COVID-19: Your Medical Coding and Compliance Headquarters


Medical coding related to COVID-19 (coronavirus disease 2019) is an evolving area, including new CPT®, HCPCS Level II, and ICD-10-CM codes with varying effective dates. Payers, such as Medicare and Medicaid, are also releasing billing and coding guidance for services related to COVID-19.

Healthcare organizations, and medical coders in particular, need a strategy for staying up to date to ensure proper reporting for testing, treatment, and diagnoses as the situation changes. The information below summarizes the updates to streamline your research on COVID-19 coding.

Terminology: COVID-19 and SARS-CoV-2

COVID-19 is the name for an infectious disease that most commonly causes fever, tiredness, and a dry cough, according to the World Health Organization (WHO). Most people do not require special treatment to recover from COVID-19, but older people and those with underlying medical problems are more prone to serious illness that involves difficulty breathing. On March 11, 2020, WHO characterized COVID-19 as a pandemic, meaning the worldwide spread of a new disease. The term pandemic does not refer to the threat level involved.

COVID-19 is caused by a virus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), states the Centers for Disease Control and Prevention (CDC). SARS-CoV-2 and the virus that caused the 2003 outbreak of SARS are genetically related, but the diseases are different.

Medical code descriptors and guidance may use terms related to COVID-19 or SARS-CoV-2, so you need to watch for both to avoid missing a relevant code or instruction.

CPT® Code for SARS-CoV-2/COVID-19 Testing

The American Medical Association (AMA) CPT® Editorial Panel has approved a new COVID-19 test code, 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.

A publicly available CPT® Assistant special edition about 87635 provides guidance on proper use of the new code. Here are some examples:

  • The AMA published the new code March 13, 2020, and the code is effective immediately.
  • Healthcare organizations should check third-party payer policy on retroactive billing and reimbursement.
  • Some payers may require use of a HCPCS Level II code instead of 87635 (see the next section).
  • Labs should follow the guidelines for microbiology codes that state when performing separate assays on multiple specimens, append modifier 59 Distinct procedural service. For instance, if a lab tests a nasopharyngeal specimen and a separate oropharyngeal specimen, it may be appropriate to report 87635, 87635-59.

HCPCS Level II Codes for SARS-CoV-2/COVID-19 Testing

Two HCPCS Level II codes for COVID-19 testing have an implementation date of April 1, 2020, which is when Medicare claims processing systems will be able to accept the codes. Dates of service can go back to Feb. 4, 2020. Private payers may accept these codes, as well, so healthcare organizations that report these tests should confirm payer preference.

According to the April 2020 file on the Centers for Medicare & Medicaid Services (CMS) HCPCS Quarterly Update page, these are the descriptors for the new codes:

U0001 CDC 2019 novel coronavirus (2019-ncov) real-time rt-pcr diagnostic panel
U0002 2019-ncov coronavirus, sars-cov-2/2019-ncov (covid-19), any technique, multiple types or subtypes (includes all targets), non-CDC

Code U0001 is appropriate for the use of tests developed by the CDC. Code U0002 will allow labs to bill for non-CDC tests.

CMS has released a document with test pricing for U0001 and U0002. For U0001 (CDC tests), the test prices listed are $35.91 or $35.92, depending on the Medicare Administrative Contractor (MAC) jurisdiction. The U0002 test prices listed are $51.31 or $51.33.

ICD-10-CM Code for COVID-19, Effective April 1, 2020

In January 2020, WHO established a new ICD-10 code, U07.1 2019-nCoV acute respiratory disease. The organization acknowledged that the disease name was likely to change, which it later did to COVID-19.

ICD-10-CM is the United States’ clinical modification of ICD-10. The code sets are not identical, but the CDC has announced that a new ICD-10-CM code will be effective April 1, 2020: U07.1 COVID-19.

The original plan was for the code to have an effective date of Oct. 1, 2020, but the CDC changed the date to April 1, 2020, to assist with claims and surveillance data.

This news comes from the CDC because the CDC National Center for Health Statistics is the federal agency responsible for use of ICD-10 in the U.S. The agency is one of the four Cooperating Parties for ICD-10-CM, along with CMS, the American Hospital Association, and the American Health Information Management Association.

The new COVID-19 diagnosis code, descriptor, and related addenda were included in the agenda and meeting proposal for the March 2020 ICD-10 Coordination and Maintenance Committee meeting.

ICD-10-CM Coding for COVID-19 Before April 1, 2020

The CDC has provided official interim diagnosis coding guidance to assist with proper reporting before the ICD-10-CM code for COVID-19 is effective. This guidance is posted on the CDC’s National Center for Health Statistics ICD-10-CM page.

Table 1 summarizes this interim coding guidance, which has an effective date of Feb. 20, 2020. Healthcare organizations should use this guidance in conjunction with the 2020 ICD-10-CM Official Guidelines. Note that the guidance states B34.2 Coronavirus infection, unspecified, which is part of category B34.- Viral infection of unspecified site, would “generally not be appropriate for the COVID-19, because the cases have universally been respiratory in nature, so the site would not be ‘unspecified.’”

Table 1: ICD-10-CM Interim Coding Guidance for COVID-19



Confirmed Cases

Pneumonia due to COVID-19

J12.89 Other viral pneumonia

B97.29 Other coronavirus as the cause of diseases classified elsewhere

Acute bronchitis due to COVID-19

J20.8 Acute bronchitis due to other specified organisms


Bronchitis not otherwise specified (NOS) due to COVID-19

J40 Bronchitis, not specified as acute or chronic


Lower or acute respiratory infection NOS associated with COVID19

J22 Unspecified acute lower respiratory infection


Respiratory infection NOS associated with COVID-19

J98.8 Other specified respiratory disorders


Acute respiratory distress syndrome (ARDS) that develops with COVID-19

J80 Acute respiratory distress syndrome


Exposure to COVID-19

Concern about possible exposure, ruled out by evaluation

Z03.818 Encounter for observation for suspected exposure to other biological agents ruled out

Exposure confirmed

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

Signs and Symptoms Without Definitive Diagnosis


R05 Cough

Shortness of breath

R06.02 Shortness of breath


R50.9 Fever, unspecified

Medicare and Medicaid Coverage and News

CMS’ “Current emergencies” page provides links to a long list of resources under the header “Coronavirus.” Healthcare professionals in a variety of roles will find helpful information here. For instance, the “Clinician & technical guidance” section offers documents about infection control in nursing homes, home health, hospice, and dialysis facilities. Other examples include links related to protective mask use, blanket waivers, and telehealth benefits.

The page also includes a “Billing & coding guidance” category, which features fact sheets on coverage and payment, and a COVID-19 FAQs document that answers questions like “Does Medicare pay for a doctor or non-physician practitioner (NPP) to furnish care in a beneficiary’s home?” The FAQ covers issues relevant to hospital services, vaccinations, and ambulance services, as well.

As you review the CMS page, you should check the date next to each link to be sure you’re applying the latest guidance. (Keep in mind that COVID-19 information likely will move from this “Current emergencies” site in the future.)

For providers who report to Medicaid, national Medicaid’s COVID-19 page is a good starting point for research. The Medicaid page includes targeted advice, such as a fact sheet on Medicaid coverage and benefits related to COVID-19 and a document titled “Medicaid State Plan Fee-for-Service Payments for Services Delivered Via Telehealth.” Many of these links are available on the CMS “Current emergencies” page, as well.

AAPC Knowledge Center Articles Related to COVID-19

AAPC Knowledge Center posts updates relevant to the healthcare industry as news is announced. All articles related to COVID-19 are on a single page to make access more convenient. Topics include the expansion of telehealth coverage for Medicare beneficiaries, new codes for testing, guidance for hospices and home health agencies, and more.

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