Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration
This repository contains the data and the analysis workflow for the manuscript "Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration".
The repository is divided into 3 sections:
1). Production - containing all the commands used to produce data for analyses.
2). Analysis - containing all the commands used to analyse data.
3). Figures - containing scripts (1 script per figure) used to plot the results.
Control and elimination of the parasitic disease schistosomiasis relies on mass administration of praziquantel. Whilst these programmes reduce infection prevalence and intensity, their impact on parasite transmission and evolution is poorly understood. Here we examine the genomic impact of repeated mass drug administration on Schistosoma mansoni populations with documented reduced praziquantel efficacy. We sequenced whole-genomes of 198 S. mansoni larvae from 34 Ugandan children from regions with contrasting praziquantel exposure. Parasites infecting children from Lake Victoria, a transmission hotspot, form a diverse panmictic population. A single round of treatment did not reduce this diversity with no apparent population contraction caused by long-term praziquantel use. We find evidence of positive selection acting on members of gene families previously implicated in praziquantel action, but detect no high frequency functionally impactful variants. As efforts to eliminate schistosomiasis intensify, our study provides a foundation for genomic surveillance of this major human parasite.
Berger, D.J., Crellen, T., Lamberton, P.H.L. et al. Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration. Nat Commun 12, 4776 (2021).
Sequencing data generated in this study have been deposited in the European Nucleotide Archive (ENA) repository under accession code PRJEB31375. Source data to reproduce these figures can be found at:
