{
  "topic": "long-covid-viral-persistence",
  "completed": true,
  "provider_mode": "Consensus Pro browser-thread plus Consensus keyword search/fetch leads; original-source checks independently opened on PubMed",
  "queries": [
    "Through 9 October 2026, critically assess whether persistent SARS-CoV-2 antigen or RNA causally maintains established Long COVID symptoms. Distinguish detection and correlations from an ongoing replication-competent reservoir, acute prevention from treatment of established disease, and tissue target engagement from clinical response. Compare primary tissue cohort studies and randomized trials STOP-PASC, PAXLC and RECOVER-VITAL, including negative results and strongest alternative mechanisms. Provide DOI/PMID. Restrict analysis to clinical causal evidence, without operational laboratory methods.",
    "Long COVID SARS-CoV-2 persistence tissue reservoirs antiviral randomized trials target engagement symptoms viral persistence causality"
  ],
  "raw_paths": [
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    "deliverables/consensus_consistency_audit_2026-10-09/checks/long-covid-viral-persistence/consensus-search-leads.md",
    "deliverables/consensus_consistency_audit_2026-10-09/checks/long-covid-viral-persistence/consensus-addendum.md"
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  "primary_comparisons": [
    {
      "pmid": "38663423",
      "doi": "10.1016/S1473-3099(24)00171-3",
      "access_depth": "abstract_metadata",
      "result": "RNA in sampled tissues associated with later symptom reporting in cross-sectional cohort; source authors call for mechanistic verification.",
      "grade_changed": false
    },
    {
      "pmid": "38848477",
      "doi": "10.1001/jamainternmed.2024.2007",
      "access_depth": "abstract_metadata",
      "result": "15-day randomized regimen had no significant symptom benefit at 10 weeks; no reservoir clearance shown.",
      "grade_changed": false
    },
    {
      "pmid": "40188838",
      "doi": "10.1016/S1473-3099(25)00073-8",
      "access_depth": "abstract_metadata",
      "result": "PAX LC 15-day regimen had null day-28 primary outcome; no tissue clearance shown.",
      "grade_changed": false
    },
    {
      "pmid": "42673984",
      "doi": "10.1016/S1473-3099(26)00406-8",
      "access_depth": "abstract_metadata",
      "result": "RECOVER-VITAL 15/25-day arms had no significant primary endpoint benefit across three phenotypes; no tissue clearance shown.",
      "grade_changed": false
    }
  ],
  "conclusion": "No SC1/SC2/SC3 score or confidence change. Consensus surfaced sources already in the archived inventory. Correct Consensus's STOP-PASC PMID typo (38848147 to 38848477) in this audit mapping; preserve raw answer unchanged. Flag its unsupported inference from antiviral nonbenefit to reservoir eradication/target engagement. Prior visible; not blind.",
  "addendum_path": "deliverables\\consensus_consistency_audit_2026-10-09\\checks\\long-covid-viral-persistence\\consensus-addendum.md",
  "grade_changed": false,
  "additional_original_source_receipts": [],
  "primary_comparison_count": 4,
  "status": "completed_retrospective_original_source_reconciliation",
  "score_before": {
    "hsef_level": "Γ",
    "hsef_descriptor": "Mechanistically plausible, partial system support",
    "confidence": "Moderate",
    "confidence_rationale": "56 primary reports with 3 selected partial-body examinations; density, heterogeneous controls and incomplete access set the confidence, not correctness.",
    "rests_on_non_peer_reviewed_work": false,
    "rationale": "Overall Γ follows SC3. Human tissue associations and mechanistic models supply partial support, but primary clinical maintenance by persistent SARS-CoV-2 has not been identified. Antiviral nulls are important counterevidence to accessible replication, not evidence that every tissue reservoir was eliminated."
  },
  "score_after": {
    "hsef_level": "Γ",
    "hsef_descriptor": "Mechanistically plausible, partial system support",
    "confidence": "Moderate",
    "confidence_rationale": "56 primary reports with 3 selected partial-body examinations; density, heterogeneous controls and incomplete access set the confidence, not correctness.",
    "rests_on_non_peer_reviewed_work": false,
    "rationale": "Overall Γ follows SC3. Human tissue associations and mechanistic models supply partial support, but primary clinical maintenance by persistent SARS-CoV-2 has not been identified. Antiviral nulls are important counterevidence to accessible replication, not evidence that every tissue reservoir was eliminated."
  },
  "raw_receipts": [
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  "manifest_source": "deliverables\\consensus_consistency_audit_2026-10-09\\checks\\long-covid-viral-persistence\\structured-consensus-validation.json",
  "literature_cutoff_preserved": true,
  "independent_blinded_audit": false
}