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Acute Vector-Borne Viral Infection: Zika and MinION Surveillance *

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  • Authors: Jaqueline Goes de Jesus1, Marta Giovanetti2,3, Nuno Rodrigues Faria4, Luiz Carlos Junior Alcantara5,6
  • Editors: Lee W. Riley7, Ronald E. Blanton8
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Laboratory of Experimental Pathology, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia 40296-710, Brazil; 2: Laboratory of Flaviviruses, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro 21040-900, Brazil; 3: Laboratory of Cellular and Molecular Genetics, ICB, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; 4: Department of Zoology, University of Oxford, Oxford OX1 3SZ, United Kingdom; 5: Laboratory of Flaviviruses, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro 21040-900, Brazil; 6: Laboratory of Cellular and Molecular Genetics, ICB, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; 7: Divisions of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA; 8: Center for Global Health & Diseases, Case Western Reserve University, Cleveland, OH
  • Source: microbiolspec August 2019 vol. 7 no. 4 doi:10.1128/microbiolspec.AME-0008-2019
  • Received 21 March 2019 Accepted 15 May 2019 Published 09 August 2019
  • Luiz Carlos Junior Alcantara, [email protected]
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  • Abstract:

    The MinION sequencer was launched by the Oxford Nanopore Technologies start-up as a disruptive technology for genome sequencing based on single-molecule synthesis. Its characteristics as a portable device, low cost, and simple library preparation have made it a good candidate for field researchers. MinION has been used to sequence a number of microorganisms, such as bacteria, viruses, and fungi. Based on the experience that characterized the Ebola virus genetic diversity in Guinea during the 2014-2015 outbreak, the ZiBRA (Zika in Brazil Real-time Analysis) project aimed to sequence a large number of Zika virus genomes during a mobile laboratory trip in northeast Brazil to provide important epidemiological information about the spread of this disease in this country. In response to the positive and rapid results obtained by the ZiBRA project, the Brazilian Ministry of Health and many leading institutions, such as the Pan American Health Organization and WHO, have shown interest in expanding the strategy used in this project to other countries dealing with arbovirus infection.

    *This article is part of a curated collection.

  • Citation: de Jesus J, Giovanetti M, Rodrigues Faria N, Alcantara L. 2019. Acute Vector-Borne Viral Infection: Zika and MinION Surveillance * . Microbiol Spectrum 7(4):AME-0008-2019. doi:10.1128/microbiolspec.AME-0008-2019.

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2019-08-09
2019-08-18

Abstract:

The MinION sequencer was launched by the Oxford Nanopore Technologies start-up as a disruptive technology for genome sequencing based on single-molecule synthesis. Its characteristics as a portable device, low cost, and simple library preparation have made it a good candidate for field researchers. MinION has been used to sequence a number of microorganisms, such as bacteria, viruses, and fungi. Based on the experience that characterized the Ebola virus genetic diversity in Guinea during the 2014-2015 outbreak, the ZiBRA (Zika in Brazil Real-time Analysis) project aimed to sequence a large number of Zika virus genomes during a mobile laboratory trip in northeast Brazil to provide important epidemiological information about the spread of this disease in this country. In response to the positive and rapid results obtained by the ZiBRA project, the Brazilian Ministry of Health and many leading institutions, such as the Pan American Health Organization and WHO, have shown interest in expanding the strategy used in this project to other countries dealing with arbovirus infection.

*This article is part of a curated collection.

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FIGURE 1

MinION device, Oxford Nanopore Technologies, available at https://nanoporetech.com/products/minion. Image courtesy of Oxford Nanopore Technologies.

Source: microbiolspec August 2019 vol. 7 no. 4 doi:10.1128/microbiolspec.AME-0008-2019
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Image of FIGURE 2
FIGURE 2

Overview of the second- and third-generation sequencing technologies. Sanger’s method was the first-generation sequencing method, followed by 454 and Solexa techniques, which marked the second generation. After Helicos and Pacific Biosciences releases, Illumina and ION Torrent were used to generate a large amount of data. More recently, nanopore sequencing techniques have interested researchers working on field research and real-time analysis.

Source: microbiolspec August 2019 vol. 7 no. 4 doi:10.1128/microbiolspec.AME-0008-2019
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FIGURE 3

ZIKV MinION sampling and library prep workflow. Shown are average times for ZIKV sampling and library preparation using the Primal Scheme-derived multiplex PCR and Oxford Nanopore Technologies SKL-108 sequencing kit. From RNA extraction to library load on a flow cell, the time spent is around 8 h, with at least 3 h of hands-on time.

Source: microbiolspec August 2019 vol. 7 no. 4 doi:10.1128/microbiolspec.AME-0008-2019
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FIGURE 4

Overview of multiplex primer design using the Primal Scheme online primer design tool. Submission box for online primer design tool. Primer table of results. Schematic showing expected amplicon products for each pool in genomic context for the Zika Asian scheme. Adapted from reference ( 60 ), with permission.

Source: microbiolspec August 2019 vol. 7 no. 4 doi:10.1128/microbiolspec.AME-0008-2019
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