Integrating COVID-19 into Coding and Clinical Documentation Integrity

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)
Facebook
Twitter
LinkedIn

Alba Kuqi, MD, RHIA, CDIP, CCS, CSMC, CICA, CRCR, CCDS , CCM

Alba Kuqi, MD is a CDI manager who grew up in Albania, coming to the United States to pursue her career. She loves the coding and clinical documentation side of the industry and prides herself in her medical knowledge and CDI experience of over 8 years.

Related Stories

Leave a Reply

Please log in to your account to comment on this article.

Featured Webcasts

Inpatient Ulcers and Gangrene: Avoid FY 2027 ICD-10-CM Coding, Sequencing, and Documentation Errors

Avoid costly inpatient coding errors involving ulcers and gangrene. This practical FY 2027 ICD-10-CM webcast clarifies pressure injury staging, non-pressure ulcer severity, diagnosis sequencing, documentation requirements, and POA reporting. Through real-world cases, gain the confidence to make defensible coding decisions, reduce denials, strengthen compliance, and support accurate reimbursement.

November 4, 2026

One Chart, Five Truths: How CDI Prevents the Same Diagnosis from Becoming Five Different Outcomes

What happens when everyone reviews the same chart, but reaches a different conclusion? In this case-based clinical documentation integrity (CDI) webcast, Penny Jefferson examines how documentation involving clinical support, timing, causation, linkage, and terminology can produce very different outcomes for ICD-10 coding, reimbursement, quality, risk adjustment, medical necessity, denials, and compliance. Using cases involving postoperative respiratory failure, severe malnutrition, and encephalopathy, you’ll learn the practical CLEAR framework to help attendees learn to evaluate whether a diagnosis is codeable, consistent, specific, reportable, and ultimately defensible across the different teams and systems that rely on the medical record.

September 30, 2026

Mastering Spinal Fusion Coding for Inpatient Facilities: ICD-10-PCS Precision, Documentation, and MS-DRG Impact

Spinal fusion cases are among the most complex inpatient procedures to code, where even minor ICD-10-PCS errors can affect MS-DRG assignment, reimbursement, compliance, and audit outcomes. This practical webcast provides a step-by-step framework for interpreting operative reports, assigning accurate ICD-10-PCS codes, recognizing documentation gaps, and confidently coding complex fusion procedures. You’ll leave with practical tools that improve coding accuracy, reduce denials and audit risk, and strengthen documentation-driven reimbursement decisions.

July 29, 2026

AI, Audits, and the Future of the Revenue Cycle

Artificial intelligence is rapidly transforming healthcare revenue cycle operations, from coding and auditing to compliance and denials. Join industry leaders Pam Warren (MaineHealth) and Raemarie Jimenez (AAPC) for a live fireside chat exploring how AI is changing workflows, workforce roles, payer-provider dynamics, and compliance risk—and what organizations should be doing now to prepare.

Webcast Only Available On ICD10monitor Subscription – Subscribe Below

June 17, 2026

Trending News

Featured Webcasts

Radiation Oncology Fundamentals: Coding, Billing & Compliance for Hospital Outpatient & Professional Services

Join Michael Calahan, PA, MBA for this radiation oncology coding and compliance webcast as he explains the fundamentals of coding, billing, reporting, and documentation for hospital outpatient and professional services. Learn how the 2026 radiation therapy coding changes affect current practices, how to distinguish technical and professional services, and how to address bundling, units, frequency, modifiers, and documentation requirements. Michael will also help you identify radiation oncology coding and billing vulnerabilities that could lead to denials, overpayments, repayment demands, or federal audit exposure.

October 20, 2026

Preparing for 2027: Inpatient & Outpatient Policy Changes for Case Management and Utilization Review

The 2027 CMS policy changes will impact case management, utilization review, reimbursement, and patient status decision-making long before they officially take effect. Join nationally recognized physician advisor Dr. Ronald Hirsch as he explains the finalized and proposed inpatient and outpatient rule changes, expanding bundled payment initiatives, payment updates, and evolving payer expectations. Gain practical guidance to help your organization prepare early, strengthen compliance, reduce reimbursement risk, and confidently navigate the transition to 2027.

September 17, 2026

The Two-Midnight Rule: Strengthening Compliance Through the Fundamentals, 2026 Updates, & 2027 Proposed Changes.

The Two-Midnight Rule continues to be one of Medicare’s most closely monitored compliance areas and now the rules are changing again. Join compliance expert Michael Calahan for a practical review of the latest 2026 policy updates, the proposed 2027 OPPS changes affecting inpatient-only procedures, and the best practices hospitals need to reduce audit risk, strengthen admission decisions, and protect reimbursement. Leave with actionable strategies you can immediately apply to improve compliance and confidently prepare for increased federal and Medicare Advantage scrutiny.

August 11, 2026

Trending News

Prepare for the 2025 CMS IPPS Final Rule with ICD10monitor’s IPPSPalooza! Click HERE to learn more

Get 15% OFF on all educational webcasts at ICD10monitor with code JULYFOURTH24 until July 4, 2024—start learning today!

This Memorial Day, we honor those who gave all for our freedom. Take 20% off sitewide through May 29 with code MEMORIAL26 at checkout

CYBER WEEK IS HERE! Don’t miss your chance to get 20% off now until Dec. 1 with code CYBER25

CYBER WEEK IS HERE! Don’t miss your chance to get 20% off now until Dec. 2 with code CYBER24