A Tangled Mess

By Monique Griffin for For the Record

From sequencing to recognizing manifestations, coding  for COVID-19 is no easy task.

When the pandemic emerged, the World Health Organization (WHO), the American Medical Association (AMA), and the Centers for Medicare & Medicaid Services (CMS) scrambled to update codes for the diagnosis, testing, and tracking of COVID-19.

Prior to the outbreak, ICD-10 featured only a handful of codes for coronavirus diagnoses: SARS-associated coronavirus as the cause of diseases classified elsewhere (B97.21), excluding pneumonia due to SARS-associated coronavirus (J12.81), and other coronavirus as the cause of diseases classified elsewhere (B97.29). Neither of the B codes would act as a primary diagnosis. The catch-all for the remaining cases is coronavirus infection, unspecified (B34.2).

You Can Thank Vaping

Typically, new codes are implemented in October, but a sharp increase in diseases and injuries related to vaping prompted the WHO to quickly add a new ICD-10-CM code: U07. 0, Vaping-related disorder. Due in part to this rapid turnaround, COVID-19 received similar treatment, with a new code (U07.1) added to the chapter encompassing codes for special purposes (U00–U85). The new section, Codes U00–U49, is designed for the provisional assignment of new diseases of uncertain etiology or for emergency use.

Diagnosis Coding

With regard to COVID-19, the Centers for Disease Control and Prevention (CDC) released several variations of the ICD-10-CM Coding and Reporting Guidelines, the final of which is effective through September 30. The CDC addressed both CPT codes (those related to diagnosis and symptoms) and HCPCS codes, which address testing and procedures related to COVID-19.

For COVID-19 infections due to SARS-CoV-2, code only a confirmed diagnosis as documented by the provider, documentation of a positive COVID-19 test result, or a presumptive positive COVID-19 test result. A confirmed diagnosis is assigned code U07.1.

“In the guideline that talks about presumptive positive, our previous guidelines tell us that we can code ‘probable’ or ‘suspected’ cases as if they already existed, so it’s very confusing for coders, especially when we first began [coding for COVID-19],” says Tammy Trombley, RHIT, CDIP, CCDS, compliance manager at GHR RevCycle. “Some physicians were documenting presumptive positive but they were not referring to a positive test result at the local or state level. There was confusion regarding the meaning of ‘presumptive positive’ in the coding guidelines.”

A presumptive positive test result is defined as a patient testing positive for the virus at a local or state level but the result having not yet been confirmed by the CDC. However, CDC confirmation is no longer required, which allows coders to code presumptive positive results as confirmed diagnoses.

“From a coding perspective, you have to know where the physician is getting presumptive positive from,” Trombley says. “Is he just saying probable? A query would be a good idea to see if he thought the test result was a false-negative by his clinical judgment. You would then want to be able to support it with all the conditions and symptoms that you have.”

For coding confirmed cases, the provider’s documentation that the patient has COVID-19 is sufficient and does not require documentation of the type of test performed that yielded the positive result.

“If the doctor says the patient is positive for COVID-19—even if the test shows negative—then you can code the COVID because the doctor might feel it is a false-negative. The patient could have all the symptoms and just that test didn’t show positive,” says Meredith McCollum, MBA, RHIA, CCS, an ICD-10-CM/PCS trainer and director of coding compliance at GHR RevCycle.

If an individual is asymptomatic and tests positive for COVID-19, assign code U07.1. Although the individual is showing no signs or symptoms of the virus, they have tested positive and are considered to have the COVID-19 infection.

However, do not assign code U07.1 if the provider documents “suspected,” “possible,” “probable,” or similar indeterminate language. This is an exception to the ICD-10-CM hospital inpatient guideline Section II, H, which states to code indeterminate language regarding a diagnosis as though it existed or was already established. Instead, code the signs or symptoms, such as a fever, that led to the individual to seek care as unspecified (R50.9), cough (R05), shortness of breath (R06.02), etc.

Z Code Clarification

“Where I am seeing the most confusion is coders are not understanding when to use the different Z codes associated with COVID-19,” McCollum says. The Z codes pertaining to COVID-19 cover patients who have had contact with COVID, had possible exposure, or are asymptomatic with no exposure.

“I think with those three, the coders are having issues in knowing which one to use,” McCollum says.

In absence of a positive test result, if a patient is exposed to someone who is either confirmed or suspected, not ruled out, of having COVID-19, code Z20.828, Contact with and (suspected) exposure to other viral communicable diseases. Do not use code Z20.828 in conjunction with code U07.1. If the patient later tests positive for COVID-19, assign code U07.1.

A provider may document a “probable” or “possible” encounter with someone who has COVID-19. If, after evaluation, this is ruled out, use code Z03.818, Encounter for observation for suspected exposure to other biological agents ruled out. While observation codes are used as the principal/first-listed diagnosis, FY2021 ICD-10-CM Guidelines makes allowances for Z03.818 to be used as a secondary code after October 1, 2020. The guidelines give the example of incidental COVID-19 testing for a patient who was in an automobile accident with negative results.

It is currently acceptable to assign code Z11.59, Encounter for screening for other viral diseases in the following cases:

• A patient fears they have COVID-19 but does not display signs or symptoms of the disease, tests negatively, has no known encounters with an infected person, and does not have a mental illness that would be listed as a primary diagnosis.

• An individual is being screened for COVID-19, is asymptomatic, and has no known exposure to the virus, and the test results are either unknown or negative.

“Coders should be assigning Z11.59 (encounter for screening for other viral diseases) to this scenario as a secondary code,” Trombley says. “Some of the coders have confused Z20.828, suspected exposure, with Z11.59. It’s important to learn the difference between the codes and noting whether the patient was symptomatic vs the physician was just screening and the patient was asymptomatic.”

However, effective October 1, 2020, the new guidelines state that code Z11.59, Encounter for screening for other viral diseases should be replaced with code Z20.828, Contact with and (suspected) exposure to other viral communicable diseases when coding COVID-19. According the guidelines, during the COVID-19 pandemic, a screening code is generally not appropriate. Also use code Z20.828 also for preoperative screening.


Sequence code U07.1, COVID-19, first when it meets the definition of principal diagnosis followed by appropriate codes for associated manifestations as well as comorbidities.

“What happened was people didn’t read the guidelines thoroughly,” says Laurie Johnson, MS, RHIA, FAHIMA, an AHIMA-approved ICD-10-CM/PCS trainer at Revenue Cycle Solutions. “The guidelines say this will be a first-listed code when it meets the definition of principal diagnosis. And it’s that last little tagline that people miss when they immediately code COVID-19 first.

“But what happens when my patient comes in and they have sepsis and they have COVID? The sepsis is sequenced first. We need to use our critical thinking skills and remember the rules.”

In the case of obstetrics patients, codes from Chapter 15 take precedence.

When the principal diagnosis of an inpatient or office encounter is because of COVID-19 for a patient during pregnancy, childbirth, or the puerperium, the encounter should be assigned code O98.5-, Other viral diseases complicating pregnancy, childbirth, and the puerperium. Code U07.1 is sequenced next, followed by the appropriate codes for associated manifestations.

If the reason for the admission or encounter is unrelated to COVID-19 but the patient tests positive for the virus, the new guidelines state that the reason for the encounter is sequenced first, followed by O98.5-, U07.1, as well as the codes for the associated COVID-19 manifestations.

FY2021 guidelines include a new section (h) in Chapter 16: Certain Conditions Originating in the Perinatal Period specifically for coding COVID-19 in newborns. When coding the birth episode, use code Z38, Live born infants according to place of birth and type of delivery, as the principal diagnosis.

If a newborn tests positive for COVID-19 and the specific type of transmission is absent or unknown, code U07.1 and associated manifestation codes. For newborns that test positive and the provider documents the infection was contracted in utero or during the birth process, code P35.8, Other congenital virus diseases, and U07.1, COVID-19.

For other respiratory illnesses confirmed as due to COVID-19 in individuals who are not obstetric or newborn patients, U07.1 should be coded first, followed by the manifestation.

“Many coders are not coding the associated manifestations,” McCollum says. “They are just coding COVID and that’s it. They are not really getting down to the manifestations. I understand that some are included but I think that this is a great source of confusion.”

If a patient develops pneumonia as a result of the virus, assign codes U07.1, COVID-19, and J12.89, Other viral pneumonia.

For acute bronchitis due to COVID-19, assign codes U07.1 and J20.8, Acute bronchitis due to other specified organisms. Bronchitis not otherwise specified (NOS) in the record should be coded U07.1, followed by J40, Bronchitis, not specified as acute or chronic.

A lower respiratory infection (NOS) or an acute respiratory infection (NOS) documented as relating to COVID-19 is coded U07.1 and J98.8, Other specified respiratory disorders. Assign codes U07.1 and J80 for patients diagnosed with acute respiratory distress syndrome (ARDS) due to COVID-19.

Because of the many respiratory complications caused by COVID-19, Trombley advises coders to be aware of the difference between coding acute respiratory failure and ARDS.

“The coding of acute respiratory failure when the patient also has ARDS is something that has been confusing to coders,” she says. “There is an Excludes 1 note and they should be coding the ARDS instead of the acute respiratory failure based on that coding guideline. I don’t think that coders clinically understand that ARDS is a type of acute respiratory failure which is why we code only the ARDS.

The other confusing part about that is finding the present on admission [POA] status,” Trombley continues. “For example, the patient comes in in acute respiratory failure, so that was POA. Let’s say the ARDS develops five days later. We have [learned] that ARDS would be POA even though it developed five days later. Because it is the extension of the acute respiratory failure, the POA status is yes.”

When COVID-19 is also present, Trombley says, “Regarding sequencing guidelines, when COVID-19 and acute respiratory failure or ARDS are both POA, the guidelines tell us that if COVID-19 meets the definition of principal diagnosis, code U07.1 should be sequenced first followed by the codes for the manifestations.”

Personal History of COVID-19 and Follow-Up Visits

For a time, there had been questions of whether or not to code COVID-19 in patient history.

“What I’m seeing from my facilities is they are coding COVID-19 from the patient history,” McCollum says. “I’ve seen it coded from the patient history because they are coming back and testing negative.”

And now, the new guidelines reflect that, stating, “For patients with a history of COVID-19, assign code Z86.19, Personal history of other infectious and parasitic diseases.”

For follow-up evaluations of individuals who previously had COVID-19 and are now testing negative for the virus, code Z09, Encounter for follow-up examination after completed treatment for conditions other than malignant neoplasm, and Z86.19.

Reporting for Patient Assessment, Swabbing, Testing, Counseling

The AMA released a CPT coding flow chart to aid in the reporting of COVID-19 testing based on where the patient is assessed, where the swab is collected, and where the test is performed.

If the patient is assessed in the office, use CPT evaluation/management (E/M) codes 99201–99205 (new patient) or 99212–99215 (established patients).

For E/M telehealth, use 99201–99205 for new patients following the established typical time in the code descriptor, with the exception of code 99205 with a typical time of 45 minutes as opposed to 60 minutes. For established patients using E/M telehealth, use codes 99212–99215 following the established typical time in the code descriptor.

If the patient is assessed via telephone, use codes 99441–99443 based on the time length of the assessment. If the patient does a virtual check-in or has an online visit and is a new or established patient, use codes 99421–99423 based on the time spent.

In situations where the qualified health care professional reviews recorded video and/or images for an established Medicare patient, use HCPCS code G2010. For virtual check-ins featuring a five- to 10-minute medical discussion for an established patient, code G2012.

Because they are captured in the E/M code, swab collections taken during an in-person visit require no additional code.

“If they get swabbed and the test is run [in the doctor’s office], the swab is included in the E/M service and so they can’t bill separately for that,” McCollum says.

Code 99000, handling and/or conveyance of specimen for transfer from the office to a laboratory, may also be coded.

“If it is collected in the office and sent to a lab, then you can add CPT code 99000 for that to be billed. I don’t know that in the physician’s offices they are understanding all the ins and outs of what they should be coding,” McCollum says.

If the patient is directed to a testing site established by the office or group practice, code 99211. Code 99001, Handling and/or conveyance of specimen for transfer from the patient in other than an office to a laboratory (distance may be indicated) is another coding possibility.

Recently, CMS and CDC announced that reimbursement will be made available for counseling patients at the time of testing about the importance of self-isolating and other CDC recommendations to slow the spread of the virus. Existing E/M codes will be utilized by CMS for counseling regardless of testing location.

Microbiology Coding

The AMA expedited the release of several new CPT codes, revised another as well as a guideline, and added three proprietary laboratory analyses codes and five parenthetical notes for the coding, testing, and tracking of COVID-19. These codes and updates cover polymerase chain reaction laboratory testing as well as serologic laboratory testing.

CPT code 87635, Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), amplified probe technique is used to report and track testing services related to COVID-19 and aids in the reporting of testing and reimbursement.

Although other coronavirus testing codes already exist in CPT, 87635 differs from those in that it is specifically for detecting COVID-19 and any pan-coronavirus types or subtypes. It can be reported from multiple manufacturers, nonproprietary.

The CDC has published interim guidelines for the collecting, handling, and testing of patients suspected of having COVID-19 in which it recommends both nasopharyngeal and oropharyngeal swabs for initial diagnostic testing. To report laboratory testing on multiple separate specimens for the same virus on the same day from the same patient, assign code 87635 and a second unit of code 87635 appended with Modifier 59 (distinct procedural service) to indicate the additional testing as a separate service.

87426, a new child code under parent code 87301, reads (including parent code wording): Infectious agent antigen detection by immunoassay technique, (eg, enzyme immunoassay [EIA], enzyme-linked immunosorbent assay [ELISA], immunochemiluminometric assay [IMCA]) qualitative or semiquantitative, multiple-step method; severe acute respiratory syndrome coronavirus (eg, SARS-CoV, SARS-CoV-2 [COVID-19]).

For Medicare patients, CMS has created two new HCPCS codes for coronavirus testing and two new HCPCS codes for specimen collection. HCPCS code U0001 is used specifically for CDC testing laboratories to test patients for COVID-19 and to track new cases of the virus. HCPCS code U0002 is for use with non-CDC laboratory tests for COVID-19.

HCPCS code G2023 is for specimen collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), any specimen source. Code G2024 is for 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 April, CMS waived cost sharing for COVID-19 testing and reintroduced the CS modifier. Originally used for the 2010 Gulf of Mexico oil spill, the CS modifier has been appended to COVID-19 testing and other related testing services. When appended, providers will receive full reimbursement from Medicare and patients will not bear any cost sharing for the testing/services.

“If a patient comes in and is suspected of having COVID—for example, they have respiratory symptoms—then coders are going to need to add modifier CS to the office visit or [emergency department] visit in which they order the test for COVID,” says Betsy Nicoletti, MS, CPC, a coding consultant. “That will allow that visit to be paid without cost sharing. There shouldn’t be any patient due amount from either Medicare or the insurance company.”

Experts say private payers are generally following CMS guidelines for CS modifiers but should be queried directly for their guidelines. According to an AMA fact sheet, CPT and HCPCS codes for COVID-19 testing should never be reported together; the code should be determined by the third-party payer.

Immunology Coding

Because of the urgent need to report and track COVID-19 antibody testing, several changes were made to the CPT code set in the Immunology subsection of the Pathology and Laboratory section.

Code 86318 was revised to include the plural “antibodies” in addition to “antibody” in the description and now acts as a parent code to the new code, 86328, which reads, “Immunoassay for infectious agent antibody(ies), qualitative or semiquantitative, single step method (eg, reagent strip).”

New code 86328, which is a child code to 86318, deals specifically with COVID-19 as a single-step method. Parenthetical notes direct coders to use code 86769 for antibody testing through a multistep method. 86769, which was created to report an antibody test for COVID-19 using a multistep method, is a child code under parent code 86710, Antibody; influenza virus.

Guidelines for codes 86602–86804 have been updated to include new codes 86328 and 86769 and a parenthetical note has been added to direct coders from 86635, Antibody; Coccidioides to COVID-19 codes 86328 and 86769.

Moving Forward

“I’m a big proponent of writing facility guidelines,” Johnson says. “You don’t want to rewrite the official coding guidelines, but this is where facilities think about what kind of data they need to run their facilities.”

Johnson also sees other logistical issues moving forward. “The World Health Organization has stopped updating ICD-10 and have developed ICD-11,” she notes. “They weren’t adding new codes to ICD-10, but when this became a pandemic, they had to create a code for it.”

The fluctuating guidelines for coding COVID-19 has played havoc with physician practices, Nicoletti says. “The most difficult thing for practices is that [the guidelines] have changed so much,” she says. “Medicare has come out with two major rules and there’s no consistency from insurance to insurance about whether you need a modifier [and] which place of service to use.”

To keep abreast of the rapid changes, coders are advised to reference their facility guidelines (where available), follow AMA and CDC updates, and refer to AHIMA, AAPC, and other organizations. In addition, a hefty dose of critical thinking is recommended.

“In trying to educate people, it’s like a moving target,” Johnson says. “It’s not only diagnosis—it’s telehealth, CPT development, HCPCS codes. It’s bombardment in trying to keep track.”

— Monique Griffin is a sports, marketing, and content writer who recently earned her CPC-A.


Centers for Disease Control and Prevention. ICD-10-CM official coding and reporting guidelines — April 1, 2020 through September 30, 2020. https://www.cdc.gov/nchs/data/icd/COVID-19-guidelines-final.pdf

COVID-19 coding and guidance. American Medical Association website. https://www.ama-assn.org/practice-management/cpt/covid-19-coding-and-guidance. Updated June 25, 2020.

Remer EE. We now have a code for COVID-19; here’s how to use it correctly. ICD10monitor website. https://www.icd10monitor.com/we-now-have-a-code-for-covid-19-here-s-how-to-use-it-correctly. Updated June 11, 2020.

Centers for Disease Control and Prevention. ICD-10-CM tabular list of diseases and injuries — April 1, 2020 addenda. https://www.cdc.gov/nchs/data/icd/ICD-10-CM-April-1-2020-addenda.pdf

Centers for Medicare & Medicaid Services. COVID-19 emergency declaration blanket waivers for health care providers. https://www.cms.gov/files/document/summary-covid-19-emergency-declaration-waivers.pdf. Published July 28, 2020.

CMS interim final rule 2 COVID-19 response: telehealth. Association of Community Cancer Centers website. https://www.accc-cancer.org/acccbuzz/blog-post-template/accc-buzz/2020/05/08/cms-interim-final-rule-2-covid-19-response-telehealth. Published May 8, 2020.

American Medical Association. CPT reporting for COVID-19 testing. https://www.ama-assn.org/system/files/2020-05/cpt-reporting-covid-19-testing.pdf. Updated May 6, 2020.

Centers for Medicare & Medicaid Services. FAQs about Families First Coronavirus Response Act and Coronavirus Aid, Relief, And Economic Security Act implementation part 42. https://www.cms.gov/files/document/FFCRA-Part-42-FAQs.pdf. Published April 11, 2020.

AHIMA and AHA FAQ: ICD-10-CM/PCS Coding for COVID-19. Journal of AHIMA website. https://journal.ahima.org/ahima-and-aha-faq-on-icd-10-cm-coding-for-covid-19/. Updated July 30, 2020.

Centers for Disease Control and Prevention. ICD-10-CM official coding guidelines – supplement — coding encounters related to COVID-19 coronavirus outbreak — effective: February 20, 2020. https://www.cdc.gov/nchs/data/icd/ICD-10-CM-Official-Coding-Gudance-Interim-Advice-coronavirus-feb-20-2020.pdf

American Medical Association. CPT Assistant Special Edition: June Update. https://www.ama-assn.org/system/files/2020-06/cpt-assistant-guide-coronavirus-june-2020.pdf


What We Didn’t Know We Would Be Coding With COVID-19

When the World Health Organization gave the worldwide pandemic a name—severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), COVID-19—much of the focus was on the disease’s respiratory complications.

“When they came up with the codes for COVID-19, under the index, it was all these respiratory issues, so it shows they had no idea all these other diseases can be part of this,” says Tammy Trombley, RHIT, CDIP, CCDS, compliance manager at GHR RevCycle. “Now physicians know to look for a bacterial pneumonia on top of COVID pneumonia. They know to look for those deep vein thrombosis and pulmonary embolisms because they’ve discovered it has a coagulopathy type of effect. Patients could get anemia, low white blood cells, platelets are lower. It’s also circulatory and could be quite extensive.”

Deep vein thrombosis and pulmonary embolisms are not the only clot hazards being attributed to COVID-19.

“We are seeing a lot of strokes that are occurring in younger patients. I recently reviewed the patient record of a 9-year-old, positive for COVID, who had a stroke,” says Meredith McCollum, MBA, RHIA, CCS, an ICD-10-CM/PCS trainer and director of coding compliance at GHR RevCycle. “They’re saying COVID is causing blood clots which are then being thrown to the brain. We are seeing clots in the brain, the lungs, even in the legs.”

McCollum says a study published in The Lancet (www.thelancet.com/journals/lanpsy/article/PIIS2215-0366(20)30287-X/fulltext) found neurological and neuropsychiatric complications can also result from COVID-19. And younger patients, originally not characterized as at-risk, are developing multisystem inflammatory syndrome in children (MIS-C).

“MIS-C is an individual less than 21 years old, presenting with fever, lab evidence of inflammation, and evidence of severe illness requiring hospitalization with multisystem organ involvement and no other plausible diagnosis and positive for current or recent COVID infections or exposure to COVID within the four weeks prior to the onset of symptoms. There are currently no coding guidelines on coding MIS-C,” McCollum says.

The severity of infection has some COVID-19 patients needing extracorporeal membrane oxygenation (ECMO) and/or hemodialysis. And although many coders will have seen and coded both of these, COVID-19 patients are needing these services for much longer duration.

When coding ECMO, Trombley points out that “coders have to know if it is central or peripheral, arterial or venous. They need to look for VA (venous-arterial) or VV (venous-venous) in the documentation. Sometimes we may see a conversion from VV to VA if the patient develops cardiopulmonary failure or cardiogenic shock.

“We have to code for central ECMO, which is an open chest procedure. We have to code for veno-arterial ECMO, which is when there are problems with both the heart and lungs. Lastly, we have to code ECMO for when the problems are only in the lungs.

“Another COVID-related procedure that I think could be challenging is hemodialysis coding. Most of your end-stage renal disease patients that are not COVID-19 usually have their hemodialysis done in under six hours. Therefore, most coders are probably used to choosing that code,” Trombley adds. “But there’s different hemodialysis procedure coding depending on the hours per day. COVID-19 patients may be on hemodialysis for 16 to 20 hours a day. When coding severely ill COVID-19 cases, this is where we need to pay close attention to the type of hemodialysis given to capture the correct procedure code.”

Complicating matters further, patients who had COVID-19 have begun seeking care for other diseases. In all likelihood, it’s going to require a lot of time, research, tracking, and data before the health care community can assemble the puzzle pieces to determine COVID-19’s long-lasting effects on all of the body’s systems.

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