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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

Williams, Simon H. and Cordey, Samuel and Bhuva, Nishit and Laubscher, Florian and Hartley, Mary-Anne and Boillat-Blanco, Noémie and Mbarack, Zainab and Samaka, Josephine and Mlaganile, Tarsis and Jain, Komal and d'Acremont, Valerie and Kaiser, Laurent and Lipkin, W. Ian. (2018) 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. mSphere, 3 (4). e00311-18.

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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.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Medicine > Clinical Research (Reither)
UniBasel Contributors:D'Acremont, Valérie
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:American Society for Microbiology
ISSN:2379-5042
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
Last Modified:11 Sep 2018 13:10
Deposited On:11 Sep 2018 13:10

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