Coding Guidelines for SARS-CoV-2 (COVID-19)Testing in Health Centers

By: Lisa Messina, Corporate Compliance Officer, PMG & Ray Jorgensen, Co-Founder, PMG

Categories: FQHC, Industry News, PMG Insights Blog

June 16, 2020

Updated 8/27/2020

On May 24, 2020 the Department of Health and Human Services presented a COVID-19 Strategic Testing Plan to Congress which describes, among other things;  detailed information on various testing methodologies; medical device and test availability; and, research and advice designed to inform the government as plans for re-opening the country are made and implemented. Guidance to health care providers has remained fluid as more is learned about the virus and how best to test for active infection (COVID-19) and for the presence of antibodies indicating a past infection.  The types of tests available, the settings in which they may be provided and/or processed, and the CMS coding, billing, and payment available for the various test-related scenarios is important for health centers to understand.  While CMS has provided definition and guidance in these areas, health centers need to check with their MACs and other payers in order to understand how best to bill and be reimbursed for the testing services.


The FDA has been issuing Emergency Use Authorizations to allow for the use of unapproved medical devices or unapproved medical products to be used for testing, treatment and prevention of the SARS-COV-2 infection during this COVID Public Health Emergency. There are currently several types of tests associated with the detection of the SARS-COV-2 virus and antibodies.  There are differences in how specimens are collected and processed as it relates to the sophistication of the approved laboratory instruments and testing kits. Health centers that hold a CLIA Certificate of Waiver, Certificate of Compliance, or Certificate of Accreditation may perform tests that the FDA has authorized under a EUA.

There are flexibilities offered to laboratories processing specimens during the COVID PHE. This CLIA   guidance issued by CMS outlines those flexibilities that may be helpful for health centers to review to understand how they may impact patient testing. Testing may occur in laboratories, including those found in hospitals, and in provider offices.

Laboratory Based Test

Point of Care Test

Molecular Diagnostic Testing

A molecular test (i.e., PCR) tells if the patient currently has an infection by detecting the presence of viral RNA. Direct collections samples include: Nasal, Throat, and/or Nasopharyngeal swabs.  It cannot tell whether a resolved patient had previously had been infected by the virus.

High and moderate complexity laboratories process the specimens using sophisticated laboratory instruments found in CLIA certified laboratories, hospitals, or other health care facilities currently in use across the country.  Molecular testing may also be performed as a point of care (POC) test. POC tests are commonly used for diagnosing strep throat and influenza.  A health center that holds a CLIA Waiver and EUA equipment (e.g., Abbott ID NOW) may perform molecular tests using EUA approved test kits.

Antigen Diagnostic Testing

Antigen tests look for part of the SARS-COV-2 viral protein.  Like the molecular test, antigen tests are looking for a current infection and cannot tell if a resolved patient had been infected by the virus. Antigen tests are commonly used for point-of-care (POC) processing of specimens inside the health center.  POC tests are commonly used for strep throat and influenza. The advantage of antigen tests is the speed in which they produce results; however, they are considered less accurate than a PCR test.  Companies are designing SARS-COV-2 antigen tests to be used with existing equipment (e.g., Quidel’s Sofia 2 SARS Antigen FIA). A CLIA-waived health center may have existing equipment that has been EUA-approved for running the tests using the company’s cartridges.  The current list of EUA approved devices and products can be found on the FDA’s website.


CMS has created CPT code 87635 for providers to use to bill for testing performed using respiratory swabbing.  It is the code health centers would use if they are performing the POC diagnostic viral test. This code became available for reporting on March 13, 2020 and will be part of the complete coding set in the 2021 data file set for release later this year. CPT 87471 is the parent code for 87635 and the full definition includes the language from the parent 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.”

If testing requires two swabs from two different sources (e.g., nasopharyngeal swab and an oropharyngeal swab), the 87635 code would be used twice with the 59 modifier associated with the second assay, following the rules for microbiology coding of separate assays on multiple specimens. Health centers who do not provide POC diagnostic testing would not bill using this code.

UPDATED July 30, 2020: A new CPT code, 87426 was approved at the end of June for providers to use for proper coding and billing of COVID-19 antigen tests performed on patients suspected of being infected with the novel coronavirus. The new code, with an effective date of June 25, 2020, can be used for the immunoassay that detects antigenic proteins for either SARS-CoV or SARS-CoV-2, meaning that it is not specific to the novel coronavirus. CPT code 87426 is now a child code under parent code 87031.
The long description of this code is:

  • 87426: Infectious agent antigen detection by immunoassay technique, (e.g. enzyme immunoassay [EIA], enzyme-linked immunosorbent assay [ELISA], immunochemiluminometric assay [IMCA]) qualitative or semi-quantitative, multiple-step method; severe acute respiratory syndrome coronavirus (e.g., SARS-CoV, SARS-CoV-2 [COVID-19]).

Antibody (Serology) Testing

Simply put, antibody testing tells if a patient has already had the virus and built up the defenses in the blood. An antibody test runs on a laboratory instrument to detect immunoglobulins (e.g., IgM, IgG). So, while they can detect if a person has been exposed to the virus, they cannot used to determine if a patient is infectious.  Health centers can perform a blood draw and send the specimen out to a laboratory for processing, but for POC testing approved (e.g., Chembio Diagnostics) through the EUA process, health centers can bill using the new antibody testing codes.

The CPT codes 86328 and 86769 were created for COVID-19 antibody testing performed by providers to test patients for the novel coronavirus using blood, serum, or plasma. They became available for reporting on April 10, 2020 and will appear in the full CPT code set in the 2021 data file available later this year. The full code descriptions for the CPT codes are:

  • 86328: 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, single-step method.
  • 86769: 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, multi-step method.

CPT 86328 is used for a single-step reagent test, whereas CPT 86769 is used for a multi-step reagent test.  CPT 86328 is the code that would be appropriate for a POC format. Again, in order to bill a CPT 86328 the health center would have to use a EUA approved device and cartridge. Health centers not able to perform testing will perform a blood collection and send the specimen out to a laboratory for processing.


For services provided on March 18, 2020 through to the end of the COVID PHE CMS will pay the reasonable costs for the specified Evaluation and Management E/M services that result in the “order for or administration of a COVID-19 test that relates to the furnishing or administration of such test or the evaluation of an individual for purposes of determine the need for such test.” Telehealth services are included in this definition. In order to qualify, health centers must waive the collection of the co-insurance from the patient. The use of the “CS” modifier is required when health centers waive the co-insurance for COVID-19 testing related services. Claims will be automatically reprocessed July 1, 2020. These claims will be paid with the coinsurance applied.  Health centers will need to submit claims for various visit types according to the time table, codes, and modifiers (e.g., modifier 95) prescribed by CMS. Our CMS Telehealth guidance blog provides an interpretation of the most current CMS MLN.

The April 28, 2020 IFR (beginning on page 184) includes CMS approval for the use of 99211 by providers for the assessment and specimen collection for COVID-19 Diagnostic Testing for new and established patients. Health centers have historically been unable to bill Medicare (CMS/MAC) using CPT 99211. However, if the coding requirements are met a swab collected at the health center’s testing site or at an independent testing site it appears that health centers can submit 99211 for payment. PMG is seeking further clarification on whether this Medicare guidance applies to health centers and suggests health centers maintain a potentially billable list of claims for which specimen conveyance could be billed.  Remember too that commercial payers and Managed Medicaid\Medicare may reimburse for specimen collection via 99211.

The AMA provides excellent CPT reporting scenarios based upon where the patient is assessed and where the swab is collected. The AMA has also created an excellent guide regarding the various scenarios for both molecular and serologic testing for SARS-CoV-2. The guide can no longer be directly hyperlinked to so please find it by going to this AMA website, scroll to the bottom and click on “Coding scenarios and how to apply best coding practices (PDF”). Below is a chart to show how coding might look from the perspective of the testing process flow by location. It is important to note the CMS MLN SE20016 is clear that a Telephone (audio only) E/M service cannot be billed if it originates from a related E/M provided within the previous 7 days or leads to an E/M service or procedure within the next 2 hours or soonest available appointment.

Molecular and Antigen Diagnostic POC Test at the Health Center

Assessment New or Established E/M Visit code New or Established E/M Visit code 99421-99423


(PPS G0071)



Swab Collection at the health center Included








POC Testing At Health Center 87635 87635 87635 87635

Molecular and Antigen Testing Not Performed at the Health Center

Assessment New or Established E/M Visit code New or Established E/M Visit code 99421-99423


(PPS G0071)



Swab Collection at the health center Included 99211* 99211* 99211*


Specimen Conveyance from health center to laboratory 99000* 99000** 99000** 99000**

* May be able to bill if visit is on a separate day from the Telehealth visit. Source:

** Check with Payer. CPT 99000 is not covered by Medicare

Serology Antibody POC Test at the Health Center

Assessment New or Established E/M Visit code New or Established E/M Visit code 99421-99423


(PPS G0071)



Blood Collection at the health center Included








POC Testing At Health Center 86328 or 86769* 86328 or 86769* 86328 or 86769* 86328 or 86769*

* CPT 86328 is used for a single-step reagent test as would be typical with POC testing whereas CPT 86769 is used for a multi-step reagent test processed on more sophisticated laboratory instruments.

Serology Antibody Testing Not Performed at the Health Center

Assessment New or Established E/M Visit code New or Established E/M Visit code 99421-99423


(PPS G0071)



Blood Collection at the health center Included 99211* 99211* 99211*


Specimen Conveyance from health center to laboratory 99000** 99000** 99000** 99000**

* May be able to bill if visit is on a separate day from the Telehealth visit. Source:

** Check with payer. CPT 99000 is not covered by Medicare

Depending upon the type of POC test performed at the health center CPT 87635 or 86328 or 86769 can be billed. If the health center is sending the specimen out to a laboratory, the laboratory would bill the applicable testing code.


On April 1, 2020, the CDC finalized guidelines for diagnostic coding for encounters for COVID-19 confirmed and suspected cases as well as those related to exposure, screening, and other respiratory illness associated with infection.  A confirmed diagnosis will have the newly created U07.1, COVID-19 assigned to it. Patients who are asymptomatic and test positive for COVID-19 are assigned U07.1, COVID-19. A patient who is asymptomatic, exposure is not known, test is negative or unknown, code Z11.59. For someone who has been exposed to the virus and tests negative for infection Z20.828, “contact with and (suspected) exposure to other viral communicable disease”. Where possible exposure is a concern but is ruled out after evaluation, assign code Z03.818 for “Encounter for observation for suspected exposure to other biological agents ruled out.” Follow coding guidelines, also outlined in this same CDC document, for when to code symptoms.


This CMS guide explains that testing (and use of 99211) can be provided to both new and established patients and by whom specimens can be collected and locations where specimen collection and testing can occur. In addition, there are flexibilities for COVID-19 and RSV/Influenza tests for which Medicare does not require a practitioner order during the PHE. Local coverage determinations still apply, and health centers will need to check with other payers to see if they have adopted this flexibility with regard to test ordering. If the code you intend to use is not on this list, then an order is still required.


Any clinical staff involved in specimen collection and testing must be properly trained and supervised in accordance with the health center’s credentialing and privileging practices. Federal and state laws must also be adhered to as it relates to personnel and training requirements for laboratory testing and specimen collection. States may be temporarily allowing health practitioners to provide these services outside their normal scope of practice; therefore, it is important for health centers to check with state laws for guidance. In addition, temporary privileging can be used to expand the scope of services, as allowable under federal and state laws, and still fall under the FTCA.

In addition, while volunteer providers are not automatically covered by the FTCA, health centers can apply for protection.

FTCA coverage extends to providers of services to established patients and to those individual who are not patients of the health center.


Payment for testing is set through the MACs. This recently published payment guide will assist health centers in pricing tests and in determining payment. There is agreement across the country that CMS reimbursement will be:

CPT 87635 CPT 86328 CPT 86769
$51.31 $45.23 $42.13

The QW Modifier is typically appended to all CLIA-waived tests. Health centers are strongly urged to check with their MACs and other payers to determine if this modifier is required for the testing codes.

Updated July 30, 2020: CMS added the requirement of the QW modifier to CPT 87426 effective June 25, 2020 with the MLN released July 24, 2020.


With the goal of placing “Patients Over Paperwork”, the government has created flexibilities to permit expansion of services within communities to allow for better access to care and testing.  During the COVID PHE, CMS is removing the location restrictions to allow flexibility for existing health centers to expand services locations, which may be outside of the location requirements, to meet the needs of Medicare beneficiaries. Where the provision of in-scope health center services are already within the health center’s approved scope of project, HRSA approval is not required. Services that are not within the project scope can be submitted to the health center’s Project Officer. It is important for health centers to check the criteria for better understanding of temporary expansion site provisions. As there are requirements for when health centers should apply for temporary site approval, centers should check the HRSA program requirements to make sure they are following the necessary steps for expansion. In addition, health centers should also check with FTCA provisions or malpractice insurance carriers to make sure any questions have been addressed before temporary expansion sites become operational.  Temporary locations that appear to be commonly used for assessment and testing are on current health center property in ‘pop-up’ tents, mobile units, and trailers. FTCA coverage also expands for health centers conducting testing on patients who are in their cars.


During the COVID PHE, health centers can make home visits in areas that are part of its service area plan, where there is a shortage of home visit agencies, and where no request for the determination is required. In addition, telehealth services (CPT 99342-99350) using audio and visual technology may be performed for homebound patients and health centers would bill the applicable HCPCS PPS G code for those services.  However, a health center nurse visit for the sole purpose of obtaining a swab is not considered a nursing visit as that service can be provided by a person of lesser training (e.g., lab technician).  If a FQHC home visit nurse is already established then the nurse can take the swab and send it for testing. This testing is permitted for homebound patients, which CMS defines as follows: “A beneficiary is considered homebound when their physician advises them not to leave the home because of a confirmed or suspected COVID-19 diagnosis or if the patient has a condition that makes them more susceptible to contract COVID-19. As a result, if a beneficiary is homebound due to COVID-19 and needs skilled services, an HHA can provide those services under the Medicare Home Health benefit.”


Q: We have been using G2023 to bill our specimen collections at our health center. Can we use this code?

A: HCPCS G2023 would not be used by health centers to code specimen collection. CMS established two new HCPCS codes, G2023 and G2024 to capture specimen collection services performed by independent laboratories. They became available for reporting on March 1, 2020 and are used by clinical diagnostic laboratories for any type of specimen collection. Laboratories must use one of these HCPCS codes when billing Medicare for the nominal specimen collection fee for COVID-19 testing for the duration of the PHE for the COVID-19 pandemic. The full description of these code are:

  • G2023, specimen collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), any specimen source
  • G2024, specimen collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), from an individual in a SNF or by a laboratory on behalf of a HHA, any specimen source

Q:  Where can I find information about the HHS Program for COVID-19 Testing and Treatment for the Uninsured Program?

A:  Information on the HHS COVID-19 Testing and Treatment for the Uninsured Program may be found on the HHS Website. A good summary of the program was written by Feldesman Tucker and describes the basic features.

Q:  If a Telephone E/M visit (99441-99443) using G2025 is not billable until July 1, 2020, and we provide at the health center POC molecular testing for a patient who received testing resulting from a Telephone E/M visit, do we hold the claim until July 1, 2020?

A:  In this scenario, the claim for the Telephone E/M using G2025 with the CS modifier should be held until July 1, 2020.  The 87635 POC test can be billed separately.

Q:  If an E/M Telehealth visit, Virtual Check-in, E-Visit or Telephone E/M is held one day and then on a separate day a patient arrives at the office for a specimen collection that is sent to a laboratory for testing, can we bill the 99211 and 99000 codes?

A:   The interpretation is that if a patient comes to the health center a separate day from the Telehealth visit for specimen collection then the health center can bill the 99211 and 99000 codes.  It is important to check with your payer. Source:

Please also note that according to CMS, “if the brief communication technology-based service originates from a related E/M service provided within the previous 7 days by the same physician or other qualified health care professional the service would be considered bundled into the previous E/M service and would not be separately billable” to Medicare.

Q: If a patient previously received testing for COVID-19, can a provider be reimbursed by Medicare if retesting prior to a procedure is determined to be needed?

A: CMS has not provided any guidance on retesting patients prior to procedures. Without this national policy, it is up to the MACs to determine coverage.

FAQs Added on June 18, 2020

 Q: Is the CS modifier required for 99211 when this code is used for swabbing only?

A: In the June 18, 2020 issue of MLN Connects, CMS provides this clarification for Physicians and Non-Physician Practitioners (NPPs): “Here are several reminders related to billing for COVID-19 symptom and exposure assessment and specimen collection performed on and after March 1, 2020:

  • Use CPT code 99211 to bill for assessment and collection provided by clinical staff (such as pharmacists) incident to your services, unless you are reporting another Evaluation and Management (E/M) code for concurrent services. This applies to all patients, not just established patients.
  • Submit the CS modifier with 99211 (or other E/M code for assessment and collection) to waive cost sharing.
  • Contact your Medicare Administrative Contractor if you did not include the CS modifier when you submitted 99211 so they can reopen and reprocess the claim.
  • We will automatically reprocess claims billed for 99211 that we denied due to place of service editing.”

Q: If the patient has insurance that will cover COVID-19 testing only if the patient is symptomatic could the patient be covered under the HRSA Uninsured Program?

A: The vast majority of payers are covering testing even if a patient is asymptomatic and the provider has determined that the testing is medically necessary.  Many states are also now encouraging testing based upon an individual’s profession regardless of whether an individual is symptomatic, and states have set up funds to cover this testing.  The HRSA Uninsured Program is strictly for patient who are uninsured and providers are required to check for health care eligibility and confirm that the patient is uninsured.

FAQ Added on August 27, 2020

Q: For which services should I apply the CS Modifier?

A: Information about the use of the CS Modifier can be found in a separate blog on our website. In short, the CS modifier must be used for COVID testing and testing related services and also for preventive health telehealth services where the cost sharing has been waived. CMS released a list of HCPCS/CPT codes that require the CS modifier in order for FQHCs to be reimbursed for services.  The list currently may only be accessed by clicking on the link inside this education release in the “Claims, Pricers, and Codes” section. In addition, they clarified that any claims submitted with the CS modifiers for services not on this list will be returned for correction and resubmission.  The CMS MLN SE20011 was also updated to reflect this change.

PMG will continue to provide updates as information becomes available.  Contact our team of experts to learn more about how PMG can help your FQHC.