Updated on: March 11, 2021

Integrating COVID-19 into Coding and Clinical Documentation Integrity

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Original story posted on: March 8, 2021

There are certain key elements of consideration during CDI review of COVID-19 patients. 

Understanding how to clinically validate sepsis and differentiate between sepsis and septicemia is not easy, and requires a lot of time and effort. Sepsis is an overwhelming non-homeostatic response of the immune system to infection causing organ dysfunction. On the other hand, septicemia is an infection with pathogenic organisms (bacteria, virus, etc.) in the blood. Whether or not sepsis or U07.1 is assigned as the principal diagnosis depends on the circumstances of admission and whether sepsis meets the definition of the principal diagnosis (AHA, 2020). Clinical documentation integrity (CDI) professionals need to check if sepsis meets the definition of the principal diagnosis. The code for viral sepsis (A41.89) should be assigned as principal diagnosis, followed by other codes, such as U07.1 and J12.89, as secondary diagnoses.



CDI professionals need to look for signs and symptoms of sepsis present on admission (POA). Furthermore, they need to query for clarification of sepsis POA, if clinically supported. Ensuring an entire clinical picture of a septic patient, and that “sepsis” is a theme throughout the body of the record, is beneficial because it can lower the risk of a denial. When unclear, query the physician if sepsis is an appropriate diagnosis. A clinical validity query may be necessary if the provider confirms a sepsis diagnosis, but clinical evidence is lacking in the documentation. Surgical cases with a secondary diagnosis of sepsis may qualify for PSI-13 Postoperative Sepsis Rate. To ensure accurate reporting in this area, look for clinical indicators and/or documentation of:

  • Sepsis POA or as principal diagnosis.
  • Whether the principal diagnosis or secondary diagnosis present on the admission for infection is incomplete. Additionally, cases assigned to MDC-14 or DRG 999 will be excluded from reporting.

Grasping how cytokine storm relates to sepsis is important, because it helps capture an accurate clinical picture in patients with COVID-19. COVID-19 is a new and poorly understood disease, so much of our current understanding of organ dysfunction in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is extrapolated from other disorders with similar clinical features. Several studies have reported elevated serum concentrations of inflammatory cytokines, including interleukin (IL)-6, in severe COVID-19 (The Lancet, 2020). Cytokine release syndrome (CRS) with secondary haemophagocytic lymphohistiocytosis (sHLH) is a type of cytokine storm/hyperinflammatory syndrome characterized by a fulminant and fatal hypercytokinaemia with multi-organ failure. Pathogenesis involves defective granule-mediated cytotoxicity and uncontrolled T-cell activation, leading to an exaggerated inflammatory response.

Capturing all comorbid conditions is very important in patients with COVID-19, because it helps capture these patients' highest acuity levels and arrive at the correct reimbursement for facilities. The most common diagnoses associated with COVID-19 infections are as follows:

  • Pneumonia
  • Acute respiratory failure
  • Acute respiratory distress syndrome (ARDS)
  • Acute exacerbation of chronic obstructive pulmonary disease (COPD)
  • Viral sepsis with organ dysfunction, ranging from encephalopathy to acute kidney injury, and shock
  • Leukopenia
  • Procedures for Intubation for mechanical ventilation
  • Cardiac injury to infarction (often non-ST elevation myocardial infarction [NSTEMI])

It is important to note the fact that “COVID-19 test results will be an important clinical indicator to ensure appropriate documentation exists for payment purposes, since sepsis is one of the most frequently denied (diagnoses)” (ACDIS, 2020). If you lose the source of infection with sepsis, the diagnosis of sepsis is at an even higher risk for denial. CDI professionals need to look for the cause of infection, such as a complication of a device, implant, or graft. When due to a device, implant, or graft, infection is reported as a complication and always sequenced as the principal diagnosis, with sepsis listed as a secondary diagnosis. The diagnosis of sepsis should be based on the physician’s clinical judgment and a full clinical picture of the patient, not on any one set of criteria. Furthermore, procalcitonin could be negative, since it is widely sensitive to bacteria and not viruses.

The third consensus definitions for sepsis and septic shock (Sepsis-3) require organ dysfunction to be present, making the term “severe sepsis” redundant. The potential risk factors of older age, high Sequential Organ Failure Assessment (SOFA) score, and d-dimer greater than 1 μg/mL could help clinicians identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future (Zhou et al., 2020). COVID-19 is classified into four categories, based on the severity of symptoms: mild, moderate, severe, and critical. Eighty percent of COVID-19-positive patients have mild features without radiologic features. Moderate patients present with fever, respiratory symptoms, and radiologic features. Severe patients meet one of three criteria:

    1. Dyspnea, respiratory rate (RR) > 30 breaths/min;
    2. Oxygen saturation < 93 percent in ambient air; or
    3. PaO2/FiO2 < 300 mmHg and/or lung infiltrates > 50 percent of lung fields within 24-48 hrs.

Critical patients also meet one of three criteria:

    1. Respiratory failure;
    2. Septic shock; or
    3. Multiple organ failure.

According to the World Health Organization (WHO, 2018), “most estimates of fatality ratios have been based on cases detected through surveillance and calculated using crude methods, giving rise to widely variable estimates of CFR by country – from less than 0.1 percent to over 25 percent.”

PCR (polymerase chain reaction) methods can generate false-positive or false-negative results, which cause challenges for isolating patients and determining hospitalization days. PCR seems to have a sensitivity somewhere to the order of about 75 percent. A single negative PCR doesn’t exclude COVID-19, especially if obtained from a nasopharyngeal source or collected relatively early in the disease course. If the PCR is negative and suspicion for COVID-19 remains, then continued isolation of the patient and resampling several days later is recommended. Two negative tests 24 hours apart are required to take the patient out of isolation precaution.

Patients with the principal or secondary diagnosis of sepsis, severe sepsis, or septic shock are included in the Severe Sepsis and Septic Shock: Management Bundle measures. Hospitals are required to identify patients with severe sepsis and septic shock early, and implement a set of evidenced-based measures within three and six hours to meet sepsis bundle requirements satisfactorily. CDI professionals need to look for comfort care or palliative care documentation, and COVID-19 as reporting of these conditions will exclude patients from this measure. Moreover, CDI professionals should be querying the providers if documentation is unclear and clinical evidence supports it. Data elements reported for this measure are consistent with the Surviving Sepsis Campaign treatment guidelines.

Surviving Sepsis Campaign Hour-1 Bundle of Care Elements:

  • Measure lactate level.
  • Obtain blood cultures before administering antibiotics.
  • Administer broad-spectrum antibiotics.
  • Begin rapid administration of 30mL/kg crystalloid for hypotension or lactate level ≥ 4 ​mmol/L.
  • Apply vasopressors if hypotensive during or after fluid resuscitation to maintain MAP ≥ 65 mm Hg (SSC, 2020)
Alba Kuqi, MD, RHIA, CDIP, CCS, CSMC, CICA, CRCR, CCDS , CCM

Alba Kuqi, MD, RHIA, CDIP, CCS, CSMC, CICA, CRCR, CCDS , CCM has extensive healthcare experience in revenue cycle operations, revenue integrity, HIM operations, compliance, quality control, clinical documentation programs, managed care, utilization review, denial management, public health, clinical research, CDI/audit experience, and provider education. Areas of focus include clinical documentation improvement, compliance, revenue integrity, relationship management, and coordination of services, among other healthcare disciplines. 

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