Nanopore direct RNA sequencing (DRS) coupled with Dorado modification-aware basecalling enables mapping of epitranscriptomic modifications including N6-methyladenosine (m6A) at the level of individual RNAs. However, a lack of systematic benchmarking continues to raise questions regarding the sensiti...

The factors influencing the establishment of the gut bacterial community in early life are fairly well studied. However, the factors shaping the infant gut virome remain elusive. Interestingly, ear...

AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi

In this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.

DOI Not Found 10.1038/s41586-025-08489-2 This DOI cannot be found in the DOI System. Possible reasons are: The DOI is incorrect in your source. Search for the item by name, title, or other metadata using a search engine. The DOI was copied incorrectly. Check to see that the string includes all the c...

Analysis of RNA polymerase hallmark gene phylogenies supported by protein structure relationships of flaviviruses and ‘flavi-like’ viruses underpins the taxonomic expansion and reorganization of Flaviviridae.

Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2–99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples’ virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.

Background Epstein–Barr virus (EBV) is strongly implicated in Multiple Sclerosis (MS), but how its influence varies across MS clinical types remains unclear. Methods We developed VirTrack , a computational framework that integrates experimentally validated EBV–host protein–protein interactions...

Antimicrobial resistance (AMR) is one of the greatest threats to global health. If unaddressed, it is projected to cause over 39 million cumulative deaths globally by 2050 (1). While resistance is a broad and evolving problem, a small group of bacteria, collectively known as ESKAPEE pathogens, has e...

Author summary Lassa fever is a viral illness that causes yearly outbreaks in West Africa and has the potential to spread internationally, with cases recently reported in several countries outside the region. Quickly identifying the genetic lineage of the virus responsible is critical for inferring the source of outbreaks and guiding medical and public health responses. However, tools designed specifically for rapid Lassa virus lineage identification are almost non-existent. In this study, we introduce CLASV, a fast and user-friendly tool that uses machine learning to identify the major circulating lineages of Lassa virus from genetic sequences. Validated on real-world data, CLASV achieved high accuracy even when working with incomplete sequences. It runs in minutes on a standard computer, making it practical for deployment in local low-resource laboratories. By providing timely and reliable lineage information, CLASV has the potential to enhance outbreak response and enable more targeted public health interventions—both in West Africa and in countries managing imported cases.

An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbiotic interactions.

Background Whole blood samples are often used to generate whole genome sequences, which provide valuable insights into the genetic make-up of viruses. However, the collection and management present si...

Scheme for the labeling of the cell membrane. The scattering tags, gold nanoparticles of two different diameters (Ø20 nm and Ø40 nm), target the biotinylated lipids inserted in the cellular membrane,...

Background Ebolavirus and related filoviruses are feared pathogens due to high mortality rates, and cases are confirmed using reverse transcription-polymerase chain reaction (RT-PCR) testing. Compared...

The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...