tetano
Editor, Senior Moderator
Cell Rep
. 2021 Jul 28;109530.
doi: 10.1016/j.celrep.2021.109530. Online ahead of print.
No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing
Nathan Smits[SUP] 1 [/SUP], Jay Rasmussen[SUP] 2 [/SUP], Gabriela O Bodea[SUP] 3 [/SUP], Alberto A Amarilla[SUP] 4 [/SUP], Patricia Gerdes[SUP] 1 [/SUP], Francisco J Sanchez-Luque[SUP] 5 [/SUP], Prabha Ajjikuttira[SUP] 2 [/SUP], Naphak Modhiran[SUP] 4 [/SUP], Benjamin Liang[SUP] 4 [/SUP], Jamila Faivre[SUP] 6 [/SUP], Ira W Deveson[SUP] 7 [/SUP], Alexander A Khromykh[SUP] 8 [/SUP], Daniel Watterson[SUP] 8 [/SUP], Adam D Ewing[SUP] 1 [/SUP], Geoffrey J Faulkner[SUP] 9 [/SUP]
Affiliations
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.
. 2021 Jul 28;109530.
doi: 10.1016/j.celrep.2021.109530. Online ahead of print.
No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing
Nathan Smits[SUP] 1 [/SUP], Jay Rasmussen[SUP] 2 [/SUP], Gabriela O Bodea[SUP] 3 [/SUP], Alberto A Amarilla[SUP] 4 [/SUP], Patricia Gerdes[SUP] 1 [/SUP], Francisco J Sanchez-Luque[SUP] 5 [/SUP], Prabha Ajjikuttira[SUP] 2 [/SUP], Naphak Modhiran[SUP] 4 [/SUP], Benjamin Liang[SUP] 4 [/SUP], Jamila Faivre[SUP] 6 [/SUP], Ira W Deveson[SUP] 7 [/SUP], Alexander A Khromykh[SUP] 8 [/SUP], Daniel Watterson[SUP] 8 [/SUP], Adam D Ewing[SUP] 1 [/SUP], Geoffrey J Faulkner[SUP] 9 [/SUP]
Affiliations
- PMID: 34380018
- DOI: 10.1016/j.celrep.2021.109530
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.