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The Oral Microbiome pp 119–137Cite as

Whole-Genome Sequencing of Pathogens in Saliva : A Target-Enrichment Approach for SARS-CoV-2

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2327))

Abstract

Outbreak analysis and transmission surveillance of viruses can be performed via whole-genome sequencing after viral isolation. Such techniques have recently been applied to characterize and monitor SARS-CoV-2 , the etiological agent of the COVID-19 pandemic. However, the isolation and culture of SARS-CoV-2 is time consuming and requires biosafety level 3 containment, which is not ideal for many resource-constrained settings. An alternate method, bait capture allows target enrichment and sequencing of the entire SARS-CoV-2 genome eliminating the need for viral culture. This method uses a set of hybridization probes known as “baits” that span the genome and provide sensitive, accurate, and minimal off-target hybridization. Baits can be designed to detect any known virus or bacteria in a wide variety of specimen types, including oral secretions. The bait capture method presented herein allows the whole genome of SARS-CoV-2 in saliva to be sequenced without the need to culture and provides an outline of bait design and bioinformatic analysis to guide a bioinformatician.

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Acknowledgments

D.J.S. was supported by McMaster University’s Michael G. DeGroote Initiative for Innovation in Healthcare. J.A.N. was supported by funds from the Comprehensive Antibiotic Resistance Database. D.E.A. is supported by a National Medical Research Council grant (COVID19RF2-0001). We thank Ben Tan Kiang Thong and Tanu Chawla (Duke-NUS Medical School, Singapore) for preparing Fig. 1 and Kathy Luinstra (St. Joseph’s Healthcare Hamilton, Canada) for technical advice.

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Authors and Affiliations

  1. Department of Laboratory Medicine, St. Joseph’s Healthcare Hamilton, Hamilton, ON, Canada

    David J. Speicher

  2. M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada

    David J. Speicher & Jalees A. Nasir

  3. Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia

    David J. Speicher

  4. CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China

    Peng Zhou

  5. Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore

    Danielle E. Anderson

Authors
  1. David J. Speicher
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  2. Jalees A. Nasir
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  3. Peng Zhou
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  4. Danielle E. Anderson
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Corresponding author

Correspondence to David J. Speicher .

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Editors and Affiliations

  1. College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA

    Guy R. Adami

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Speicher, D.J., Nasir, J.A., Zhou, P., Anderson, D.E. (2021). Whole-Genome Sequencing of Pathogens in Saliva : A Target-Enrichment Approach for SARS-CoV-2 . In: Adami, G.R. (eds) The Oral Microbiome. Methods in Molecular Biology, vol 2327. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1518-8_8

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  • DOI: https://doi.org/10.1007/978-1-0716-1518-8_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1517-1

  • Online ISBN: 978-1-0716-1518-8

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