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Apollo is a GPU-accelerated simulator of within-host viral evolution, spanning host populations, tissues, and cells. It scales to millions of viral genomes and supports complex demographic and population genetic models.

Matthew M. Hernandez and Ana S. Gonzalez-Reiche and colleagues report evidence of SARSCoV-2 infections in respiratory pathogen-negative nasopharyngeal specimens collected in New York, which date back to over one month before the first officially documented case in the state. The findings provide insights in to the origins of the virus in New York.

Highly pathogenic H5N1 avian influenza lineage 2.3.4.4b has spread through the Americas in birds since 2021 with frequent spillover into mammals. Here, the authors characterise the dissemination of the virus in Chile and find evidence of sustained transmission between mammals.

In a phase 1 trial, patients with pancreatic ductal adenocarcinoma who were treated with surgery and bespoke neoantigen mRNA vaccines combined with anti-PD-L1 and chemotherapy exhibited marked long-lived persistence of neoantigen-specific CD8⁺ T cell clones, which correlated with prolonged recurrence-free survival at a 3.2-year follow-up.

IL-33 induces tertiary lymphoid structures.

Experiments at the National Ignition Facility show how delocalization of K-shell electrons is driven by extreme pressure and temperature.

Solid organ transplant recipients are at increased risk of infectious disease and have unique molecular pathophysiology. Here the authors use host-microbe profiling to assess SARS-CoV-2 infection and immunity in solid organ transplant recipients, showing enhanced viral abundance, impaired clearance, and increased expression of innate immunity genes.

Continued monitoring of population SARS-CoV-2 seroprevalence can reveal infection and vaccination patterns. Here, the authors report data from a prospective hospital-based sero-monitoring study in New York City from 2020–2023, including ~55,000 individuals.

The role of IgG glycosylation in the immune response has been studied, but less is known about IgM glycosylation. Here the authors characterize glycosylation of SARS-CoV-2 spike specific IgM and show that it correlates with COVID-19 severity and affects complement deposition.

Deconvolution methods infer levels of immune infiltration from bulk expression of tumour samples. Here, authors assess 6 published and 22 community-contributed methods via a DREAM Challenge using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells.

Roberts syndrome (RBS) is an autosomal recessive disorder with profound growth deficiency and limb reduction caused by ESCO2 loss-of-function variants. Here, the authors show that the pathogenesis of limb reduction in an Esco2 cohesinopathy mouse model of Roberts syndrome has an underlying vascular etiology that is mediated by p53-signaling, sharing commonality with thalidomide embryopathy.

There is limited understanding of SARS-CoV-2 intra-host evolution and subsequent transmission and adaptations in the context of persistent infection. Here, the authors describe sequential persistent SARS-CoV-2 infections that led to the emergence, transmission and further evolution of a novel Omicron BA.1.23 lineage.

The photocurrent generated in organic photodetectors and solar cells can be enhanced by increasing light absorption in the active layer. It is now shown that an extended persistence length can increase the oscillator strength of conjugated polymers.

A collaborative study demonstrates that, compared with previous SARS-CoV-2 variants, B.1.1.529 isolates cause less infection and disease in mice and hamsters, in agreement with preliminary data from studies in humans.

Sera from unvaccinated, vaccinated, and previously infected and vaccinated individuals show reduced neutralizing and spike protein-binding activity towards the Omicron (B.1.1.529) variant of SARS-CoV-2 compared to other variants.

Post-acute sequelae of SARS-CoV-2 (PASC) is still not well understood. Here the authors provide patient reported outcomes from 590 hospitalized COVID-19 patients and show association of PASC with higher respiratory SARS-CoV-2 load and circulating antibody titers, and in some an elevation in circulating fibroblast growth factor 21.

The plasma membrane can expand the blades of the PIEZO1 ion channel, impacting channel activation.

Heterogeneous reactions associated with porous films are vital in nature and industry. A hierarchical-structure-accelerated interfacial dynamic strategy is reported to improve interfacial gas transfer on conductive metal-organic framework films.

Craniofacial development depends on formation and maintenance of sutures between bones of the skull. Here the authors identify enriched expression of the hedgehog inhibitor Hhip, specifically in the mesenchyme of the murine coronal suture, and show sutural dysgenesis in Hhip−/− mutants.

Swarm Learning is a decentralized machine learning approach that outperforms classifiers developed at individual sites for COVID-19 and other diseases while preserving confidentiality and privacy.

The secondary structure of mRNAs can slow or even halt protein synthesis. Single-molecule FRET studies of distinct steps in the translation elongation cycle now reveal that unfolding of mRNA secondary structures is more closely coupled to tRNA dissociation from the ribosomal exit site, with little effect on tRNA translocation within the ribosome.

Echo-enabled harmonic generation in a free-electron laser enables 45th harmonic pulses from a 264 nm wavelength seed, yielding 5.9 nm wavelength coherent output.

A strategy exploiting species-specific miRNA expression may provide another layer of biosafety in gain-of-function influenza experiments.

Laser-driven free-electron lasers use laser pulses instead of magnetostatic undulators, enabling x-ray amplification with lower electron energies and shorter interaction lengths. Here, the authors show that a flying-focus pulse, with an intensity peak moving opposite to its phase fronts, provides the uniformity needed for high-gain X-ray generation using 20 × less energy than conventional laser pulses

By amplifying a soliton in a multistage cascade, few-femtosecond extreme-ultraviolet free-electron laser pulses are achieved.

Using a spectroscopy streaking technique at LCLS (Linac Coherent Light Source), researchers demonstrate temporal characterization of X-ray pulses with sub-femtosecond resolution.

The SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme provides a real-time risk assessment of SARS-CoV-2 variants with the potential to affect transmission, virulence and resistance to infection- and vaccine-induced immunity.

PIONEER is a European network of excellence for big data in prostate cancer, which brings together private and public stakeholders from nine countries in one multidisciplinary research consortium. In this Perspectives, members of the consortium detail the achievements of PIONEER and describe its goal of maximizing the potential of big data to improve prostate cancer care in the future.