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New York State Medicaid Coverage Policy and Billing Guidance for the Administration of COVID-19 Vaccines Authorized for Emergency Use July 2021

Ann Finn

This guidance sets forth New York State (NYS) Medicaid’s reimbursement policy for the administration of COVID-19 vaccines authorized for emergency use and instructions for providers to bill the cost of administration of authorized COVID19 vaccine.

NYS Guidance found here

This coverage policy applies to both Medicaid fee-for-service (FFS) and Medicaid Managed Care (MMC).

Current billing guidance for administering the COVID vaccine for the NYS Hospital Outpatient clinics, D&TC’s and FQHC’s including NYS SBHC’s:

1) Reimbursement for administration of COVID-19 vaccines may be based on a patient-specific order or non-patient specific order (“standing order”). These orders must be kept on file by the provider.

2) Ordering provider’s National Provider Identifier (NPI) is required on the Medicaid claim.

3) Can’t charge a co-pay or any cost sharing.

4) Bill an Ordered Ambulatory Fee claim only for the administration with CPT codes below depending on vaccine brand: (Do not include a vaccine code or claim will deny.)

  • Pfizer 1st dose- bill CPT 0001A

  • Pfizer 2nd dose - CPT 0002A

  • Moderna 1st dose - CPT 0011A

  • Modera 2nd dose - CPT 0012A

  • Janssen - CPT 0013A

5) Current reimbursement post 4/1/2021: $40.00; Prior to 4/1/2021: $13.23

6) The COVID-19 vaccine administration CPT codes above include the actual work of administering the vaccine, including all necessary counseling provided to patients and/or caregivers, required vaccination reporting, and updating of electronic records.

7) If a separate and distinct E/M service is provided on same day, bill an APG or PPS claim for the E/M or other service(s). Still the administration to a separate Ordered Ambulatory Fee claim per above

See guidance for other rate-based providers, pharmacy and ambulance billing.

2021 E/M Guidance Updated - AMA

Ann Finn

The American Medical Association updated its guidance on E/M coding changes for 2021 on March 9th.

One area that was not clear to many providers I’ve met with is when using the MDM method to calculate the E/M code, how to count / apply lab tests to determine the level of the data element. A few tips for family planning providers include I’ve found most helpful include:

  • Do not include Point of Care tests (POCT) that are separately reported during the visit as a unique test in data (i.e., Urine pregnancy tests, rapid testing, microscopy, in office ultrasounds)

  • Ordering and reviewing the test result (i.e., Chlamydia and Gonorrhea) regardless of when it is reviewed - counts as 1 point total for each test

  • Count reviewing test results only for tests you did not order

  • A panel is considered 1 unique test

E/M Coding Changes - January 1, 2021

Ann Finn

This January 2021, CMS and AMA will be updating the guidance for assigning Evaluation and management codes based on Medical Decision Making or total time. These changes will impact code selection and billing. See more here

Key changes include:

The 1995 and 1997 E/M guidelines that have been used in the past no longer apply. 

CPT 99201 has been deleted and is no longer accepted for billing. Other E/M code descriptors have been updated.

New and established client codes (99202-99205, 99212-99215) no longer require the 3 key components or reference typical face-to-face time. Instead, each service includes “a medically appropriate history and/or examination,” and code selection will be based on:

  • an updated MDM (medical decision making) level; OR 

  • time including both face-to-face and non-face-to-face the provider(s) spent in care of the client on the day of the encounter

While not common in family planning settings, revisions to prolonged service codes (e.g. over 74 minutes) have also been made.


New ICD-10-CM code for the 2019 Novel Coronavirus (COVID-19), April 1, 2020

Ann Finn

The Centers for Disease Control (CDC), under the National Emergencies Act Section 201 and 301, is announcing a change in the effective date of new diagnosis code U07.1, COVID-19, from October 1, 2020 to April 1, 2020. This off-cycle update is unprecedented and is an exception to the code set updating process established under HIPAA.

NYS Medicaid: Comprehensive Guidance Regarding Use of Telehealth including Telephonic Services During the COVID-19 State of Emergency

Ann Finn

Effective for dates of service on or after March 1, 2020, for the duration of the State Disaster Emergency declared under Executive Order 202, herein referred to as the “State of Emergency”, New York State Medicaid will reimburse telephonic assessment, monitoring, and evaluation and management services provided to members in cases where face-to-face visits may not be recommended and it is appropriate for the member to be evaluated and managed by telephone. This guidance is to support the policy that members should be treated through telehealth provided by all Medicaid qualified practitioners and service providers, including telephonically, wherever possible to avoid member congregation with potentially sick patients. Telephonic communication will be covered when provided by any qualified practitioner or service provider. All telephonic encounters documented as appropriate by the provider would be considered medically necessary for payment purposes in Medicaid FFS or Medicaid Managed Care. All other requirements in delivery of these services otherwise apply.

Telehealth services will be reimbursed at parity with existing off-site visit payments (clinics) or face-to-face visits (i.e., 100% of Medicaid payment rates). This guidance relaxes rules on the types of clinicians, facilities, and services eligible for billing under telehealth rules.

This guidance additionally addresses some technological barriers to telehealth by allowing clinicians and health care organizations to bill for telephonic services if they cannot provide the audiovisual technology traditionally referred to as “telemedicine.” See update here