Biology subjects

Lavezzo, E.

Publications and source records attributed to Lavezzo, E..

5 recordsLinked to original sources

bioRxiv2026

Extensive and heterogeneous viral circular RNA production during Zika virus infection

Circular RNAs (circRNAs) are covalently closed RNA molecules with regulatory functions. Although virus-derived circRNAs (vcircRNAs) are well characterized in DNA viruses, their occurrence in RNA viruses remains poorly understood. Recent reports in coronaviruses and hepatitis C virus suggest that vcircRNA production extends beyond nuclear-replicating viruses. Here, we show that Zika virus (ZIKV), a vector-borne orthoflavivirus, produces vcircRNAs during infection of neural stem cells. Using a custom computational pipeline optimized for viral back-splice junction detection, we identified at 72 hours post infection a core set of 113 putative vcircRNAs shared across three biological replicates and distributed throughout the viral genome. Eight candidates spanning different genomic regions and abundance levels were experimentally validated by rolling-circle reverse transcription and Nanopore sequencing. These findings provide the first evidence of vcircRNA production in an orthoflavivirus, suggesting that circular RNA biogenesis may represent a previously underappreciated feature of RNA virus biology.

microbiology↗

bioRxiv2026

First detection and characterization of Alongshan virus in Ixodes ricinus ticks from Italy, 2021-2022

Alongshan virus (ALSV) is an emerging tick-borne segmented RNA virus belonging to the Jingmenvirus group and has been reported in humans, ticks, and vertebrates across Asia and Europe. Despite its potential public health relevance, its distribution and genetic diversity remain poorly characterized in several European regions where tick-borne pathogens are endemic. In this study, we developed a specific TaqMan-based real-time RT-PCR assay targeting a conserved region of ALSV segment 2 and used it to investigate the presence of ALSV RNA in Ixodes ricinus ticks collected in northeastern Italy. The assay showed high linearity over a broad dynamic range and no cross-reactivity with related flaviviruses. A total of 212 archival tick samples collected between March 2021 and November 2022 were screened, and 28 samples (13.2%) tested positive for ALSV RNA. Positive ticks were detected in the provinces of Belluno and Vicenza and included individual adult males and nymph pools. A subset of positive samples was further characterized by nested PCR and Sanger sequencing of all four genomic segments. Phylogenetic analyses showed that Italian ALSV sequences clustered within the broader European ALSV diversity and were closely related to strains from Central and Northern Europe, without forming a distinct country-specific lineage. Sequence comparisons suggested purifying selection and revealed differences in predicted structural proteins between European and Chinese strains. These findings provide the first molecular evidence of ALSV circulation in Italy and support further studies to clarify its epidemiology, host range, genetic diversity, and potential clinical relevance. IMPORTANCEAlongshan virus (ALSV) is an emerging tick-borne virus identified in febrile patients in China and subsequently detected in ticks in Russian Federation and several European countries. Although severe disease has not yet been reported in humans, surveillance and elucidation of the virus distribution are essential to assess its pathogenicity and potential public health impact. We developed a specific real-time RT-PCR protocol and detected ALSV in Ixodes ricinus ticks collected in northeastern Italy. Sequence analyses suggested multiple introductions and revealed differences in structural proteins between European and Chinese strains, suggesting potential adaptation and differences in pathogenicity. Since the clinical signs of ALSV infection in humans may overlap with those of tick-borne encephalitis (TBE), differential diagnostic procedures should be developed to improve patient management, particularly in TBE-endemic regions such as northeastern of Italy.

microbiology↗

bioRxiv2024

VirNA: a novel Minimum Spanning Networks algorithm for investigating viral evolution

Next Generation Sequencing technologies are essential in public health surveillance for tracking pathogen evolution, spread, and the emergence of new variants. However, the extensive sequencing of viral genomes during recent pandemics has highlighted the limitations of traditional molecular phylogenetic algorithms in capturing fine-grained evolutionary details, emphasizing the urge for more effective approaches to manage these large-scale data. VirNA (Viral Network Analyzer) addresses this challenge by reconstructing detailed mutation patterns and tracing pathogen evolutionary routes in specific regions through Minimum Spanning Networks. It analyzes thousands of sequences, generating networks where nodes represent identical genomic sequences linked to their metadata, while edges represent evolutionary pathways. AUTHOR SUMMARYThe authors present Viral Network Analyzer (VirNA), a new tool designed to help track the spread of viruses during pandemics. During recent outbreaks, researchers faced challenges due to the sheer volume of viral genome data. Traditional tools struggled to process this massive amount of information effectively. VirNA solves this problem by using a powerful method called Minimum Spanning Networks (MSN) with enhanced features to analyze large datasets quickly and accurately. VirNA allows scientists to map how viruses spread in specific areas, providing critical insights that other tools couldnt achieve. It complements traditional phylogenetic methods, offering a detailed look at viral transmission routes. This makes it a valuable asset for public health surveillance, helping experts understand and respond to pandemics more effectively. Already tested in previous studies, VirNA represents a significant breakthrough for future pandemic preparedness, offering new ways to handle and interpret big data in viral research.

bioinformatics↗

bioRxiv2021

Rapid longitudinal SARS-CoV-2 intra-host emergence of novel haplotypes regardless of immune deficiencies

On February 2020, the municipality of Vo, a small town near Padua (Italy), was quarantined due to the first coronavirus disease 19 (COVID-19)-related death detected in Italy. The entire population was swab tested in two sequential surveys. Here we report the analysis of the viral genomes, which revealed that the unique ancestor haplotype introduced in Vo belongs to lineage B and, more specifically, to the subtype found at the end of January 2020 in two Chinese tourists visiting Rome and other Italian cities, carrying mutations G11083T and G26144T. The sequences, obtained for 87 samples, allowed us to investigate viral evolution while being transmitted within and across households and the effectiveness of the non-pharmaceutical interventions implemented in Vo. We report, for the first time, evidence that novel viral haplotypes can naturally arise intra-host within an interval as short as two weeks, in approximately 30% of the infected individuals, regardless of symptoms severity or immune system deficiencies. Moreover, both phylogenetic and minimum spanning network analyses converge on the hypothesis that the viral sequences evolved from a unique common ancestor haplotype, carried by an index case. The lockdown extinguished both viral spread and the emergence of new variants, confirming the efficiency of this containment strategy. The information gathered from household was used to reconstructs possible transmission events. AUTHOR SUMMARYIt is of great interest and importance to understand SARS-CoV-2 ability to mutate generating new viral strains, and to assess the impact of containment strategies on viral transmission. In this study we highlight the rapid intra-host haplotype evolution regardless of symptom severity and immune deficiencies that we observed during the first wave of the pandemic in the municipality of Vo in Italy. The confirmation that all the haplotypes found in this small community derive from a common ancestor haplotype, has allowed us to track the rapid emergence of new variants but lockdown and mass testing efficiently prevented their spread elsewhere.

evolutionary biology↗

bioRxiv2018

G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide

G-quadruplexes are non-canonical nucleic acid structures that control transcription, replication, and recombination in organisms. G-quadruplexes are present in eukaryotes, prokaryotes, and viruses. In the latter, mounting evidence indicates their key biological activity. Since data on viruses are scattered, we here present a comprehensive analysis of putative G-quadruplexes in the genome of all known viruses that can infect humans. We show that the presence, distribution, and location of G-quadruplexes are features characteristic of each virus class and family. Our statistical analysis proves that their presence within the viral genome is orderly arranged, as indicated by the possibility to correctly assign up to two-thirds of viruses to their exact class based on the G-quadruplex classification. For each virus we provide: i) the list of all G-quadruplexes formed by GG-, GGG- and GGGG-islands present in the genome (positive and negative strands), ii) their position in the viral genome along with the known function of that region, iii) the degree of conservation among strains of each G-quadruplex in its genome context, iv) the statistical significance of G-quadruplex formation. This information is accessible from a database (http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus) to allow the easy and interactive navigation of the results. The availability of these data will greatly expedite research on G-quadruplex in viruses, with the possibility to accelerate finding therapeutic opportunities to numerous and some fearsome human diseases.

bioinformatics↗