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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American Society for Microbiology
2018
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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) |
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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 |
| work_keys_str_mv |
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| _version_ |
1718427987298222080 |