Viral evolution articles from across Nature Portfolio

Tracking influenza virus populations over 72 passages, the authors show that hundreds of defective viral genomes compete for dominance, ultimately resolving into a single variant carrying an adaptive mutation that enhances replication and interference, enabling it to outcompete other defective genomes.

The role of giant viruses in freshwater habitats is less well studied. Here, using metagenomes collected over 20 years in Lake Mendota, the authors show that giant virus genomes adapt to environmental change via gene duplication and horizontal gene transfer, revealing genomic stability and increased virus-host interactions.

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.

By integrating DMS profiles, evolutionary trajectories and epidemiological data, a deep-learning framework enables the spatiotemporal prediction of emerging dominant SARS-CoV-2 variants.

Understanding HIV evolution during early infection is important for prevention strategies. Here, leveraging deep sequencing during acute infection, the authors show a higher-than-expected frequency of multiple transmitted viruses, highlighting fluctuating viral lineages, which may inform future vaccine development.

In this Review, Tran and Vignuzzi examine how molecular processes and evolutionary pressures shape RNA virus diversity and adaptation. They outline how genome structure, mutational pathways and viral interactions influence evolutionary outcomes, offering insights relevant to the design of better vaccines and antiviral strategies.

This Genome Watch article explores how taking into account known phylogenetic relationships can improve computational efficiency for genomics, enabling improved genome data compression and faster sequence search as datasets continue to expand.

Funk and colleagues show that acquisition of a multibasic cleavage site in H5 haemagglutinin is the result of the combination of insertion-prone RNA sequences and the formation of transient RNA structures during replication by the viral RNA polymerase.

The release of a more genetically stable form of a live, attenuated oral polio vaccine, nOPV2, was heralded as a major advance towards global polio eradication. Virus recombination events can undo all the hard work.

Understanding the emergence, evolution and spread of viral pathogens is central to improving global health. This Focus issue highlights advances in our understanding of evolving viral pathogens and the surveillance and preparedness strategies that are needed to control them.

A powerful technique for probing the effects of amino acid substitutions on protein function sheds light on the evolutionary constraints of a rapidly evolving influenza virus glycoprotein.

This study reports the emergence of a novel, highly pathogenic feline–canine recombinant coronavirus responsible for a rapidly spreading outbreak of feline infectious peritonitis, which originated in Cyprus.