Rapid identification of human-infecting viruses

Transboundary and Emerging Diseases
Zheng ZhangYousong Peng

Abstract

Viruses have caused much mortality and morbidity to humans and pose a serious threat to global public health. The virome with the potential of human infection is still far from complete. Novel viruses have been discovered at an unprecedented pace as the rapid development of viral metagenomics. However, there is still a lack of methodology for rapidly identifying novel viruses with the potential of human infection. This study built several machine learning models to discriminate human-infecting viruses from other viruses based on the frequency of k-mers in the viral genomic sequences. The k-nearest neighbor (KNN) model can predict the human-infecting viruses with an accuracy of over 90%. The performance of this KNN model built on the short contigs (≥1kb) is comparable to those built on the viral genomes. We used a reported human blood virome to further validate this KNN model with an accuracy of over 80% based on very short raw reads (150 bp). Our work demonstrates a conceptual and generic protocol for the discovery of novel human-infecting viruses in viral metagenomics studies. This article is protected by copyright. All rights reserved.

References

Mar 5, 2002·Bulletin of the History of Medicine·Niall P A S Johnson, Juergen Mueller
Apr 9, 2004·The Proceedings of the Nutrition Society·John C Mathers
Mar 9, 2005·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Janet G Baseman, Laura A Koutsky
Oct 4, 2005·Proceedings·Stefan Riedel
Nov 23, 2007·Critical Reviews in Microbiology·Mark Woolhouse, Eleanor Gaunt
Jun 12, 2009·The New England Journal of Medicine·Mark R DuffyEdward B Hayes
Nov 26, 2009·The Journal of Immunology : Official Journal of the American Association of Immunologists·Rama S AkondyRafi Ahmed
Jul 6, 2010·NeuroImage·Ariana AndersonMark S Cohen
Apr 8, 2011·American Journal of Respiratory and Critical Care Medicine·Sharon Chao WoottonHarold R Collard
Oct 9, 2012·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·V M CormanC Drosten
Apr 13, 2013·The New England Journal of Medicine·Rongbao GaoYuelong Shu
Sep 3, 2013·Indian Journal of Virology : an Official Organ of Indian Virological Society·S V Alavandi, M Poornima
Feb 11, 2014·Lancet·Adolfo García-Sastre, Mirco Schmolke
Oct 16, 2014·The New England Journal of Medicine·Gaël D MagangaEric M Leroy
Nov 25, 2014·Cellular and Molecular Life Sciences : CMLS·Ronald Rosenberg
Sep 25, 2015·Emerging Infectious Diseases·Gubio S CamposSilvia I Sardi
Dec 15, 2015·FEMS Microbiology Reviews·Robert A EdwardsBas E Dutilh
Feb 11, 2016·The New England Journal of Medicine·Jernej MlakarTatjana Avšič Županc
Mar 5, 2016·Viruses·Tomoko MiharaHiroyuki Ogata
Mar 22, 2016·Antiviral Research·Scott C WeaverNikos Vasilakis
Aug 18, 2016·Nature·David Paez-EspinoNikos C Kyrpides
Mar 23, 2017·PLoS Pathogens·Ahmed MoustafaAmalio Telenti
Feb 24, 2018·Science·Dennis CarrollJonna A K Mazet
Jan 9, 2019·Bulletin of the World Health Organization
Feb 10, 2019·Tropical Medicine and Infectious Disease·Rebecca ShipleyAshley C Banyard

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Citations

Feb 9, 2021·NAR Genomics and Bioinformatics·Jakub M BartoszewiczBernhard Y Renard
Jul 24, 2021·Briefings in Bioinformatics·Jakub M BartoszewiczBernhard Y Renard
Sep 29, 2021·PLoS Biology·Nardus MollentzeDaniel G Streicker

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blastx
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BalanceBaggingClassifier
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imbalanced
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BalanceRandomForest
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