FY 2027 MEDESUN®
Home›Chapter 1 Certain Infectious and Parasitic Diseases
Section I.C.1 · A00-B99, U07.1, U09.9 · FY 2027

Chapter 1 — Certain Infectious and Parasitic Diseases

HIV, sepsis, MRSA, Zika and COVID-19 — the chapter that holds three exceptions to the inpatient uncertain-diagnosis rule, and the sepsis sequencing every auditor checks.

Dr. Santosh Kumar Guptha, CCS, CPC, COC, CIC, CRC, CPMA, CDIP, CPCO — AHIMA-Approved ICD-10-CM/PCS Trainer, MEDESUN® Medical Coding Academy Guidelines effective October 1, 2026 – September 30, 2027

Chapter 1 carries three “code only confirmed cases” exceptions to the inpatient uncertain-diagnosis rule — HIV, Zika virus and COVID-19 — plus the sepsis sequencing rules, the MRSA rules, and the organism and resistance codes used by every other chapter. Confirmation never requires a positive test: the provider's diagnostic statement is what confirms the diagnosis.

GuidelineCovers
I.C.1.aHIV infections — code only confirmed cases, selection and sequencing
I.C.1.bInfectious agents as the cause of diseases classified to other chapters (B95, B96, B97)
I.C.1.cInfections resistant to antibiotics (Z16)
I.C.1.dSepsis, severe sepsis and septic shock
I.C.1.eMethicillin resistant Staphylococcus aureus (MRSA) conditions
I.C.1.fZika virus infections
I.C.1.gCoronavirus infections — COVID-19

Which three infections must be confirmed before you code them?#

HIV (B20), Zika virus disease (A92.5) and COVID-19 (U07.1). All three are explicit exceptions to Section II.H, the inpatient rule that uncertain diagnoses are coded as if established. For these three, “suspected”, “possible” or “probable” is never enough — but the provider's diagnostic statement is, with no test result required.

InfectionConfirmed codeWhat counts as confirmationIf suspected / possible / probable
HIV diseaseB20The provider's diagnostic statement that the patient is HIV positive or has an HIV-related illness. Positive serology or culture is not required.Code the signs and symptoms, or Z21 if positive status only. R75 for inconclusive HIV serology.
Zika virus diseaseA92.5The provider's diagnostic statement that the condition is confirmed. The type of test performed need not be documented. Assigned regardless of the stated mode of transmission.NEVER Do not assign A92.5. Code the reason for the encounter — fever, rash, joint pain — or Z20.821 contact with and (suspected) exposure to Zika virus.
COVID-19U07.1The provider's documentation that the individual has COVID-19. A positive test result is not required.NEVER Do not assign U07.1 for suspected, possible, probable or inconclusive COVID-19. Code the presenting signs and symptoms, adding Z20.822 if there is actual or suspected exposure.

HIV — how are the codes selected and sequenced?#

CircumstanceCodesSequencing
AIDS or HIV disease documented; or the patient is treated for any HIV-related illness; or described as having a condition resulting from HIV positive statusB20B20 is assigned
Admitted for an HIV-related conditionB20 + all reported HIV-related conditions1B202codes for every reported HIV-related condition
EXCEPTION Admitted for hemolytic-uremic syndrome associated with HIV diseaseD59.31 + B201D59.31 Infection-associated hemolytic-uremic syndrome2B20
HIV disease patient admitted for an unrelated condition, such as a traumatic injurythe unrelated condition + B201the unrelated condition — for example the nature of injury code2B20 as a secondary diagnosis3other documented conditions
Newly diagnosed versus previously diagnosed—Irrelevant to the sequencing decision
“HIV positive”, “HIV test positive” or similar, with no symptoms and no HIV-related illness documentedZ21Z21 Asymptomatic HIV infection status
Inconclusive HIV serology documentedR75R75
Prior diagnosis of an HIV-related illnessB20ALWAYS B20 on every subsequent admission or encounter. NEVER Such a patient is never assigned R75 or Z21
Symptomatic HIV disease or HIV-related illness in pregnancy, childbirth or the puerperiumO98.7- + B20 + HIV-related illness(es)1O98.7-2B203codes for any HIV-related illness
Asymptomatic HIV infection status, or HIV positive, in pregnancy, childbirth or the puerperiumO98.7- + Z211O98.7-2Z21
HIV testing and managementCode
Screening — patient without signs or symptoms tested for HIVZ11.4, plus codes for any associated high-risk behaviour
Patient with signs or symptoms of HIV presents for testingCode the signs and symptoms. Z71.7 may be added if counselling was provided. NEVER Z11.4 is not assigned when HIV signs or symptoms are present
Follow-up for HIV test results, result negativeZ71.7 HIV counselling
Follow-up for HIV test results, result positiveApply the HIV selection and sequencing guidelines above
HIV disease, HIV-related illness or AIDS managed on antiretroviral medicationB20, optionally with Z79.899 for long-term antiretroviral use
HIV positive status managed on antiretroviral medication, with no documentation of HIV disease, HIV-related illness or AIDSZ21, optionally with Z79.899
Pre-exposure prophylaxis (PrEP) administrationZ29.81 Encounter for HIV pre-exposure prophylaxis, plus any risk factors for HIV

Organism codes and antibiotic resistance#

CategoryUse
B95Streptococcus, Staphylococcus and Enterococcus as the cause of diseases classified to other chapters
B96Other bacterial agents as the cause of diseases classified to other chapters
B97Viral agents as the cause of diseases classified to other chapters
Z16Resistance to antimicrobial drugs — assigned following the infection code, and only if the infection code does not itself identify drug resistance

Certain infections are classified outside Chapter 1 and no organism is identified in the infection code. In those cases an additional code from Chapter 1 is necessary to identify the organism, and an instructional note at the infection code will say so.

Sepsis, severe sepsis and septic shock#

Sepsis is one code — the underlying systemic infection. Severe sepsis is a minimum of two codes — the systemic infection plus R65.2-, and a code for each acute organ dysfunction. A code from R65.2 can never be the principal diagnosis.

Provider documents sepsis1. Code the underlyingsystemic infectionA41.9 if organism unspecifiedIs acute organ dysfunctiondocumented and linked?NO → stopdo not add a code from R65.22. Add R65.2- Severe sepsisR65.21 when septic shock is present3. Add a code for each acuteorgan dysfunctionNot clearly linked?query the providerR65.2- and R65.21 can NEVER be the principal diagnosis — the systemic infection is sequenced first
Section I.C.1.d — the sepsis decision path
SituationCodes and sequence
Sepsis, organism or type of infection not further specifiedA41.9 Sepsis, unspecified organism
Sepsis with no documented severe sepsis or acute organ dysfunctionNEVER Do not assign a code from R65.2
Severe sepsis1the underlying systemic infection (A41.9 if the organism is not documented)2R65.2- Severe sepsis3a code for each associated acute organ dysfunction
Septic shock1the systemic infection2R65.21 Severe sepsis with septic shock, or T81.12 Postprocedural septic shock3codes for other acute organ dysfunctions
Severe sepsis present on admission and meeting the definition of principal diagnosis1the underlying systemic infection as principal diagnosis2R65.2-
Severe sepsis develops after admissionThe underlying systemic infection and R65.2- are both secondary diagnoses
Sepsis or severe sepsis and a localised infection, both the reason for admission1the underlying systemic infection2the localised infection as a secondary diagnosis3R65.2- if severe sepsis is present
Admitted with a localised infection; sepsis develops after admission1the localised infection2the sepsis / severe sepsis codes
Sepsis or severe sepsis associated with a noninfectious condition (burn, serious injury) meeting the definition of principal diagnosis1the noninfectious condition2the resulting infection3R65.2- and organ dysfunction codes if severe sepsis is present
EXCEPTION Hemolytic-uremic syndrome associated with sepsis is the reason for admission1D59.31 as principal diagnosis2the underlying systemic infection and any other conditions, including severe sepsis, as secondary diagnoses

Sepsis due to a postprocedural infection

Source of the infectionSequence
Postprocedural wound (surgical site) infection1T81.41–T81.43, T81.49, or O86.00–O86.03 / O86.09 identifying the site of the infection, if known2T81.44 sepsis following a procedure, or O86.04 sepsis following an obstetrical procedure3an additional code to identify the infectious agent4R65.2- plus acute organ dysfunction codes if severe sepsis is present
Infection following infusion, transfusion, therapeutic injection or immunisation1T80.2-, or T88.0- infection following immunisation2the code for the specific infection3R65.2- plus acute organ dysfunction codes if severe sepsis is present
Postprocedural infection resulting in postprocedural septic shock1the codes above for sepsis due to a postprocedural infection2T81.12- Postprocedural septic shock — NEVER do not assign R65.213codes for any acute organ dysfunction

MRSA and MSSA#

SituationCodeDo not also assign
Infection due to MRSA where a combination code exists — for example sepsis or pneumoniaThe combination code: A41.02 Sepsis due to MRSA, J15.212 Pneumonia due to MRSANEVER B95.62, and NEVER a code from Z16.11 resistance to penicillins — the combination code already carries both the infection and the organism
Current infection due to MRSA with no combination code — wound infection, stitch abscess, urinary tract infectionThe code for the condition plus B95.62NEVER A code from Z16.11
MRSA colonisation — documented as “MRSA screen positive” or “MRSA nasal swab positive”Z22.322 Carrier or suspected carrier of MRSA—
MSSA colonisationZ22.321 Carrier or suspected carrier of MSSA—
Both MRSA colonisation and MRSA infection during the same admissionZ22.322 and the code for the MRSA infection — both may be assigned—

COVID-19 — the full sequencing table#

COVID-19 — code U07.1 only for a provider-confirmed diagnosis (no test result required)Respiratory manifestationU07.1 first, then J12.82,J20.8, J22, J80, J96.0-Non-respiratory manifestationU07.1 first, then themanifestation codeSuspected, possible,probable, inconclusivedo NOT assign U07.1 —code the signs and symptomsExposure onlyZ20.822Screening: Z11.52Sequela / condition after a previous infectionthe specific condition + U09.9Personal history, no residualZ86.16 — with Z09 for a follow-up visitMIS with COVID-19U07.1 first, then M35.81Sequencing exceptions: obstetrics (O98.5- first), sepsis, and transplant complications outrank U07.1. Asymptomatic positive test with no provider diagnosis → query the provider.
Section I.C.1.g.1 — COVID-19 coding at a glance
CircumstanceCodesSequence
COVID-19 meets the definition of principal diagnosisU07.1 + manifestationsU07.1 first, then codes for associated manifestations — except where another guideline requires certain codes first, such as obstetrics, sepsis or transplant complications
Pneumonia confirmed as due to COVID-19U07.1 + J12.821U07.12J12.82
Acute bronchitis confirmed as due to COVID-19U07.1 + J20.81U07.12J20.8
Bronchitis NOS due to COVID-19U07.1 + J401U07.12J40
Lower respiratory infection NOS, or acute respiratory infection NOS, due to COVID-19U07.1 + J221U07.12J22
Respiratory infection NOS due to COVID-19U07.1 + J98.81U07.12J98.8
ARDS due to COVID-19U07.1 + J801U07.12J80
Acute respiratory failure due to COVID-19U07.1 + J96.0-1U07.12J96.0-
Non-respiratory manifestation, for example viral enteritisU07.1 + the manifestation1U07.12the manifestation code
Asymptomatic, actual or suspected exposureZ20.822—
Symptomatic, exposure actual or suspected, infection ruled out or results inconclusive or unknownZ20.822—
Screening, including preoperative testingZ11.52—
Signs and symptoms without a definitive diagnosisR05.1 or R05.9 cough, R06.02 shortness of breath, R50.9 fever — plus Z20.822 if there was exposure—
Personal history of COVID-19Z86.16—
Follow-up after resolution, no residual, test negativeZ09 + Z86.161Z092Z86.16
Antibody testing not to confirm current infection and not a follow-up testZ01.84—
Multisystem inflammatory syndrome with COVID-19U07.1 + M35.811U07.12M35.813codes for associated complications of MIS
MIS in a patient with a history of COVID-19M35.81 + U09.91M35.812U09.9
MIS after known or suspected exposure only, no current infection and no historyM35.81 + Z20.8221M35.812Z20.822
Post COVID-19 condition — sequela, or symptoms or conditions developing after a previous infectionthe specific condition(s) + U09.9NEVER U09.9 is not assigned for manifestations of an active infection
Condition from a previous infection and a new active infectionU09.9 with U07.1, plus codes for the previous condition(s) and for the new manifestation(s)—
Unvaccinated for COVID-19Z28.310—
Partially vaccinated for COVID-19 per the CDC schedule in place at the timeZ28.311—

Practice questions#

Q1A patient with a documented history of Pneumocystis pneumonia two years ago, an HIV-related illness, is admitted this month for a displaced fracture of the left femur after a fall. How is the HIV reported?

  1. AZ21, because the patient is currently asymptomatic
  2. BB20 as a secondary diagnosis, with the fracture as principal diagnosis
  3. CB20 as the principal diagnosis, because chapter 1 codes take priority
  4. DR75, because the HIV was not evaluated at this admission
Show answer & rationale

Correct answer: B. B20 as a secondary diagnosis, with the fracture as principal diagnosis

Rationale. Two rules combine. Guideline I.C.1.a.2.g states that once an HIV-related illness has developed, B20 should always be assigned on every subsequent admission or encounter, and such a patient may never be assigned Z21 or R75. Guideline I.C.1.a.2.c states that where an HIV disease patient is admitted for an unrelated condition such as a traumatic injury, the unrelated condition is the principal diagnosis and B20 is reported as a secondary diagnosis.

Q2A patient is admitted with Escherichia coli sepsis. The record documents acute kidney injury, and the nephrology note attributes the acute kidney injury to the patient's long-standing obstructive uropathy rather than to the sepsis. What is assigned?

  1. AThe sepsis code, R65.20, and the acute kidney injury code
  2. BThe sepsis code and the acute kidney injury code, with no code from R65.2
  3. CR65.20 as principal diagnosis
  4. DThe sepsis code, R65.11, and the acute kidney injury code
Show answer & rationale

Correct answer: B. The sepsis code and the acute kidney injury code, with no code from R65.2

Rationale. Guideline I.C.1.d.1.a.iv states that if a patient has sepsis and an acute organ dysfunction but the documentation indicates the acute organ dysfunction is related to a medical condition other than the sepsis, a code from R65.2 is not assigned. The acute organ dysfunction must be associated with the sepsis to justify the severe sepsis code. Where the documentation is unclear on that link, the provider is queried — here it is not unclear, it is documented as unrelated.

Q3A patient develops sepsis following a postoperative surgical site infection of the abdominal wall. Severe sepsis with acute respiratory failure is documented. What is the correct sequence?

  1. AA41.9, T81.44, R65.20, J96.00
  2. BT81.41- or the applicable site code, T81.44, the infectious agent, R65.2-, J96.0-
  3. CR65.21, T81.44, J96.00
  4. DT81.44, A41.9, R65.20
Show answer & rationale

Correct answer: B. T81.41- or the applicable site code, T81.44, the infectious agent, R65.2-, J96.0-

Rationale. Guideline I.C.1.d.5.b directs that for sepsis following a postprocedural wound infection, a code from T81.41 to T81.43, or T81.49, identifying the site of the infection is sequenced first if known, followed by T81.44 sepsis following a procedure, with an additional code to identify the infectious agent. If the patient has severe sepsis, R65.2- is also assigned with codes for any acute organ dysfunction.

Q4An admission screening nasal swab is positive for MRSA. The patient has no documented MRSA infection. What is reported?

  1. AB95.62
  2. BZ22.322
  3. CZ16.11
  4. DNothing — colonisation is not coded
Show answer & rationale

Correct answer: B. Z22.322

Rationale. Guideline I.C.1.e.1.c states that Z22.322, carrier or suspected carrier of MRSA, is assigned for patients documented as having MRSA colonisation, and names “MRSA screen positive” and “MRSA nasal swab positive” as the typical documentation. Colonisation is not necessarily indicative of a disease process unless the provider documents it as such, so no infection or resistance code is assigned.

Q5A pregnant patient in the second trimester is admitted because of COVID-19 pneumonia. What is sequenced first?

  1. AU07.1
  2. BJ12.82
  3. CO98.5-
  4. DZ20.822
Show answer & rationale

Correct answer: C. O98.5-

Rationale. Guideline I.C.1.g.1.b states that U07.1 is sequenced first when COVID-19 meets the definition of principal diagnosis except where another guideline requires certain codes to be sequenced first, naming obstetrics among them. Guideline I.C.15.s is that guideline: O98.5- is sequenced as the principal diagnosis, followed by U07.1 and the codes for associated manifestations. Chapter 15 codes always take sequencing priority.

Scenarios#

Scenario 1Severe sepsis present on admission, with two organ dysfunctions

A patient is admitted from the emergency department with Klebsiella pneumoniae sepsis arising from a urinary tract infection. The provider documents severe sepsis with acute kidney injury and acute encephalopathy, both attributed to the sepsis. Severe sepsis was present on admission.

Show coded answer & rationale
SeqCodeDescription
1A41.51Sepsis due to Escherichia coli — here, the applicable A41.5- code for Klebsiella: A41.50 / A41.59 as verified in the Tabular List, as principal diagnosis
2R65.20Severe sepsis without septic shock
3N17.9Acute kidney failure, unspecified
4G93.41Metabolic encephalopathy, or the encephalopathy code the record supports
5N39.0Urinary tract infection, site not specified — the localised infection, as a secondary diagnosis

Rationale. Guideline I.C.1.d.1.b requires a minimum of two codes for severe sepsis: the underlying systemic infection followed by a code from R65.2, with additional codes for each associated acute organ dysfunction. Guideline I.C.1.d.3 directs that where severe sepsis is present on admission and meets the definition of principal diagnosis, the underlying systemic infection is the principal diagnosis followed by R65.2-, which can never itself be principal. Guideline I.C.1.d.4 adds the localised infection as a secondary diagnosis. Verify the organism-specific sepsis code in the Tabular List rather than relying on the Index alone.

Guideline: Section I.C.1.d.1.b, I.C.1.d.3, I.C.1.d.4

Scenario 2Sepsis after a burn

A patient is admitted with a third-degree burn of the right forearm sustained three days earlier. The burn wound is infected and the provider documents sepsis due to Pseudomonas aeruginosa associated with the burn. The burn is the condition chiefly responsible for the admission. No organ dysfunction is documented.

Show coded answer & rationale
SeqCodeDescription
1T22.311-Burn of third degree of right forearm, with the appropriate 7th character — principal diagnosis
2A41.52Sepsis due to Pseudomonas
3T31.-Burn extent code, if used for burn-unit reporting
4X codeExternal cause code identifying the source, intent and place of the burn

Rationale. Guideline I.C.1.d.6 covers sepsis associated with a noninfectious process: where sepsis is documented as associated with a noninfectious condition such as a burn or serious injury, and that condition meets the definition of principal diagnosis, the noninfectious condition is sequenced first followed by the code for the resulting infection. No code from R65.2 is assigned because no severe sepsis or acute organ dysfunction is documented, and it is not necessary to assign R65.1 for these cases. Guideline I.C.19.d.4 requires an additional code for the infected burn site, and I.C.19.d.9 requires an external cause code with burns.

Guideline: Section I.C.1.d.6, I.C.19.d.4, I.C.19.d.9

Scenario 3A condition after COVID-19, and then COVID-19 again

A patient who had COVID-19 eight months ago has persistent post-COVID fatigue and dyspnoea documented by the provider as related to that infection. At this encounter the patient is diagnosed with a new, active COVID-19 infection with acute bronchitis.

Show coded answer & rationale
SeqCodeDescription
1U07.1COVID-19 — the new active infection
2J20.8Acute bronchitis due to other specified organisms — the manifestation of the current infection
3U09.9Post COVID-19 condition, unspecified
4R53.83 / R06.00Codes for the specific conditions related to the previous infection, as documented

Rationale. Guideline I.C.1.g.1.m states that U09.9 should not be assigned for manifestations of an active COVID-19 infection, but that if a patient has a condition associated with a previous infection and develops a new active infection, U09.9 may be assigned together with U07.1 to identify that the patient also has a condition associated with a previous infection — with codes for both the previous conditions and the current manifestations. Sequencing of U07.1 first follows I.C.1.g.1.b and I.C.1.g.1.c.ii for bronchitis.

Guideline: Section I.C.1.g.1.b, I.C.1.g.1.c.ii, I.C.1.g.1.m

Primary sources#