DOI: 10.5061/dryad.d58b8
title: Data from: Whole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection

description: The trypanosome Trypanosoma brucei gambiense (Tbg) is a cause of human
 African trypanosomiasis (HAT) endemic to many parts of sub-Saharan Africa.
 The disease is almost invariably fatal if untreated and there is no
 vaccine, which makes monitoring and managing drug resistance highly
 relevant. A recent study of HAT cases from the Democratic Republic of the
 Congo reported a high incidence of relapses in patients treated with
 melarsoprol. Of the 19 Tbg strains isolated from patients enrolled in this
 study, four pairs were obtained from the same patient before treatment and
 after relapse. We used whole genome sequencing to investigate whether
 these patients were infected with a new strain, or if the original strain
 had regrown to pathogenic levels. Clustering analysis of 5938 single
 nucleotide polymorphisms supports the hypothesis of regrowth of the
 original strain, as we found that strains isolated before and after
 treatment from the same patient were more similar to each other than to
 other isolates. We also identified 23 novel genes that could affect
 melarsoprol sensitivity, representing a promising new set of targets for
 future functional studies. This work exemplifies the utility of using
 evolutionary approaches to provide novel insights and tools for disease
 control.
description: 15RE_R1First read pairs for Sample 15 BT-RE, in fastq format. See Table 1 in text.15RE_R2Second read pairs for Sample 15 BT-RE, in fastq format. See Table 1 in text.45BT_R1First read pairs for Sample 45 BT, in fastq format. See Table 1 in text.45BT_R2Second read pairs for Sample 45 BT, in fastq format. See Table 1 in text.57AT_R1First read pairs for Sample 57 AT, in fastq format. See Table 1 in text.57AT_R2Second read pairs for Sample 57 AT, in fastq format. See Table 1 in text.85BT_R1First read pairs for Sample 85 BT, in fastq format. See Table 1 in text.85BT_R2Second read pairs for Sample 85 BT, in fastq format. See Table 1 in text.141BT_R1First read pairs for Sample 141 BT, in fastq format. See Table 1 in text.141BT_R2Second read pairs for Sample 141 BT, in fastq format. See Table 1 in text.146AT_R1First read pairs for Sample 146 AT, in fastq format. See Table 1 in text.146AT_R2Second read pairs for Sample 146 AT, in fastq format. See Table 1 in text.146BT_R1First read pairs for Sample 146 BT, in fastq format. See Table 1 in text.146BT_R2Second read pairs for Sample 146 BT, in fastq format. See Table 1 in text.148AT_R1First read pairs for Sample 148 AT, in fastq format. See Table 1 in text.148AT_R2Second read pairs for Sample 148 AT, in fastq format. See Table 1 in text.148BT_R1First read pairs for Sample 148 BT, in fastq format. See Table 1 in text.148BT_R2Second read pairs for Sample 148 BT, in fastq format. See Table 1 in text.163AT_R1First read pairs for Sample 163 AT, in fastq format. See Table 1 in text.163AT_R2Second read pairs for Sample 163 AT, in fastq format. See Table 1 in text.163REL_R1First read pairs for Sample 163 AT-RE, in fastq format. See Table 1 in text.163REL_R2Second read pairs for Sample 163 AT-RE, in fastq format. See Table 1 in text.340AT_R1First read pairs for Sample 340 AT, in fastq format. See Table 1 in text.340AT_R2Second read pairs for Sample 340 AT, in fastq format. See Table 1 in text.346AT_R1First read pairs for Sample 346 AT, in fastq format. See Table 1 in text.346AT_R2Second read pairs for Sample 346 AT, in fastq format. See Table 1 in text.346REL_R1First read pairs for Sample 346 AT-RE, in fastq format. See Table 1 in text.346REL_R2Second read pairs for Sample 346 AT-RE, in fastq format. See Table 1 in text.346BT_R1First read pairs for Sample 346 BT, in fastq format. See Table 1 in text.346BT_R2Second read pairs for Sample 346 BT, in fastq format. See Table 1 in text.348BT_R1First read pairs for Sample 348 BT, in fastq format. See Table 1 in text.348BT_R2Second read pairs for Sample 348 BT, in fastq format. See Table 1 in text.349AT_R1First read pairs for Sample 349 AT, in fastq format. See Table 1 in text.349AT_R2Second read pairs for Sample 349 AT, in fastq format. See Table 1 in text.349BT_R1First read pairs for Sample 349 BT, in fastq format. See Table 1 in text.349BT_R2Second read pairs for Sample 349 BT, in fastq format. See Table 1 in text.378BT_R1First read pairs for Sample 378 BT, in fastq format. See Table 1 in text.378BT_R2Second read pairs for Sample 378 BT, in fastq format. See Table 1 in text.