Medical coding for COVID-19 changed a lot over time, including new CPT^®, HCPCS Level II, and ICD-10-CM codes with varying effective dates. Payers such as Medicare and Medicaid also posted and modified a variety of billing and coding guidance related to COVID-19.

The information below is a quick snapshot to streamline your research on COVID-19 coding, particularly for physician coders.

For information from the time of the pandemic, check AAPC Knowledge Center, which posted updates relevant to the healthcare industry as news was 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, the end of the public health emergency (PHE), and more.

Terminology: COVID-19 and SARS-CoV-2

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 relevant codes and instructions.

COVID-19, which stands for coronavirus disease 2019, is the name for an infectious disease that most commonly causes fever, chills, and sore throat, according to the World Health Organization (WHO). The symptoms may vary based on the variant of the virus.

Most people do not require special treatment to recover from COVID-19, and some patients who test positive do not experience symptoms. Older people and those with underlying medical problems are more prone to require medical attention, but patients of all ages may become seriously ill with COVID-19, possibly leading to death. 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). SARS-CoV-2 and the virus that caused the 2003 outbreak of SARS are genetically related, but the diseases are different.

CPT^® Codes for SARS-CoV-2/COVID-19 Services

The American Medical Association (AMA) CPT^® Editorial Panel approved several new Category I and proprietary laboratory analyses (PLA) CPT^® codes connected to COVID-19. Examples of services represented by these codes include lab tests to check for current infection, lab tests to check for antibodies to the SARS-CoV-2 virus (which may indicate past infection and possible current immunity), and vaccine and immunization administration.

Because of the urgency of the situation, the code updates did not follow the usual release and implementation schedule. Instead, the codes were typically effective as soon as the AMA posted them. For instance, the first new 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 — was published and effective March 13, 2020. The vaccine and immunization codes may include a note indicating they are effective once the vaccine receives Emergency Use Authorization or approval from the Food and Drug Administration.

The AMA posts new codes on its COVID-19 CPT^® Vaccine and Immunizations Codes page. The page also includes links to CPT^® Assistant guides for many of the codes.

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

Medicare released HCPCS Level II codes in response to the COVID-19 pandemic, covering services such as specimen collection and testing. Check with non-Medicare payers to confirm their policies on use and coverage of these codes. Also ensure you’re using codes appropriate for your date of service, including confirming whether the code has been deleted.

As an example, two HCPCS Level II codes for COVID-19 testing (U0001 and U0002) had an implementation date of April 1, 2020, which is when Medicare claims processing systems were able to accept the codes. Dates of service for these codes can go back to Feb. 4, 2020.

Healthcare organizations also need to watch for changes to medical coding modifiers. A case in point is modifier CS Cost-sharing waived for specified covid-19 testing-related services that result in and order for or administration of a covid-19 test and/or used for cost-sharing waived preventive services furnished via telehealth in rural health clinics and federally qualified health centers during the covid-19 public health emergency. Medicare revised this descriptor for use when cost-sharing does not apply to certain COVID-19 testing-related services and certain telehealth services.

Medicare posts updates to HCPCS Level II codes and modifiers on the HCPCS Quarterly Update page.

ICD-10-CM Coding for COVID-19

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.

Consequently, the CDC announced the creation of ICD-10-CM code U07.1 COVID-19, which was effective April 1, 2020. ICD-10-CM is the United States’ clinical modification of ICD-10. The code sets are not identical, and ICD-10-CM is the code set U.S. providers should use for third-party payer claims.

This coding news came 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 original plan was for ICD-10-CM code U07.1 to have an effective date of Oct. 1, 2020. October 1 is the date when annual ICD-10-CM updates occur each year. But the CDC announced a change to April 1, 2020, to assist with claims and surveillance data for COVID-19.

ICD-10-CM added more codes specific to COVID-19 effective Jan. 1, 2021, to represent screening, exposure, personal history, and pneumonia, as well as multisystem inflammatory syndrome, a condition that may be associated with COVID-19. And another update effective April 1, 2022, added ICD-10-CM codes for underimmunization and post COVID-19 conditions.

The rules for COVID-19 ICD-10-CM coding vary depending on the date of service. Links to authoritative guidance are available on the CDC’s ICD-10-CM page. The ICD-10-CM Official Guidelines for Coding and Reporting address issues such as sequencing codes, coding suspected COVID-19 cases, and reporting follow-up visits.

Medicare and Medicaid Coverage and News

CMS’ page on past infectious disease emergencies provides links to a long list of resources under the header “Coronavirus Disease 2019 (2020-2023).” Healthcare professionals in a variety of roles will find helpful information here. For instance, the “Clinical & technical guidance” section offers documents about the Quality Payment Program, patient counseling, and a toolkit for mitigating COVID-19 in nursing homes.

The page also includes a “Billing & coding guidance” category, which features fact sheets on coverage and payment and provides a COVID-19 FAQs document. As you review the CMS page, check the date next to each link to be sure you’re aware of when the update was posted.

For providers who report to Medicaid, a good starting point is the page "Unwinding and Returning to Regular Operations after COVID-19."

Last reviewed on Jan. 9, 2025, by the AAPC Thought Leadership Team