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mSphere. 2018 Aug 22;3(4). pii: e00311-18. doi: 10.1128/mSphere.00311-18.

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.

Author information

1
Center for Infection & Immunity, Columbia University, New York, New York, USA.
2
Laboratory of Virology, University Hospitals of Geneva, Geneva, Switzerland.
3
University of Geneva Medical School, Geneva, Switzerland.
4
Department of Ambulatory Care and Community Medicine, University of Lausanne, Lausanne, Switzerland.
5
University of Lausanne Medical School, Lausanne, Switzerland.
6
Swiss Tropical and Public Health Institute, University of Basel, Lausanne, Switzerland.
7
Infectious Diseases Service, University Hospital of Lausanne, Lausanne, Switzerland.
8
Mwananyamala Hospital, Dar es Salaam, United Republic of Tanzania.
9
Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.
10
Center for Infection & Immunity, Columbia University, New York, New York, USA wil2001@cumc.columbia.edu.
#
Contributed equally

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.

KEYWORDS:

UHTS; VirCapSeq-VERT; febrile illness; sequencing; virology

PMID:
30135221
PMCID:
PMC6106054
DOI:
10.1128/mSphere.00311-18
[Indexed for MEDLINE]
Free PMC Article

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