40 (bronchitis, not specified as acute or chronic)
  • J80 (acute respiratory distress syndrome)
  • J98.8 (other specified respiratory disorders)

Use appropriate codes for the signs and symptoms, e.g., R05 (cough), R06.02 (shortness of breath), or R50.9 (fever, unspecified).

For more detailed guidance regarding diagnosis coding for COVID-19 and guidelines for pregnant patients, see this CDC guideline.

CPT and Lab Codes

Below are the CPT and HCPCS codes specific to COVID-19 testing. For a complete list of COVID-19, influenza, and RSV clinical diagnostic laboratory tests for which Medicare does not require a practitioner order during the PHE, click here.

For a summary of Medicare payments for lab testing by type of test and location, see here.  

86328 - ​Immunoassay for infectious agent antibody(ies), qualitative or semiquantitative, single step method (eg, reagent strip); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (COVID-19).

86413 – Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]) antibody, quantitative. (Note: This is a new code as of September 8, 2020. For more information about this new code, see this article.)

86769 - Antibody; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (COVID-19)(multi-step method).

87426 – Infectious agent antigen detection by immunoassay technique, (eg, enzyme immunoassay [EIA], enzyme-linked immunosorbent assay [ELISA], immunochemiluminometric assay [IMCA]) qualitative or semiquantitative, multiple-step method; severe acute respiratory syndrome coronavirus (eg, SARS-CoV, SARSCoV-2 [COVID-19]).  (Short Descriptor: CORONAVIRUS AG IA) (This rapid test code is new so some payers and MACs may not be set up yet)

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.

99000 - ​Handling and/or conveyance of specimen for transfer from the physician’s office to a laboratory. (Use if the specimen is prepared by your office and sent to an outside lab, report the specimen collection code.)

99001 - Handling and/or conveyance of specimen for transfer from the patient in other than an office to a laboratory (distance may be indicated). (Use when directing patient to a testing site.)

99072 – Additional supplies, materials, and clinical staff time over and above those usually included in an office visit or other non-facility service(s), when performed during a Public Health Emergency as defined by law, due to respiratory-transmitted infectious disease. (Note: 99072 may be reported with code 99070 when the requirements for both codes have been met. Paymentand coverage policy will vary by payer.) (Note: This code was released by AMA on Sept. 8 and it will take time for CMS and other payers to begin accepting this code. For more information about this new code, see this article.)

The Centers for Medicare & Medicaid Services (CMS) developed these lab testing codes:

U0001​ - Use to report coronavirus testing using the CDC 2019 Novel Coronavirus Real Time RT-PCR Diagnostic Test Panel.

U0002 - ​​Use to report validated non-CDC laboratory tests for SARS-CoV-2/2019-nCoV (COVID-19).

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.  Note: Use for tests that would otherwise be identified by CPT code 87635 but for being performed with high throughput technologies.

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. Note: Use for tests that would otherwise be identified by U0002 but for being performed with these high throughput technologies.

C9803 - ​Specimen collection only. For use by outpatient hospital departments when no other services were provided. Physician offices should use 99211.

Modifiers

-CS: Use on applicable claim lines subject to the cost-sharing waiver (i.e., COVID-19 testing-related services). Medicare beneficiaries should not be charged for any coinsurance or deductible for those services. The -CS modifier will signal the Medicare Administrative Contractors (MACs) to pay 100% of the Medicare-approved amount for the service. Physicians should contact their MACs and request to resubmit applicable claims with dates of service on or after March 18, 2020, that were submitted without the -CS modifier. The -CS modifier should not be used for services unrelated to COVID-19.

-DR and -CR:  -DR (disaster related) modifier is for institutional claims and the -CR (catastrophic/disaster related) modifier is for Part B billing, both institutional and non-institutional.  For clarification on when to use each modifier, see this guidance released June 1, including a chart of blanket waivers and flexibilities that require the modifier or condition code.  Note: The CR modifier is not for use on telehealth services.

Coding Scenarios

This article, “COVID-19 diagnosis coding explained in a flowchart” helps determine which codes to use based on symptoms (or not) and test results (positive, negative, or not available).

The AMA has issued some coding guidance that includes how to code different scenarios (Updated May 4). The scenarios include examples specifically related to COVID-19 testing. For example, coding for when a patient comes to the office for E/M visit, and is tested for COVID-19 during the visit; receives a telehealth visit re COVID-19 and is directed to come to physician office or physician’s group practice site for testing; receives a virtual check-in/online visit re COVID-19 (not related to E/M visit), and is directed to come to physician office for testing; and more. [Note: These only address coding and are not a guarantee of reimbursement.]