It is critical that the CDISs compose their queries to get codable verbiage in response.

In my most recent consulting project, I read many cases and queries regarding pneumonia related to COVID-19, and our Talk Ten Tuesdays listeners have been sending me cases soliciting my opinion as to how to code them.

There are two basic problems with this condition: first, clinically, providers are not sure whether the current pneumonia is from an active case of COVID-19; and second, the providers don’t know how to document it such that the coder can derive the appropriate code.

Let me give you a few examples of the clinical indicators, as presented by the clinical documentation integrity specialists (CDISs) in their queries:

Case 1: Patient with a recent episode of COVID-19 treated with remdesivir and steroids, presents with shortness of breath and fatigue two weeks later. SARS-CoV-2 antibody test negative, PCR negative.

New patchy ground glass infiltrates.

Pulmonary documented “relapsing COVID-19 pneumonia.” Discharge summary states “recently treated for COVID-19 pneumonia.”

Case 2: Admitted with pneumonia (community versus hospital-acquired – Gram negative versus MRSA versus COVID-related). Had been in hospital for seven days, two weeks prior, for COVID-19 pneumonia. CXR with developing bilateral infiltrates.

Pulmonary consult: possible bacterial pneumonia, history of COVID-19 pneumonia, possible sepsis.

DC summary: Pneumonia due to recent COVID-19 infection.

Case 3: Patient admitted with agonal breathing, hypotensive, tachycardic, hypoxic with RLL pneumonia. PCR positive on admission.

COVID-19 infection about a month ago. Attending documented, “the positive test today could be a viral remnant. Also, reportedly the patient has been vaccinated.”

Patient expired within a day. Death summary noted: “death is probably related to sepsis and respiratory failure, probably secondary to pneumonia or COVID-19.”

You can find more examples posed in the Coding Clinic FAQs.

Many COVID-19 infections run their course, and the manifestations resolve promptly. The literature seems to suggest that in some cases, however, there is incomplete eradication of virus from the tissues, and the pathogen burrows deep in clusters of alveoli, the air-filled sacs in the lungs. An abnormal immune response mediated by SARS-CoV-2 may actually spread the infection throughout the lungs. Bronchoscopy sampling may detect the virus, but it may not be replication-competent. If there is no infectivity, is it still considered an active infection, U07.1? Furthermore, patients with severe COVID-19 pneumonia can have tissue damage and fibrosis induced by the virus, resulting in an organizing pneumonia, even after the virus is no longer present.

The length of stay for patients with severe COVID-19 infection can be prolonged, often two weeks or more. If the patient waited before presenting for medical care, their discharge date could be almost a month after onset of symptoms. It is conceivable, even likely, that by the time of discharge, their PCR test could be negative. That would not negate the original etiology of the pneumonia. If the patient were admitted for COVID-19 pneumonia, their principal diagnosis would be U07.1, COVID-19 with J12.82, Pneumonia due to coronavirus disease 2019 as a secondary condition, even if the patient no longer tests positive for SARS-CoV-2 upon discharge.

However, it becomes particularly dicey when the patient has an index admission for COVID-19, is treated and released, and returns after deterioration. A Centers for Disease Control and Prevention (CDC) study found that one in 11 patients hospitalized for COVID-19 were readmitted to the same hospital within two months (March-August 2020). Is the pneumonia still a manifestation of the original COVID-19 infection, or has another clinical process intervened?

ICD-10-CM incorporated the new code, J12.82, Pneumonia due to coronavirus disease 2019, in October 2020. There is a “code first” instruction for U07.1, COVID-19. This means that if the provider is diagnosing the patient with COVID-19 pneumonia, the patient is to be coded with underlying COVID-19 at the same time.

We are getting a code for “post-COVID-19 condition” on Oct. 1, 2021, U09.9, straight from the World Health Organization’s (WHO’s) version of ICD-10. The ICD-10-CM instruction will be to code first the specific condition that resulted from COVID-19. ICD-10-CM is pretty clear that sequelae do not occur during acute episodes of illness. Additionally, WHO’s instructional note cautions that “this code is not to be used in cases that still are presenting COVID-19.” My interpretation is that J12.82 will not be used with U09.9. This leaves us with the question of what to do with patients who have a delayed pneumonia presentation after completed treatment for acute COVID-19 infection. This is the condition that causes providers to use variable and often conflicting terminology like “relapsing,” “recurrent,” “recent,” and “post-COVID-19.”

If the patient has a secondary bacterial infection and is not believed to have COVID-19 presently, they should have the appropriate code assigned for a different form of pneumonia. If it is documented as “probable gram-negative pneumonia,” J15.6, Pneumonia due to other gram-negative bacteria, would be used. Other bacterial pneumonias would have their corresponding specific codes if an organism was identified, and J15.9, Unspecified bacterial pneumonia, would be the correct way to capture “secondary bacterial pneumonia.” If a viral pneumonia is diagnosed, the code would be J12.9, Viral pneumonia, unspecified. The code that identifies the component of a prior COVID-19 infection would be Z86.16, Personal history of COVID-19.

The situation that proves problematic is the post-acute COVID-19 patient. A categorization schema I found out of the United Kingdom breaks down the three phases seen in this viral scourge best (COVID-19 rapid guideline: managing the long-term effects of COVID-19):

  • Acute COVID-19 (signs and symptoms of COVID-19 for up to four weeks);
  • Ongoing symptomatic COVID-19 (signs and symptoms from four weeks to 12 weeks); and
  • Post-COVID-19 syndrome (signs and symptoms that develop during or after an infection consistent with COVID-19, continue for more than 12 weeks, and are not explained by an alternative diagnosis).

I really like the “ongoing symptomatic COVID-19” description. It explains that the symptoms are persisting longer than typical acute COVID-19, but it establishes that the practitioner still believes there is current COVID-19 infection. This gives the coder permission to pick up U07.1, in my opinion.

Organizing pneumonia (OP) is the entity formerly known as bronchiolitis obliterans with organizing pneumonia, or BOOP. OP is a process of pulmonary tissue repair that can occur secondary to a lung injury caused by an issue such as an infection, toxin, or radiation; can be associated with other pulmonary diseases, such as vasculitis, lung cancer, or interstitial pneumonitis; or can be idiopathic, referred to as cryptogenic. OP is characterized by lung inflammation and scarring with obstruction of small airways and destruction of alveoli. It seems to be occurring with some frequency, post-COVID-19.

The American Hospital Association/American Health Information Management Association (AHA/AHIMA) FAQs, Question 53, address this patient:

“The provider’s final diagnostic statement lists, ‘Post-COVID-19 organizing pneumonia,’ and the advice is to assign J84.89, Other specified interstitial pulmonary diseases, followed by code B94.8, Sequelae of other specified infectious and parasitic diseases. It is likely that in the future, U09.9 will supplant B94.8, because that code will identify the infectious disease sequela as a post-COVID-19 condition.”

When the documentation is confusing, a query is indicated. It is critical that the CDIS compose their queries to dispel the confusion and get codable verbiage in response. I never condone leading, but we need to give the providers choices that can help them define the current circumstances. Some of this may require education to give them the words they need; e.g., they may not be familiar with the entity of OP. What we don’t want is for the response to the query to set up a clinical validation issue (or, worse yet, to not resolve the question in a codable format).

Let me give you some verbiage that is specific and codable. I recommend you use the same order each time: e.g., current, ongoing symptomatic (which is coded as current); or sequela of previous infection, historical infection. Also, be sure to organize the choices the same way each time, preventing the provider having to search for the choice that applies for today’s patient. The parenthetical codes would not appear in the query – they are included in this article for the CDIS’s and the coder’s reference. I am also including some verbiage that is not specifically for pneumonia:

  • Manifestation of acute COVID-19 infection (U07.1);
  • Current acute COVID-19 pneumonia; COVID-19 pneumonia; pneumonia from COVID-19 (U07.1 + J12.82);
  • Manifestation of ongoing symptomatic COVID-19 infection (U07.1);
  • Manifestation of pneumonia due to ongoing symptomatic COVID-19 infection (U07.1 + J12.82);
  • Manifestation of pneumonia due to persistent COVID-19 infection (U07.1 + J12.82);
  • Pneumonia due to prolonged manifestation of COVID-19 infection (U07.1 + J12.82);
  • Sequela of previous, resolved COVID-19 infection (B94.8…U09.9, as of October);
  • Condition unrelated to previous history of COVID-19 (Z86.16);
  • Superimposed secondary pneumonia on COVID-19 pneumonia (J18.9 (or other specified PNA) + U07.1 + J12.82);
  • Secondary bacterial pneumonia following previous COVID-19 infection (J18.9 (or other specified PNA) + Z86.16);
  • Organizing pneumonia due to previous COVID-19 (J84.89 + B94.8…U09.9 as of October); and
  • Organizing pneumonia as a post-COVID-19 condition (J84.89 + B94.8…U09.9 as of October).

My opinion is that the linkage of the words “due to,” “secondary to,” “from,” or “as a result of” indicate a sequela, whereas “following,” “after,” or “subsequent to” would indicate personal history. If it is unclear, you need to obtain clarity.

I would not offer an uncertain qualifier in a query, such as “presumed” or “likely.” We can’t code uncertain COVID-19 as definitive. Case 3 set up this issue:

Patient expired within a day. Death summary noted: death is probably related to sepsis and respiratory failure, probably secondary to pneumonia or COVID-19.

A query would be needed to resolve the uncertainty, because “probably COVID-19 pneumonia” must be coded as J18.9, Pneumonia, unspecified organism.

I would check the radiology report; if it notes “viral” or “organizing” or some other descriptor that has a specific ICD-10-CM code, it can be compliantly included in the choices.

Beware of adding in the element of present-on-admission status. If you have too many questions in a single query, your provider may miss one. Don’t give them excessive permutations. Give them the words they need, but don’t put words in their mouths (or on their computers).

Let’s take Case 1 as an example:

Patient with a recent episode of COVID-19 treated with remdesivir and steroids, presents with shortness of breath and fatigue two weeks later. SARS-CoV-2 antibody negative, PCR negative.

New patchy ground glass infiltrates.

Pulmonary documented “relapsing COVID-19 pneumonia.” Discharge summary states “recently treated for COVID-19 pneumonia.”

My query would look something like:

Please clarify the status of current pneumonia and COVID-19:

  • Pneumonia believed to be a manifestation of current COVID-19 infection
  • Pneumonia believed to be a manifestation of an ongoing symptomatic COVID-19 infection
  • Organizing pneumonia believed to be a sequela of a previous COVID-19 infection that has resolved
  • Pneumonia unrelated to personal history of COVID-19 (please specify type of pneumonia, if possible)
  • Secondary pneumonia following previous COVID-19 pneumonia (please specify type of pneumonia, if possible)
  • Other ______________________________________________________

If unraveling the mystery of COVID-19 status seems daunting, you may need to do a verbal query. Help the provider come to an educated decision. If you would like a downloadable CDI tip on this topic, go to my website,, and navigate to Free Pointers for a CDI tip.

Better yet, let’s all get vaccinated, eradicate this ghastly virus, and not have to query anyone about COVID-19 ever again!

Programming Note: Listen to Dr. Erica Remer when she co-hosts Talk Ten Tuesdays with Chuck Buck, Tuesdays at 10 a.m. Eastern.

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