Biology subjects

Mastriani, E.

Publications and source records attributed to Mastriani, E..

4 recordsLinked to original sources

bioRxiv2026

ViroSeek: a viral detection pipeline for second-generation sequencing

Arbovirus emergences represent a rising public health issue and are exacerbated by climate change and globalization. Virome analysis has become a key approach for monitoring and managing infectious diseases, yet existing tools often remain technically complex and inaccessible to non-specialists. In this context, we present ViroSeek, a reproducible and accessible bioinformatics pipeline specifically designed for the taxonomic analysis of second-generation sequencing data from target-enriched libraries. ViroSeek performs a series of automated steps: quality control, trimming, host and bacterial sequence removal, assembly, taxonomic assignment, read remapping for quantification, and PCR duplicate removal. The whole process is designed to produce a clear, usable viral taxonomy table that is suitable for diversity studies. ViroSeek was empirically validated on enriched control samples containing a known panel of viruses. All the expected viruses were correctly detected. Bacterial and host contaminant sequences were effectively removed. The pipeline is freely available and fully documented, supporting its adoption and adaptation by the research community.

bioinformatics↗

bioRxiv2021

Unsupervised Clustering characterizes the CPG dinucleotides distribution of the Andes hantavirus

Hantaviruses belong to the family of Bunyaviridae, and small mammals host them. Humans are infected either by inhaling virus-containing aerosols or through contact with animal droppings. Even if rodents host the pathogenic species and humans are dead-end hosts, they get accidentally infected. Andes Orthohantavirusus (ANDV) seems to be the only species with documented person-to-person transmission. Hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS) are both serious syndromes associated with hantavirus infections. For both syndromes, the mortality rate is near 40%. Decades of studies already highlighted the CpG repression in RNA viruses, and both the estimation of the CpG odds ratio and the correlation with their genome polarity were dominant factors to figure out the CpG bias. We conducted the differential analysis of the CpG odds ratio for all the orthohantaviruses on the full segmented genomes (L, M, S). The results suggested the statistical significance of the three groups. The "Small" genomes resulted in the more informative from the CpG odd ratio point of view. We calculated the CpG odds ratio for all the Orthohantaviruses within these segments, and besides, we estimated the correlation coefficient with the relative coding sequences (CDS). Preliminary results firstly confirmed the CpG odds ratio as the lowest among all the nucleotides. Second, highlighted the Andes virus as that whose CpG odds ratio within CDS is highest. The use of these two measures as features for unsupervised clustering algorithms has brought to the identification of four different sub-groups inside of the Orthohantaviridae family. The evidence is that the Andes Hantavirus exhibits a peculiar CpG odds ratio distribution, probably linked to its unique prerogative to pass from human-to-human.

bioinformatics↗

bioRxiv2020

An evolutionary analysis of the SARS-CoV-2 genomes from the countries in the same meridian

In the current study we analyzed the genomes of SARS-CoV-2 strains isolated from Italy, Sweden, Congo (countries in the same meridian) and Brazil, as outgroup country. Evolutionary analysis revealed codon 9628 under episodic selective pressure for all four countries, suggesting it as a key site for the virus evolution. Belonging to the P0DTD3 (Y14_SARS2) uncharacterized protein 14, further investigation has been conducted showing the codon mutation as responsible for the helical modification in the secondary structure. According to the predictions done, the codon is placed into the more ordered region of the gene (41-59) and close the area acting as transmembrane (54-67), suggesting its involvement into the attachment phase of the virus. The predicted structures of P0DTD3 mutated and not confirmed the importance of the codon to define the protein structure and the ontological analysis of the protein emphasized that the mutation enhances the binding probability.

genomics↗

bioRxiv2020

HamHeat: A fast and simple package for calculating Hamming distance from multiple sequence data for heatmap visualization

The problem of fast calculation of Hamming distance inferred from many sequence datasets is still not a trivial task. Here, we present HamHeat, as a new software package to efficiently calculate Hamming distance for hundreds of aligned protein or DNA sequences of a large number of residues or nucleotides, respectively. HamHeat uses a unique algorithm with many advantages, including its ease of use and the execution of fast runs for large amounts of data. The package consists of three consecutive modules. In the first module, the software ranks the sequences from the most to the least frequent variant. The second module uses the most common variant as the reference sequence to calculate the Hamming distance of each additional sequence based on the number of residue or nucleotide changes. A final module formats all the results in a comprehensive table that displays the sequence ranks and Hamming distances. Availability and implementationHamHeat is based on Python 3 and AWK, runs on Linux system and is available under the MIT License at: https://github.com/alexeyrakov/HamHeat. Contactrakovalexey@gmail.com

bioinformatics↗