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FQHC Coding for COVID-19 Vaccines

October 12, 2023

On September 11, 2023, the FDA authorized, for emergency use (EUA), the 2023-2024 formulations of the Pfizer-BioNTech and Moderna COVID-19 vaccines for individuals ages 6 months and older. This new formulation includes a monovalent component corresponding to the Omicron XBB.1.5 variant. The FDA simultaneously rescinded the authorization for bivalent vaccines for use in the United States.

The FDA set forth the following guidelines for vaccination by age of the eligible individual:

  • 6 months through 4 years: If previously vaccinated are eligible to receive 1 or 2 doses of the new vaccine depending upon the timing and number of previous vaccine doses.
  • 6 months through 4 years: If previously unvaccinated are eligible to receive 3 doses of the new Pfizer-BioNTech vaccine or 2 doses of the new Moderna vaccine.
  • 5 years and older: Regardless of vaccination history are eligible to receive 1 dose of the new vaccine at least 2 months after the last dose of any previous vaccine.

The FDA also approved:

  • Comirnarty COVID-19 vaccine (2023-2024 formula) change to a single dose for individuals, ages 12 and older.
  • Spikevax COVID-19 vaccine (2023-2024 formula) change to a single dose for individuals ages 18 and older; and, approval for a single dose for individuals, ages 12 – 17 years.

Providers are advised to remove and dispose of all bivalent vaccines in their inventory, even if they are not expired. The Bureau of Primary Care advises health centers that have ordered vaccines through the COVID-19 Vaccine Program to update their stock and wastage via the Health Partner Order Portal which may be found through the Health Center Program Community.

The AMA, in August 2023, approved new vaccine product codes and deleted over 45 previously approved ones to streamline the coding for COVID-19 vaccines. This follows the Vaccines and Related Biological Products Advisory Committee decision that COVID-19 vaccinations be updated annually. In addition, the AMA created one administration code to be used with any vaccine for any patient, regardless of patient age, thereby replacing all previously issued administration codes. The effective date of the new codes coincides with the FDA approval date of September 11, 2023.

With the streamlining of the COVID-19 vaccine code set, the AMA deleted Appendix Q, effective November 1, 2023. Appendix Q and the deleted codes will appear in the CPT® 2024 codebook because the decision to delete them came after the codebook was finalized. Health centers should refer to the AMA website for the most up-to-date information.

As of September 12, 2023, Medicare will no longer pay for the deleted CPT codes. Most state programs and commercial payors are also no longer paying for the deleted CPT codes, and health centers should check with their individual payors.

Medicare will continue to pay FQHCs 100% of the reasonable cost for administering COVID-19 vaccines through the cost report. Health centers should continue to submit administration claims to the relevant Medicare Advantage plan. Check with your payors or vaccine programs for policies specific to your health center.


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