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No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing.
Smits, Nathan; Rasmussen, Jay; Bodea, Gabriela O; Amarilla, Alberto A; Gerdes, Patricia; Sanchez-Luque, Francisco J; Ajjikuttira, Prabha; Modhiran, Naphak; Liang, Benjamin; Faivre, Jamila; Deveson, Ira W; Khromykh, Alexander A; Watterson, Daniel; Ewing, Adam D; Faulkner, Geoffrey J.
  • Smits N; Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia.
  • Rasmussen J; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
  • Bodea GO; Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
  • Amarilla AA; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
  • Gerdes P; Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia.
  • Sanchez-Luque FJ; GENYO, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK.
  • Ajjikuttira P; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
  • Modhiran N; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
  • Liang B; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
  • Faivre J; INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France.
  • Deveson IW; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
  • Khromykh AA; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD 4072, Australia.
  • Watterson D; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD 4072, Australia.
  • Ewing AD; Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia.
  • Faulkner GJ; Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia. Electronic address: faulknergj@gmail.com.
Cell Rep ; 36(7): 109530, 2021 08 17.
Article in English | MEDLINE | ID: covidwho-1330686
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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ABSTRACT
A recent study proposed that 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 apply deep (>50×) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2 and do not find the virus integrated into the genome. By examining ONT data from separate HEK293T cultivars, we completely resolve 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 by ONT sequencing. That we find no evidence of SARS-CoV-2 integration suggests that such events are, at most, extremely rare in vivo and therefore are unlikely to drive oncogenesis or explain post-recovery detection of the virus.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA, Viral / Genome, Human / Virus Integration / Sequence Analysis, DNA / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Evidence synthesis Topics: Long Covid Limits: Aged / Animals / Humans / Male Language: English Journal: Cell Rep Year: 2021 Document Type: Article Affiliation country: J.celrep.2021.109530

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Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA, Viral / Genome, Human / Virus Integration / Sequence Analysis, DNA / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Evidence synthesis Topics: Long Covid Limits: Aged / Animals / Humans / Male Language: English Journal: Cell Rep Year: 2021 Document Type: Article Affiliation country: J.celrep.2021.109530