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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 LU orcid ; Sanchez-Luque, Francisco J ; Ajjikuttira, Prabha ; Modhiran, Naphak ; Liang, Benjamin and Faivre, Jamila , et al. (2021) In Cell Reports 36(7). p.1-8
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... (More)

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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publishing date
type
Contribution to journal
publication status
published
subject
keywords
Aged, Animals, COVID-19/diagnosis, Carcinoma, Hepatocellular/virology, Chlorocebus aethiops, DNA, Viral/genetics, Genome, Human, HEK293 Cells, Hepatitis B virus/genetics, Host-Pathogen Interactions, Humans, Liver Neoplasms/virology, Long Interspersed Nucleotide Elements, Male, Nanopore Sequencing, SARS-CoV-2/genetics, Sequence Analysis, DNA, Vero Cells, Virus Integration
in
Cell Reports
volume
36
issue
7
article number
109530
pages
1 - 8
publisher
Cell Press
external identifiers
  • scopus:85111892448
  • pmid:34380018
ISSN
2211-1247
DOI
10.1016/j.celrep.2021.109530
language
English
LU publication?
no
additional info
Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.
id
8caa4b8f-ca61-4659-80f0-20c52f348831
date added to LUP
2024-06-10 16:06:59
date last changed
2024-06-12 03:06:27
@article{8caa4b8f-ca61-4659-80f0-20c52f348831,
  abstract     = {{<p>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 (&gt;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.</p>}},
  author       = {{Smits, Nathan and Rasmussen, Jay and Bodea, Gabriela O and Amarilla, Alberto A and Gerdes, Patricia and Sanchez-Luque, Francisco J and Ajjikuttira, Prabha and Modhiran, Naphak and Liang, Benjamin and Faivre, Jamila and Deveson, Ira W and Khromykh, Alexander A and Watterson, Daniel and Ewing, Adam D and Faulkner, Geoffrey J}},
  issn         = {{2211-1247}},
  keywords     = {{Aged; Animals; COVID-19/diagnosis; Carcinoma, Hepatocellular/virology; Chlorocebus aethiops; DNA, Viral/genetics; Genome, Human; HEK293 Cells; Hepatitis B virus/genetics; Host-Pathogen Interactions; Humans; Liver Neoplasms/virology; Long Interspersed Nucleotide Elements; Male; Nanopore Sequencing; SARS-CoV-2/genetics; Sequence Analysis, DNA; Vero Cells; Virus Integration}},
  language     = {{eng}},
  month        = {{08}},
  number       = {{7}},
  pages        = {{1--8}},
  publisher    = {{Cell Press}},
  series       = {{Cell Reports}},
  title        = {{No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing}},
  url          = {{http://dx.doi.org/10.1016/j.celrep.2021.109530}},
  doi          = {{10.1016/j.celrep.2021.109530}},
  volume       = {{36}},
  year         = {{2021}},
}