joyreuben/ebola-bdbv-rtpcr-coverage

In silico inclusivity/exclusivity analysis of five filovirus RT-PCR assays against 2026 DRC/Uganda BDBV outbreak genomes # In silico inclusivity/exclusivity analysis of five filovirus RT-PCR assays vs. Bundibugyo virus An in silico inclusivity and exclusivity analysis asking whether five published filovirus RT-PCR assays still match Bundibugyo virus (BDBV) genomes from the 2007, 2012, and 2026 outbreaks — including the ongoing 2026 DRC/Uganda outbreak. No laboratory work; purely computational. Follows the AOAC International Appendix Q framework, the FDA molecular diagnostic assay evaluation template, and reports assay design information consistent with MIQE guidelines. **Status:** analysis complete (Steps 1–7), manuscript in draft. See manuscript_draft.md for the full methods/results write-up and CLAUDE.md for the detailed project log. ## Headline finding The Panning/Sanchez shared FiloB primer mismatch against BDBV (4 mismatches, ~19.7°C predicted duplex Tm shift) is **not unique to the 2026 lineage** — it is already present, uniformly, in the founder 2007 outbreak genomes and in 2012. This points to a species-level gap between the assay design (EBOV/SUDV-based) and BDBV, rather than new-lineage escape in the current outbreak. All findings are in silico predictions of reduced amplification compatibility, not proof of assay failure — wet-lab confirmation is the necessary final step. ## Dataset 70 curated BDBV genomes (Pathoplexus `ebola-bdbv` collection, OPEN data-use terms, downloaded 2026-08-22): 12 from the 2007 outbreak (Uganda), 23 from 2012 (DRC), 35 from 2026 (DRC, Uganda, Germany). 8 records were excluded as GenBank Patent-division deposits or automated ingest artifacts rather than clinical isolates — see CLAUDE.md for the full exclusion audit trail. ## Assay panel Five published RT-PCR assays (22 oligonucleotides total), targeting the L or NP gene: | Assay | Gene | Type | DOI | |---|---|---|---| | Panning 2007 | L | pan-filovirus TaqMan (primer mix) | 10.1086/520600 | | Ogawa 2010 | NP | EBOV-specific conventional | 10.1016/j.jviromet.2010.11.010 | | Sanchez 1999 | L …