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COVID-19 Testing and Diagnosis Codes and your EHR

CPT Test Procedure Codes for COVID-19 Testing

COVID-19 testing and diagnosis codes are an essential component to collecting and analyzing data to understand the pandemic.   U.S. Health and Human Services Secretary Alex Azar declared a public health emergency for the United States on January 27th 2020.   U.S. Government and the largest medical association in the U.S. responded in record time. CMS made new medical billing codes effective retroactive to February 4, 2020.  This compares favorably with the World Health Organization (WHO) who did not declare a global pandemic until March 11, 2020. 

New data Standards in the form of medical codes to track testing and diagnosis for the virus were approved within 60 days by the American Medical Association and 90 days by the Centers for Medicare and Medicaid.  The codes could be used by many healthcare claims adjudication systems by April to June but could be used to bill for tests as far in the past as February 2020. 

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The American Medical Association held an expedited meeting to approve medical billing codes specific to laboratory testing to determine whether test subjects/patients have SARS-CoV-2 for Coronavirus disease, also known as COVID-19. 

The AMA also approved new Proprietary Laboratory Analyses (PLA) Codes are an addition to the CPT® codes for COVID-19 testing.  PLA codes are alpha-numeric CPT codes with a corresponding descriptor for labs or manufacturers that want to identify their test more specifically.

The American Medical Association reviewed the SARS-CoV-2 related CPT codes and approved them for the 2021 CPT code set, but also declared on an expedited basis that they are active immediately.

    •  87635 – This CPT code is used for COVID-19 Testing for an infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease or COVID-19), amplified probe technique. The new code was valid on March 13, 2020.
    •  86318 – This CPT code is used for COVID-19 Testing as an immunoassay for infectious agent antibody or antibodies. 
    • 87426 – This CPT code is used for tests for an infectious agent antigen detection by immunoassay technique of SARS-CoV and SARS-CoV-2. 
      • Single and multiple-step antibody testing “child” codes of 86318:
        • The addition of code 86328 is used for single-step antibody testing.  
        • Also, a child code 86769 may be used to report multiple-step antibody testing. These new codes and revisions were valid on April 10, 2020.
    •  PLA code 0202U to report the BioFire® Respiratory Panel 2.1 (RP2.1) test. The new code was effective on May 20, 2020.
    • PLA codes (0223U and 0224U) were accepted for the detection of SARS-CoV-2.

New PLA Code Approval by a Provider

We note that Mt. Sinai has applied for and received approval for its own COVID-19 Antibody Test. It is listed as PLA code – Mt Sinai, Mount Sinai Laboratory 0224U was approved for use starting in June 2020 and was approved for publication starting in 2022

We note that child CPT codes are already in use. For example, 86769 is listed in this published list by the University of Washington list of tests for virology

HCPCS Level II Test Procedure Codes 

Some health plans, such as Medicare, may require the use of HCPCs codes.

CMS announced that it had approved two HCPCS codes for COVD-10 Testing valid (implemented) as of April 1, 2020. CMS also states that the date of service for COVID-19 HCPCs codes can be as far in the past as February 4, 2020.

Commercial insurers may require or accept these codes also, or in substitution for CPT codes. The new codes are:

    1. U0001 CDC 2019 – is used specifically for CDC testing laboratories to test patients for SARS-CoV-2a HCPCS code for novel coronavirus (2019-ncov) real-time rt-pcr diagnostic panel
    2. U0002 2019 – allows laboratories to bill for non-CDC laboratory tests. This HCPCS code for novel ncov COVID-19 using any technique, multiple types or subtypes (includes all targets).

WHO Approved Two International ICD-10 Diagnosis Codes for Patients who Test Positive after COVID-19,but this is not the U.S. Standard Approved by the CDC.

In January 2020, the World Health Organization instantiated ICD-10 code U07.1  but WHO introduced more than one code.  In fact, WHO approved two codes and approved both as a code for cause of death.

  • An emergency ICD-10 code of ‘U07.1 COVID-19, virus identified’ is assigned to a disease diagnosis of COVID-19 confirmed by laboratory testing.
  • An emergency ICD-10 code of ‘U07.2 COVID-19, virus not identified’ is assigned to a clinical or epidemiological diagnosis of COVID-19 where laboratory confirmation is inconclusive or not available.
  • Both U07.1 and U07.2 may be used for mortality coding as a cause of death. See the International guidelines for certification and classification (coding) of COVID-19 as the cause of death is on the WHO web site.

The CDC has Approved One Standard ICD-10 CM Code and Differentiates between Confirmed and Suspected Diagnoses

According to the CDC, “Code only confirmed cases

Code only a confirmed diagnosis of the 2019 novel coronavirus disease (COVID-19) as documented by the provider, documentation of a positive COVID-19 test result, or a presumptive positive COVID-19 test result. For a confirmed diagnosis, assign code U07.1, COVID-19. This is an exception to the hospital inpatient guideline Section II, H. In this context, “confirmation” does not require documentation of the type of test performed; the provider’s documentation that the individual has COVID-19 is sufficient.

Presumptive positive COVID-19 test results should be coded as confirmed. A presumptive positive test result means an individual has tested positive for the virus at a local or state level, but it has not yet been confirmed by the Centers for Disease Control and Prevention (CDC). CDC confirmation of local and state tests for COVID-19 is no longer required.

If the provider documents “suspected,” “possible,” “probable,” or “inconclusive” COVID- 19, do not assign code U07.1. Assign code(s) explaining the reason for encounter (such as fever) or Z20.828, Contact with and (suspected) exposure to other viral communicable diseases.”  See Official ICD-10 CM coding guidelines from the CDC.

With respect to conditions caused by COVID-19:

Acute respiratory illness due to COVID-19

  1. Pneumonia

“For a confirmed pneumonia case due to the 2019 novel coronavirus (COVID-19), assign codes U07.1, COVID-19, and J12.89, Other viral pneumonia.”

  1. Acute bronchitis – For a patient with acute bronchitis confirmed as due to COVID-19, assign codes U07.1, and J20.8, Acute bronchitis due to other specified organisms.Bronchitis not otherwise specified (NOS) due to COVID-19 should be coded using code U07.1 and J40, Bronchitis, not specified as acute or chronic.
  2.  Lower respiratory infection – If the COVID-19 is documented as being associated with a lower respiratory infection, not otherwise specified (NOS), or an acute respiratory infection, NOS, codes U07.1 and J22, Unspecified acute lower respiratory infection, should be assigned.If the COVID-19 is documented as being associated with a respiratory infection, NOS, codes U07.1 and J98.8, Other specified respiratory disorders, should be assigned.
  3. Acute respiratory distress syndrome – For acute respiratory distress syndrome (ARDS) due to COVID-19, assign codes U07.1, and J80, Acute respiratory distress syndrome.” See Official ICD-10 CM coding guidelines from the CDC.

Exposure to COVID-19

“For cases where there is a concern about possible exposure to COVID-19, but this is ruled out after evaluation, assign code Z03.818, Encounter for observation for suspected exposure to other biological agents ruled out.

For cases where there is an actual exposure to someone who is confirmed or suspected (not ruled out) to have COVID-19, and the exposed individual either tests negative or the test results are unknown, assign code Z20.828, Contact with and (suspected) exposure to other viral communicable diseases.” See Official ICD-10 CM coding guidelines from the CDC.

Diagnosis Code to use When Testing for COVID-19

Since health plans only pay claims for medically necessary tests, the diagnosis code used with the bill and procedure code is important.  CDC guidelines state that “When screening a patient who is asymptomatic and who are being screened for COVID-19 with no known exposure to the virus, and the test results are either unknown or negative, assign code Z11.59, Encounter for screening for other viral diseases.”  Generally, logic suggests that this code should be used with those CPT and HCPCS codes noted above for testing, but see the specific guidelines for the healthcare payer.

Coding for Isolation

The criteria for coding isolation in section O has not changed with the advent of COVID-19. Skilled nursing and hospice centers have been impacted by COVID and need to document and code appropriately.

Part of that criteria is the presence of active disease.  If a patient tests negative for COVID-19 then it would not be appropriate to code isolation in section O. CMS clarified recently.

0100M, isolation or quarantine for active infectious disease (does not include standard body/fluid precautions)  The guidelines state, that providers should code only when the resident requires strict isolation or quarantine in a separate room because of active infection (i.e., symptomatic and/or have a positive test and are in the contagious stage) with a communicable disease, in an attempt to prevent spread of illness.  Providers should not not code this item if the resident only has a history of infectious disease, but facility policy requires cohorting of similar infectious disease conditions.

American Healthcare Association and CDC Guidelines indicate transmission-based precautions must be considered regarding the type and clinical presentation related to the specific communicable disease. The three types of transmission-based precautions are contact, droplet, and airborne. More information related to the types of transmission-based precautions can be found in the 2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Healthcare Settings

EHR Updates – Contact your Electronic Health Record Vendor to Capture  Testing and Diagnoses Codes in Patient Documentation and Billing

Health care providers should contact their electronic health record vendors. Because these codes were added before the scheduled update that occurs each October 1, EHR and billing systems will require interim updates to their code libraries to ensure that they are available for clinician code selection and reporting. 

CPT is a registered trademark of the American Medical Association

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Michael F. Arrigo

Michael is Managing Partner & CEO of No World Borders, a leading healthcare management and IT consulting firm. He serves as an expert witness in Federal and State Court and was recently ruled as an expert by a 9th Circuit Federal Judge. He serves as a patent expert witness on intellectual property disputes, both as a Technical Expert and a Damages expert. His vision for the firm is to continue acquisition of skills and technology that support the intersection of clinical data and administrative health data where the eligibility for medically necessary care is determined. He leads a team that provides litigation consulting as well as advisory regarding medical coding, medical billing, medical bill review and HIPAA Privacy and Security best practices for healthcare clients, Meaningful Use of Electronic Health Records. He advises legal teams as an expert witness in HIPAA Privacy and Security, medical coding and billing and usual and customary cost of care, the Affordable Care Act and benefits enrollment, white collar crime, False Claims Act, Anti-Kickback, Stark Law, physician compensation, Insurance bad faith, payor-provider disputes, ERISA plan-third-party administrator disputes, third-party liability, and the Medicare Secondary Payer Act (MSPA) MMSEA Section 111 reporting. He uses these skills in disputes regarding the valuation of pharmaceuticals and drug costs and in the review and audit of pain management and opioid prescribers under state Standards and the Controlled Substances Act. He consults to venture capital and private equity firms on mHealth, Cloud Computing in Healthcare, and Software as a Service. He advises ERISA self-insured employers on cost of care and regulations. Arrigo was recently retained by the U.S. Department of Justice (DOJ) regarding a significant false claims act investigation. He has provided opinions on over $1 billion in health care claims and due diligence on over $8 billion in healthcare mergers and acquisitions. Education: UC Irvine - Economics and Computer Science, University of Southern California - Business, studies at Stanford Medical School - Biomedical Informatics, studies at Harvard Medical School - Bioethics. Trained in over 10 medical specialties in medical billing and coding. Trained by U.S. Patent and Trademark Office (USPTO) and PTAB Judges on patent statutes, rules and case law (as a non-attorney to better advise clients on Technical and Damages aspects of patent construction and claims). Mr. Arrigo has been interviewed quoted in the Wall Street Journal, New York Times, and National Public Radio, Fortune, KNX 1070 Radio, Kaiser Health News, NBC Television News, The Capitol Forum and other media outlets. See and for more about the company.

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