Purpose

Define user requirements for a standalone FUZKK utility that accepts laboratory CSV data, evaluates the records using limits embedded in code, and produces LabWare-compatible JSON.

Scope

The utility is intended for preliminary QC/QA review, integration testing, LIMS/LabWare flow and evidence-trail preparation. Final release decisions remain under the laboratory's validated procedure and responsible personnel.

Users

QC analyst, QA reviewer, CSV/validation engineer, LIMS/LabWare integration engineer, responsible laboratory specialist.

User requirements

1. The utility shall run without arguments and print its self-description, a built-in input.csv example from GetDemoData(), and demo evaluation for the embedded records.
2. The utility shall run with two arguments: input.csv output.json.
3. The utility shall not read input.csv and shall not write output.json when started without arguments.
4. CSV numeric values shall be parsed using CultureInfo.InvariantCulture.
5. Output shall be generated as LabWare-compatible JSON with Header, Samples, Results, Status, StatusCode, ErrorMessage, Description and DescriptionEN.
6. For PASS records, ErrorMessage shall be an empty string.
7. Embedded limits shall follow this priority: Ph. Eur. → British Pharmacopoeia / UK implementation → EAEU / regional requirements → EMA/ICH/EU guidance → USP fallback.
8. If an exact monograph is not known, strict standard API limits are used where applicable: assay 98–102%, total impurities ≤1.0%, individual impurity ≤0.5%.
9. For biologics and mAb-like products, aggregation, sterility and endotoxin checks shall be included where relevant to the utility purpose.
10. If a parameter may arrive in different units, the unit shall be represented as a separate input field or explicitly reflected in the input.csv field name.

Input CSV

BatchNumber,ProductName,AssayType,Gag_CopyNumber,Pol_CopyNumber,VSV_G_CopyNumber,E1_CopyNumber,LOD_Copies,Input_Volume_uL,Total_Batch_Volume_L,Positive_Control_Detected,Negative_Control_Clear
CGT-SAFE-2026-001,Lentiviral-CAR-T,qPCR,0.0,0.0,0.0,0.0,10.0,50.0,2.0,true,true
CGT-SAFE-2026-002,Adenoviral-Oncolytic,qPCR,0.0,0.0,0.0,5.0,5.0,100.0,5.0,true,true
CGT-SAFE-2026-003,AAV-Hemophilia,CellBased,0.0,0.0,0.0,0.0,1.0,1000.0,10.0,true,true

input.csv fields

Utility description

RCL/RCA Safety Screen — Replication Competent Virus Safety Screen

RCL/RCA Safety Screen — Replication Competent Virus Safety Screen

ℹ️ Utility analyzes vector safety test data:
• Gag/Pol detection (for lentiviruses)
• E1/E3 detection (for adenoviruses)
• VSV-G detection (for pseudotyping)
• Assay control validation

⚠️ CRITICAL: Presence of RCL/RCA leads to uncontrolled patient infection!
This is an absolute contraindication for batch release.

Usage:
RCLRCA SafetyScreen.exe → demo mode (console output)
RCLRCA SafetyScreen.exe input.csv output.json → evaluate your data

Input format:
BatchNumber,ProductName,AssayType,Gag_CopyNumber,Pol_CopyNumber,VSV_G_CopyNumber,E1_CopyNumber,LOD_Copies,Input_Volume_uL,Total_Batch_Volume_L,Positive_Control_Detected,Negative_Control_Clear

Example:
CGT-SAFE-2026-001,Lentiviral-CAR-T,qPCR,0.0,0.0,0.0,0.0,10.0,50.0,2.0,true,true

— WHY IS THIS NEEDED?
RCL/RCA control is critical for viral vectors (Novartis, BioNTech, Oxford Biomedica):
• Replication Competent Lentiviruses (RCL) or Adenoviruses (RCA) may arise from recombination of production plasmids
• Such viruses can replicate in patient cells, causing severe diseases or oncogenesis
• Regulators (FDA/EMA) require mandatory screening of each clinical batch
• Tests include molecular methods (qPCR) and functional infectivity assays

⚠️ CRITICAL:
• Result must be below Limit of Detection (LOD) of the method
• Gag and Pol are key markers for lentiviral vectors
• E1 and E3 are key markers for first-generation adenoviral vectors
• VSV-G is envelope marker used in pseudotyping
• Positive control must trigger, negative must be clear

Key features:
• Support for various vector types (Lenti, Adeno, AAV)
• qPCR and cell-based bioassay data analysis
• Strict assay validity control (controls)
• Risk calculation based on batch volume and LOD

Critical parameters:
• Gag/Pol/VSV-G/E1: < LOD (usually 0 copies)
• Positive control: Detected
• Negative control: Clear

💡 Usage tips:
1. Use high-sensitivity methods (ddPCR) to lower LOD
2. Perform testing at early production stages (Master Bank) and on final product
3. For cell-based tests, use lines sensitive to specific virus type
4. If signal detected, perform sequencing to confirm product nature
5. Document every negative result for regulatory dossier

⚠️ Note: Unlike other impurities, presence of even one replication-competent particle is considered a critical safety defect. The utility applies "Zero Tolerance" principle for these specific markers.

Traceability and limitations

• The URS is used as the source document for functional specification, CSV review and later validation work.
• This document does not replace an approved pharmacopoeial monograph, validated analytical method or internal product specification.
• For product-specific limits, the approved customer specification takes priority.

The functional specification describes the behaviour of the standalone FUZKK console utility, input-data format, evaluation algorithm and output JSON structure.

Functional flow

1. Main() checks the number of arguments.
2. If no arguments are provided: PrintHello() prints the description and built-in input.csv example, then RunDemoEvaluation() executes Evaluate() over GetDemoData() and prints demo JSON.
3. If two arguments are provided: RunWithFiles(input.csv, output.json) reads CSV, evaluates each record and writes LabWare-compatible JSON.
4. LoadData() uses CultureInfo.InvariantCulture and shall not be called in no-arguments mode.
5. Evaluate() returns a named tuple with BatchNumber, ProductName, Parameters, CriticalFailCount, WarningCount, Recommendation and RecommendationEN.
6. GetIssues() builds messages for ErrorMessage in WARNING/FAIL cases.

Evaluation rules

• PASS: CriticalFailCount = 0 and WarningCount = 0.
• WARNING: CriticalFailCount = 0 and WarningCount > 0.
• FAIL: CriticalFailCount > 0.
• ERROR: exception during reading or processing.
• ErrorMessage remains empty for PASS.
• Limits are embedded in Program.cs; no external limit configuration is required.

Input and fields

BatchNumber,ProductName,AssayType,Gag_CopyNumber,Pol_CopyNumber,VSV_G_CopyNumber,E1_CopyNumber,LOD_Copies,Input_Volume_uL,Total_Batch_Volume_L,Positive_Control_Detected,Negative_Control_Clear
CGT-SAFE-2026-001,Lentiviral-CAR-T,qPCR,0.0,0.0,0.0,0.0,10.0,50.0,2.0,true,true
CGT-SAFE-2026-002,Adenoviral-Oncolytic,qPCR,0.0,0.0,0.0,5.0,5.0,100.0,5.0,true,true
CGT-SAFE-2026-003,AAV-Hemophilia,CellBased,0.0,0.0,0.0,0.0,1.0,1000.0,10.0,true,true

Output JSON

{
  "Header": {
    "UtilityName": "RCL_RCA_Safety_Screen",
    "Version": "1.0.0",
    "Timestamp": "UTC",
    "InstrumentID": "FUZKK-QC-WORKSTATION",
    "OperatorID": "Admin"
  },
  "Samples": [
    {
      "SampleID": "from BatchNumber",
      "BatchNumber": "from CSV",
      "ProductName": "from CSV",
      "TestName": "utility-specific test",
      "AnalysisCode": "utility-specific code",
      "Status": "PASS | WARNING | FAIL | ERROR",
      "StatusCode": "1 | 2 | 0 | -1",
      "ErrorMessage": "",
      "Description": "Russian recommendation",
      "DescriptionEN": "English recommendation",
      "Results": [
        {
          "ParameterName": "parameter",
          "ResultValue": 0.0,
          "UnitOfMeasure": "unit",
          "SpecificationLimit": "limit",
          "IsWithinSpec": true
        }
      ]
    }
  ]
}