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.

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 the virus integrated into the genome. By examining ONT data from separate HEK293T cultivars, we completely resolved 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 are, at most, extremely rare in vivo, and therefore are unlikely to drive oncogenesis or explain post-recovery detection of the virus.