No evidence of human genome integration of SARS-CoV-2 found by long-read DNA 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

doi:10.1016/j.celrep.2021.109530

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

Cell Rep. 2021 Aug 17;36(7):109530. doi: 10.1016/j.celrep.2021.109530. Epub 2021 Jul 28.

Authors

Affiliations

¹ Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia.
² Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
³ Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
⁴ School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
⁵ 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.
⁶ INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France.
⁷ 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.
⁸ 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.
⁹ Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia. Electronic address: [email protected].

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.

Keywords: COVID-19; L1; LINE-1; SARS-CoV-2; hepatitis B virus; retrotransposon.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

Aged
Animals
COVID-19 / diagnosis
COVID-19 / virology*
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*

Substances

DNA, Viral