Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology
- Mathew A. Beale
- Vignesh Shetty
- Kirsty E. Ambridge
- George Lacey
- Sam Dougan
- William Roberts-Sengier
- Beth Sampher
- Florent Lassalle
- Matthew J. Dorman
- Mahlape P. Mahlangu
- Johanna M. E. Venter
- Bianca Da Costa Dias
- Martha Chipinduro
- Tendai M. Washaya
- Luanne Rodgers
- Beauty Makamure
- Ethel Dauya
- Michael Marks
- Etienne E. Müller
- Rashida A. Ferrand
- Nicholas R. Thomson
2026-07-09
Genomic pathogen surveillance is a powerful tool for public health and research, but is costly and unachievable in low-resource settings. Most sub-genomic typing methods sacrifice resolution whilst remaining costly. We developed “Phylo-Plex”, a novel approach that identifies information-rich genomic regions to maximise phylogenetic information whilst minimising the number of regions. Applied to Treponema pallidum and Neisseria gonorrhoeae , we designed a high-resolution multiplex PCR sequencing scheme for lineage tracking pathogens with different extremes of genome variation. For Treponema pallidum , we also designed and evaluated the Phylo-Plex scheme in the laboratory and field settings by sequencing 72 clinical samples using MinION Flongle cells. Our T. pallidum scheme comprising 59 multiplex amplicons achieved high discrimination of fine-scale sublineages comparable to those defined using whole genomes, and demonstrating a qPCR detection limit ≤Ct 32. Variant calls from MinION amplicon sequencing were highly correlated with Illumina whole genome sequencing. We successfully deployed the method in a low-resource laboratory in Zimbabwe, costed at <£300/24 samples (£12.47/sample). Phylo-Plex enables low-cost tracking of priority pathogenic lineages in low resource settings and at scale.