Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance
Por:
Deng X., Achari A., Federman S., Yu G., Somasekar S., Bártolo I., Yagi S., Mbala-Kingebeni P., Kapetshi J., Ahuka-Mundeke S., Muyembe-Tamfum J.-J., Ahmed A.A., Ganesh V., Tamhankar M., Patterson J.L., Ndembi N., Mbanya D., Kaptue L., McArthur C., Muñoz-Medina J.E., Gonzalez-Bonilla C.R., López S., Arias C.F., Arevalo S., Miller S., Stone M., Busch M., Hsieh K., Messenger S., Wadford D.A., Rodgers M., Cloherty G., Faria N.R., Thézé J., Pybus O.G., Neto Z., Morais J., Taveira N., R. Hackett J., Jr., Chiu C.Y.
Publicada:
1 ene 2020
Resumen:
Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use. © 2020, The Author(s), under exclusive licence to Springer Nature Limited.
Filiaciones:
Deng X.:
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
UCSF–Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, United States
Achari A.:
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
UCSF–Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, United States
Federman S.:
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
UCSF–Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, United States
Yu G.:
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
UCSF–Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, United States
Somasekar S.:
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
UCSF–Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, United States
Bártolo I.:
Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
Yagi S.:
Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, United States
Mbala-Kingebeni P.:
Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic Congo
Kapetshi J.:
Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic Congo
Ahuka-Mundeke S.:
Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic Congo
Muyembe-Tamfum J.-J.:
Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic Congo
Ahmed A.A.:
Boston Children’s Hospital, Boston, MA, United States
Harvard Medical School, Boston, MA, United States
Ganesh V.:
Massachussetts General Hospital, Boston, MA, United States
Tamhankar M.:
Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
Patterson J.L.:
Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
Ndembi N.:
Institute for Human Virology Nigeria, Abuja, Nigeria
Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
Mbanya D.:
Universite de Yaoundé I, Yaoundé, Cameroon
University of Bamenda, Bamenda, Cameroon
Kaptue L.:
Université des Montagnes, Bangangté, Cameroon
McArthur C.:
University of Missouri-Kansas City, Kansas City, MO, United States
Muñoz-Medina J.E.:
Instituto Mexicano del Seguro Social, Mexico City, Mexico
Gonzalez-Bonilla C.R.:
Instituto Mexicano del Seguro Social, Mexico City, Mexico
López S.:
Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
Arias C.F.:
Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
Arevalo S.:
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
Miller S.:
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
Stone M.:
Blood Systems Research Institute, San Francisco, CA, United States
Busch M.:
Blood Systems Research Institute, San Francisco, CA, United States
Hsieh K.:
Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, United States
Messenger S.:
Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, United States
Wadford D.A.:
Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, United States
Rodgers M.:
Abbott Laboratories, Abbott Park, IL, United States
Cloherty G.:
Abbott Laboratories, Abbott Park, IL, United States
Faria N.R.:
Department of Zoology, University of Oxford, Oxford, United Kingdom
Thézé J.:
Department of Zoology, University of Oxford, Oxford, United Kingdom
Pybus O.G.:
Department of Zoology, University of Oxford, Oxford, United Kingdom
Neto Z.:
Angolan National Institute of Health Research, Luanda, Angola
Morais J.:
Angolan National Institute of Health Research, Luanda, Angola
Taveira N.:
Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
Instituto Universitário Egas Moniz (IUEM), Monte de Caparica, Portugal
R. Hackett J.:
Abbott Laboratories, Abbott Park, IL, United States
Jr.:
Abbott Laboratories, Abbott Park, IL, United States
Chiu C.Y.:
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
UCSF–Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, United States
Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, United States
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