RNA polymerase III transcribes essential non-coding RNAs, but many aspects of this biology remain unclear. Here, the authors develop DRAP3R, a nanopore sequencing method that captures Pol III transcripts and RNA modifications, revealing new RNAs and dynamic modification patterns.

HCMV infection can become productive or latent. Here the authors show that variations in the number of incoming viral particles across cell types is a key factor of this decision, identifying entry efficiency as a key regulator of latency.

SIMPLICITY models multi-scale SARS-CoV-2 evolution by integrating within-host viral dynamics and population-level transmission. Our adaptive fitness landscape model reveals how immune escape prompts evolutionary dynamics akin to the real-world evolution of SARS-CoV-2.

Patient-specific induced pluripotent stem cells (iPSCs) can be differentiated into alveolar type II cells (iAT2s), expanded as 3D alveolospheres, and grown at physiologically relevant air–liquid inte...

Direct studies of long-term RNA virus evolution are largely limited to chemically-fixed specimens from natural history and pathology museums collected over the past two centuries. Detecting genomic traces of RNA viruses in older, buried remains is generally considered highly unlikely. The cold, dry conditions of Antarctica may represent an exception. Under such circumstances, natural mummification of penguins and seals—animals that form large colonies where RNA viruses circulate—is common and may facilitate the recovery of RNA virus genomes. Here, we show that Adélie penguin ( Pygoscelis adeliae ) mummies, ranging in age from recent to nearly two millennia, indeed contain fragments of such ancient viral genomes. Metatranscriptomic analyses yielded near-complete genome sequences of a picornavirus ( Megrivirus epengu ) and a rotavirus D ( Rotavirus deltagastroenteritidis ) from relatively recent specimens. We further retrieved rotavirus D sequences from a 280-year-old individual and a near-complete rotavirus G ( Rotavirus gammagastroenteritidis ) genome from a 1900-year-old one. These findings pave the way to direct studies of RNA virus evolution across millennia. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Transregio Collaborative Research Centre 410 “WETSCAPES2.0”, Project-ID 531801029 – TRR 410 National Science Foundation, ANT 1443386, OPP 9909274 US National Institutes of Health, R01 AI153044 Research Foundation - Flanders (‘Fonds voor Wetenschappelijk Onderzoek - Vlaanderen’, G0D5117N, G0B9317N, G051322N Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Germany's Excellence Strategy - EXC 2155 - project number 390874280 Helmholtz Association’s Initiative and Network Fund, KA1-Co-02 “CoViPa”

Poly(A) tails are present on most cellular and viral mRNAs, providing a platform for poly(A)-binding proteins that stimulate translation and regulate the deadenylation and stability of transcripts in the cytoplasm. Here we leverage nanopore direct RNA sequencing to analyse the distribution of poly(A) tail lengths on cellular and viral mRNAs across Herpesviridae and other DNA and RNA virus infections. We find that herpesvirus mRNA poly(A) tails are consistently longer than those on cellular and other viral transcripts, presenting a previously unrecognized yet widespread mechanism to advantage herpesviral gene expression. This contrasts with the templated poly(A) tails on coronavirus RNAs and those on cytoplasmically transcribed poxviral mRNAs, which are more similar in length to those on host mRNAs. Herpesviral noncoding RNAs display differential poly(A) tailing patterns which do not correlate with nuclear localisation while individual herpesviral mRNAs also show variation in the extent to which their poly(A) tail lengths change during the virus lifecycle, suggestive of additional uncharacterised layers of poly(A) tail length regulation. Importantly, while we detect non-adenosine nucleotides within herpesviral poly(A) tails, which are known to oppose deadenylase activity, this “mixed tailing” is not at sufficient frequency to explain the widespread extended tails of herpesvirus mRNAs. ### Competing Interest Statement The authors have declared no competing interest.

This study assessed the durability of immunity in humans after vaccination with an MVA-based MERS vaccine. The data show that antibodies and T cells persist for at least two years, with the antibodies capable of cross-neutralizing MERS-CoV variants.

Fourier Transform Infrared (FTIR) and Circular Dichroism (CD) spectroscopies are powerful and rapid techniques that provide valuable insights into the conformational properties of nucleic acids (NA). These spectroscopic methods, sensitive to vibrational and...

Background The evolutionary history of retroviruses and their impact on vertebrate evolution remains poorly understood, particularly in non-mammalian hosts. In this study, we explore retroviruses associated with Amphibia through analysis of 169 RNA sequencing datasets from 102 amphibian species. Using a BLAST-based approach, we identified retroviral transcripts from assembled transcriptomes and phylogenetically characterise both their pol and env regions to elucidate their evolutionary history. Results We identified the transcription of 18 novel and two previously described retroviruses with closest relatives in gammaretrovirus, epsilonretrovirus, betaretrovirus and spumaretrovirinae. Despite their differing pol phylogenies, we found that all amphibian retroviruses belong to the gamma-type envelope group (GTE). This suggests a common selection pressure for amphibian retroviruses to retain GTEs. Within these GTEs we also observed a new clade of alpharetrovirus-like envelopes in amphibians which form a sister clade to avian alpharetrovirus envelopes. Furthermore, we observe correlations between amphibian taxonomical order and retroviral diversity, with Gymnophiona (caecilians) harbouring the widest diversity of retroviruses whilst Anura (frogs and toads) harbour the fewest. Through mapping these transcribed retroviruses to their respective genomes (seven available) supplemented with observing ORF intactness, we determined that 14 of the 20 retroviruses are likely endogenous in origin yet are still transcribed in many amphibian tissues. These amphibian endogenous retroviruses (ERVs) have high genomic copy numbers: most (5/7) ERVs investigated have > 100 copies, and one of which has 9,219 integrations within the Ichthyophis bannanicus caecilian genome. This high retroviral load in amphibian genomes may suggest that these retroviruses have low pathogenicity, or may reflect a lack of transposon control mechanisms in amphibian cells. Conclusions Through the characterisation of metatranscriptomic and genomic data from retroviruses in this study, we provide insights into their evolution in amphibians and exemplify the diversity of Retroviridae in vertebrate genomes. The identification of novel retroviral clades, widespread transcription of endogenous retroviruses in amphibians and abundance of ERV copies suggests that Retroviridae have played a significant role in amphibian evolution.

The Evaluation and Enhancement (EVEN) method optimizes automatically the quality of multichannel microscopy images affected by uneven illumination, enabling accurate visual interpretation and image an...

Cheng et al., use non-infectious stable viral replicon cell lines in genome-wide CRISPR KO screens across diverse viral pathogens to identify host factors specifically involved in the intracellular stages of viral replication.

The family Geminiviridae comprises 15 genera and over 500 species of diverse plant-infecting viruses. Previous studies on this virus’s diversity primarily focused on the members’ selection without considering the entire genomic divergence. This study presents comprehensive comparative genomic analyses and a global distribution map using 17,718 complete genomes and 28,185 geminivirus-associated metadata records. Intergeneric pairwise identity among monopartite and Begomovirus DNA-A is ≥ 40%, while interspecies identity among Begomovirus DNA-B is ≥ 41%, corresponding to genetic variations of ≤60% and ≤59%, respectively. Begomovirus and Mastrevirus are the only genera detected across all continents, with Asia exhibiting the highest genus diversity (11 genera). However, in Africa, geminiviruses from six genera are more broadly distributed across individual countries. To our knowledge, this is the first geographical map constructed using all genera from the Geminiviridae family. Phylogenetic reconstructions of complete genomes, coat proteins, and replication-associated proteins (Rep) underscored distinct clustering patterns consistent with genus-level classification but revealed exceptions, including misclassified viral species and potential new taxa. Notably, French bean severe leaf curl virus with accession KC699544 was reclassified from Capulavirus to Begomovirus with the proposed name Corchorus yellow vein mosaic virus. Additionally, two unclassified begomovirus-like viruses, named “begomovirus spathoglottis 1” and “2,” are proposed for reclassification within Maldovirus under the tentative names “maldovirus spathoglottis 1” and “2.” The Begomovirus Rep showed phylogenetic affinity with Rep from Maldovirus, Curtovirus, Turncurtovirus, and Topocuvirus, supporting potential evolutionary relationships among these genera. Recombination analyses confirmed high-frequency interspecies and intergeneric recombination events, predominantly involving Begomovirus, underscoring its pivotal role in geminivirus evolution. Furthermore, we hypothesized specific vector transmission: Opunvirus, Welwivirus, and Topilevirus are transmitted via treehopper species, whereas Citlodavirus and Eragrovirus are transmitted via leafhopper species. Accurate identification and classification of plant viruses and their transmission vectors are essential for developing effective surveillance and management strategies to safeguard global agriculture.

A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms

The forces driving virus evolution are central to understanding cross-species transmission and virus emergence. It is well established that the adaptive immune system drives virus evolution in mammals...