Background Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as recent or non-recent within a window of several months, and cannot assess the cumulative impact of an intervention. Results We developed a Random Forest Regression model, HIV-phyloTSI, which combines measures of within-host diversity and divergence to generate continuous TSI estimates directly from viral deep-sequencing data, with no need for additional variables. HIV-phyloTSI provides a continuous measure of TSI up to 9 years, with a mean absolute error of less than 12 months overall and less than 5 months for infections with a TSI of up to a year. It performs equally well for all major HIV subtypes based on data from African and European cohorts. Conclusions We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.

Germany is worldwide one of the largest hop (Humulus lupulus L.) producers, an essential crop for the brewing industry. However, infections caused by viruses and viroids can severely impact hop yield and quality. In 2019, citrus bark cracking viroid (CBCVd) – a highly aggressive pathogen in hop – was first reported in Germany, raising concerns about its spread and prompting a broader investigation of the German hop virome.To investigate the viro-diversity in German hops, we started with a pilot study in 2021 targeting three hopyards in the Hallertau region (Bavaria), where CBCVd was previously detected. This study was expanded in 2022 and 2023 to include other main hop growing regions of Tettnang (Baden-Wuerttemberg) and Elbe-Saale (Saxony, Saxony-Anhalt, Thuringia). Leaf samples were collected from hop as well as non-hop plants inside and outside the hopyard, pooled, and proceeded for double-stranded RNAs extraction. High-throughput sequencing (HTS) was used as a diagnostic tool, followed by RT-PCR confirmation. Our analysis identified four viruses infecting hops; hop latent virus (HpLV), hop mosaic virus (HpMV), apple mosaic virus (ApMV), arabis mosaic virus (ArMV) – and two viroids; hop latent viroid (HLVd) and CBCVd. HpLV, HpMV, and HLVd were consistently found across all targeted hopyards, while CBCVd was confined to the Hallertau region. ArMV was only detected in one hopyard at one sampling timepoint. ApMV was the only virus detected in both hop and non-hop plants. Additional analysis of hop pool datasets revealed the presence of other potential hop pathogens, i.e., fungi and bacteria. The results showed a low diversity of viruses and viroids infecting hops. However, this study provides a comprehensive overview on the major viruses and viroids in German hopyards. The results may serve as a useful resource for the development of disease management strategies in hop cultivation and highlight the valuable implementation of HTS in plant pathogen surveillance.

Bovine leukemia virus (BLV) causes Enzootic bovine leukosis (EBL) in approximately 1%–5% of infected cattle after a long latent period. Few biomarkers effectively distinguish non-EBL from EBL cattle....

Phylogenetic studies examining the origins, emergence, and spread of viruses have arguably been one of the most active and successful areas of evolutionary biology and form the bedrock of the flourishing field of genomic epidemiology. This, in part, reflects the ability of viruses, particularly thos...

Implementing high-throughput sequencing (HTS) in virus detection has recently become widespread. Bioinformatic expertise, programming skills, and access to high-capacity computers are essential for HTS data analysis. The E-Probe Diagnostic Nucleic Acid Analysis, a bioinformatic detection system that...

Viruses are integral to every biome on Earth, yet we still need a more comprehensive picture of their identity and global distribution. Global metagenomics sequencing efforts revealed the genomic content of tens of thousands of environmental samples, however identifying the viral sequences in these...

Arboviruses are climate sensitive, and their global distributions are changing. Here, the authors describe results of a One Health study programme to investigate the occurrence of Usutu and West Nile Virus in the Netherlands, a previously non-endemic area.

Label-free Raman spectroscopy is utilized for an in-depth characterization of alveolar macrophages directly within intact precision-cut human lung slices. Characteristic biochemical changes in indivi...

This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn 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.

Some viruses affect us humans, like the now all-too-familiar coronavirus SARS-CoV-2, while others mainly affect animals, such as pestiviruses that can infect pigs, cows, and even wild animals. And …

Phage therapy, which involves treating bacterial infections using bacteriophages (phage), has shown promise as an alternative to antibiotics and can offer a solution for treating infections caused by antibiotic-resistant bacteria. However, phages are not ...

The ability to study mature neuronal cells ex vivo is complicated by their non-dividing nature and difficulty in obtaining large numbers of primary cells from organisms. Thus, numerous transformed progenitor models have been developed that can be routinely cultured, then scaled, and differentiated to mature neurons. In this paper, we present a new method for differentiating one such model, the Lund human mesencephalic (LUHMES) dopaminergic neurons. This method is two days faster than some established protocols, results in nearly five times greater numbers of mature neurons, and involves fewer handling steps that could introduce technical variability. Moreover, it overcomes the problem of cell aggregate formation that commonly impedes high-resolution imaging, cell dissociation, and downstream analysis. While recently established for herpes simplex virus type 1, we demonstrate that LUHMES neurons can facilitate studies of other herpesviruses, as well as RNA viruses associated with childhood encephalitis and hemorrhagic fever. This protocol provides an improvement in the generation of large-scale neuronal cultures, which may be readily applicable to other neuronal 2D cell culture models and provides a system for studying neurotrophic viruses. We named this method the Streamlined Protocol for Enhanced Expansion and Differentiation Yield, or SPEEDY, method.

BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistical inference.