The detection of viral DNA is considered crucial in both diagnosis and prognosis. Nowadays, molecular diagnostic approaches represent the most promising tools for the clinical detection of viral infections. This review aims to investigate the most used and promising DNA-based technologies for viral detection, focusing on herpesviruses because of their ability to undergo latent and reactivation cycles, persisting lifelong in the host in association with several diseases. Molecular technologies, such as PCR-based assays, enhance sensitivity and specificity in identifying viral DNA from clinical samples such as blood, cerebrospinal fluid and saliva, indicating PCR and its derivatives as the gold standard methods for herpesvirus detection. In conclusion, this review underscores the need for continuous innovation in diagnostic methodologies to address the complexities of herpesvirus identification in different clinical samples.

Flaviviruses, such as dengue and West Nile, cause diverse clinical symptoms and trigger varied clinical outcomes, partly driven by the secreted nonstructural sNS1 protein (sNS1). This study examined how sNS1 from neurotropic and hemorrhagic flaviviruses affects coagulation and inflammation using human monocytic (THP-1) cells. sNS1 from neurotropic viruses (e.g., West Nile, Japanese encephalitis) increased tissue factor (TF) expression and the release of TF-bearing microvesicles, promoting procoagulant activity. In contrast, sNS1 from hemorrhagic viruses (e.g., dengue) showed anticoagulant effects. These divergent responses correlated with the virus-specific modulation of interleukin-6 (IL-6), suggesting that inflammation plays a central role in sNS1-mediated vascular changes. The findings identify sNS1 as a key virulence factor influencing flavivirus pathogenesis through hemostatic and immune pathways, offering a potential target for therapeutic intervention.

Human Leukocyte Antigen-G (HLA-G) is a key immunomodulatory molecule with multiple isoforms, including recently identified variants lacking the α1 domain (HLA-G Δα1). The absence of the α1 domain may reduce immune inhibition, particularly of Natural Killer (NK) cells, which are often suppressed during viral infections such as SARS-CoV-2. This suggests a novel immune regulatory mechanism that could mitigate COVID-19-related complications, including coagulopathies. This study investigates the influence of full-length and Δα1 HLA-G isoforms in NK-cell activity in vitro during SARS-CoV-2 infection and whether their expression associates with viral persistence and coagulopathy in COVID-19 patients, using vascular specimens retrieved from surgical procedures. RCC7 cell lines engineered to express either the full-length or Δα1 form of HLA-G were infected with Omicron SARS-CoV-2 to assess NK cell-mediated cytotoxicity in a co-culture system. Contrary to full-length, Δα1 HLA-G only partially inhibited NK activation, allowing greater cytotoxicity and higher IFN-I/II expression. To evaluate clinical relevance, vascular tissues from coagulopathic COVID-19 patients were analyzed for in situ SARS-CoV-2 persistence and HLA-G isoform expression. SARS-CoV-2 negative tissues more frequently expressed Δα1 and displayed higher systemic interferon (IFNs) levels. Among infection-positive cases, Δα1 expression was also associated with stronger IFN-β and IFN-γ responses. These in vivo trends mirror in vitro findings, supporting a model in which full-length HLA-G dampens NK-mediated clearance of infected vascular cells, favoring viral persistence and potentially contributing to immunothrombosis, while Δα1 permits enhanced antiviral immunity. Overall, these findings identify distinct immunomodulatory roles for HLA-G isoforms in SARS-CoV-2 infection. The Δα1 variant exhibits reduced inhibitory potency, partially preserving NK-cell antiviral functions and modulating interferon responses, whereas full-length HLA-G may facilitate vascular viral persistence and coagulopathy. HLA-G isoform profiling may thus represent a novel biomarker and therapeutic target in COVID-19 associated vascular pathology.

Natural killer (NK) cells are central to antiviral immunity through a balance of activating and inhibitory receptors, including killer immunoglobulin-like receptors (KIRs). We have previously observed that an increased frequency of the inhibitory receptor KIR2DL2 and its ligand HLA-C1 is associated with heightened susceptibility to human herpesvirus (HHV) infection, supporting a role for KIR-mediated NK cell regulation in host–virus interactions. We investigated whether the co-infection of SARS-CoV-2 and human herpesvirus 6 (HHV-6) might be connected to the expression of KIR2DL2/HLA-C1. We analyzed 110 SARS-CoV-2-positive subjects and 109 SARS-CoV-2-negative subjects for the KIR2DL2 and HLA-C1 genotype and for HHV-6A/B reactivation in plasma samples. SARS-CoV-2-positive subjects showed a significantly higher frequency of the KIR2DL2/HLA-C1 haplotype and increased reactivation of HHV-6A. Among deceased and comorbid patients, the co-occurrence of the KIR2DL2/HLA-C1 haplotype and HHV-6A DNAemia was more frequent, particularly in those with cardiovascular disorders. These findings suggest that the KIR2DL2/HLA-C1 haplotype might promote NK cell inhibition, facilitating HHV-6A persistence and contributing to immune dysregulation during SARS-CoV-2 infection. The combined presence of KIR2DL2/HLA-C1 and HHV-6A may, therefore, represent a molecular signature of COVID-19 outcomes.

Polyomaviruses are a family of small DNA viruses capable of establishing persistent infections, and they can pose significant pathogenic risks in immunocompromised hosts. While traditionally studied in the context of viral reactivation and immune suppression, recent evidence has highlighted the gut microbiota as a critical regulator of host immunity and viral pathogenesis. This review examines the complex interactions between polyomaviruses, the immune system, and intestinal microbiota, emphasizing the role of short-chain fatty acids (SCFAs) in modulating antiviral responses. We explore how dysbiosis may facilitate viral replication, reactivation, and immune escape and also consider how polyomavirus infection can, in turn, alter microbial composition. Particular attention is given to the Firmicutes/Bacteroidetes ratio as a potential biomarker of infection risk and immune status. Therapeutic strategies targeting the microbiota, including prebiotics, probiotics, and fecal microbiota transplantation (FMT), are discussed as innovative adjuncts to immune-based therapies. Understanding these tri-directional interactions may offer new avenues for mitigating disease severity and improving patient outcomes during viral reactivation.