Virus Evolution病毒进化
Virus Evolution(英文缩写 VIRUS EVOL),ISSN 2057-1577,eISSN 2057-1577,中文译名:病毒进化 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-11-01 至 2026-10-31，按本站收录文献的发表日期统计。
期刊介绍
Virus Evolution 最新收录文献
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1. Phylogeography and evolutionary dynamics of Nairobi sheep disease virus.
PMID:日期:2026-09-21Nairobi sheep disease virus (NSDV) is a tick-borne 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 (L) to 6.81 × 10 (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 , 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.
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2. Reconstructing the molecular epidemiology of rabies in Switzerland from outbreak to elimination (1967-97).
PMID:日期:2026-09-04Rabies 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.
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3. Shared quasispecies architecture in experimental and natural RNA virus populations.
PMID:日期:2026-09-03RNA 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 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.
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4. {"_":"Discovery of novel viruses related to the family reveals expanded diversity, a broad host range, and evidence of fungal and oomycete infections.","i":["Potyviridae"]}
PMID:日期:2026-08-27The family 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 , 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 , 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.
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5. Slowdown of synonymous substitution rate preceding the emergence of multiple SARS-CoV-2 variants.
PMID:日期:2026-08-20The 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.
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6. {"_":"Discovery of the order '' redefines the evolution of RNA replication and transcription in the phylum .","i":["Quisvirales","Pisuviricota"]}
PMID:日期:2026-08-18Genome 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 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 ''. 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 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 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 ' demonstrates that viruses employing large replicase polyproteins of nidovirus-like complexity and discontinuous transcription may have evolved repeatedly from an 3CLpro-RdRp-encoding ancestor.
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7. Virus-host associations of bat coronaviruses along a land-use gradient in the Yucatán Peninsula, México.
PMID:日期:2026-08-18Coronavirus (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 . Juvenile bats were more likely to be CoV-positive, a pattern particularly pronounced in but absent in . 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.
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8. Correction to: Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies.
PMID:日期:2026-08-14[This corrects the article DOI: 10.1093/ve/veaf104.].
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9. Correction to: ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods.
PMID:日期:2026-08-14[This corrects the article DOI: 10.1093/ve/veaf071.].
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10. Emergence and spread of multirecombinant enterovirus A71 lineages C1.3/RF5 and C1.3/RF6 associated with neurological diseases in Europe, 2016-2022, ENPEN multicentre study.
10. 与欧洲神经系统疾病相关的多重重组肠道病毒A71谱系C1.3/RF5和C1.3/RF6的出现与传播，2016-2022年，ENPEN多中心研究PMID:日期:2026-08-08Since 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.