Persistent DNA methylation changes after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a population-based setting

Epigenetic mechanisms are responsible for regulating gene expression independent from changes in DNA sequence. DNA methylation (DNAm) is an epigenetic mechanism involving the enzymatic addition of a methyl group to cytosine residues at cytosine-guanine positions. This mechanism plays an important role in the regulation of gene expression and human development and alterations in its patterns have been identified in diseases like cancer, immune and metabolic disorders (PMID: 30479381). Infectious agents have also been observed to alter the host’s epigenetic landscape, where viral agents profit from the host’s epigenetic mechanisms to allow for viral replication, as well as for the spread and persistence of disease (PMID: 33087172, 24890513, 27173930). DNA methylation changes have been observed to regulate the viral activity of DNA and RNA viruses (e.g. human papillomavirus [HPV], hepatitis B, herpes viruses [EBV, KS], HIV) (PMID: 19208682, 32991266, 32712664). Altered methylation patterns have been observed in respiratory tract infections due to influenza and coronaviruses (e.g. Middle Eastern respiratory syndrome coronavirus [MERS-CoV] and SARS-CoV-1) (PMID: 29339515, 33087172). Importantly, DNAm measured in blood reflects methylation patterns from circulating immune cells and thus offers a snapshot of the underlying immunological processes. Considering the significant multi-dimensional impact of the ongoing pandemic and the heterogeneity of COVID-19 disease and related outcomes, a better understanding of the molecular mechanisms and identification of potential biomarkers related to disease severity and long-term outcomes is required.
    A few studies investigating DNAm changes in relation to COVID-19 infection have been conducted with samples from the acute phase of hospitalized moderate-to-severe patients, mostly within the first 14 days after admission. These studies have identified COVID-19-specific differentially methylated regions in comparison to healthy controls and other viral infections (PMID: 33296687, 33464637, 34034806, 33867313). Hypomethylation of regulatory regions of genes involved in inflammatory and cytokine response and changes in blood cell proportions have been reported (PMID: 33464637, 33296687), as well as worse outcomes have been related to hypermethylation of specific regions (PMID: 34034806). Epigenetic age acceleration has also been identified as associated with COVID-19 infection and poorer health outcomes (PMID: 33464637), although no significant differences in epigenetic aging were identified when comparing pre-pandemic healthy controls to individuals who acquired COVID-19 (PMID: 34034806). A first DNAm signature to predict mild and severe progression of COVID-19 infections, EPICOVID, has been developed in patients free of additional comorbidities (PMID: 33867313). All in all, previous research has focused on the initial days after infection and/or hospitalization, with relatively small samples of hospitalized patients (12 samples in PMID: 33296687, 32 samples in PMID: 33464637, 124 samples in PMID: 34034806) and cases with mild disease but no comorbidities (up to 407 patients in PMID: 33867313). These recent reports offer evidence that DNAm is modulated as a consequence of SARS-CoV-2 infection, although it is unclear how these changes translate to the general population – a setting in which comorbidities are present and a wide range of disease severity has been observed –, and if immune function-associated epigenetic patterns persist over time.
    In view of the novelty of the disease and scarcity of population-based data, the aim of this project is to identify epigenetic changes associated to disease severity by comparing DNAm profiles from individuals with asymptomatic and mild/moderate infections to those of age- and sex-matched controls up to 4 months after infection. Likewise, a secondary aim is to assess whether these changes replicate DNAm findings from acute infections or if these reflect a distinct convalescent immunological scenario, thus contributing to better understanding the longitudinal trajectory of DNAm changes in COVID-19. Addressing these research questions will enable the identification of epigenetic sub-phenotypes present in the general population, as well as offer epidemiological insights into COVID-19 susceptibility and prognosis.