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Using machine learning to detect coronaviruses potentially infectious to humans

Georgina Gonzalez-Isunza, M. Zaki Jawaid, Pengyu Liu, Daniel L. Cox, Mariel Vazquez, Javier Arsuaga
doi: https://doi.org/10.1101/2022.12.11.520008
Georgina Gonzalez-Isunza
1University of California, Department of Microbiology & Molecular Genetics, Davis, CA, USA
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M. Zaki Jawaid
4Department of Physics, University of California, Davis, USA
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Pengyu Liu
1University of California, Department of Microbiology & Molecular Genetics, Davis, CA, USA
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Daniel L. Cox
4Department of Physics, University of California, Davis, USA
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Mariel Vazquez
1University of California, Department of Microbiology & Molecular Genetics, Davis, CA, USA
3Department of Mathematics, University of California, Davis, CA, USA
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Javier Arsuaga
2University of California, Department of Molecular & Cellular Biology, Davis, CA, USA
3Department of Mathematics, University of California, Davis, CA, USA
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  • For correspondence: jarsuaga@ucdavis.edu
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Abstract

Establishing the host range for novel viruses remains a challenge. Here, we address the challenge of identifying non-human animal coronaviruses that may infect humans by creating an artificial neural network model that learns from the binding of the spike protein of alpha and beta coronaviruses to their host receptor. The proposed method produces a human-Binding Potential (h-BiP) score that distinguishes, with high accuracy, the binding potential among human coronaviruses. Two viruses, previously unknown to bind human receptors, were identified: Bat coronavirus BtCoV/133/2005 (a MERS related virus) and Rhinolophus affinis coronavirus isolate LYRa3 a SARS related virus. We further analyze the binding properties of these viruses using molecular dynamics. To test whether this model can be used for surveillance of novel coronaviruses, we re-trained the model on a set that excludes SARS-COV-2 viral sequences. The results predict the binding of SARS-CoV-2 with a human receptor, indicating that machine learning methods are an excellent tool for the prediction of host expansion events.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/Arsuaga-Vazquez-Lab/h-BiP

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 12, 2022.
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Using machine learning to detect coronaviruses potentially infectious to humans
Georgina Gonzalez-Isunza, M. Zaki Jawaid, Pengyu Liu, Daniel L. Cox, Mariel Vazquez, Javier Arsuaga
bioRxiv 2022.12.11.520008; doi: https://doi.org/10.1101/2022.12.11.520008
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Using machine learning to detect coronaviruses potentially infectious to humans
Georgina Gonzalez-Isunza, M. Zaki Jawaid, Pengyu Liu, Daniel L. Cox, Mariel Vazquez, Javier Arsuaga
bioRxiv 2022.12.11.520008; doi: https://doi.org/10.1101/2022.12.11.520008

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