Coronavirus: Clinical and Coding Considerations

Zoonotic diseases can be caused by viruses that infect one species and evolve through genetic mutations allowing them to make the leap to other species, including humans, where they spread.  The Coronavirus is the latest example of a zoonotic disease spreading rapidly through a new host population lacking any immunity to fight back.

This is no new evolutionary phenomenon. The best-known historical case occurred about 20,000 years ago when bovine tuberculosis made the jump to humans when we first turned to agriculture as our food source.  HIV may have done the same in Africa, originating in other primates (simian immunodeficiency virus).

Coronaviruses are a large group of viruses that cause illness ranging from the common cold to more severe diseases. This particular coronavirus is officially called “severe acute respiratory syndrome coronavirus 2” (SARS-CoV-2) in contrast to the SARS-CoV-1 that emerged in 2002. The word “corona” means “like a crown.” Under the electron microscope, the spherical coronavirus is lined with small projections resembling a small crown.

The 2019 coronavirus disease (COVID-19) is the collective term for all respiratory infections caused by SARS-CoV-2. Initial symptoms are much like almost any significant respiratory infection such as fever and/or respiratory-like symptoms like cough, sneezing, shortness of breath and difficulty breathing. In more severe cases, infection can cause pneumonia, respiratory failure, acute kidney injury and even death especially among people over age 60 and/or those with significant chronic diseases. The disease appears to be less severe in children and people less than age 60.

When COVID-19 attacks it settles down in the body’s cells where it multiplies exponentially before causing symptomatic infection. This period between invasion and disease is called the “latent” (silent) period lasting 2-14 days during which the host is infectious to others.

The apparently healthy, unsuspecting host goes around as usual all the while shedding viruses that infect others. Just like the flu, transmission occurs via aerosol droplets from coughing and sneezing and also by contact with contaminated surfaces. Hand-to-hand and hand-to-surface are the primary mechanisms of contact transmission, hence the important of frequent hand washing and sanitary gels.

The availability of testing kits is currently limited so CDC has strict testing guidelines. The results usually take 2-3 days. Production of testing kits is beginning to accelerate.

Treatment is primarily supportive focusing on the complications. There are no known effective anti-viral drugs but some are being tested. Prevention is the best defense. The following are recommended by the CDC for everyone:

Surgical face masks will limit, but not eliminate, the chance of inhaling large infectious particles circulating near the face produced by patients who cough and sneeze, which is the primary way the virus is spread. A face mask should be worn by people who have COVID-19 or are symptomatic to protect others from infection. The CDC recommends that the N95 particulate filtering facepiece respirators be reserved for protecting healthcare workers in the riskiest situations. A vaccine is currently being developed but will take several months for production and testing. It could take a year or more to produce enough doses for every American.

The ICD-10 code for COVID-19 is B97.29 (Other coronavirus as the cause of diseases classified elsewhere). Only cases confirmed as COVID-19 are coded.  According to the new guidelines, do not assign code B97.29 if the provider documents “suspected,” “possible,” or “probable” COVID-19. Instead, assign codes explaining the reason or symptoms for the encounter (such as fever, cough, shortness of breath). The COVID-19 respiratory infections associated with SARS-CoV-2 and the corresponding codes are: For ARDS associated with COVID-19:

For pneumonia associated with COVID-19:

For acute bronchitis associated with COVID-19:

For acute or lower respiratory infections associated with COVID-19:

Other ICD-10 codes associated with COVID-19 include:

CDC plans to include a new code for COVID-19 (the disease) in the 2021 ICD-10-CM and will probably create a unique B97.2- code for SARS-CoV-2 itself as it did for SARS-CoV-1 coronavirus.

CDC maintains a Coronavirus home page to provide all the information and advice you need to know and do about the coronavirus epidemic.  It includes recommendations for infected persons, healthy people and in all social settings like the workplace, schools and colleges, public events, certain specific communities, travel, and “high-risk” populations. The situation is fluid and CDC recommendations will continue to evolve, so periodically monitor the site to keep up with any changes.


Official Coding Guidelines FY2020

Official Coding Guidelines FY2020

Who Owns Sepsis?

A recent “Opinion” article by three distinguished professors from Harvard and Washington University in St. Louis titled “Who Owns Sepsis?” was published in the January 2020 issue of the Annals of Internal Medicine addressing the limitations of the Sepsis-3 definition.  

Widespread skepticism in the general medical community outside the critical care specialty has been expressed about the Sepsis-3 definition of sepsis as “life-threatening organ dysfunction” due to infection.  These clinicians worry that the requirement for acute organ dysfunction will result in missed opportunities to identify “early” sepsis before acute organ dysfunction develops requiring ICU admission with its associated morbidity and mortality.

The authors forcefully and convincingly argue that the clinical concept of “early” sepsis preceding acute organ dysfunction is clinically valid and cannot be omitted from a sepsis definition.

While Sepsis-3 proposed a quick-SOFA (qSOFA) screening tool to prompt full SOFA scoring, it is not designed to identify “early” sepsis without organ dysfunction.  Shannon et al. published a study in the February 20, 2018 issue of the Annals of Internal Medicine showing that the SIRS criteria were more accurate than qSOFA in predicting organ dysfunction.

The authors also expressed concern about the risk of over-treatment from a single management protocol for patients that may present with a broad range for severity.  One size does not fit all even with acute organ dysfunction. A more balanced approach to sepsis diagnosis and management informed by the urgency and intensity of therapy needed is suggested.

They also point out that 50 of the 59 members of the Surviving Sepsis Campaign (SSC) panel, which adopted the Sepsis-3 criteria, are critical care specialists while 85% of sepsis cases are managed by non-intensivists. 

Since SSC has been the authoritative custodian for a unified international definition and management protocol for sepsis, the authors advocate the inclusion of more Emergency Physicians, Internal Medicine and Family Medicine specialists on the SSC panel.

Download the original article published on

Multi-drug Resistance

For the 2020 ICD-10-CM, new codes were created to capture antibiotic resistance in clinical settings. The intent is to identify antibiotic resistance in the U.S. for our health care database. There are multiple databases both public and private brought together by AHRQ under the Healthcare Cost and Utilization Project (HCUP). The National (Nationwide) Inpatient Sample (NIS) is the largest publicly available all-payer hospital inpatient care database in the United States. Researchers and policymakers use NIS data to identify, track, and analyze trends in health care utilization, access, charges, quality, and outcomes.  

Multidrug-resistant (MDR) infections are associated with increased mortality, length of stay, and hospital costs. MDR is defined as organisms with resistance to one or more antibiotics in three or more antibiotic/antimicrobial drug classes. To identify multidrug resistance, clinicians should have a working knowledge of the drug class of commonly used antibiotics and antimicrobials reported on culture sensitivity testing.

Methicillin-resistant Staphylococcus aureus (MRSA) accounts for up to 80% of bacterial MDR infections. Other commonly encountered MDR bacteria are vancomycin-resistant enterococci (VRE), Acinetobacter, Klebsiella, Pseudomonas, and coliforms, particularly E. coli and Clostridioides (formerly Clostridium) difficile.

MDR tuberculosis infection is increasingly common and particularly worrisome because many strains are resistant to all known antitubercular drugs. MDR Candida are also becoming problematic. Parasites and many viral pathogens are also becoming resistant to many antimicrobials.

High-risk MDR circumstances (Table 2) include immunosuppression from any cause, history of an MDR infection, known colonization by an MDR organism, and exposure to an MDR-infected person even at home. Structural lung disease, as in cystic fibrosis and bronchiectasis, is typically associated with Pseudomonas colonization and pneumonia, often with multi-drug resistance.

The three most common inpatient situations associated with multi-drug resistance are ventilator-associated pneumonia (VAP), catheter-related bloodstream infection (CRBSI), and catheter-associated urinary tract infection (CAUTI).

The new Category Z16 was created for the new drug resistance codes identifying the antibiotics to which the infectious organism is resistant (Table 3). The codes do not require the clinical MDR definition of resistance to 3 or more classes of antibiotics. In most cases, the codes specify an entire class of drugs keeping in mind there may be only a single drug in a class like vancomycin and clindamycin.

The provider must document the drug resistance in the record. If the provider documents resistance to multiple drug classes, a code is assigned for each of the drugs identified. If only “multi-drug resistance” is documented, code Z16.24 (multidrug resistance) is assigned.  Category Z16 codes are classified as CCs but not assigned to an HCC.

It’s the coder’s responsibility to assign a code for the correct drug class based on the antibiotics specified. For example, if the clinician documents resistance to gentamicin based on sensitivity testing, the coder must know that the aminoglycoside code (Z16.29) should be used. Table 1 should be helpful but coding software ought to lead the coder from a specific antibiotic to the correct drug-class code.

The type of infection is coded first, followed by a code for the organism—unless the infection code itself describes the organism (e.g. code J13, pneumococcal pneumonia)—and then the drug resistance code. In the case of MRSA, a drug resistance code is not assigned because the infection code identifies the antibiotic. In contrast, codes for infections caused by other drug-resistant organisms do not include the drug and require the additional Z16 code. For example, VRE sepsis is coded A41.81 (sepsis due to enterococcus) + Z16.21 (resistance to vancomycin).

Table 1. Antibiotic drug classes 

Source: CDC. Antimicrobial Use and Resistance (AUR) Module—Appendix B.

Table 2. Circumstances posing high risk of multi-drug resistance (MDR)

Derived from multiple sources. 

Table 3. Selected ICD-10-CM drug resistance codes

Drug Code
Multi-drug Z16.24
Penicillins Z16.11
Cephalosporins Z16.19
Quinolones Z16.23
Vancomycin Z16.21
Aminoglycosides Z16.29
Antifungal Z16.32
Antimycobacterial, multiple drugs Z16.342
Antiparasitic Z16.31
Antiviral Z16.33

Source: ICD-10-CM.

MCC-CC Listings for MS-DRGs FY2020

Complete MCC-CC Listings for MS-DRGs FY2020

FY2020 MCC-CC List


MS-DRG Tables 2008 through 2020



CMS-HCC Listing Version 24.0 with ICD-10 Codes

CMS-Version 24.0 list and HCCs sorted by ICD-10 codes and HCC.

Note that CMS has not updated the HCC listing with the FY2020 ICD-10 codes.

CMS-HCC V24.0 List and ICD-10 codes

Everything you need to know about P/F Ratio and how to calculate PaO2/FIO2

What is the P/F Ratio?

The P/F ratio is a powerful objective tool to identify acute hypoxemic respiratory failure when supplemental oxygen has already been administered and no room air ABG is available, or pulse oximetry readings are unreliable.

The diagnostic criteria for acute hypoxemic respiratory failure is:

The P/F ratio indicates what the PaO2 would be on room air (if patient was taken off oxygen): [table id=1 /]

A normal P/F Ratio is ≥ 400 and equivalent to a PaO2 ≥ 80 mmHg. 

The P/F ratio should not be used to diagnose acute on chronic respiratory failure since many patients with chronic respiratory failure already have a P/F ratio < 300 (PaO2 < 60) in their baseline stable state which is why they are treated with chronic supplemental home oxygen.

Note that PaO2 and pO2 are synonymous.

How to Calculate the P/F Ratio:  PaO2 / FIO2

“P” represents PaO2 (arterial pO2) from the ABG. “F” represents the FIO2 – the fraction (percent) of inspired oxygen that the patient is receiving expressed as a decimal (40% oxygen = FIO2 of 0.40).  P divided by F = P/F ratio.

PaO2 = 90 on 40% oxygen (FIO2 = 0.40):   90 / 0.40 = P/F ratio = 225.
A P/F ratio of 225 is equivalent to a pO2 of 45 mmHg, which is significantly < 60 mmHg on room air.


How to Calculate FIO2 from Liters

A nasal cannula provides oxygen at adjustable flow rates in liters of oxygen per minute (L/min or “LPM”).  The actual FIO2 (percent oxygen) delivered by nasal cannula is somewhat variable and less reliable than with a mask but can be estimated as shown in the Table below as the accepted clinical standard for the conversion. The FIO2 derived from nasal cannula flow rates can then be used to calculate the  P/F ratio. Note:  Assumes room air is 20% (0.20) and each L/min of oxygen = +4% (0.04).   [table id=2 /]

Example: A patient has a pO2 of 85mmHg on ABG while receiving 5 liter/minute of oxygen. 5 L/min = 40% oxygen  = FIO2 of 0.40, the P/F ratio = 85 divided by 0.40 = 212.5.

How to Calculate SpO2 to PaO2 (when no ABG available)

When the PaO2 is unknown because an ABG is not available, the SpO2 measured by pulse oximetry can be used to approximate the PaO2, as shown in the Table below.

*Note the SpO2/PaO2 conversion becomes unreliable when SpO2 is > 98%, but PaO2 of 110 mmHg for 97% may be used as a substitute avoiding an overestimation.

Conversion of SpO2 to PaO2

[table id=3 /] Note that the patient may be stable and asymptomatic while receiving 40% oxygen, but still has severe acute respiratory failure.  If oxygen were withdrawn leaving the patient on room air, the PaO2 would only be 40 mmHg (much less than 60 mmHg criteria on room air for acute respiratory failure).  Clinicians commonly lose sight of this fact.

Patient has a pulse oximetry SpO2 of 95% on 40% oxygen:  SpO2 95% is equal to PaO2 of 80mmHg.
P/F ratio = 80 divided by 0.40 = 200.

For more information about the P/F ratio, respiratory failure, and many other pertinent topics, check out our CDI Pocket Guide, the #1 best-selling resource for CDI.  

Copyright (c) 2019 Pinson & Tang LLC.

Acute Kidney Injury (AKI): Creatinine Baseline Explained

AKI Diagnostic Criteria: 1.5x Baseline

A CDI Pocket Guide customer recently sent us a question regarding the 1.5x diagnostic criteria for acute kidney injury, and we thought others may benefit:

The CDI Pocket Guide on page 62 includes one of the AKI diagnostic criteria as: “Increase in Creatinine > 1.5x baseline (historical or measured) which is known or presumed to have occurred within the prior 7 days.”

However, on page 63 the Guidelines for applying this AKI criterion states: The 1.5x diagnostic criteria “can be applied prospectively and retrospectively with broad interpretation of the baseline level which may be one from 6 months or even one year previously if there is no known CKD.”

How we can have a baseline up to one year old but the diagnostic criteria states within the prior 7 days?

Known vs. “Presumed” Baseline

A creatinine level from 6 months to as much as a year before may be used as a baseline to identify AKI at the time of admissionif the patient did not have preexisting CKD or another dramatic change in health since then.  If a patient is admitted for an acute illness and the creatinine is > 1.5x the past baseline level, it is “presumed” to have occurred within the prior 7 days, and AKI can be diagnosed.

For example, a previously healthy patient is admitted for nausea, vomiting, diarrhea and dehydration. His creatinine level was 2.0, and his creatinine level four months ago was 1.0. It is presumed that the creatinine increased to twice the previous level during this acute illness (within 7 days) confirming AKI.

In such circumstances the elevated admission creatinine would also be expected to return to or near the historical baseline further confirming it as acute. For example, if the prior baseline were 1.0 and the admission creatinine of 2.0 returned to 1.2 at discharge, the diagnosis of AKI is indisputable.

Should the elevated admission creatinine unexpectedly remain well above the prior baseline, AKI is not fully substantiated.  Further investigation is necessary to determine the cause. For example, an admission creatinine of 2.0 (with a prior baseline of 1.0) that remains elevated between 1.7−2.0 does not confirm AKI.

How to apply to CKD

Patients with CKD may also have AKI if the patient is admitted with a creatinine level that is 1.5x their baseline. For example, a patient with CKD and a stated baseline of 1.8 is admitted with a creatinine of 2.5 which decreases to 1.6 with IV fluids. The true baseline is now 1.6 and 2.5 is > 1.5x this level, confirming AKI with chronic CKD.

MCC-CC Listings – MS-DRG FY2019 Tables 6I & 6J

CMS MS-DRG Complete MCC-CC Listings for FY2019

MCC-CC List FY 2019