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Coding High-Throughput COVID-19 Testing

Coding High-Throughput COVID-19 Testing

The Centers for Medicare & Medicaid Services (CMS) created two new HCPCS Level II codes for lab tests that use high-throughput technologies to detect SARS-CoV-2, the virus that causes COVID-19. The rate for these codes is $100, roughly twice the rate of similar tests that don’t use high-throughput technologies.

Consider New Codes in Place of 87635 and U0002

The descriptors for both new codes specify that they apply to the use of high-throughput technologies. They also reference the April 14 ruling, CMS-2020-01-R, that announced their creation.
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 as described by CMS-2020-01-R.
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 as described by CMS-2020-01-R.
The ruling states that you should report U0003 when high-throughput technology is used to perform a test that would otherwise fall under CPT® 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.
Code U0004 is appropriate when reporting the use of high-throughput technology for tests that you would otherwise code using U0002 2019-ncov coronavirus, sars-cov-2/2019-ncov (covid-19), any technique, multiple types or subtypes (includes all targets), non-cdc.
To clarify, U0003 and U0004 do not make 87635 and U0002 obsolete. The point of the new codes is to provide more specific options for high-throughput technology tests.
And here’s one more coding tip: You should not use new codes U0003 or U0004 for tests that detect COVID-19 antibodies, the ruling states.

Which Tests Qualify as High Throughput?

Some clinical diagnostic laboratory tests (CDLTs) that detect SARS-CoV-2 involve sophisticated high-throughput machines that require special training and use intensive processes for quality purposes. The technology allows automated processing of more than 200 specimens in a day for rapid diagnosis of large numbers of cases. This technology may be useful in testing vulnerable populations, such as nursing home patients.
In the ruling, CMS listed the following as examples of high-throughput technology:

  • Roche cobas® 6800 System
  • Roche cobas® 8800 System
  • Abbott m2000TM System
  • Hologic Panther Fusion® System
  • GeneXpert® Infinity System
  • NeuMoDxTM 288 Molecular

Know the Criteria for $100 Rate

Medicare Part B pays for CDLTs using the Clinical Laboratory Fee Schedule (CLFS or CLAB). Medicare will pay a rate of $100 for CDLTs that meet these criteria:

  • Use high-throughput technologies (as the ruling defines them);
  • Are administered during the ongoing emergency period, which began March 18, 2020;
  • Are used “for the detection of SARS-CoV-2 or the diagnosis of the virus that causes COVID-19;” and
  • Are CDLT types paid under Medicare Part B using 87635 or U0002.

Medicare will continue to pay other CDLTs at their current levels. CMS plans to make quick assessments about payment rates as new COVID-19 tests that use high-throughput technology emerge.

Learn More About Implementation

The conclusion of the CMS ruling directs Medicare Administrative Contractors “to engage in whatever processes are necessary to make determinations or policies to process claims in accordance with this Ruling.” The ruling will expire when the emergency period officially ends.
The effective date of the ruling is April 14, 2020, but as of April 20, 2020, CMS has not posted updated HCPCS Level II or CLAB files that include the new codes. Check with payers to confirm their policies regarding use of U0003 and U0004.
Disclaimer: Information related to COVID-19 changes rapidly. For the latest updates, keep an eye on AAPC Knowledge Center’s COVID-19 posts and CMS’ current emergencies page.

Deborah Marsh

10 Responses to “Coding High-Throughput COVID-19 Testing”

  1. Jeff Grancorbitz says:

    Can any of these codes be billed by the physician group providing the test to their surgery patients or do these codes only get reimbursed if billed by the Lab vendor themselves? Thank you.

  2. Patti Westergard says:

    My provider started doing blood finger sticks for Covid 19. Is there a CPT code?

  3. Renee Dustman says:

    “My provider started doing blood finger sticks for Covid 19. Is there a CPT code?”

    This article from the AAFP may answer your question: https://www.aafp.org/journals/fpm/blogs/gettingpaid/entry/covid_antibody_coding.html

  4. Renee Dustman says:

    CMS, in an April 30 press release, says they will pay hospitals and practitioners to assess patients and collect lab samples for COVID-19 testing. https://www.cms.gov/newsroom/press-releases/trump-administration-issues-second-round-sweeping-changes-support-us-healthcare-system-during-covid

  5. NISHA TANEJA says:


  6. Renee Dustman says:

    The BD Veritor™ System for Rapid Detection of SARS-CoV-2 is a chromatographic immunoassay for the direct and qualitative detection of SARS-CoV-2 antigens in nasal swabs from patients with signs and symptoms who are suspected of COVID-19. Therefore, 87426 is correct.

  7. Carolyne says:

    What about the BD Veritor Plus combo now testing for Influenzaand Nasopharyngeal Swab

  8. Vincent Donatacci says:

    My lab is questioning if they can charge for high through put technology for CPT 87636.
    This would be based on whether they are using high through put technology machines correct.?

  9. Renee Dustman says:

    Do you mean 87635? Yes, the lab must use the type of test described in the code in order to bill the code.