Whole-Genome Sequencing for High-Consequence Emerging RNA Viruses: Strategy Selection for Bundibugyo Virus Disease Under 2026 Outbreak Constraints

Whole-genome sequencing (WGS) is central to outbreak response for high-consequence ribonucleic acid (RNA) viruses, but useful genomes depend on workflow design, sample quality, biosafety, diagnostic breadth, infrastructure, and bioinformatics as much as sequencing platform. The 2026 Bundibugyo virus disease outbreak in the Democratic Republic of the Congo and Uganda provides a case example. Bundibugyo virus (BDBV) was already known from the 2007–2008 Uganda and 2012 Democratic Republic of the Congo outbreaks, but sparse historical genome sampling, Ebola virus-centered diagnostic assumptions, non-specific febrile and viral hemorrhagic fever presentations, and difficult field conditions created a need for broad differential diagnosis, rapid species assignment, and representative genome generation. This Review compares outbreak WGS strategies by the degree of prior viral sequence knowledge required, distinguishing direct RNA sequencing, random-primed complementary DNA (cDNA) sequencing, sequence-independent amplified cDNA sequencing, background-depleted or particle-enriched cDNA sequencing, probe-based hybrid capture, tiled amplicon sequencing, portable field sequencing, culture-derived sequencing, and associated bioinformatics workflows. For BDBV-like outbreaks, the most defensible strategy is staged and adaptive: broad viral hemorrhagic fever and febrile-illness differential testing at recognition; Filoviridae-wide testing when filovirus disease remains plausible; divergence-tolerant first-genome recovery; quantification-cycle-informed sequencing prioritization without BDBV-only diagnostic narrowing; validated amplicon scale-up; and representative sequencing across locations and time.