Abstract Viruses represent a primary source of biological diversity, yet the specific mechanisms by which viral proteins shape host range remain unclear. Members of the family Partitiviridae offer a minimalist model to address this question: despite their collectively broad host range, they typically encode only an RNA-dependent RNA polymerase (RdRP) and a capsid protein (CP). Here, we integrate sequence phylogenetics with structural analyses of solved and AlphaFold-predicted structures for both proteins to reconstruct their evolutionary trajectories. We show that CPs feature a conserved Reo-like shell core alongside a genus-specific, highly variable protrusion (P) domain. Similarly, the RdRP retains a conserved catalytic core, with terminal variations giving rise to additional elements within the finger domain. Evolutionary analysis indicates that these two proteins originated independently: an ancestral Betapartitivirus-like RdRP triggered the origin of partitiviruses, while a repurposed totivirus-like CP provided the original capsid—traces of which remain evident in Epsilonpartitivirus. Furthermore, structural and phylogenetic similarities reveal subclusters within established genera and suggest three independent insertion events shaping the P domain. Ultimately, this detailed dual-protein framework demonstrates how structural minimalism and modular adaptability facilitate viral survival and cross-kingdom spread, providing a structural explanation for the exceptional ecological breadth of partitiviruses.
Abstract The family Potyviridae represents the largest and most economically important group of plant-infecting RNA viruses. Despite extensive study of crop-associated members, the full diversity, host range, and evolutionary history of potyvirids remain poorly understood. Here, we conducted a large-scale mining of publicly available RNA-seq datasets to systematically search for novel potyvirid sequences. This approach enabled the identification and assembly of 47 previously undescribed members of the family, distributed across 8 recognized genera and, importantly, putative new groups. Beyond expanding the known genetic diversity of Potyviridae, our analyses revealed a distinct and deeply divergent lineage of potyvirid-like viruses associated with fungi and oomycetes. These viruses possess compact genomes and atypical genomic organizations, including the absence of canonical plant cell-to-cell movement factors and the presence of HCPro-like proteins arranged in tandem. Comparative structural and phylogenetic analyses indicate that these leader proteases are more closely related to fungal hypoviral counterparts than to canonical potyvirid HCPro factors. Together, our findings substantially expand the host range of Potyviridae, provide compelling evidence that potyvirid-like viruses likely infect fungi and oomycetes in nature, and offer new insights into the evolutionary pathways that have shaped this major virus family.
Abstract Rabies virus (RABV) is a lethal zoonotic pathogen that remains endemic in some parts of the world despite long-standing vaccination efforts. We present a comprehensive genomic and evolutionary analysis of the sylvatic rabies epidemic in Switzerland (1967–1997) and propose a molecular epidemiological framework describing RABV dynamics from emergence to elimination, with relevance for countries pursuing wildlife rabies elimination. We generated almost whole-genome sequences from 88 RABV-positive brain samples collected across 17 Swiss cantons and 13 host species over three decades. Using Illumina sequencing, 76 genomes were recovered at high coverage, enabling robust Single Nucleotide Polymorphism (SNP) and molecular clock analyses. Phylogenetic reconstruction based on Swiss whole genomes and glycoprotein sequences including additional European strains identified three temporally structured RABV lineages—red (1967–1976), blue (1976–1988), and green (1984–1996)—each consistent with independent introductions from neighbouring countries. Evolutionary analyses indicated a slow substitution rate and predominant purifying selection, with limited adaptive amino-acid change. However, four mutations emerged during the epidemiological peak, suggesting possible modest fitness effects. We found no evidence of major genomic changes associated with cross-species spillovers. Four synonymous variants were underrepresented in carnivore hosts; however, larger datasets may provide stronger evidence for host-associated genetic differences. Genetic divergence showed a strong temporal signal and moderate correlation with geographic distance, consistent with natural and vaccination-induced barriers limiting RABV dispersal, in agreement with the known ecology and control history of the epidemic. These findings provide a genomic framework for understanding sylvatic rabies emergence and elimination and may inform strategies to achieve and sustain the World Health Organization (WHO) goal of zero human deaths from dog-mediated rabies.
Genome replication in positive-stranded RNA (ssRNA+) viruses is mediated by cognate enzymes, including ubiquitous RNA-dependent RNA polymerase (RdRp). In ssRNA+ viruses with multiple open reading frames (ORFs) in their genomes, replication often is accompanied by synthesis of subgenomic RNAs (transcription) for expression of 3'-proximal ORFs. In addition, all ssRNA+ viruses with genomes larger than ~7 kb encode helicases, linking helicases to RNA genome expansion. Helicases are essential ATPases that unwind nucleic acids and are classified into six recognized superfamilies (SF1-SF6). In the phylum Pisuviricota that includes important pathogens, helicases of SF1-SF3 are integrated into multi-enzyme replicase polyprotein(s) including 3C(-like) protease (3CLpro) and RdRp. Here, large-scale mining of invertebrate metatranscriptomes and targeted genome sequence assembly uncovered six spider-associated ssRNA+ viruses that, based on their conserved 3CLpro-RdRp module in replicase polyproteins, genome size (20-22 kb), and phylogeny, form a family-like cluster in a putative order, named 'Quisvirales'. Quisviruses have similar genome and replicase architectures to enveloped coronaviruses and other nidoviruses. Notably, quisviruses encode ORFs 1a and 1b with predicted -1 programmed ribosomal frameshifting elements in the ORF1a/b overlap region. Using an original mapping approach for detecting chimeric sequencing reads, we obtained evidence that 3'-proximal ORFs are expressed via 5'-coterminal, leader-containing subgenomic RNAs. This suggests that the quisvirus subgenomic RNAs are generated through discontinuous transcription-a mechanism otherwise exclusively found in nidoviruses among the many ssRNA+ virus orders that synthesize subgenomic RNAs. Striking differences between nido- and quisviruses are, however, the RdRp being the only common core ORF1b-encoded enzyme and the replacement of the nidovirus SF1 helicase by a novel superfamily helicase. This quisvirus SF7 helicase, like the Picornavirales SF3 helicase, comprises an AAA+ (ATPase-like) domain typical for ring-forming helicases and thus must play an essential role in replication. The discovery of the order 'Quisvirales' demonstrates that viruses employing large replicase polyproteins of nidovirus-like complexity and discontinuous transcription may have evolved repeatedly from an 3CLpro-RdRp-encoding ancestor.
Human adenovirus type C (HAdV-C) causes upper respiratory infections in children and may lead to severe pneumonia. During the implementation and subsequent relaxation of non-pharmaceutical interventions, HAdV-C emerged as a transiently dominant circulating strain in Beijing. However, the fine-scale genomic architecture and the evolutionary trajectories governing its recombination remains insufficiently characterized. Between March 2023 and August 2024, respiratory samples from Beijing patients were collected and screened by quantitative PCR. In conjunction with high-throughput whole-genome sequencing, five complete HAdV-C genomes were characterized, predominantly identified as genotypes C1 and C108, maintaining over 98% intra-typic sequence identity. Phylogenetic analysis based on whole genomic sequences revealed at least five evolutionary branches within C108. Phylogenetic reconstruction revealed a complex diversification within C108, delineating at least five distinct evolutionary clades. Specifically, the four C108 strains partitioned into two divergent sub-lineages, exhibiting close phylogenetic affinities with sequences from China and the United States. Furthermore, recombination analysis identified six discrete recombination patterns. Selection pressure analysis further demonstrated heterogenous evolutionary constraints across the genome; notably, immune-relevant early genes such as E1a_26KD exhibited elevated dN/dS ratios, harbouring multiple positive selection sites. These adaptive mutations were distributed across 23 of 33 annotated genes (69.7%), suggesting extensive diversifying selection. These findings elucidate that HAdV-C evolution is synergistically driven by frequent recombination events and potent selective pressures. This study provides critical evidence for the spatiotemporal dynamics and genomic surveillance of the emerging HAdV-C variants.
