Encephalopathy is common in critically ill patients with COVID-19. According to a recent report, a study of 817 older patients (median age 78 years) evaluated in the emergency department diagnosed with COVID-19 infection, encephalopathy was present in 28 percent of the patients.1 It is essential to review the emergency department (ED) note in the charts of these patients to check for clinical evidence for the present on admission (POA) indicator. Diagnoses must be documented and clinically supported to meet the Universal Hospital Discharge Data Set (UHDDS) definition of a secondary diagnosis. Looking for the underlying condition causing the encephalopathy is beneficial because it can help in the identification of the principal diagnosis.

Here is one example: Say encephalopathy due to COVID-19 is documented by the clinician, and the coder captures ICD-10-CM code G93.40, Encephalopathy, unspecified. CDI professionals need to look for a specific type of encephalopathy, such as metabolic (G93.41), toxic (G92), toxic-metabolic (G92), septic encephalopathy (G93.41), hepatic encephalopathy (K72.90), hypertensive encephalopathy (I67.4), hypoxic encephalopathy (G93.1), or hypoxic ischemic encephalopathy (P91.60). If encephalopathy is attributed to a specific condition, for example, “Encephalopathy due to COVID-19,” but a specific type of encephalopathy is not documented, the CDI professional should be assigning code G93.49, Other encephalopathy.

Another possible scenario is that of a male patient admitted with a chief complaint (CC) of altered mental status. The final impression listed on the discharge summary was: “Hyponatremia, encephalopathy, moderate protein-calorie malnutrition, dehydration, vitamin B12 deficiency.”

The patient was COVID-19 positive. Based on the coding guidelines, the coder assigned U07.1 as a principal diagnosis (Pox) followed by another diagnosis: G93.40, Encephalopathy, unspecified; E44.0, Moderate protein-calorie malnutrition; E86.0, Dehydration; and E53.8, Deficiency of other specified B group vitamins. The facility assigned the Medicare severity diagnosis related group (MS-DRG) 178 with a relative weight (RW) or 1.2059 ALOS=5 GLOS=4.

After reviewing the chart, the clinical documentation integrity (CDI) professional decided to submit a query request asking for the specific encephalopathy type. The attending physician responded to the query request as “Metabolic encephalopathy.” After the discharge summary was amended by the physician and the new diagnosis was documented, the new code (G93.41) was captured by the coder. The new DRG assigned by the facility was (MS-DRG) 177 with a relative weight of 1.8453 ALOS=6.8 GLOS=5.4.

Combing the chart for incomplete, imprecise, illegible, conflicting, or absent documentation of diagnoses, procedures, and treatments, as well as supporting clinical indicators, is the core responsibility of the CDI professional. Furthermore, it is essential to cultivate a medical record that stands alone as an accurate story of a patient’s encounter and provides a full picture of the patient’s illness and record of treatment. Many CDI programs began with the goal of DRG optimization. Today, CDI has evolved—it takes a holistic view of all aspects of patient comorbidities. Having a strong denials management team is critical for facilities. If providers do not leverage proper resources to generate strong appeals, the third-party payers will uphold their decisions to remove and change diagnosis or procedure codes.

A question that can come up in situations like this is whether it’s required for a patient to return to their mental status baseline before a CDI specialist can query the provider for a diagnosis of encephalopathy. A couple of things need to be addressed before we can fully answer this question. First, what is the patient’s normal baseline? Older age, vision impairment, history of Parkinson’s disease or stroke, and prior psychoactive medication use are some of the risk factors associated with the diagnosis of encephalopathy.

For example, one recent study2 showed that of 12,601 hospitalized COVID-19 patients, 1,092 (or 8.7 percent) developed acute encephalopathy. Hospitalized COVID-19 patients with acute encephalopathy are more likely to need critical care, intubation, and have higher 30-day mortality even after matching for age and comorbidities as surrogates for the severity of infection, according to the study.

In my reviews of records, I’ve often seen physicians write “Encephalopathy due to COVID-19.” I would highly suggest mentioning the type of encephalopathy because it can turn a CC (encephalopathy) into an MCC (toxic-metabolic encephalopathy). On the other hand, if the physician notes the specific type of encephalopathy (metabolic encephalopathy due to COVID-19), the CDI professional will be assigning G93.41 (MCC).

The study referenced above3 notes that “A spectrum of neuroimaging abnormalities have been described in patients with COVID-19-related encephalopathy; some but not all of these findings indicate a specific, alternative diagnosis for the patient’s mental state, such as stroke, encephalitis, posterior reversible encephalopathy (PRES), and others.” As such, CDI specialists should consider capturing appropriate chronic conditions that are relevant to this admission. Furthermore, looking for radiology reports is important because it can lead to significant findings, such as whether the findings are diagnosed and documented in the record. And it can help determine whether the report is copy and pasted or corroborated by the provider’s documentation.

Encephalopathy may be the primary symptom of COVID-19 and its etiology is often multifactorial. When COVID-19 meets the definition of principal or first-listed diagnosis, code U07.1, COVID-19, should be sequenced first and 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.

  1. Elkind, Mitchell SV, Brett L. Cucchiara, and Igor J. Koralnik.Coronavirus disease 2019 (COVID-19): Neurologic complications and management of neurologic conditions,” UpToDate. January 2021.
  2. Shah, Vishank Arun et al. “Acute encephalopathy is associated with worse outcomes in COVID-19 patients.” Brain, Behavior & Immunity – Health. October 2020.
  3. Elkind, Mitchell SV, Brett Cucchiara, and Igor J. Koralnik.Coronavirus disease 2019 (COVID-19): Neurologic complications and management of neurologic conditions,”

Association of Clinical Documentation Integrity Specialist. “How to Conduct a Medical Record Review.” October 2018.

American Hospital Association. Frequently Asked Questions Regarding ICD-10-CM/PCS Coding for COVID-19.


Alba Kuqi ( is an ACDIS Leadership Council member, PHIMA member, American Urological Association member, and an AHIMA Foundation Research Network Volunteer.