Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues

Abstract

Prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and recurrence of PCR-positive tests have been widely reported in patients after recovery from COVID-19, but some of these patients do not appear to shed infectious virus. We investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the DNA of human cells in culture and that transcription of the integrated sequences might account for some of the positive PCR tests seen in patients. In support of this hypothesis, we found that DNA copies of SARS-CoV-2 sequences can be integrated into the genome of infected human cells. We found target site duplications flanking the viral sequences and consensus LINE1 endonuclease recognition sequences at the integration sites, consistent with a LINE1 retrotransposon-mediated, target-primed reverse transcription and retroposition mechanism. We also found, in some patient-derived tissues, evidence suggesting that a large fraction of the viral sequences is transcribed from integrated DNA copies of viral sequences, generating viral–host chimeric transcripts. The integration and transcription of viral sequences may thus contribute to the detection of viral RNA by PCR in patients after infection and clinical recovery. Because we have detected only subgenomic sequences derived mainly from the 3′ end of the viral genome integrated into the DNA of the host cell, infectious virus cannot be produced from the integrated subgenomic SARS-CoV-2 sequences.

Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome

“…However, one recent study revealed that SARS-CoV-2 infection induced retrotransposon activation, leading to the formation of chimeric virus-retrotransposon RNA (Yin et al, 2021 ). Zhang et al also observed the host genome integration of SARS-CoV-2 under overexpressing LINE1 in cultured human cells (Zhang et al, 2021 ). These reports indicate a likely chance of SARS-CoV-2 integration into host genome (Yin et al, 2021 ; Zhang et al, 2021 ), which have fueled concerns about its potential long-term health threat in the infected individuals.…”

“…Zhang et al also observed the host genome integration of SARS-CoV-2 under overexpressing LINE1 in cultured human cells (Zhang et al, 2021 ). These reports indicate a likely chance of SARS-CoV-2 integration into host genome (Yin et al, 2021 ; Zhang et al, 2021 ), which have fueled concerns about its potential long-term health threat in the infected individuals. Thus, more evidences are explicitly required to address this issue.…”

“…Recently, Zhang et al reported that SARS-CoV-2 RNA might integrate into host genome via reverse-transcription, and overexpressed LINE1 might stimulate the reverse-transcribed SARS-CoV-2 integration into host genome (Zhang et al, 2021 ), which prompted us to determine whether or not the correlation of chimeric events with high expression of host genes was attributed to the viral integration into the locations of DNA elements, such as promoters and enhancers. We first analyzed the number of chimeric genes in each chromosome, and didn’t identify any evidence of preferred viral integration into some chromosomes (Fig.…”

Immunological profiling of COVID-19 patients with pulmonary sequelae

“…Prolonged viral RNA shedding may induce clonal expansion of NK cells in an antigen-specific manner, similar to the response to cytomegalovirus infection to acquiring memory features (38). Since reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues (39), there might also be latent SARSCoV-2 virus in the reservoir cells in PPSs that could lead to the prolonged expansion of NK cells. Although our study confirms some findings and provides new data on the innate and adaptive immune landscape of patients with PS who have recovered from COVID-19 one year after discharge, we recognize limitations that might be overcome with larger sample sizes and matched control populations.…”

Clinical Validation of Automated and Rapid MariPOC SARS-CoV-2 Antigen Test

“…Their data suggests that virion and subgenomic RNAs are stable in cellular doublemembrane vesicles and, therefore, can be detected long after the acute infection 22 . Furthermore, Zhang et al (2021) found that parts of the reverse-transcribed SARS-CoV-2 RNA can integrate into the human genome without the ability to yield infectious viruses and suggest that this could explain at least partly the long term RNA shedding 23 .…”