COVID-19: Physician Coding and Reporting Guidance


Medical coding for COVID-19 requires staying up to date on a large number of changes, including new CPT®, HCPCS Level II, and ICD-10-CM codes with varying effective dates. Payers such as Medicare and Medicaid also have been posting and modifying billing and coding guidance related to COVID-19.

Healthcare organizations, and medical coders in particular, need a strategy for staying informed to ensure proper reporting for testing, treatment, and diagnoses as the situation changes. The information below is a starting point to streamline your research on COVID-19 coding, particularly for physician coders.

For the latest information, check AAPC Knowledge Center, which 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, the end of the public health emergency (PHE), agencies, 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, fatigue, and a dry cough, according to the World Health Organization (WHO). Aches and pains, headache, sore throat, and loss of taste or smell are among other possible symptoms, which 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), the Centers for Disease Control and Prevention (CDC) states. 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 has 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 have not followed the usual release and implementation schedule. Instead, the codes are typically effective as soon as the AMA posts 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 pages also include links to CPT® Assistant guides for many of the codes.

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

Medicare has 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.

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. In some cases, the Centers for Medicare & Medicaid Services (CMS) may post the codes in announcements rather than updating the official file, so healthcare organizations need to pay close attention to payer news. Many of the codes are also available on the CMS COVID-19 Vaccines and Monoclonal Antibodies 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, 2020ICD-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, adds 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’ “Current emergencies” page provides links to a long list of resources under the header “Coronavirus Disease 2019.” 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 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 FAQs document covers issues relevant to hospital services, labs, vaccinations, and ambulance services, as well. Medicare updates the FAQs document as new information is released.

Some of the other COVID-19 topics on the CMS emergencies page include telehealth guidance, a list of blanket waivers, and marketplace and Medicare Advantage plan guidance.

As you review the CMS page, check the date next to each link to be sure you’re applying the latest guidance. (Also 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, including a link to the page "Unwinding and Returning to Regular Operations after COVID-19."

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