HIV Viral Load Pooling — Abbott m2000 Pipeline
BCHPR · TB Reference Laboratory Bamenda (ISO 15189:2022) · 2023 – present
4,785-line pipeline (the 3,595-line VIRAL LOAD DATA CLEANING.py is the largest single file in the project) ingesting Abbott m2000 HIV-1 viral-load results through REDCap — powers the 12,396-specimen pooled-testing study published in Scientific Reports 2025 (+80% testing capacity, 0.01% misclassification).
Highlights
- Multi-form REDCap consolidation across 7 forms (demographics · reception · results · verification · dispatch etc.) merged into one unified specimen record.
- Robust HTTPAdapter with exponential backoff for REDCap API reliability; chunked 10-day incremental imports handle large result volumes.
- ThreadPoolExecutor parallel API calls for faster multi-form export.
- User activity tracking with post-dated detection — flags data entered long after the test event for QA.
- Temporal analysis: hours / days between test performed and data entry.
- Pools of 3 with method validation: Bland–Altman mean bias –0.51 log copies/mL, 0.01% unsuppressed misclassification under ≥ 40 copies/mL cutoff.
- Automatic patient-result generation at refresh time — reduces patient wait time by 85%.
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