Virus Evolution最新文献

{"title":"Molecular epidemiology of paediatric respiratory adenovirus infections in Île-de-France: findings from whole-genome sequencing.","authors":"Maud Salmona, Elise Diaz, Linda Feghoul, Abdeljalil Senhaji Rachik, Héloïse Delagrèverie, Honorine Fenaux, Aurélie Schnuriger, Audrey Baron, Lamia Limam, Séverine Mercier-Delarue, Elyanne Gault, Jérôme LeGoff","doi":"10.1093/ve/veag064","DOIUrl":"10.1093/ve/veag064","url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Aim: </strong>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.</p><p><strong>Methods: </strong>We retrospectively analysed 6 956 respiratory samples from patients < 18 years, collected at five hospitals (Jan-June 2022). HAdVs were detected by multiplex PCR. Viral loads were quantified in mono-infections, and whole-genome sequencing (WGS) was performed on samples with sufficient viral load.</p><p><strong>Results: </strong>HAdVs were detected in 14% of samples, making them the second most prevalent virus after rhinovirus/enterovirus. Co-infections were frequent (64%), particularly in younger children. Among the 254 mono-infected samples with viral-load quantification, 110 (43%) had low or undetectable viral loads. WGS of 122 samples revealed HAdV species B (62.3%), C (34.4%), and F (3.3%). Species distribution varied by age: HAdV-C predominated in children under 2 years, while HAdV-B was more common in older children. The most frequent genotypes were B3 (76.3%), B66 (18.4%), and B7d (5.3%) within species B, and C1 (33.3%), C89 (26.2%), and C2 (23.8%) within species C.</p><p><strong>Conclusion: </strong>HAdVs are prevalent among children with respiratory infections, with age-specific patterns and substantial genomic diversity. The circulation of diverse genotypes, including recombinants and potentially more virulent variants, highlights the importance of sustained molecular surveillance.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag064"},"PeriodicalIF":3.8,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conditions for invasion and persistence of a satellite that does not affect the replication and virulence of its helper virus.","authors":"Rafael de Andrés-Torán, Bruno Cuevas-Zuviría, Mark P Zwart, Miguel Ángel Mora, Aurora Fraile, Fernando García-Arenal","doi":"10.1093/ve/veag063","DOIUrl":"https://doi.org/10.1093/ve/veag063","url":null,"abstract":"<p><p>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 <i>Nicotiana glauca</i> 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 <i>N. glauca</i>. 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 <i>N. glauca</i>. 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag063"},"PeriodicalIF":3.8,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of codon usage bias revealed natural selection-driven evolution and host adaptation of infectious haematopoietic necrosis virus.","authors":"Yu-Meng Yang, Fang Liu, Liu-Yi Yu, He Sun, Adili Abudu, Jian-Yong Hu, Yue Zhuo, Cui-Lan Hao, Cheng Yue","doi":"10.1093/ve/veag062","DOIUrl":"https://doi.org/10.1093/ve/veag062","url":null,"abstract":"<p><p>The infectious haematopoietic necrosis virus (IHNV) is an important threat for global salmonid aquaculture, particularly <i>Oncorhynchus mykiss</i>. 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 < 0.78), while CpA, GpA, and TpC were overrepresented in both the G gene and the whole genome (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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag062"},"PeriodicalIF":3.8,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeography and evolutionary dynamics of Nairobi sheep disease virus.","authors":"Han-Zheng Mu, Si-Qian Wu, Mei-Qi Zhang, Gui-Yan Shi, Jia-Yi Wang, Ming Chen, Yun-Dong Shi, Hong Su, Xiao-Ai Zhang, Wei Liu","doi":"10.1093/ve/veag061","DOIUrl":"https://doi.org/10.1093/ve/veag061","url":null,"abstract":"<p><p>Nairobi sheep disease virus (NSDV) is a tick-borne <i>orthonairovirus</i> 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 <i>a posteriori</i>, 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag061"},"PeriodicalIF":3.8,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13628517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A divergent hepatitis A virus lineage in wild western lowland gorillas and central chimpanzees supports localized circulation and expands HAV diversity.","authors":"Charles Sanctorum, Matheus A C Cosentino, Amandine Esteban, Christelle Butel, Innocent Ndong Bass, Simon-Pierre Ndimbo-Kumugo, Steve Ahuka-Mundeke, Eric Leroy, Charles Kouanfack, Ahidjo Ayouba, Martine Peeters","doi":"10.1093/ve/veag060","DOIUrl":"https://doi.org/10.1093/ve/veag060","url":null,"abstract":"<p><p>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 (<i>Gorilla gorilla gorilla</i>) from southern Cameroon, sampled in 2006, and another from a central chimpanzee (<i>Pan troglodytes troglodytes</i>) 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag060"},"PeriodicalIF":3.8,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Substantial deceleration of adaptation of HIV-1 within 1500 generations in an experimental evolution: a genomic perspective.","authors":"Ali Movasati, Christine Leemann, Kathrin Neumann, Rongfeng Chen, Lygeri Sakellaridi, Karin J Metzner, Roland R Regoes","doi":"10.1093/ve/veag059","DOIUrl":"https://doi.org/10.1093/ve/veag059","url":null,"abstract":"<p><p>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 <i>via</i> 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag059"},"PeriodicalIF":3.8,"publicationDate":"2026-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reconstructing the molecular epidemiology of rabies in Switzerland from outbreak to elimination (1967-97).","authors":"Farzane Shams, Claudia Bachofen, Alex Popinga, Monika Hilbe, Michele Wyler, Torsten Seuberlich","doi":"10.1093/ve/veag058","DOIUrl":"https://doi.org/10.1093/ve/veag058","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag058"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13598893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shared quasispecies architecture in experimental and natural RNA virus populations.","authors":"Samuel Martínez-Alcalá, Iker Atienza-Diez, Pilar Somovilla, Brenda Martínez-González, Celia Perales, Luis F Seoane, Ester Lázaro, Susanna Manrubia","doi":"10.1093/ve/veag053","DOIUrl":"10.1093/ve/veag053","url":null,"abstract":"<p><p>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 <i>Qβ</i> 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag053"},"PeriodicalIF":3.8,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13591489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149019022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of novel viruses related to the <i>Potyviridae</i> family reveals expanded diversity, a broad host range, and evidence of fungal and oomycete infections.","authors":"Bernardo Rodamilans, Mario Rincón Barrado, Alberto Cobos Piñuela, Carmen Simón Mateo, Adrian A Valli","doi":"10.1093/ve/veag057","DOIUrl":"https://doi.org/10.1093/ve/veag057","url":null,"abstract":"<p><p>The family <i>Potyviridae</i> 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 <i>Potyviridae</i>, 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 <i>Potyviridae</i>, 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag057"},"PeriodicalIF":3.8,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Slowdown of synonymous substitution rate preceding the emergence of multiple SARS-CoV-2 variants.","authors":"Jennifer L Havens, Karthik Gangavarapu, Jade C Wang, Faten Taki, Elizabeth Luoma, Jonathan E Pekar, Helly Amin, Steve Di Lonardo, Enoma Omoregie, Scott Hughes, Kristian G Andersen, Tetyana I Vasylyeva, Marc A Suchard, Joel O Wertheim","doi":"10.1093/ve/veag054","DOIUrl":"10.1093/ve/veag054","url":null,"abstract":"<p><p>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<i>.</i> 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<i>.</i> 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag054"},"PeriodicalIF":3.8,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}