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Human genome integration of SARS-CoV-2 contradicted by long-read sequencing

Nathan Smits, Jay Rasmussen, Gabriela O. Bodea, Alberto A. Amarilla, Patricia Gerdes, Francisco J. Sanchez-Luque, Prabha Ajjikuttira, Naphak Modhiran, Benjamin Liang, Jamila Faivre, Ira W. Deveson, Alexander A. Khromykh, Daniel Watterson, View ORCID ProfileAdam D. Ewing, View ORCID ProfileGeoffrey J. Faulkner
doi: https://doi.org/10.1101/2021.05.28.446065
Nathan Smits
1Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia
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Jay Rasmussen
2Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia
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Gabriela O. Bodea
1Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia
2Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia
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Alberto A. Amarilla
3School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia
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Patricia Gerdes
1Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia
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Francisco J. Sanchez-Luque
4GENYO, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain
5MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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Prabha Ajjikuttira
2Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia
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Naphak Modhiran
3School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia
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Benjamin Liang
3School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia
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Jamila Faivre
6INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
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Ira W. Deveson
7Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
8St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney NSW 2052, Australia
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Alexander A. Khromykh
3School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia
9Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane QLD 4072, Australia
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Daniel Watterson
3School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia
9Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane QLD 4072, Australia
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Adam D. Ewing
1Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia
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Geoffrey J. Faulkner
1Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia
2Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia
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  • ORCID record for Geoffrey J. Faulkner
  • For correspondence: faulknergj@gmail.com
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Abstract

A recent study proposed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we applied deep (>50×) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2, and did not find any evidence of the virus existing as DNA. By examining ONT data from separate HEK293T cultivars, we resolved the complete sequences of 78 L1 insertions arising in vitro in the absence of L1 overexpression systems. ONT sequencing applied to hepatitis B virus (HBV) positive liver cancer tissues located a single HBV insertion. These experiments demonstrate reliable resolution of retrotransposon and exogenous virus insertions via ONT sequencing. That we found no evidence of SARS-CoV-2 integration suggests such events in vivo are highly unlikely to drive later oncogenesis or explain post-recovery detection of the virus.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://www.ncbi.nlm.nih.gov/sra/?term=PRJEB44816

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 30, 2021.
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Human genome integration of SARS-CoV-2 contradicted by long-read sequencing
Nathan Smits, Jay Rasmussen, Gabriela O. Bodea, Alberto A. Amarilla, Patricia Gerdes, Francisco J. Sanchez-Luque, Prabha Ajjikuttira, Naphak Modhiran, Benjamin Liang, Jamila Faivre, Ira W. Deveson, Alexander A. Khromykh, Daniel Watterson, Adam D. Ewing, Geoffrey J. Faulkner
bioRxiv 2021.05.28.446065; doi: https://doi.org/10.1101/2021.05.28.446065
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Human genome integration of SARS-CoV-2 contradicted by long-read sequencing
Nathan Smits, Jay Rasmussen, Gabriela O. Bodea, Alberto A. Amarilla, Patricia Gerdes, Francisco J. Sanchez-Luque, Prabha Ajjikuttira, Naphak Modhiran, Benjamin Liang, Jamila Faivre, Ira W. Deveson, Alexander A. Khromykh, Daniel Watterson, Adam D. Ewing, Geoffrey J. Faulkner
bioRxiv 2021.05.28.446065; doi: https://doi.org/10.1101/2021.05.28.446065

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