Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches

ABSTRACT High-throughput sequencing can provide insights into epidemiology and medicine through comprehensive surveys of viral genetic sequences in environmental and clinical samples. Here, we characterize the plasma virome of Tanzanian patients with unexplained febrile illness by using two high-thr...

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Autores principales: Simon H. Williams, Samuel Cordey, Nishit Bhuva, Florian Laubscher, Mary-Anne Hartley, Noémie Boillat-Blanco, Zainab Mbarack, Josephine Samaka, Tarsis Mlaganile, Komal Jain, Valerie d’Acremont, Laurent Kaiser, W. Ian Lipkin
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Publicado: American Society for Microbiology 2018
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spelling oai:doaj.org-article:fce50eef830b46e2a859069fb4d9ca8b2021-11-15T15:25:50ZInvestigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches10.1128/mSphere.00311-182379-5042https://doaj.org/article/fce50eef830b46e2a859069fb4d9ca8b2018-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00311-18https://doaj.org/toc/2379-5042ABSTRACT High-throughput sequencing can provide insights into epidemiology and medicine through comprehensive surveys of viral genetic sequences in environmental and clinical samples. Here, we characterize the plasma virome of Tanzanian patients with unexplained febrile illness by using two high-throughput sequencing methods: unbiased sequencing and VirCapSeq-VERT (a positive selection system). Sequences from dengue virus 2, West Nile virus, human immunodeficiency virus type 1, human pegivirus, and Epstein-Barr virus were identified in plasma. Both sequencing strategies recovered nearly complete genomes in samples containing multiple viruses. Whereas VirCapSeq-VERT had better sensitivity, unbiased sequencing provided better coverage of genome termini. Together, these data demonstrate the utility of high-throughput sequencing strategies in outbreak investigations. IMPORTANCE Characterization of the viruses found in the blood of febrile patients provides information pertinent to public health and diagnostic medicine. PCR and culture have historically played an important role in clinical microbiology; however, these methods require a targeted approach and may lack the capacity to identify novel or mixed viral infections. High-throughput sequencing can overcome these constraints. As the cost of running multiple samples continues to decrease, the implementation of high-throughput sequencing for diagnostic purposes is becoming more feasible. Here we present a comparative analysis of findings from an investigation of unexplained febrile illness using two strategies: unbiased high-throughput sequencing and VirCapSeq-VERT, a positive selection high-throughput sequencing system.Simon H. WilliamsSamuel CordeyNishit BhuvaFlorian LaubscherMary-Anne HartleyNoémie Boillat-BlancoZainab MbarackJosephine SamakaTarsis MlaganileKomal JainValerie d’AcremontLaurent KaiserW. Ian LipkinAmerican Society for MicrobiologyarticleUHTSVirCapSeq-VERTfebrile illnesssequencingvirologyMicrobiologyQR1-502ENmSphere, Vol 3, Iss 4 (2018)
institution DOAJ
collection DOAJ
language EN
topic UHTS
VirCapSeq-VERT
febrile illness
sequencing
virology
Microbiology
QR1-502
spellingShingle UHTS
VirCapSeq-VERT
febrile illness
sequencing
virology
Microbiology
QR1-502
Simon H. Williams
Samuel Cordey
Nishit Bhuva
Florian Laubscher
Mary-Anne Hartley
Noémie Boillat-Blanco
Zainab Mbarack
Josephine Samaka
Tarsis Mlaganile
Komal Jain
Valerie d’Acremont
Laurent Kaiser
W. Ian Lipkin
Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
description ABSTRACT High-throughput sequencing can provide insights into epidemiology and medicine through comprehensive surveys of viral genetic sequences in environmental and clinical samples. Here, we characterize the plasma virome of Tanzanian patients with unexplained febrile illness by using two high-throughput sequencing methods: unbiased sequencing and VirCapSeq-VERT (a positive selection system). Sequences from dengue virus 2, West Nile virus, human immunodeficiency virus type 1, human pegivirus, and Epstein-Barr virus were identified in plasma. Both sequencing strategies recovered nearly complete genomes in samples containing multiple viruses. Whereas VirCapSeq-VERT had better sensitivity, unbiased sequencing provided better coverage of genome termini. Together, these data demonstrate the utility of high-throughput sequencing strategies in outbreak investigations. IMPORTANCE Characterization of the viruses found in the blood of febrile patients provides information pertinent to public health and diagnostic medicine. PCR and culture have historically played an important role in clinical microbiology; however, these methods require a targeted approach and may lack the capacity to identify novel or mixed viral infections. High-throughput sequencing can overcome these constraints. As the cost of running multiple samples continues to decrease, the implementation of high-throughput sequencing for diagnostic purposes is becoming more feasible. Here we present a comparative analysis of findings from an investigation of unexplained febrile illness using two strategies: unbiased high-throughput sequencing and VirCapSeq-VERT, a positive selection high-throughput sequencing system.
format article
author Simon H. Williams
Samuel Cordey
Nishit Bhuva
Florian Laubscher
Mary-Anne Hartley
Noémie Boillat-Blanco
Zainab Mbarack
Josephine Samaka
Tarsis Mlaganile
Komal Jain
Valerie d’Acremont
Laurent Kaiser
W. Ian Lipkin
author_facet Simon H. Williams
Samuel Cordey
Nishit Bhuva
Florian Laubscher
Mary-Anne Hartley
Noémie Boillat-Blanco
Zainab Mbarack
Josephine Samaka
Tarsis Mlaganile
Komal Jain
Valerie d’Acremont
Laurent Kaiser
W. Ian Lipkin
author_sort Simon H. Williams
title Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
title_short Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
title_full Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
title_fullStr Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
title_full_unstemmed Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
title_sort investigation of the plasma virome from cases of unexplained febrile illness in tanzania from 2013 to 2014: a comparative analysis between unbiased and vircapseq-vert high-throughput sequencing approaches
publisher American Society for Microbiology
publishDate 2018
url https://doaj.org/article/fce50eef830b46e2a859069fb4d9ca8b
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