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COVID-19: Important Coding Updates

This article is being updated as new information becomes available. It was originally published on April 3rd and was most recently updated on May 1st with additions to the Specimen Collections section based on updates from CMS on April 30th.

In response to the COVID-19 pandemic, the CMS, the CDC, and the AMA have each issued billing codes for reporting COVID-19 related to:

  • Laboratory testing and specimen collection,
  • Condition code DR (disaster relief), and
  • New ICD-10-CM codes.

Please refer to our summary below related to these important updates.

Laboratory Testing and Specimen Collection

New CPT Codes

Currently, there are three available codes for COVID-19 testing:


Medicare Reimbursement: 51.31

Description:  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.


Medicare Reimbursement: $35.92

Description: CDC 2019 Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel.


Medicare Reimbursement: $51.31

Description: 2019-nCoV Coronavirus, SARS-CoV-2/2019-nCoV (COVID-19), any technique, multiple types or subtypes (includes all targets), non-CDC.

Guidelines for Medicare reporting:

  • If your laboratory uses the CDC test kit, report U0001.
  • If your laboratory uses the method specified by CPT 87635, the appropriate code to use would be CPT 87635. If your laboratory has a test that uses a method not described by CPT 87635, the appropriate code to use would be HCPCS code U0002.

These codes are new. Laboratories can begin billing for the performance of these tests using these codes immediately via standard fee-for-service billing practices. Medicare Administrative Contractors (MACs) are being instructed to hold claims submitted for these tests using these codes until April 1, 2020, at which time claims will be released so the adjudication process can continue.


Charge Amounts

As with any new test (CPT code), common hospital charge setting methods include:

  • Medicare fee schedule amount, plus mark-up
  • Reference lab cost, plus mark-up
  • Review of market comparative amounts. We suggest the Hospital monitor chargemaster charge amounts posted on-line by individual hospitals to understand if the hospital is within market range. Until this information is available, the hospital may wish to consider charge amounts published for common test with similar technology.

For example:

  • 87641 MRSA DNA AMP PROBE; National charge average = $238
  • 87634 RSV DNA/RNA AMP PROBE = $338
  • 87640 STAPH A DNA AMP PROBE = $182

For Medicare, the hospital’s reimbursement will be limited to its charge amount if set below the fee schedule payment amounts from Medicare and other applicable payers.

Specimen Collections

To identify and reimburse specimen collection for COVID-19 testing, the following codes apply to the collection of test samples, including nasopharyngeal (NP) or oropharyngeal (OP) aspirates or washes, NP or OP swabs, bronchoalveolar lavage (BAL), etc.

Coding – Independent Laboratories


Medicare Reimbursement $23.46

Description: Specimen collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), any specimen source.


Medicare Reimbursement: $25.46

Description: Specimen collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), from an individual in a skilled nursing facility or by a laboratory on behalf of a home health agency, any specimen source.

In interim final rule CMS-1744-IFC, CMS states that it is changing Medicare payment policies for the duration of the COVID-19 pandemic.

This change allows Medicare-enrolled independent laboratories to bill Medicare for the COVID-19 specimen collection “G” codes.  If the patient is “confined to the home” (that is, “homebound”), laboratories may also bill for the travel allowance with the current HCPCS codes set forth in Section 60.2 of the Medicare Claims Processing Manual (P9603 and P9604). CMS-1744-IFC clarifies the context of “homebound” for the COVID-19 pandemic.


Coding – Hospital Outpatient and Physician Offices

On April 30, 2020, CMS clarified that Medicare is separately paying hospitals and practitioners to assess patients and collect laboratory samples for COVID-19 testing even when that is the only service the patient receives. The applicable collection codes include:

  • C9803 – Specimen collection billed by hospital outpatient department. Medicare reimbursement is approximately $23 – $25.
  • 99211 – Specimen collection billed by physician office. Medicare reimbursement is approximately $23 – $25.

HCPCS code C9803 was not included on the April 2020 HCPCS update table, so it is unclear when contractors will be able to accept this code for reimbursement.  It is also unclear if C9803 will be paid separately (or OPPS packaged) when performed in conjunction with an ED visit or other separately payable procedures on the same day.

During the public health emergency, we suggest COVID-19 testing and collections for outpatients are reported with modifier CR.

Physician Orders

To ensure that Medicare beneficiaries have broad access to testing, for Medicare payment purposes, Medicare no longer requires an order from the treating physician or other practitioner for beneficiaries to get both COVID-19 testing and laboratory tests for influenza and respiratory syncytial virus that may be part of a COVID-19 diagnosis. COVID-19 tests may be covered when ordered by any healthcare professional authorized to do so under state law.  For details, please refer to the resources below.


Disaster Relief (DR/CR Code) Reporting

The CMS is issuing blanket waivers consistent with those issued for past Public Health Emergencies (PHE) declarations. These waivers prevent gaps in access to care for beneficiaries impacted by the emergency. Special billing requirements for indicating payment is based on “formal waiver.” For Medicare reporting:

  • Condition Code DR (Disaster Relief)
    • “DR” applies to institutional (UB-04) claims only; inpatient and outpatient.
    • Use of the DR condition code is required when a service is affected by an emergency or disaster and Medicare payment for such service is conditioned on the presence of a “formal waiver”.
      • As an example, for SNF claims to process without the three-day qualifying hospital stay, condition code “DR” should be included on the UB-04 claim. MLN Matters Number: SE20011 Revised includes a listing of waivers.
    • Unlike other claims for which Medicare payment is based on a “formal waiver,” telehealth claims don’t require the “DR” condition code or “CR” modifier. CMS is not requiring additional or different modifiers associated with telehealth services furnished under these waivers.
  • Modifier CR (Catastrophe/Disaster Related)
    • The “CR” modifier is used for Part B items and services only but may be used in either institutional or non-institutional billing (UB-04 or CMS-1500).
    • Use of the CR modifier as needed for applicable HCPCS codes on any claim for which Medicare Part B payment is conditioned on the presence of a “formal waiver.”
  • Other payers may have different requirements


ICD-10 CM Codes

Effective April 1, 2020, the CDC is implementing a new diagnosis code, U07.1, COVID-19, into the ICD-10-CM. If diagnosis code U07.1, COVID-19, is reported as a principal diagnosis, it will only exclude itself from acting as a MCC under the CC Exclusions List.

If diagnosis code U07.0, Vaping-related disorder, is reported as a principal diagnosis, the following diagnosis codes will be excluded from acting as a MCC when reported as a secondary diagnosis under the CC Exclusions List.

Principal Diagnosis Code U07.0

Exclude Secondary Diagnosis:

  • J67.8 –  Hypersensitivity pneumonitis due to other organic dusts
  • J67.9 – Hypersensitivity pneumonitis due to unspecified organic dust
  • J68.0 – Bronchitis and pneumonitis due to chemicals, gases, fumes, and vapors
  • J68.1 –  Pulmonary edema due to chemicals, gases, fumes and vapors
  • J69.1 – Pneumonitis due to inhalation of oils and essences

For cases where there is a concern about a possible exposure to COVID-19, but this is ruled-out after evaluation, it would be appropriate to assign the 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 to have COVID-19, it would be appropriate to assign the code Z20.828, Contact with and (suspected) exposure to other viral communicable diseases. Depending on the circumstances, COVID-19 can also be coded with B97.29, Other coronavirus as the cause of diseases classified elsewhere. Only report B97.29 for confirmed cases of COVID-19.

ICD-10-CM Official Coding Guidelines – Chapter 22
Codes for special purposes (U00-U85)
Provisional assignment of new diseases of uncertain etiology or emergency use (U00-U49)

Add         Note: Codes U00-U49 are to be used by WHO for the provisional assignment of new diseases of uncertain etiology. U07 Conditions of uncertain etiology

New codes     U07.1 COVID-19        U07.0 Vaping-related disorder

Add         Use additional code to identify pneumonia or other manifestations.

Add         Excludes1: Coronavirus infection, unspecified site (B34.2)

Add         Coronavirus as the cause of diseases classified to other chapters (B97.2-)

Add         Severe acute respiratory syndrome [SARS], unspecified (J12.81)

Possible exposure to COVID-19 – Z03.818

Actual exposure to COVID -19 – Z20.828

Other coronavirus as the cause of diseases classified elsewhere. B97.29

CMS stated MS-DRG v37.1 will be effective on April 1, 2020. This applies to all discharges April 1 or later: https://edit.cms.gov/files/document/icd-10-ms-drgs-version-371-r1-effective-april-1-2020-updated-march-23-2020.pdf

The Centers for Disease Control and Prevention (CDC) published the final guidelines for the new diagnosis code U07.1, COVID-19, effective April 1 to September 30, 2020. This provides coding scenarios for reporting the new COVID-19 codes: ICD-10-CM Official Coding and Reporting Guidelines April 1, 2020 through September 30, 2020

Please contact us if you have questions about your hospital, and visit our Coronavirus Resources & Information for additional guidance on related items. 

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