{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T04:28:34Z","timestamp":1789187314359,"version":"build-2803163510"},"reference-count":42,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2016,1,9]],"date-time":"2016-01-09T00:00:00Z","timestamp":1452297600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5T32AI007404\u201023"],"award-info":[{"award-number":["5T32AI007404\u201023"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Evolutionary Applications"],"published-print":{"date-parts":[[2016,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The trypanosome <jats:italic>Trypanosoma brucei gambiense<\/jats:italic> (<jats:italic>Tbg<\/jats:italic>) is a cause of human African trypanosomiasis (<jats:styled-content style=\"fixed-case\">HAT<\/jats:styled-content>) endemic to many parts of sub\u2010Saharan 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 <jats:styled-content style=\"fixed-case\">HAT<\/jats:styled-content> cases from the Democratic Republic of the Congo reported a high incidence of relapses in patients treated with melarsoprol. Of the 19 <jats:italic>Tbg<\/jats:italic> 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.<\/jats:p>","DOI":"10.1111\/eva.12338","type":"journal-article","created":{"date-parts":[[2015,10,13]],"date-time":"2015-10-13T22:59:44Z","timestamp":1444777184000},"page":"381-393","source":"Crossref","is-referenced-by-count":14,"title":["Whole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection"],"prefix":"10.1111","volume":"9","author":[{"given":"Joshua B.","family":"Richardson","sequence":"first","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven CT USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Evans","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven CT USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patient P.","family":"Pyana","sequence":"additional","affiliation":[{"name":"Department de Parasitologie Institut National de Recherche Biomedicale Kinshasa Gombe Democratic Republic of the Congo"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nick","family":"Van Reet","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Sistrom","sequence":"additional","affiliation":[{"name":"School of Natural Sciences University of California Merced Merced CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"B\u00fcscher","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences Institute of Tropical Medicine Antwerp Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serap","family":"Aksoy","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Public Health Yale School of Public Health New Haven CT USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adalgisa","family":"Caccone","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven CT USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2016,1,9]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth0410-248"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2013.06.005"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature10771"},{"key":"e_1_2_7_5_1","unstructured":"Andrews S.2010.FastQC a quality control tool for high throughput sequence data. Available fromhttp:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/(accessed on 24 September 2013)."},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp851"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1202885109"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.actatropica.2008.06.006"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-3156.2001.00710.x"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1128\/EC.1.1.137-151.2002"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm238"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/361173a0"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/1741-7007-10-82"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.2147\/RRTM.S34399"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0002475"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000658"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-10-482"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr521"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2156-11-94"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0166-6851(99)00101-2"},{"key":"e_1_2_7_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.actatropica.2007.07.007"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11174"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.285.5425.242"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-3156.2001.00712.x"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0166-6851(01)00332-2"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2013.08.003"},{"key":"e_1_2_7_31_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-3156.2001.00714.x"},{"key":"e_1_2_7_32_1","doi-asserted-by":"publisher","DOI":"10.1086\/649917"},{"key":"e_1_2_7_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(09)61117-X"},{"key":"e_1_2_7_34_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0003212"},{"key":"e_1_2_7_35_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0001025"},{"key":"e_1_2_7_36_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-ecolsys-110411-160248"},{"key":"e_1_2_7_37_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2002.02831.x"},{"key":"e_1_2_7_38_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182012000169"},{"key":"e_1_2_7_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evu222"},{"key":"e_1_2_7_40_1","unstructured":"Smit A. F. A. R.Hubley andP.Green2013\u20132015.RepeatMasker Open\u20104.0. Available fromhttp:\/\/www.repeatmasker.org(accessed on 11 February 2014)."},{"key":"e_1_2_7_41_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-3156.2001.00724.x"},{"key":"e_1_2_7_42_1","first-page":"1","article-title":"From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline","volume":"11","author":"Auwera G. A.","year":"2013","journal-title":"Current Protocols in Bioinformatics"},{"key":"e_1_2_7_43_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-11-124"}],"container-title":["Evolutionary Applications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Feva.12338","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/eva.12338","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/eva.12338","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/eva.12338","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T11:10:54Z","timestamp":1696245054000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/eva.12338"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1,9]]},"references-count":42,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2016,2]]}},"alternative-id":["10.1111\/eva.12338"],"URL":"https:\/\/doi.org\/10.1111\/eva.12338","archive":["Portico"],"relation":{},"ISSN":["1752-4571","1752-4571"],"issn-type":[{"value":"1752-4571","type":"print"},{"value":"1752-4571","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,1,9]]}}}