Clinical Commander

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id.covid19.core.v1

COVID-19 inpatient management

infectious_diseaseacutechronicadultacuteinpatient
Start encounter →Print handoutPRODUCTION

id.covid19.core.v1 covers adult COVID-19 management across the outpatient → ED → ward → ICU continuum, with post-acute long-COVID surveillance. Severity-tiered per WHO 2024 ordinal scale: mild (nirmatrelvir-ritonavir; EPIC-HR Hammond NEJM 2022; PANORAMIC molnupiravir alternative; PINETREE 3-day IV remdesivir alternative), moderate (remdesivir + dexamethasone; ACTT-1 Beigel NEJM 2020 + RECOVERY Horby NEJM 2021), severe (dexamethasone + tocilizumab/baricitinib + remdesivir + awake prone per RECOVERY-RS Perkins NEJM 2022; REMAP-CAP Gordon NEJM 2021 + COV-BARRIER Marconi Lancet RM 2021), critical (+ lung-protective ventilation ARDSnet Brower NEJM 2000 + prone ≥16 h/d PROSEVA Guérin NEJM 2013 + ECMO consideration EOLIA Combes NEJM 2018). VTE prophylaxis axis reflects REMAP-CAP/ACTIV-4a/ATTACC anticoagulation trials (NEJM 2021): therapeutic dose benefits non-critically ill with elevated D-dimer (PMID 34351721) but NOT critically ill (PMID 34351722). Status downgraded 2026-05-14 from INTEGRATED to AUTHORED to match operational reality: declared INTEGRATED requires manifest pointer to resolve, and the manifest path prisma/seed/manifests/id.covid19.core.v1.ts is not yet on disk; shard-5-obped-id contract forbids prisma/seed/ authoring. The dossier meets AUTHORED criteria fully (design brief, flow, required inputs, entry points, ≥1 workup). PRODUCTION/INTEGRATED blockers: manifest not yet created (out-of-shard-scope), RxCUI verification pending (npm run research:rxnav:validate), no end-to-end protocol test for COVID severity-escalation ladder, COVID-specific registry entries (calc.who_ordinal_scale, calc.pf_ratio, protocol.covid_rapid_desaturation, protocol.covid_cytokine_storm, workup.covid_pe_screen / covid_superinfection / covid_myocarditis / covid_aki) pending — currently repointed to existing-registry equivalents (workup.pe_full, workup.hap_vap, workup.aki; calc.news2 + calc.psi_port + calc.rox + calc.sofa for severity / HFNC failure / multi-organ; protocol.septic_shock for the cytokine-storm → shock continuum) and inline severity_triggers. Deepened 2026-05-14 (shard-5-obped-id depth-pass-1): added co-located _briefs/id.covid19.core.v1.md + _research-bundles/id.covid19.core.v1.md. Repointed design_brief to the new in-scope brief; repointed package to existing tier3 src/lib/tier3/problem-package/packages/coronavirus-disease-2019-covid-19 directory (which exists on disk; closes that broken pointer). Added outpatient setting playbook (oral antiviral initiation ≤5 d for high-risk per EPIC-HR/PANORAMIC/PINETREE — nirmatrelvir-ritonavir first-line + molnupiravir alternative when CYP3A interaction + IV remdesivir 3-d alternative when oral contraindicated; home pulse-oximetry teaching with return precautions for SpO2 <94% sustained / ≥4% exertional drop; rebound-on-paxlovid counseling per Anderson NEJM 2022 / Pandit JAMA 2022 — ~5-15% rebound, NO retreatment per NIH 2024; long-COVID screen at 4-6 wk per NICE NG188 / WHO 2021 post-COVID-19 condition — PHQ-9 + GAD-7 + Chalder/FACIT-fatigue + mMRC dyspnea + cognitive checklist + DePaul post-exertional malaise; vaccination reconciliation post-infection per current ACIP). Added severity triggers: rapid_desaturation_event (life-threatening, distinct from severe covid_rapid_desaturation by gradient — sustained SpO2 <92% OR ≥4% exertional drop), pe_risk_features_in_covid (severe — D-dimer rising above already-elevated COVID baseline + clinical features; CT-PA threshold elevated per Klok TR 2020), and covid_secondary_bacterial_pneumonia (severe — new fever after defervescence + procalcitonin rise + new infiltrate; routes to workup.hap_vap and id.sepsis.core.v1 if shock features develop). Appended outpatient/proning anchors at depth-pass-1. (2026-05-22 build campaign: promoted AUTHORED→INTEGRATED; live-verified all 13 PMIDs and removed 2 mis-attributed (36780967=Pickering-emulsion food science, 34433228=hepatology thioesterase) leaving 11 verified COVID-trial anchors; molnupiravir + awake-proning retained as named prose. RxCUIs corrected: dexamethasone 1311524→3264 (was aspartame), tocilizumab 1658168→612865, baricitinib 2267577→2047232 (was Enhertu), nirmatrelvir-ritonavir 2587902→2587899 (was molnupiravir), unfractionated heparin 8163→5224 (was phenylephrine); remdesivir 2284718 + enoxaparin 67108 RxNav-verified.) Phenotype matrix (severity × O2 × host × variant × prior immunity × complications — 5×5×4×variant×3×7 collapsed cells) is encoded indirectly via severity_triggers (covid_rapid_desaturation, covid_cytokine_storm, covid_ards, covid_pe_vte, covid_mis_a, rapid_desaturation_event, pe_risk_features_in_covid, covid_secondary_bacterial_pneumonia) and via setting_playbook drug logic. First-class TS field for phenotype matrix is schema-blocked — deferred to shard schema proposal cache (see co-located _briefs/id.covid19.core.v1.md). Bayesian linkage (NAAT LR+ ~100 / LR- ~0.05 per Cochrane Dinnes 2020 PMID 32845525; rapid antigen LR+ ~50-100 / LR- ~0.4-0.6 per Cochrane Dinnes 2021 PMID 33760236; typical CT GGO LR+ ~4-7 per RSNA Simpson Radiology 2020; lymphopenia <800/µL LR+ ~2-3 for severe; D-dimer for PE elevated COVID-baseline poorly performant at standard cutoff — use ≥3-5 µg/mL + clinical features per Klok TR 2020; CRP >75 + ferritin >1000 LR+ ~3-5 for cytokine-storm phenotype + ICU progression per REMAP-CAP; T_treat ≈ 30% post-test probability + high-risk-for-progression + ≤5 d onset → start oral antiviral; T_test → supportive care if low-risk + improving + no hypoxia; cross-dossier routing to id.sepsis.core.v1 for superinfection + shock, pulm.ards.core.v1 for ARDS ventilation, neph.aki.core.v1 for AKI, cardio.myocarditis when authored for myocarditis suspicion) is documented in the co-located _research-bundles/id.covid19.core.v1.md. ROS/DDx LR seed data audited by npm run audit:ros-ddx-coverage (cross-cutting; not touched by this shard). Spec-referenced COV-BARRIER PMID 34480854 deferred for PubMed verification — dossier carries 34480861 for Marconi Lancet RM 2021; both refer to the COV-BARRIER trial corpus / companion publications (see _research-bundles for deferred-verification entry). Prehospital recognition (home pulse-oximetry trend → ED referral via outpatient → ED transition) is rendered via the outpatient setting playbook + transitions[].admit; a first-class "prehospital" DossierSetting value is schema-blocked.

Entry points (4)

  • lab_abnormality
    SARS-CoV-2 PCR or antigen positive (WHO 2024 case definition)
    sars_cov2_positive
  • symptom
    Acute respiratory illness with COVID-19 risk factors (NIH COVID Treatment Guidelines 2024)
    covid_respiratory_illness
  • vital_abnormality
    New hypoxemia (SpO2 <94%) with confirmed/suspected SARS-CoV-2 (WHO 2024 ordinal scale ≥4)
    hypoxemia_with_covid
  • imaging
    Bilateral ground-glass opacities on CT consistent with COVID-19 pneumonia (RSNA 2020 typical pattern)
    bilateral_ggo_ct

Required inputs (19)

  • spo2required
    vital • used at CONTEXT
    WHO ordinal scale severity anchor; drives O2 escalation decisions (WHO 2024)
  • rrrequired
    vital • used at CONTEXT
    Tachypnea predicts deterioration; WHO ordinal scale component (WHO 2024)
  • temperaturerequired
    vital • used at CONTEXT
    Fever trajectory tracks disease phase and inflammatory burden (NIH COVID Treatment Guidelines 2024)
  • sbprequired
    vital • used at RED_FLAGS
    Hemodynamic instability signals cytokine storm / septic shock phenotype (NIH COVID Treatment Guidelines 2024)
  • hrrequired
    vital • used at CONTEXT
    Tachycardia + relative bradycardia pattern; VTE risk signal (NIH COVID Treatment Guidelines 2024)
  • sars_cov2_pcrrequired
    lab • used at INITIAL_WORKUP
    Confirmatory diagnostic; cycle threshold correlates with viral load (WHO 2024)
  • crprequired
    lab • used at INITIAL_WORKUP
    Inflammatory marker; CRP >75 mg/L predicts ICU need (NIH COVID Treatment Guidelines 2024)
  • d_dimerrequired
    lab • used at INITIAL_WORKUP
    Elevated D-dimer >1.0 µg/mL predicts VTE and mortality (NIH COVID Treatment Guidelines 2024)
  • ferritinrequired
    lab • used at INITIAL_WORKUP
    Hyperferritinemia >500 ng/mL signals cytokine storm / MAS phenotype (NIH COVID Treatment Guidelines 2024)
  • ldh
    lab • used at INITIAL_WORKUP
    LDH elevation correlates with disease severity and lung injury (NIH COVID Treatment Guidelines 2024)
  • lymphocyte_countrequired
    lab • used at INITIAL_WORKUP
    Lymphopenia <800/µL predicts severe disease (NIH COVID Treatment Guidelines 2024)
  • creatininerequired
    lab • used at INITIAL_WORKUP
    AKI staging (KDIGO 2026) + remdesivir renal dosing consideration (ACTT-1 Beigel NEJM 2020)
  • altrequired
    lab • used at MONITORING
    Hepatotoxicity monitoring for remdesivir (ACTT-1 Beigel NEJM 2020) + baricitinib (COV-BARRIER Marconi Lancet RM 2021)
  • il6
    lab • used at BRANCHING_WORKUP
    IL-6 >100 pg/mL supports tocilizumab decision (REMAP-CAP Gordon NEJM 2021; NIH COVID Treatment Guidelines 2024)
  • troponin
    lab • used at BRANCHING_WORKUP
    Myocardial injury screen; elevated troponin in ~20-30% of hospitalised COVID-19 (NIH COVID Treatment Guidelines 2024)
  • procalcitonin
    lab • used at BRANCHING_WORKUP
    Bacterial superinfection screen; low PCT argues against empiric antibiotics (NIH COVID Treatment Guidelines 2024)
  • vaccination_statusrequired
    history • used at CONTEXT
    Vaccination status modifies severity prediction and treatment candidacy (WHO 2024; NIH COVID Treatment Guidelines 2024)
  • symptom_onset_daterequired
    history • used at CONTEXT
    Days from symptom onset determines remdesivir eligibility (≤7d optimal; ACTT-1 Beigel NEJM 2020) and nirmatrelvir window (≤5d; EPIC-HR Hammond NEJM 2022)
  • immunocompromiserequired
    history • used at CONTEXT
    Immunocompromised patients at highest risk; extended antiviral courses considered (NIH COVID Treatment Guidelines 2024)

12-phase flow (12)

  1. 1FRAME
    Adult COVID-19 inpatient management per WHO 2024 ordinal scale; severity-tiered therapeutics from mild through critical
    advance: SARS-CoV-2 confirmed and admission criteria met (WHO 2024)
  2. 2ENTRY
    Confirm SARS-CoV-2 by PCR or rapid antigen; establish symptom onset date for antiviral eligibility (WHO 2024 case definition)
    inputs: sars_cov2_pcr
    advance: COVID-19 diagnosis confirmed (WHO 2024)
  3. 3CONTEXT
    Vaccination status, symptom duration, comorbidities (obesity, DM, CKD, immunocompromise), baseline O2 requirement, code status (NIH COVID Treatment Guidelines 2024)
    inputs: spo2, rr, temperature, hr, vaccination_status, symptom_onset_date, immunocompromise
    advance: severity tier and treatment eligibility established (WHO 2024 ordinal scale)
  4. 4RED_FLAGS
    Rapid desaturation (SpO2 <90% on room air), cytokine storm (ferritin >1000 + rising CRP + organ dysfunction), ARDS (PaO2/FiO2 <300), PE/VTE, MIS-A (NIH COVID Treatment Guidelines 2024)
    inputs: sbp, spo2
    actions: protocol.covid_rapid_desaturation
    advance: red flags actioned or excluded (NIH COVID Treatment Guidelines 2024)
  5. 5INITIAL_WORKUP
    CBC with differential (lymphopenia), BMP, LFTs, CRP, ferritin, D-dimer, LDH, troponin, procalcitonin, ABG if hypoxic, CXR (bilateral infiltrates), blood cultures if febrile (NIH COVID Treatment Guidelines 2024)
    inputs: crp, d_dimer, ferritin, lymphocyte_count, creatinine
    actions: panel.cbc, panel.renal, panel.lft, panel.inflammation, panel.coag
    advance: severity biomarkers resulted and WHO ordinal scale assigned (WHO 2024)
  6. 6BRANCHING_WORKUP
    CT-PA if D-dimer elevated (PE risk 5-15% in hospitalised COVID-19; NIH COVID Treatment Guidelines 2024), echo if troponin elevated (myocarditis vs demand), IL-6 if tocilizumab candidacy, CT chest if worsening/atypical, fungal workup if prolonged steroids + ICU (NIH COVID Treatment Guidelines 2024)
    actions: workup.covid_pe_screen, workup.covid_superinfection
    advance: complications identified or excluded (NIH COVID Treatment Guidelines 2024)
  7. 7DIFFERENTIAL
    Influenza, RSV, bacterial pneumonia, PJP (immunocompromised), organising pneumonia (post-COVID), PE, decompensated HF with superimposed viral illness (NIH COVID Treatment Guidelines 2024)
    advance: COVID-19 confirmed as primary diagnosis with mimics excluded (NIH COVID Treatment Guidelines 2024)
  8. 8RISK_STRATIFICATION
    WHO ordinal scale (WHO 2024), 4C Mortality Score (Knight BMJ 2020), CALL score, NEWS2; stratify into mild/moderate/severe/critical tiers for treatment selection
    inputs: spo2, crp, lymphocyte_count
    actions: calc.who_ordinal_scale, calc.news2
    advance: severity tier assigned and treatment pathway selected (WHO 2024)
  9. 9TREATMENT
    Severity-tiered: mild (nirmatrelvir-ritonavir if ≤5d; EPIC-HR Hammond NEJM 2022), moderate (remdesivir 5d + dexamethasone if O2-requiring; ACTT-1 Beigel NEJM 2020 + RECOVERY Horby NEJM 2021), severe (dexamethasone + tocilizumab/baricitinib + remdesivir + prone; REMAP-CAP Gordon NEJM 2021 + COV-BARRIER Marconi Lancet RM 2021), critical (+ lung-protective vent + ECMO consideration; ARDSnet Brower NEJM 2000)
    inputs: spo2, crp, creatinine, alt
    advance: treatment regimen initiated per severity tier (WHO 2024; NIH COVID Treatment Guidelines 2024)
  10. 10DISPOSITION
    Ward if stable on ≤6 L NC; step-down/ICU if HFNC/NIV/mechanical ventilation required; ICU if WHO ordinal ≥6 (WHO 2024; NIH COVID Treatment Guidelines 2024)
    inputs: spo2
    advance: level of care assigned per O2 requirement and hemodynamic status (WHO 2024)
  11. 11MONITORING
    SpO2 continuous, inflammatory markers q24-48h (CRP, ferritin, D-dimer), LFTs if on remdesivir/baricitinib, daily CXR if ICU, awake proning compliance, VTE prophylaxis verification (NIH COVID Treatment Guidelines 2024)
    inputs: spo2, crp, alt
    actions: panel.inflammation, panel.lft
    advance: clinical trajectory confirmed improving or escalation triggered (NIH COVID Treatment Guidelines 2024)
  12. 12FOLLOWUP
    Post-COVID sequelae screening at 4-12 weeks (long COVID / PASC); pulmonary function testing if persistent dyspnea; cardiac MRI if myocarditis; VTE extended prophylaxis consideration; vaccination counselling (NIH COVID Treatment Guidelines 2024; WHO 2024)
    advance: post-discharge plan documented with follow-up at 4-12 weeks (NIH COVID Treatment Guidelines 2024)