Viruses

Human adenoviruses (HAdV) comprise more than 100 genotypes with species-specific differences in tropism and immune response and can cause severe infections in immunocompromised patients. This study aimed to characterise the HAdV species involved in pediatric infections to assess their clinical impact and guide future therapeutic strategies based on AdV-specific T-cell responses. Between January and October 2024, 595 pediatric HAdV diagnoses were made at the Bambino Gesù Children’s Hospital (Rome), and whole-genome sequencing was performed on 60 samples. Most patients (91.7%) were hospitalised, including both immunocompetent (75%) and immunocompromised (25%) children. Gastrointestinal and respiratory symptoms were more common in immunocompetent patients, whereas immunocompromised patients experienced longer hospitalisations and persistent viral infections. Species F (F41) was most prevalent (63.3%), especially among immunocompetent patients, while species C and A predominated in immunocompromised children, with species A associated with severe disease. Viral loads were significantly higher for species F than for species A and C, independent of immune status. Co-infections were frequent (63.3%), with species C particularly linked to them. In conclusion, HAdV distribution differed by immune status, with species F predominating in immunocompetent children and species C and A more common in immunocompromised patients. Whole-genome sequencing may enhance surveillance, enable earlier diagnosis, and support the development of genotype-specific immunotherapies.

Merbecovirus, a subgenus of coronaviruses that includes the highly pathogenic Middle East respiratory syndrome coronavirus (MERSr-CoV), poses a significant zoonotic threat. To better understand its host adaptation and potential for cross-species transmission, we conducted a comprehensive analysis of codon usage patterns in 1967 Merbecovirus sequences. Phylogenetic analysis confirmed the division of Merbecoviruses into seven distinct clusters. Codon usage bias was found to be low and predominantly shaped by natural selection, with a consistent A/U-rich composition across the genome. Codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analyses indicate that Merbecovirus exhibits potential host adaptation to Sus scrofa (pigs), Equus caballus (horses), and Oryctolagus cuniculus (rabbits), suggesting a risk of cross-species transmission. Strikingly, this genomic-level adaptation prediction is supported by emerging functional evidence: recent studies have demonstrated that key Merbecovirus lineages utilize diverse cell entry receptors (DPP4 or ACE2), a fundamental determinant of host tropism. For instance, the ability of the HKU5 lineage to utilize ACE2 receptors from mustelids like minks (Neogale vison) provides mechanistic support for the host adaptability trends inferred from our genomic analyses. By integrating existing receptor specificity data, this study provides the first systematic, large-scale analysis of codon usage across the Merbecovirus subgenus, elucidating key mechanisms of genomic adaptation and viral evolution. Our analytical framework provides a novel comparative perspective on host diversity and pinpoints specific surveillance priorities for mitigating future spillover risks.

Enterovirus D68 (EV-D68) is a significant global pathogen associated with severe respiratory infections and acute flaccid myelitis in children. Currently, there are no vaccines or antiviral drugs available for EV-D68, and a robust model to elucidate the pathogenesis of EV-D68 and evaluate treatment methods is lacking. We developed a mouse-adapted EV-D68 strain that caused progressive limb paralysis after intramuscular inoculation in 7-day-old mice. Viral load analysis showed that the skeletal muscle and spinal cord had the highest titers and most severe injuries. RNA sequencing of the infected muscle, brain, spinal cord, and lung tissues revealed differentially expressed genes (DEGs) associated with viral infection and pathogenesis. DEGs were significantly enriched in various pathways associated with antiviral immunity, interferon responses, and cytokine signaling. In the spinal cord, DEGs highlighted mitochondrial dysfunction and oxidative stress as crucial contributors to neural damage. Flow cytometry analysis of spinal cord cells showed that EV-D68 activates the immune system, leading to systemic inflammation and significant increases in CD8⁺ and CD4⁺ T cells, but limited neutrophil and monocyte infiltration. This mouse model provides a valuable tool for studying EV-D68 pathogenesis and evaluating antiviral and vaccine efficacy, thereby advancing the understanding of its neuropathological mechanisms. Importance: We developed a novel mouse model of EV-D68 that provides a valuable tool for studying its pathogenesis and evaluating antiviral and vaccine efficacy, deepening the understanding of its neuropathological basis.