The questions

SARS-CoV-2 — the virus responsible for the COVID-19 pandemic — has a greater impact on human health than other respiratory viruses have, although the mechanisms of this are not fully understood. Further questions are the molecular basis of the long-term consequences of COVID-19, known as ‘long COVID’, and why SARS-CoV-2 seems to accelerate human aging. One potential explanation for these observations is that SARS-CoV-2 causes damage to nuclear DNA — the only irreplaceable cell component. We therefore aimed to test the hypothesis that damage to nuclear DNA might be the underlying cause of the many severe consequences of SARS-CoV-2 infection.

The discovery

To establish whether SARS-CoV-2 infection results in activation of the DNA damage response (DDR), we infected human cell lines with SARS-CoV-2 and performed immunoblot analysis of DDR markers. We showed that SARS-CoV-2 infection activated the DDR, and we confirmed the presence of DNA fragmentation through the use of comet assays. These events were accompanied by pro-inflammatory signaling and the establishment of cellular senescence (a form of cellular aging).

We next probed the molecular mechanisms that caused the DNA damage. We discovered that SARS-CoV-2 expresses proteins that, by distinct mechanisms, hijack cell nucleotide metabolism. Specifically, the viral factors ORF6 and NSP13 promoted the degradation of checkpoint kinase 1 (CHK1), an enzyme involved in coordinating the DDR. A reduction in CHK1 levels is thought to result in the accumulation of rNTPs, which we propose is needed to fuel viral replication (SARS-CoV-2 being a RNA virus). However, the accumulation of rNTPs seemed to occur at the expense of dNTPs, which we detected at lower levels after SARS-CoV-2 infection and which resulted in impaired DNA replication and DNA damage.

In addition, we found evidence that DNA breaks accumulated because they were not efficiently repaired. Indeed, we discovered that the SARS-Cov-2 nucleocapsid protein impaired focal recruitment of the binding protein 53BP1 and decreased DNA repair by competing with 53BP1 for association with damage-induced long non-coding RNAs. Overall, these findings suggest that SARS-CoV-2 both induces DNA damage and impairs its repair, ultimately causing cells to age and spread inflammation (Fig. 1). Finally, we demonstrated that these events happened in vivo in SARS-CoV-2-infected mice and in patients with COVID-19.

Fig. 1: Impact of SARS-CoV-2 infection on genome integrity and cellular senescence.
figure 1

Schematic of the events that follow SARS-CoV-2 infection and lead to reduced genomic integrity, with subsequent inflammation and cellular senescence. Two mechanisms are presented. In one (left), depletion of CHK1 leads to loss of the ribonucleoside-diphosphate reductase subunit RRM2, which results in a reduction in cellular levels of dNTPs and DNA replication stress. In the other (right), the SARS-CoV-2 nucleocapsid (N) protein binds to damage-induced long non-coding RNAs (dilncRNAs), which results in inactivation of 53BP1 and defects in DNA repair. © 2023, Gioia, U. et al., CCBY 4.0.

Full size image

The implications

Our findings reveal the profound impact that SARS-CoV-2 infection has on cellular biology, threatening the most important cellular constituent: nuclear DNA. The accumulation of DNA damage is known to be associated with cancer and aging1. Although the long-term consequences of severe COVID-19 on lung cancer incidence are unknown at present, accelerated aging phenotypes have been reported2,3. Our results may provide a mechanistic explanation for post-COVID-19 syndromes with hastened aging features, to which the establishment of cellular senescence and the triggering of inflammatory processes might be a crucial contributing factor. Indeed, chronic inflammation is thought to be the underlying cause of lung fibrosis4, brain degeneration5 and overall frailty. Thus, local events initially restricted to the respiratory system may have systemic consequences.

Our study does not exclude the possibility that additional viral gene products also threaten genome stability by hitherto unknown mechanisms. Moreover, whether the mechanisms described here are altered in the various SARS-CoV-2 variants remains unknown. In the future, it will be interesting to explore the possibility of exploiting the altered nucleotide metabolism of SARS-CoV-2-infected cells to develop anti-viral strategies or interventions aimed at taming the cellular consequences of COVID-19.

Fabrizio d’Adda di Fagagna1,2

1The AIRC Institute of Molecular Oncology (IFOM ETS), Milan, Italy.

2Institute of Molecular Genetics (IGM), National Research Institute (CNR), Pavia, Italy.

Expert opinion

“I believe that this manuscript presents important information to broadly understand host–viral pathogen interactions, as they relate specifically to the induction of a DDR. Most viruses will need to develop mechanisms to modulate the DDR, as exemplified here.” An anonymous reviewer.

Behind the paper

The trigger for this work can be traced back to attendance at a conference in 2019, where I heard that two thirds of transcripts in SARS-CoV-2-infected cells are of viral origin. This immediately sparked in my mind the idea that infected cells must be under tremendous pressure to triple their normal RNA-synthesis capacity, which cannot be without consequences on nucleotide availability for cellular functions. Although I do not lead a molecular virology group at present, I did my PhD studies on human immunodeficiency virus type 1, and it was good to resurrect my passion for this area of research and put to good use that frame of mind. Finally, having previously demonstrated the relevance of chromosomal DNA damage and DDR activation in telomere-induced and oncogene-induced cellular senescence, I am glad to have extended here the relevance of that paradigm to virus-induced senescence. F.d’A.d.F.

From the editor

“This study adds an important dimension to the understanding of the impact of SARS-CoV-2 infection on cells by describing how it interferes with DNA repair and causes lingering damage, while tying it in with the growing body of work indicating SARS-CoV-2 infection causes cellular senescence.” Melina Casadio, Senior Editor, Nature Cell Biology.