Phylo-Plex: A phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology Article Swipe

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Mathew A. Beale , Vignesh Shetty , Kirsty 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 Washaya , Logan Rodgers , Beauty Makamure , Ethel Dauya , Michael Marks , Étienne Muller , Rashida A. Ferrand , Nicholas R. Thomson ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.1101/2025.02.19.25322526

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 , we designed a high-resolution multiplex PCR sequencing scheme for lineage tracking. Using MinION Flongle cells, we sequenced 72 clinical samples. 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.

Related Topics

Computational Biology

Polymerase Chain Reaction

16S Ribosomal Rna

Remote Sensing

Concepts

Amplicon Computational biology Amplicon sequencing Biology Low resolution Genomics Genetics High resolution Computer science Evolutionary biology Genome Geography Gene Polymerase chain reaction 16S ribosomal RNA Remote sensing

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Type: preprint
Language: en
Landing Page: https://doi.org/10.1101/2025.02.19.25322526
OA Status: green
References: 47
Related Works: 10
OpenAlex ID: https://openalex.org/W4407985652

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DOI: https://doi.org/10.1101/2025.02.19.25322526

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Title: Phylo-Plex: A phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology

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Type: preprint

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Language: en

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Publication year: 2025

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Publication date: 2025-02-25

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Authors: Mathew A. Beale, Vignesh Shetty, Kirsty 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 Washaya, Logan Rodgers, Beauty Makamure, Ethel Dauya, Michael Marks, Étienne Muller, Rashida A. Ferrand, Nicholas R. Thomson

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Landing page: https://doi.org/10.1101/2025.02.19.25322526

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Concepts: Amplicon, Computational biology, Amplicon sequencing, Biology, Low resolution, Genomics, Genetics, High resolution, Computer science, Evolutionary biology, Genome, Geography, Gene, Polymerase chain reaction, 16S ribosomal RNA, Remote sensing

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abstract_inverted_index.,	55
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