Don’t Let the Codes Get You Sick! Navigating Covid-19, Flu & RSV Coding

Keisha Wilson CCS, CPC, CRC, CPB, CPMA, AAPC Approved Instructor

Has anyone else felt lately that something is going around in the air? And everyone is getting sick? I have a pretty good immune system, but in the last few weeks, I can’t get over whatever this is.  Interestingly enough, I received a text message from my local CVS pharmacy, stating they have noticed an uptake in the area with flu and encouraging many to get the vaccine.  Emergency departments, urgent care, primary care, and internal medicine doctors are packed with children and adults, coughing, sneezing, running noses, sore throats, headaches, night sweats, and fatigue.  Medical professionals are working overtime again. 

The symptoms of COVID-19, RSV (Respiratory Syncytial Virus), and the flu are so similar in their clinical presentation, particularly regarding respiratory symptoms, that some may think they have one but find out they have the other.  Let’s not forget the common cold as well.

Respiratory Symptoms

COVID-19, RSV, and the flu primarily affect the respiratory system, leading to cough, fever, congestion, and difficulty breathing. These common respiratory symptoms can overlap across different respiratory illnesses, making it challenging to differentiate based solely on symptoms.  COVID-19, RSV, and the flu are contagious respiratory viruses that can spread through respiratory droplets. People may assume they have one of these illnesses based on exposure to individuals with similar symptoms or in environments where viral transmission is likely, such as crowded indoor spaces or healthcare settings.

Some people may experience mild symptoms resembling a common cold, while others may develop more severe respiratory complications requiring medical attention. While diagnostic tests are available for COVID-19, RSV and the flu, access to testing and delays in receiving results can complicate the identification of the causative virus. Some symptoms, such as fever and cough, are nonspecific and may not conclusively differentiate between these respiratory illnesses without laboratory confirmation.

Coding for COVID-19, RSV (Respiratory Syncytial Virus), and the flu involves different diagnosis codes and coding guidelines due to their distinct nature, etiology, and documentation requirements:

COVID-19 Coding:

COVID-19, caused by the SARS-CoV-2 virus, has specific diagnosis codes in the International Classification of Diseases, Tenth Revision, and Clinical Modification (ICD-10-CM) coding system. Per ICD-10 CM guidelines, “code only a confirmed diagnosis of the 2019 novel coronavirus disease (COVID-19) as documented by the provider, or documentation of a positive COVID-19 test result.  For a confirmed diagnosis, assign code U07.1, COVID-19. This is an exception to the hospital inpatient guideline Section II, H. In this context, “confirmation” does not require documentation of a positive test result for COVID-19; the provider’s documentation that the individual has COVID-19 is sufficient.

If the provider documents “suspected,” “possible,” “probable,” or “inconclusive” COVID-19, do not assign code U07.1. Instead, code the signs and symptoms reported. See guideline I.C.1.g.1.g. When COVID-19 meets the definition of principal diagnosis, code U07.1, COVID-19, should be sequenced first, followed by the appropriate codes for associated manifestations, except when another guideline requires that certain codes be sequenced first, such as obstetrics, sepsis, or transplant complications.

Below are just some examples of COVID-19 diagnosis codes:

  • U07.1: COVID-19
  • U09.9: Post COVID-19 condition, unspecified
  • Z11.52: Encounter for screening for COVID-19.
  • Z20.822: Contact with and (suspected) exposure to COVID-19

Per ICD-10 Guidelines, additional codes may be required to specify the manifestations and severity of the illness, such as pneumonia, acute respiratory distress syndrome (ARDS), or complications affecting other organs. Documentation must support the diagnosis of COVID-19, including positive laboratory test results or a provider’s clinical diagnosis based on symptoms, exposure history, and epidemiological criteria.

RSV Coding:

Respiratory Syncytial Virus (RSV) is a common respiratory virus affecting infants and young children. Diagnosis codes for RSV include:

  • J12.1: Respiratory syncytial virus pneumonia
  • B97.4: Respiratory syncytial virus as the cause of diseases classified elsewhere

Like COVID-19, additional codes may specify complications or manifestations, such as bronchiolitis or pneumonia. Documentation should include evidence supporting the diagnosis of RSV, such as laboratory tests, clinical signs and symptoms, and patient history. RSV also has new vaccine codes for FY 2024; coders should review the CPT to ensure the correct code is reported.

Flu Coding:

Influenza, commonly known as the flu, has specific diagnosis codes in ICD-10-CM, including:

  • J09-J11: Influenza due to identified influenza virus
  • Codes may specify the type of influenza virus (e.g., influenza A, influenza B).

Similar to COVID-19 and RSV, additional codes may be used to describe complications, such as influenza pneumonia or acute respiratory failure. Documentation should include evidence of influenza infection, such as positive laboratory tests or clinical diagnosis based on symptoms and exposure history during flu season.

Per ICD-10 CM guidelines, for patients presenting with any signs/symptoms associated with COVID-19 (such as fever, etc.) but a definitive diagnosis has not been established, assign the appropriate code(s) for each of the presenting signs and symptoms such as:

R05.1: Acute cough, or R05.9, Cough, unspecified

R06.02: Shortness of breath

R50.9: Fever, unspecified

Due to these factors, healthcare providers must conduct thorough evaluations, including clinical assessments and diagnostic testing, to accurately diagnose and differentiate between RSV, COVID-19, and the flu. This helps ensure appropriate treatment and management strategies and helps mitigate the spread of contagious respiratory illnesses within communities. While COVID-19, RSV, and the flu are all respiratory illnesses, coding for each condition requires specific diagnosis codes and documentation to accurately reflect the patient’s diagnosis and ensure appropriate billing and reimbursement. Healthcare providers should adhere to coding guidelines and documentation requirements outlined in ICD-10-CM and any additional coding guidance issued by relevant authorities or organizations.


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