A vital component of the response to viral outbreaks is the classification and tracking of sub-species-level variation, which is essential for guiding public health risk assessment and communication strategies. Given this rapid and ongoing evolution of viruses, there is a need for sub-species classi...

Henipaviruses are a group of emerging human pathogens including the deadly Nipah virus. Here, the authors biochemically, biophysically, and structurally investigate the antigenicity and functionality of their surface glycoproteins.

Groundwater ecosystems host diverse microbial communities, yet the diversity and ecological roles of their associated viral genomes remain poorly characterized. Here, we investigated viral community composition, diversity, host associations, lifestyles, and auxiliary metabolic potential in groundwater from three hand pumps located in Toukh, Qalyubia, Egypt, representing distinct local surroundings and potential contamination pressures. Using complementary viral detection approaches and a quality assessment workflow, we recovered 9,534 non-redundant viral contigs spanning a wide range of viral genome quality. Taxonomic profiling revealed dominance of tailed dsDNA bacteriophages (Uroviricota/Caudoviricetes) across all pumps, with ~ 99% of contigs not assigned below the class level. Whereas the viral composition of pump 3 was distinct and its diversity was consistently higher, pumps 1 and 2 clustered together, a pattern mirrored across taxonomic scales and diversity metrics. The majority of predicted viral hosts belonged to phylum Pseudomonadota, followed by Actinomycetota, Bacillota and Bacteroidota, with levels that varied between pumps. Correlation and network analyses showed strong concordance between the relative abundance of bacteria and the abundance of viruses that potentially infect them. Lifestyle prediction indicated a descending relative abundance of viruses with lysogenic lifestyle from pumps 1 through 3. Auxiliary metabolic genes (AMGs) related mainly to nucleotide, amino acid, and cofactor metabolism were detected in all pumps, with distinct pump-specific repertoires suggesting localized viral metabolic strategies. Together, these results demonstrate that groundwater viromes are ecologically structured and highly novel, with the potential ability to modulate host metabolism, highlighting their potential role in shaping subsurface microbial communities.

Viral metagenomics is an increasingly powerful tool for understanding the function and structure of viruses across the diverse environments of our planet. However, decoding the functional potential o...

Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of...

Advances in virus genomics have made it increasingly possible to track evolutionary changes at the population level over the timescales of outbreaks and epidemics (1). Before the current era of large-scale genomic surveillance, our inferences relied on sparse, heterogeneous datasets—dozens to hund...

Convergent evolution in protein antigens is common across pathogens, including SARS-CoV-2; the most likely reason is the need to evade the selective pressure exerted by previous infection- or vaccine-elicited immunity.

High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically been bottlenecked by experimental determination. The recent revolution in artificial intelligence (A...

Author summary Poly(A) tails are found on almost all cellular mRNAs and many viral mRNAs, serving as binding platforms for proteins that enhance translation and regulate mRNA stability. In this study, we used a new RNA sequencing approach, nanopore direct RNA sequencing, that allows us to measure poly(A) tails on individual mRNAs during infections by herpesviruses and other DNA and RNA viruses. We found that herpesvirus mRNAs consistently possess longer poly(A) tails than both host and other viral mRNAs, suggesting a widespread and previously unrecognized strategy to enhance viral gene expression. By contrast, coronavirus and poxvirus mRNAs exhibit poly(A) tail lengths comparable to host mRNAs. While non-As are present within some herpesviral poly(A) tails, which could potentially slow poly(A) tail degradation, this “mixed tailing” occurs too infrequently to account for the broadly extended tails observed.

Viruses such as coronaviruses or filoviruses use their surface glycoproteins (GPs) to attach to the host cell, triggering the fusion of the viral membrane with the endosome membrane. Epitopes on the viral GP are major targets for antibody-mediated recognition and neutralization. During the fusion process, the GP undergoes conformational changes triggered by fluctuations in environmental pH. Structural states are typically classified into three distinct conformations: prefusion, intermediate, and postfusion. These conformations serve as essential templates for prediction of conformational epitopes and structure-based vaccine design. Despite their importance, many viral GP structures remain absent from the Protein Data Bank (PDB). Fortunately, recent breakthroughs in computational structure prediction have greatly enhanced the accuracy and accessibility of protein modeling. In this study, we utilized AlphaFold2-Multimer (AF2-M), version 2.3, to predict various GP structural conformations and observed that the overall frequency of predictions in the postfusion conformation is low. Therefore, we hypothesized that adapting the AF2-M protocol is necessary to enrich for specific conformations, thereby enabling the prediction of both pre- and postfusion conformations. AF2-M requires only the input sequence and internally generates multiple sequence alignments (MSAs) and optional templates before applying its pretrained model weights. We tested the use of template data to enrich pre- or postfusion conformations and demonstrated that our approach significantly increases the prediction frequency of class I fusion protein structures in both conformations, with the template dataset playing a crucial role in guiding modeling towards the intended state. Furthermore, we showed that the lack of correlation between pLDDT and TM-scores suggests that low pLDDT values may obscure the presence of valid alternative conformations.

Public viral genome resources such as the National Center for Biotechnology Information (NCBI) Virus database are central to outbreak response, evolutionary analysis, vaccine design, and genomic surveillance. Yet many high-value retrieval workflows remain optimized for interactive use rather than deterministic, reproducible programmatic interfaces. This creates a challenge for Large Language Model (LLM)-based scientific agents, where errors in metadata interpretation, filtering logic, or retrieval can propagate into incorrect datasets. To evaluate agentic viral data retrieval, we built VirBench, a manually curated benchmark of 120 queries spanning diverse pathogens, taxonomic levels, and metadata filters. When autonomous AI systems, including Biomni, Claude, GPT, and Edison Analysis, were tasked with these queries without a dedicated retrieval layer, performance varied widely: mean accuracy ranged from 16.9% for Claude Sonnet 4 to 91.3% for GPT-5.5, with newer frontier models showing progress but residual errors remaining consequential. To address this, we built gget virus, a deterministic query framework that formalizes NCBI Virus-style filtering as a reproducible programmatic system. By staging retrieval, applying metadata constraints before sequence download, and retrieving structured GenBank records, gget virus reduces data transfer by more than 98% for high-volume queries while preserving exact-match semantics. Instructing autonomous AI systems to use gget virus increased accuracy to at least 90.0% across all evaluated systems and up to 99.7% for GPT-5.5, improved response stability to 0.92-1.00, reduced error magnitude, and generally decreased runtime and tool calls. Together, this work establishes deterministic data access as critical infrastructure for reliable agentic science and provides a reproducible retrieval layer for robust human- and AI-driven viral genomics workflows.

Author summary Bacteriophages, or phages, are viruses that infect bacteria and play central roles in shaping microbial communities across ecosystems. Despite their ecological importance, the bacterial...

Theo Murphy meeting organised by Dr Katy Brown, Dr Emma Harding and Professor Rachael Tarlinton

In this Review, Abergel et al. overview infection cycles across the Nucleocytoviricota phylum, highlighting shared mechanisms and lineage-specific features spanning viral entry, viral factory formation, genome replication, virion morphogenesis and egress, and discuss key unresolved questions in the field.

npj Viruses - Sequence to structure insights into Lassa virus population-level biophysical properties and glycoprotein structure catalogue

Bacteriophages (phages) play essential roles in microbial systems, yet most phage proteins remain poorly characterised. Protein tertiary and quaternary structure information contributes valuable infor...

Event-triggered MINFLUX combines confocal monitoring with real-time analysis to selectively acquire single-molecule data, enabling nanometre-resolution studies of membrane dynamics in living cells with improved speed, efficiency and data throughput.

Scientific Data - A complete catalogue of human-infective RNA viruses

Rfam is a comprehensive database of non-coding RNA (ncRNA) families providing curated sequence alignments, consensus secondary structures, and covariance models for thousands of RNA families. The database is essential for identifying structured non-coding RNAs in newly sequenced genomes and understa...

Vaccination is a highly efficient strategy in controlling infections. Aluminum-containing adjuvants have long been used to enhance immunogenicity, but quantification of adsorbed antigens remains analytically challenging. This study uses Raman spectroscopy, a powerful, nondestructive technique, augme...

The gut microbiome of the honey bee is relatively simple, but its phages are not well studied. Here, Basler et al. use metagenomics to provide a comprehensive catalogue of honey bee gut phages across eight European countries, describing novel taxa as well as a core set of 97 prevalent phages.

Trials are beginning on several drugs that have shown promise in preliminary studies against the virus that is causing the current outbreak.