2026-09-26 · Volume 12 · Issue 1
Abstract Background: Human adenoviruses (HAdVs) are a frequent cause of respiratory tract infections in children; however, their epidemiological patterns and genomic diversity remain insufficiently characterized in Europe. As respiratory HAdVs can cause outbreaks of acute and severe disease and show periodic re-emergence, improved understanding of their circulation is needed. Aim: To investigate the epidemiology, age distribution, and genomic diversity of respiratory HAdVs in paediatric patients in Île-de-France during the first half of 2022. Methods: We retrospectively analysed 6 956 respiratory samples from patients
DOI: 10.1093/ve/veag064/88365622026-09-24 · Volume 12 · Issue 1
Abstract Satellites are subviral agents that depend on a helper virus for functions essential to complete their infection cycle, while the helper virus may infect and be transmitted in the absence of the satellite. Thus, satellites are cheats that compete with the helper virus for its resources, and may modulate its replication, infection dynamics, evolution, and the coexistence among viruses. Understanding the conditions for satellite invasion and persistence is therefore relevant to understanding both the prevalence of single viruses and virus community dynamics. This is the goal of this study, centred in satellite tobacco mosaic virus (STMV), and its helper virus tobacco mild green mosaic virus (TMGMV). We use epidemiological data on STMV occurrence and infection dynamics in TMGMV-infected Nicotiana glauca populations, and experimentally estimate relevant parameters to feed models that predict STMV invasion and persistence conditions. We show that under field conditions, STMV has no significant effects on TMGMV accumulation or pathogenesis in N. glauca . However, the presence of STMV significantly reduces the horizontal transmission rate of TMGMV, and we showed experimentally that STMV transmission occurs in only a fraction of TMGMV transmission events. Model simulations showed that a requirement for STMV invasion at realistic transmission rates was a low virulence, a condition met as shown by previous studies of the virulence of TMGMV in N. glauca . Simulations that considered variation in the density of the host plant population identified a high transmission rate as a condition for the persistence of STMV, which disappears from the TMGMV population at low plant densities. A major conclusion is that STMV interferes with TMGMV transmission despite not interfering with TMGMV accumulation. Thus, conditions favouring a high transmission rate are required for invasion and persistence of STMV, similarly to satellites that interfere with helper virus replication, suggesting these conditions may be general for other satellite-helper virus systems.
DOI: 10.1093/ve/veag063/88338192026-09-21 · Volume 12 · Issue 1
Abstract Nairobi sheep disease virus (NSDV) is a tick-borne orthonairovirus causing severe hemorrhagic gastroenteritis in small ruminants, with case fatality rate up to 90% among naive populations. Despite its veterinary and zoonotic importance, the evolution and spatiotemporal dynamics of NSDV remain poorly understood. We analysed S, M, and L segment sequences collected from the 1950s to 2024 in China, India, and Kenya, and identified three geographically structured lineages (Lineage A from India, Lineage B from China, and Lineage C from Kenya). No host-specific clustering was observed, indicating geographic isolation, rather than host adaptation, is the primary driver of diversification. Recombination events exhibited strong geographic structuring, with Jilin province as a major hotspot (likely reflecting higher sampling density in the region). Occasional intercontinental gene flow from Africa into China contributed parental lineages, and recombinant strains were detected in ticks, with parental contributions from sheep and saiga antelope hosts. Selection analyses revealed strong purifying selection on L segment (dN/dS = 0.365), but relaxed or positive selection on M glycoprotein (dN/dS = 3.020) and S segment (dN/dS = 5.360). Substitution rates ranged from 1.56 × 10 −4 (L) to 6.81 × 10 −4 (S) substitutions/site/year. Time-to-most-recent-common-ancestor (tMRCA) of all NSDV strains was estimated at ~ 1732 ce (95% highest posterior density [HPD]: 1624–1833), representing the divergence between the Chinese lineage and the common ancestor of the Indian and Kenyan lineages. The Indian and Kenyan lineages subsequently diverged from their common ancestor ~ 1763 ce (95% HPD: 1677–1845), followed by the Indian lineage (~1883 ce ) and the Chinese lineage (~1934 ce ). The ancestral location at the root node is highly uncertain (maximum a posteriori , MAP = India_Karnataka), and sparse sampling from intermediate regions limits robust phylogeographic inference. Among the well-supported intra-continental routes, migration from India (Maharashtra/Karnataka) to eastern China (Liaoning, Shandong) received moderate support (BF = 6.40–22.57). A route from Liaoning to Kenya was also detected (BF = 11.84), but this inference should be interpreted with caution given the limited Kenyan sampling and potential unsampled intermediate populations.
DOI: 10.1093/ve/veag061/88242502026-09-21 · Volume 12 · Issue 1
Abstract Hepatitis A virus (HAV) is a ubiquitous human pathogen that may cause acute liver disease. Despite the availability of effective vaccines, high prevalence rates are still reported in Southeast Asia and Africa, where sanitation conditions are poor. Although seven genotypes are known, including three in humans, three in non-human primates (NHP), and one recently identified in alpacas, the diversity, ecology, and evolutionary history of HAV remain poorly understood. In a pilot study of virome molecular characterization of wild African apes by using oligonucleotide probes enrichment, HAV sequences were detected in two animals (2/105; 1.9%): one from a western lowland gorilla ( Gorilla gorilla gorilla ) from southern Cameroon, sampled in 2006, and another from a central chimpanzee ( Pan troglodytes troglodytes ) in northeastern Gabon, sampled in 2011, approximately 450 km apart. Two near-full-length viral genomes were successfully reconstructed using specific primer sets that were developed. Phylogenetic analyses revealed that these sequences cluster within the simian HAV clade, forming a distinct cluster closely related to environmental strains from the Sanaga River in Cameroon and South Africa, yet clearly divergent from genotype V sequences (≥15.8% nucleotide divergence in the VP1 protein). Amino acid comparisons identified residues conserved in simian HAVs and, subsequently, only in African HAV strains. These results support the classification of a supplementary African simian genotype, provisionally designated HAV-VIII. HAV-positive samples (13/227; 5.7%) were detected in the same field sites, suggesting localized viral circulation in these populations. Bayesian time-scaled phylogenetic analysis estimated the most recent common ancestor of the human and simian HAV lineages at ~ 2 291 years ago and that of simian lineages at ~ 1900 years ago, with a more recent diversification (~100 years ago) within the identified lineage. This study highlights the presence of HAV in wild ape populations for the first time and also the first HAV detection among NHP species in Central Africa. These findings contribute to our current understanding of the diversity and evolution of HAV and highlight the need to extend surveillance across NHP species to better assess potential zoonotic risks.
DOI: 10.1093/ve/veag060/88242492026-09-21 · Volume 12 · Issue 1
Abstract The infectious haematopoietic necrosis virus (IHNV) is an important threat for global salmonid aquaculture, particularly Oncorhynchus mykiss . Understanding molecular mechanisms of evolution and host adaptation is crucial. This study comparatively analyses codon usage bias (CUB) between IHNV genotypes and their relations to host adaptation and evolutionary forces. Phylogenetic analysis of IHNV reveals topological differences based on whole-genome and G gene. Temporal analysis mapped major genotypic diversification to the 1950s–1970s. At the whole-genome and G gene levels, the most frequently preferred codons were related to the encoding of Leu (CTC), Ser (TCC), Pro (CCC), and Thr (ACC) across all genotypes (RSCU > 1.6). All data points fall below the expected effective number of codons (ENC) curve in ENC-plot. Codon usage for every genotype departs from the PR2-plot origin (0.5, 0.5) to varying extents in both the G gene and the whole genome. For whole-genome datasets, the selection contribution metric values for genotypes U, J, and E were 45.22%, 89.23%, and 99.52%, respectively, in Neutrality plots. Correspondingly, the selection contribution metric for G gene genotypes L, J, U, M, and E were 56.49%, 68.49%, 93.57%, 96.45%, and 85.52%, respectively. The CpG, GpC, GpT, TpT, and TpA were markedly underrepresented (Pxy 1.25). Codon adaptation index analysis shows a conserved optimal adaptation of all IHNV genotypes to salmonid hosts (rainbow trout and Chinook salmon). Bayesian skyline reconstruction shows genotype-specific population dynamics with expansion phases associated to intensive aquaculture. These results provide a molecular framework for understanding IHNV epidemiology and host specificity.
DOI: 10.1093/ve/veag062/88242512026-09-19 · Volume 12 · Issue 1
Abstract Numerous experimental evolution studies have suggested that adaptation rate of microbial populations evolving in stable environments decline over time. Despite the generality of this phenomenon across different domains of life, the timing and magnitude of decline in adaptation can vary greatly based on the idiosyncrasies of the biological system. To investigate the characteristics of adaptation deceleration in a fast-evolving virus, we propagated HIV-1 in two human T-cell lines (MT-2 and MT-4) for ~4.8 years and tracked its genome evolution through next-generation sequencing. The curated sequencing data covering the whole genome can be accessed and explored via LTEEviz, an interactive web application. Time-resolved sequencing data uncovered that despite constant fixation rate of 0.085 (MT-2) and 0.042 (MT-4) mutations per generation, the fixation kinetics of adaptive mutations changed considerably over time. The rate of fixation of adaptive parallel mutations decreased by 44% every 300 generations, while their conferred fitness gain decreased by 27% (MT-2) and 18% (MT-4) per every added adaptive mutation in their genetic background. The early and substantial deceleration of adaptation in our HIV-1 populations can, at least in part, be explained by diminishing gains of adaptive mutations. Furthermore, we identified genomic patterns consistent with a hard selective sweep that occurred in one population later in the experiment. Together, our results confirm that HIV-1 genomic evolution is characterized by a swift and substantial deceleration of adaptation while also revealing that episodes of positive selection can occur beyond the initial adaptive phase.
DOI: 10.1093/ve/veag059/88181072026-09-04 · Volume 12 · Issue 1
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 (1967–97) 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 (1967–76), blue (1976–88), and green (1984–96)—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 goal of zero human deaths from dog-mediated rabies.
DOI: 10.1093/ve/veag058/87858452026-09-03 · Volume 12 · Issue 1
Abstract RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the structural organization of viral populations in sequence space remains less explored. Here, we compare genotype network architectures in two RNA viruses with markedly different evolutionary contexts: bacteriophage $Q\beta$ evolving in controlled laboratory conditions and severe acute respiratory syndrome coronavirus 2 evolving within infected human hosts. Using deep sequencing data, we reconstruct the genotype network of mutationally coupled variants within viral populations and analyse their topological properties. Despite large differences in genome size, mutation rate, and ecological setting, both viruses exhibit a common organization: a highly abundant central haplotype surrounded by layers of variants of diminishing abundance as Hamming distance to the central haplotype increases. All reconstructed networks share qualitative and quantitative topological features, displaying a hierarchical structure. The robust organization of both populations under multiple conditions suggests that RNA viruses may share a common genotype network architecture governed by fundamental properties of sequence space and the generic mechanisms of replication and mutation. Genotype networks provide a unifying framework to describe viral population structure beyond conventional diversity measures and, by revealing how local constraints shape mutational search, offers insights into the predictability of viral evolution.
DOI: 10.1093/ve/veag053/87850532026-08-27 · Volume 12 · Issue 1
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.
DOI: 10.1093/ve/veag057/87719992026-08-20 · Volume 12 · Issue 1
Abstract The emergence of variants has shaped the COVID-19 pandemic. The lack of directly observed precursors to these variants has led to proposals that variants emerge from either persistent infections, transmission in non-human animal populations after reverse-zoonosis, or cryptic transmission in the human population. We investigated the origin of variants by analysing the molecular clock and rate of nonsynonymous and synonymous substitutions in SARS-CoV-2 circulating in human population, persistently infected individuals, non-human animals, and along variant stems: the branches preceding emergence of SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Epsilon, Iota, B.1.637, Mu, and Omicron: BA.1, BA.2/BA.4/BA.5). Along the variant stems we find evidence for an acceleration in the non-synonymous substitution rate, as compared with the non-synonymous substitution rate along branches that represent the genetic diversity of circulating virus. We also find evidence for a slowdown in the synonymous substitution rate preceding the emergence of multiple named variants (e.g . Beta, Delta, Iota, Mu, Omicron BA.1); a similar pattern was observed in some individuals with persistent infections. However, the synonymous rate slowdown was not observed for all variants, with some exhibiting an increase in synonymous substitution rates preceding their emergence compared with typical viral transmission (e.g . Alpha, Epsilon). The similarity in evolutionary dynamics preceding variant emergence and during persistent infections, but not with human to human transmission or during reverse zoonosis, supports the hypothesis that persistent infections were the likely source of many COVID-19 variants.
DOI: 10.1093/ve/veag054/87672482026-08-18 · Volume 12 · Issue 1
Abstract 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.
DOI: 10.1093/ve/veag052/87637592026-08-18 · Volume 12 · Issue 1
Abstract Coronavirus (CoV) spillover from wildlife to humans is increasing and has caused major global epidemics, facilitated by human-induced habitat alteration that promotes zoonotic emergence. This highlights the need for sustained surveillance and a better understanding of circulation patterns within wildlife reservoirs. Although Neotropical bats harbour a highly diverse CoV community, how host traits and ecological factors shape CoV circulation and virus–host associations remains poorly characterized. During 2021–3, we conducted extensive bat sampling across 12 localities along an anthropogenic land-use gradient in the Yucatan Peninsula, Mexico, to characterize bat community diversity. We then screened bats for CoVs and evaluated the association between CoV detection and host traits and ecological variables. Detected CoVs were subsequently sequenced and phylogenetically characterized. Using publicly available databases and host phylogenetic diversity metrics, we further analysed the putative host range of each identified CoV taxon and their distribution along the gradient. Bat diversity was significantly lower in urban sites. Although overall CoV positivity was low (3.2%), we identified eight divergent CoV taxa, including two novel Alphacoronavirus sequences, one of which represents the first CoV reported from Lophostoma brasiliense . Juvenile bats were more likely to be CoV-positive, a pattern particularly pronounced in Sturnira parvidens but absent in Artibeus jamaicensis . We found variation in putative host breadth among the identified CoV taxa, supported by differences in host phylogenetic distances. Notably, CoV taxa detected at sites with lower bat diversity were associated with a greater number of reported host species and higher host phylogenetic diversity. Our findings expand the known diversity of Neotropical bat CoVs and reveal distinct patterns in CoV detection and virus–host associations across viral taxa. Sustained viral surveillance, complemented by broader genomic studies and deeper investigation into variation within and among CoV taxa, is needed to clarify these patterns, guide research priorities in the Neotropical CoVs, and help mitigate the risk of future zoonotic emergence.
DOI: 10.1093/ve/veag049/87637582026-08-14 · Volume 12 · Issue 1
This is a correction to: Bowen Zheng, Paul C D Johnson, Joseph Hughes, ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods, Virus Evolution , Volume 11, Issue 1, 2025, veaf071, https://doi.org/10.1093/ve/veaf071
DOI: 10.1093/ve/veag055/87615742026-08-14 · Volume 12 · Issue 1
This is a correction to: Hugh K Haddox, Omar Abdel Aziz, Jared G Galloway, Javen Kent, Cameron R Cooper, Chris Jennings-Shaffer, Will Dumm, Seth D Temple, Jesse D Bloom, Frederick A Matsen, Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies, Virus Evolution , Volume 12, Issue 1, 2026, veaf104, https://doi.org/10.1093/ve/veaf104
DOI: 10.1093/ve/veag056/87615732026-08-08 · Volume 12 · Issue 1
Abstract Since its re-emergence in Europe in 2015, enterovirus A71 (EV-A71) has been associated with sporadic cases of severe infections and outbreaks. Currently, there is no treatment but a few Asian countries have implemented vaccination programmes. The aim of our study was to characterize the EV-A71 cases in Europe and track the evolution of the virus between 2016 and 2022.For this retrospective study, we compiled the data of confirmed EV-A71 infections collected by 19 institutes participating in the European Non-Polio Enterovirus Network between 2016 and 2022. We also sequenced whole EV-A71 genomes to follow the viral evolutionary history of the virus and its molecular changes.Between 1 January 2016 and 31 December 2022, 627 EV-A71 cases were reported in 14 European countries. Most cases (59.3%) occurred in children under two years of age. Of the 537 subjects for whom clinical information was available, 52.7% were diagnosed with neurological signs, and 10.6% presented with acute flaccid paralysis or acute flaccid myelitis. EV-A71 infections were linked to two subclades, C1.2 and C1.3, within the C1 subgenogroup. Two marked epidemic waves, in 2016 and 2019, were characterized by the predominance of C1.3 viruses. Comparisons of 153 whole genomes revealed nine recombinant forms (RFs), each arising from multiple recombination events affecting different genomic regions. Only C1.3/RF5 and C1.3/RF6 lineages achieved widespread geographic dissemination initially in Europe and subsequently in Asia and the Americas, and long-term circulation. Phylodynamic analyses indicated that C1.3 viruses emerged around 2013–2014, displacing earlier C1.1 viruses, and the effective population size closely parallels the timing of clinical cases. Molecular analyses of the capsid revealed several amino acid changes, few of which occurred within known antigenic sites.These findings document the role of the C1.3/RF5 and C1.3/RF6 multi-recombinant lineages of EV-A71 as frequent causes of neurological disease in young children in Europe. The study highlights the need for sustained genome-informed surveillance to anticipate the emergence and spread of novel epidemic lineages, and to inform the evaluation of future EV-A71 vaccination strategies.
DOI: 10.1093/ve/veag051/87569642026-08-05 · Volume 12 · Issue 1
Abstract Understanding the sources of genetic diversity in Influenza A Virus (IAV) infections is crucial for understanding the mechanisms of viral evolution and immune escape. Whereas prior studies have characterized the effects of population bottlenecks during host-to-host transmission and intrahost tissue-to-tissue dissemination, the role of intracellular replication processes on IAV genetic diversity remains largely unexplored. In this study, we used stochastic mathematical modelling to simulate the replication of genetically distinct IAV strains within individual cells and tissues. Our results reveal significant bottleneck effects within a single infection cycle of individual cells. Intracellular bottleneck effects are driven by stochastic molecular processes and lead to the expansion or elimination of neutral variants creating large-scale differences between the initial and final frequencies of genetic variants in individual cells. By expanding our findings to a population-level model, we show that IAV intracellular replication reduces the effective population size, thereby diminishing the impact of selection and increasing the role of genetic drift. Our findings highlight the impact of intracellular replication processes on IAV genetic diversity.
DOI: 10.1093/ve/veag050/87526882026-07-31 · Volume 12 · Issue 1
Abstract A virus with a circular single-stranded DNA genome, HthCRESSV1, was discovered in an oomycete, Halophytophthora thermoambigua , isolated from brackish waters off the Algarve coast in southern Portugal. Phylogenetic analyses place this virus outside of all currently classified families within the phylum Cressdnaviricota , suggesting it represents a distinct lineage. Cellular fractionation, mitochondrial marker co-enrichment, and Southern blot analyses indicate that HthCRESSV1 is associated with mitochondria and replicates episomally. The virus is stably transmitted through zoospores and is associated with a reduced host mycelial growth. Homologous sequences corresponding to both the replication-associated protein and a membrane-associated hypothetical protein were identified in the mitochondrial genomes of several oomycete species, suggesting recurrent endogenization of HthCRESSV1-like viruses in oomycete mitochondria. Together, these findings expand the known diversity of oomycete-associated DNA viruses, identify mitochondria as an unexpected niche for DNA virus replication, and highlight marine environments as underexplored reservoirs of DNA viruses in stramenopiles.
DOI: 10.1093/ve/veag047/87482882026-07-31 · Volume 12 · Issue 1
Abstract Herpesviruses are a widespread and diverse family of large double-stranded DNA viruses. Narrow host ranges maintained over long evolutionary times have fostered intimate host adaptations. However, such close virus–host associations inevitably invite conflict. Genetic conflict describes antagonistic interactions between two individuals that drive genetic changes to overcome said conflict. During the herpesvirus infectious cycle, genetic conflict—and specifically antagonistic co-evolution—can occur on multiple levels: between host and virus, between co-infecting viruses, or between genes within the same genome. This review highlights the many ways such conflict occurs and how it shapes herpesvirus evolution. Starting with attachment and entry, and continuing through gene expression, DNA metabolism, packaging, and egress, we examine how antagonistic interactions manifest at each stage of the viral life cycle. Latency and immunity receive special consideration as their inherent biology makes them focal points of sustained antagonism. Since genetic conflict is a major force in evolutionary ecology, we aim to emphasize its central role in herpesvirus biology and encourage future studies to explicitly consider the antagonistic forces shaping their evolution.
DOI: 10.1093/ve/veag048/87482972026-07-28 · Volume 12 · Issue 1
Abstract Respiratory syncytial virus (RSV) remains a leading cause of hospitalization despite the recent implementation of infant immunoprophylaxis programs. The inter- and intrahost levels of genetic variation across the genome have not been extensively investigated. Hence, the aim of this study was to characterize the whole genome of RSV strains circulating within two Italian areas during the 2024–5 RSV season, corresponding to the first season after implementation of the national nirsevimab prophylaxis program. Whole genome sequencing (WGS) was performed on 88 respiratory samples that tested positive for RSV. Clinical records showed that none of the sequenced patients had received nirsevimab prophylaxis. The WGS strains obtained in the present study were correlated with the RSV strains circulating in Europe using phylogenetic inference. A newly designed bioinformatic pipeline was developed to evaluate the extent of genetic variation within hosts and reveal the distribution of minority mutations among RSV lineages. RSV-A ( n = 54) showed significantly higher levels of nucleotide diversity than RSV-B ( n = 34). Among the RSV-A strains, lineage A.D.3 was the most prevalent (35/54, 64%), followed by A.D.1 (18/54, 33%). The A.D.5 lineage was identified in only one strain, while all 34 RSV-B strains were found to be lineage B.D.E. Analysis of variants across the major lineages (A.D.1, A.D.3, and B.D.E) revealed heterogeneous mutation patterns. The G, L, and F genes showed the highest variability. Minority viral variants (0.02–0.05 frequency) followed the same gene-specific dynamics as the broader quasispecies population. A > G transitions consistent with ADAR activity were detected in all samples, but their frequency was similar to the other nucleotide substitutions across the genomes. The analysis of minor variants also targeted mutations known to reduce nirsevimab efficacy, and none were detected. Overall, RSV-A showed substantially greater intragenotypic and intrahost diversity than RSV-B. The elevated diversity in RSV-A resulted from a wider distribution of mutations across the viral genome, including both high-frequency substitutions that shaped the consensus sequence and low-frequency variants contributing to the underlying quasispecies complexity. Although no nirsevimab-treated patients were included in this study, the observed intrahost diversity highlights the importance of continued genomic surveillance to detect potential escape variants as prophylactic programs expand.
DOI: 10.1093/ve/veag045/87441282026-07-26 · Volume 12 · Issue 1
Abstract Twice each year, a decision is made on whether to update the strains included in the seasonal influenza vaccine to better match the most recent circulating viral strains. To characterize the antigenic properties of current seasonal influenza A strains to inform the upcoming decision about which strains to include in the 2026–7 Northern Hemisphere vaccine, here we perform high-throughput sequencing–based neutralization assays using a library of 57 H3N2 and 34 H1N1 influenza hemagglutinins reflecting the circulating diversity of strains in late 2025 to early 2026. We assay this library against 302 human sera collected in late 2025. The resulting data set encompasses 27 409 titres and provides a near real-time portrait of the human neutralizing antibody landscape against influenza virus. We find that many human sera have lower titres against the K subclade of H3N2 and the D.3.1.1 subclade of H1N1; these subclades have recently become dominant among their respective subtypes. Our measurements also reveal variability in titres to different subvariants within the K subclade of H3N2, with titres especially low to subclade K strains with additional mutations in antigenic regions D and E. We make all our data and accompanying visualizations publicly available to enable their use in vaccine-strain selection and analyses of influenza evolution and immunity.
DOI: 10.1093/ve/veag046/87420492026-07-16 · Volume 12 · Issue 1
Abstract Killer yeasts secrete protein toxins that inhibit other yeast strains, a trait often encoded by M satellites of L-A dsRNA viruses. These systems serve as important molecular models, yet their adaptive significance in natural settings remains unclear. This study surveyed 60 strains from a natural Saccharomyces paradoxus population in the UK to characterize dsRNA viral genomic diversity. Our survey revealed 27% of strains showed killer activity mediated by dsRNA viruses. Additionally, five of 18 nonkiller strains also contained dsRNA viruses. Deep sequencing of pooled dsRNAs from 17 strains identified six distinct M satellite types, including three novel lineages, with single-nucleotide and structural polymorphisms creating multiple variant sequences within types. Predicted preprotoxin proteins generally contained post-translational modification sites necessary for toxin maturation, although with variable numbers among different types, potentially affecting processing and expression. Eight L-A virus sequences were also assembled. These were all closely related to each other and clustered phylogenetically with viruses from other European S. paradoxus strains. Extended 5′ sequence analysis revealed novel structural features in both L-As and their M satellites, including a pair of inverted repeats ending in a pair of inverted conserved motifs (GA 5–6 and corresponding U 5–6 C in Ms and GAAUA and corresponding UAUUC in L-As), which is, in turn, flanked by a pair of direct repeats. The pair of conserved motifs also exists in all described S. cerevisiae M satellites. The observed diversity of dsRNA satellites within a single yeast population is a challenge to explain, with many evolutionary forces potentially contributing.
DOI: 10.1093/ve/veag043/87357992026-07-16 · Volume 12 · Issue 1
Abstract It is known that several endogenous retroviruses, remnants of ancient retroviral integrations, retain envelope ( env ) genes encoding fusogenic proteins in primates. Whilst most env genes are degraded, a few have been co-opted by hosts, yet the entire evolutionary dynamics of env sequences remain poorly understood. To explore this, we screened and compared env open reading frames (ORFs) from 247 primate genomes. In total, 8683 nearly intact env -ORFs encoding 400 or more amino acids were identified, and their copy numbers ranged from 3 to 429 across primate species. Sequence similarity clustering revealed a clear evolutionary signature that distinguishes the small set of long-term co-opted env -derived genes, which are retained at low copy numbers across lineages, from the broader pool of rapidly turning-over env -ORFs. Applying this framework, we identified a previously unrecognized, single-copy env ortholog conserved across Tarsiiformes, named env-Tar1 , and experimentally demonstrated its cell fusion activity in vitro , providing the first functional evidence of an env -derived gene co-opted in a tarsier lineage. Further, we found that certain co-opted env -derived genes may have lost their functions due to nonsense or indel mutations within specific primate lineages. Considering that many env genes tend to be maintained at low copy numbers and are reported to be under purifying selection, such dynamic evolutionary turnover of env -derived genes may be driven by host-virus arms races, as viruses and endogenous retroviruses often share cell-surface receptors.
DOI: 10.1093/ve/veag044/87357922026-07-12 · Volume 12 · Issue 1
Abstract Parvoviridae (small, nonenveloped ssDNA viruses) currently includes 281 species in two vertebrate- and four invertebrate-infecting subfamilies. While parvovirus-derived sequences are frequently identified in viromes, their taxonomy and host affiliation can be challenging due to high host and genetic diversity. We investigated the faecal parvovirome of 46 bats (7 insectivorous and 1 frugivorous species) from Eswatini and identified 28 novel viral species in 29 individuals (63.0%). The majority of these (22/28, 78.6%) belonged to nine genera (including two that are previously undescribed) within the invertebrate-infecting subfamily Densovirinae . A novel virus in the genus Brevipenbrevirus (arthropod-infecting subfamily Penbrevirinae ) was found in 19.6% of the animals, including several frugivorous Epomophorus wahlbergi bats. A novel bat protoparvovirus (vertebrate-infecting subfamily Parvovirnae ) was found both in the faeces and blood of one Afronycteris nanus bat. A highly divergent virus (Swazi bat–associated megaparvovirus 1, SwaBA-MePV-1) was found in the faeces, but not in the blood, of two insectivorous bats ( Mops pumilus and Scotophilus viridis ). Compared to other parvoviruses, SwaBA-MePV-1 presented two additional coding cassettes, significantly increasing its genome size. Homology modelling showed capsid protein C-terminal elongation, a previously undescribed strategy of parvoviral particle size expansion. Exploring public repositories identified 10 related uncharacterized viruses with similar genome organization and complete endogenous viral elements (EVEs) in eight beetle species, suggesting a coleopteran host affiliation. The complete genome of another highly divergent virus (SwaBA microparvovirus 1), without any detectable exogenous or endogenous relatives, was found in the faeces, but not in the blood, of one insectivorous Mops condylurus bat. Importantly, when comparing our sequences to references in Genbank , we observed that taxonomic mislabelling in sequence repositories can seriously misguide automatic taxonomy assignments (~75% of sequences initially identified as parvoviruses were discarded as false positives). These errors are amplified as new mislabelled sequences become dominant, highlighting the importance of prioritizing taxonomy validation and correct annotations in repositories. This study demonstrates that faecal samples from insectivorous chiropterans are rich in (novel) parvoviruses from various hosts. The discovery of highly divergent lineages (outside current sub-families) and EVEs helps clarify parvovirus evolutionary history and emphasizes how much of the parvoviral world remains unexplored.
DOI: 10.1093/ve/veag042/87327542026-07-05 · Volume 12 · Issue 1
Abstract Mosquito-borne viruses are expanding their geographic range in Europe, increasingly affecting wildlife and human health. Usutu virus (USUV), a zoonotic mosquito-borne Orthoflavivirus with birds as amplifying hosts, has caused large-scale avian mortality in Europe, particularly among Eurasian Blackbirds ( Turdus merula ). Although USUV is not considered a major human health threat, it is closely related to other human-pathogenic arboviruses. Its emergence in northwestern Europe may indicate increasingly suitable conditions for other arboviruses that could follow similar transmission dynamics upon emergence in this setting. In the Netherlands, USUV was first detected in 2016, caused major outbreaks in birds until 2018, and resurged in 2022. Here, we conduct phylodynamic and phylogeographic analyses to reconstruct the emergence and persistence dynamics of USUV in the Netherlands. We analyse 298 near-full-length viral genomes obtained from birds and mosquitoes from the Netherlands, combined with publicly available USUV genomes. We identify multiple independent USUV introductions into the Netherlands region, leading to the apparent enzootic establishment of two predominant clades from lineage Africa 3 in this broader region. For these two clades, our analyses show a temporal pattern consistent with invasion followed by local persistence, associated with a substantial spatial intermixing of viral lineages circulating in the region. Landscape phylogeographic analyses further suggest a possible tendency for USUV lineages to circulate in urbanized areas and regions with higher human population density, though future work should assess whether this pattern reflects true ecological preference or reporting bias. In a context with recurrent outbreaks of West Nile virus in northwestern Europe, this study provides insight into the dynamics of emergence and establishment of a closely related mosquito-borne virus in a previously nonendemic temperate region.
DOI: 10.1093/ve/veag041/87249772026-07-01 · Volume 12 · Issue 1
Abstract Viral genes sometimes use certain codons more than others due to their nucleotide content, translational efficiency, and selection pressure from the host immune system. The rabies virus (RABV) is a negative strand RNA virus which can infect a broad range of mammalian hosts, with many of its clades circulating predominantly in specific host species. Previous work on codon usage in RABV has focused only on broader viral clades. We use publicly available RABV nucleoprotein gene sequences to investigate how dinucleotide content and codon usage biases differ between host-associated clades, and what drives these differences. We found that codon usage varies most between bat- and carnivore-associated RABV clades, and more subtly between host-species-specific minor clades within these groups. C1, GA3, and GT3 content were found to have a strong influence over codon usage patterns, and cytosine-guanine dinucleotide (CpG) content was higher in carnivore-associated RABV clades than in bat-associated clades. This, along with lower numbers of zinc-finger antiviral protein binding motifs than would be expected based on (di)nucleotide composition in bat-associated RABV sequences, suggests that bat-associated RABV clades may be under higher selection pressure from the host’s zinc-finger antiviral protein than carnivore-associated clades are, warranting further investigation of the mechanism underpinning this change.
DOI: 10.1093/ve/veag039/87232662026-07-01 · Volume 12 · Issue 1
Abstract 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.
DOI: 10.1093/ve/veag040/87232652026-06-27 · Volume 12 · Issue 1
Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the Coronavirus Disease of 2019 (COVID-19) pandemic, can productively infect a variety of animal hosts. The evidence suggests that both wild and farmed animal populations supporting continuous transmission present us with novel concerning genotypes of SARS-CoV-2. This is especially worrisome within large and dense populations of farmed animals, such as minks, for which spillbacks of ‘mink genotypes’ to the human population have been recorded on numerous occasions. In this study, we present the results of continuous clinical, virological, serological, and genomic surveillance during the period of 11 months of the SARS-CoV-2 outbreak at the largest Latvian mink farm with ˃300 000 animals. Using the One Health approach, the COVID-19 status of minks and farm workers was constantly monitored during the surveillance period. The presence of the SARS-CoV-2 genome was confirmed in 299 minks and 32 farm workers during the outbreak. The phylogenetic analysis of 188 mink and 14 human SARS-CoV-2 isolates linked to the farm provided insight into the evolution of the virus in situ and contributed to epidemiological investigation. The results revealed that SARS-CoV-2 lineage B.1.177.60 was initially introduced to the mink farm by an infected farm worker between 17 February and 23 March 2021, and subsequently spread among the minks. Surveillance in the affected farm showed fluctuating virus circulation. Although the average seroprevalence in samples taken from live minks was 76.92%, a fluctuating course of infection was observed from April 2021 to March 2022. Despite the implementation of strict preventive and control measures at the farm, several additional SARS-CoV-2 strain introductions were identified during 11 months. The initial introduction of a common viral strain circulating among the people at the time soon resulted in the co-circulation of multiple sister sublineages that have evolved some concerning spike protein amino acid substitutions. Subsequent other lineage introductions into the farm were not able to spread among minks. Several independent cases of farm workers infected with genotypes restricted to this mink farm were documented throughout the study timeframe. However, the ‘Latvian mink genotypes’ were not detected in the general human population beyond epidemiologic association with the given mink farm.
DOI: 10.1093/ve/veag038/87196382026-06-23 · Volume 12 · Issue 1
Abstract Bat sarbecoviruses include several potentially human-infective viruses, and evaluating their evolvability is therefore important for assessing emergence risks. In particular, the interaction between the viral spike protein and the host ACE2 receptor is critical for cross-species transmissibility. Here, we focused on the spike protein from Rc-o319, a bat sarbecovirus related to SARS-CoV-2 but unable to infect humans. Using a recombinant vesicular stomatitis virus (VSV), we found that Rc-o319 spike protein ACE2 usage was restricted to its natural host, Rhinolophus cornutus , and to mouse ACE2 at low levels, but not to R. sinicus , ferret, cow, or human ACE2 homologues. Experimental evolution passages of the recombinant VSV expressing the Rc-o319 spike enabled us to study spike adaptation without requiring the authentic virus or posing a risk to humans. We found rapid spike optimization for viral entry through mouse ACE2, driven by a single substitution in the receptor-binding motif. In contrast, repeated passaging under strong selective pressure failed to yield variants capable of using human ACE2, indicating substantial evolutionary constraints. Together, our results demonstrate that the Rc-o319 spike can readily optimize interactions with already permissive ACE2 receptors but is limited in its capacity to acquire usage of a new ACE2 homologue, particularly human ACE2, suggesting a low zoonotic risk. However, some evolved spikes appeared to acquire a residual capacity for ACE2-independent viral entry, although this observation remains to be conclusively demonstrated and requires further investigation.
DOI: 10.1093/ve/veag035/87141272026-06-22 · Volume 12 · Issue 1
Abstract To date, 15 species have been described within the genus Enterovirus. Previous studies suggested the existence of another species comprising strains isolated from stool specimens of non-human primates (NHPs) in Central Africa. Moreover, numerous full-length or partial genomic sequences of NHP enteroviruses (EVs) can be found in GenBank without being properly classified. To our knowledge, no comprehensive synthesis of NHP EV data exists, leaving genetic relationships between strains across independent studies unclear. To address these gaps, we sequenced the complete genome of four NHP EVs from our stool collection and conducted an extensive search of NHP EV sequences in GenBank to perform a comprehensive phylogenetic analysis. Our analyses highlight that a group of viruses closely related to simian members of the species Enterovirus betacoxsackie in the non-structural region of the genome was found to be highly divergent in the capsid. In our view, the level of divergence suggests the existence of a novel species, tentatively named Enterovirus mbel . Recombination events between members of these two distinct species would explain their close relationships downstream the capsid-encoding region, thus challenging the long-held view that recombination is confined within narrowly defined subsets of EVs belonging to the same species. We also identified new virus types within the species Enterovirus jesimi , some of which are relatively divergent from the others in the capsid and could belong to another species, tentatively named Enterovirus noa . We also performed the first comprehensive comparative analysis of full-length human and NHP EV genomes, focusing on guanine-cytosine (GC) content, dinucleotide frequencies, and codon-usage bias. GC content emerged as the most robust host-associated marker: all NHP-associated virus types within species Enterovirus alphacoxsackie and Enterovirus betacoxsackie displayed GC content below 47%, whereas human-derived virus types exhibited GC content above 47%. Dinucleotide frequency, effective number of codons, and relative synonymous codon usage highlighted distinct codon-bias clusters that mirror the phylogenetic relationships between EVs, but only partially correlate with their respective hosts. This work enhances our understanding of EVs circulating in NHPs and paves the way for future research aiming at understanding the mechanisms underlying host-adaptation among EVs.
DOI: 10.1093/ve/veag037/87132742026-06-22 · Volume 12 · Issue 1
Abstract Simultaneous genomic sequencing of multiple respiratory pathogens from clinical samples can provide real-time data on viral evolution, co-circulation, and co-infection during seasonal epidemics. Influenza is a major global respiratory pathogen, with a well-established genomic epidemiology framework, that has yet to be integrated with genomic surveillance of other co-circulating respiratory viruses. Leveraging existing well-integrated community influenza sampling during the first major Australian winter influenza season after the lifting of the Coronavirus Disease 2019 (COVID-19) pandemic restrictions in 2022, we examined the genomic epidemiology of influenza A alongside co-infections of common human respiratory viruses. Using a commercial respiratory viral sequencing method, Respiratory Virus Oligo Panel (Illumina), we recovered full-length human influenza A genomes from 75% (117/157) of samples with nucleic acid amplification test-confirmed influenza, as well as 19 genomes of co-infecting viruses from 17 samples, including respiratory syncytial virus (RSV-B), human bocavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), human metapneumovirus, and coronaviruses 229E and OC43. The observed incidence of co-infecting viruses (RSV and SARS-CoV-2) was temporally consistent with national epidemic trends. In the majority of co-infections, the viral abundance was predominated by one of the infecting viruses, which may suggest either consecutive infections, or within-host dynamics favouring the dominance of one of the infecting viruses. The dominant influenza subtype was A/H3N2, with a minority of A/H1N1 infections persisting throughout the winter season, consistent with national surveillance. We contextualize our representative sample set within the global genomic diversity of A/H3N2 and the ongoing evolution of influenza A/H3N2 in the following Northern Hemisphere 2022/2023 winter. In addition to influenza A genomic epidemiology, multi-pathogen methodology enables simultaneous detection and characterization of co-infecting respiratory pathogens, providing insights into the role of viral dynamics during overlapping epidemics.
DOI: 10.1093/ve/veag036/8719636