Virus Evolution最新文献

{"title":"Dynamic evolution of retroviral envelope-derived sequences in primates.","authors":"Koichi Kitao, Kirill Kryukov, Lihua Jin, Yuta Shintaku, Takashi Hayakawa, So Nakagawa","doi":"10.1093/ve/veag044","DOIUrl":"10.1093/ve/veag044","url":null,"abstract":"<p><p>It is known that several endogenous retroviruses, remnants of ancient retroviral integrations, retain envelope (<i>env</i>) genes encoding fusogenic proteins in primates. Whilst most <i>env</i> genes are degraded, a few have been co-opted by hosts, yet the entire evolutionary dynamics of <i>env</i> sequences remain poorly understood. To explore this, we screened and compared <i>env</i> open reading frames (ORFs) from 247 primate genomes. In total, 8683 nearly intact <i>env</i>-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 <i>env</i>-derived genes, which are retained at low copy numbers across lineages, from the broader pool of rapidly turning-over <i>env</i>-ORFs. Applying this framework, we identified a previously unrecognized, single-copy <i>env</i> ortholog conserved across Tarsiiformes, named <i>env-Tar1</i>, and experimentally demonstrated its cell fusion activity <i>in vitro</i>, providing the first functional evidence of an <i>env</i>-derived gene co-opted in a tarsier lineage. Further, we found that certain co-opted <i>env</i>-derived genes may have lost their functions due to nonsense or indel mutations within specific primate lineages. Considering that many <i>env</i> genes tend to be maintained at low copy numbers and are reported to be under purifying selection, such dynamic evolutionary turnover of <i>env</i>-derived genes may be driven by host-virus arms races, as viruses and endogenous retroviruses often share cell-surface receptors.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag044"},"PeriodicalIF":3.8,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13461226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148714914","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":"Genomic characterization and diversity of dsRNA viruses and their killer satellites in a natural population of the yeast <i>Saccharomyces paradoxus</i>.","authors":"Mahsan Nematbakhsh, Vassiliki Koufopanou, Anthony Cass, Austin Burt","doi":"10.1093/ve/veag043","DOIUrl":"10.1093/ve/veag043","url":null,"abstract":"<p><p>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 <i>Saccharomyces paradoxus</i> 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 <i>S. paradoxus</i> 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_5-6C 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 <i>S. cerevisiae</i> M satellites. The observed diversity of dsRNA satellites within a single yeast population is a challenge to explain, with many evolutionary forces potentially contributing.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag043"},"PeriodicalIF":3.8,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698413","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":"Characterizing the parvovirome of Swazi bats: novel species, highly divergent lineages, endogenous viral elements, and taxonomic challenges.","authors":"Joost T P Verhoeven, Julie Teresa Shapiro, Randi Holm Jensen, Robert A McCleery, Ara Monadjem, Anders J Hansen, Judit J Pénzes, Marta Canuti","doi":"10.1093/ve/veag042","DOIUrl":"10.1093/ve/veag042","url":null,"abstract":"<p><p><i>Parvoviridae</i> (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 <i>Densovirinae</i>. A novel virus in the genus <i>Brevipenbrevirus</i> (arthropod-infecting subfamily <i>Penbrevirinae</i>) was found in 19.6% of the animals, including several frugivorous <i>Epomophorus wahlbergi</i> bats. A novel bat protoparvovirus (vertebrate-infecting subfamily <i>Parvovirnae</i>) was found both in the faeces and blood of one <i>Afronycteris nanus</i> 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 (<i>Mops pumilus</i> and <i>Scotophilus viridis</i>). 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 <i>Mops condylurus</i> 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag042"},"PeriodicalIF":3.8,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13426907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148655028","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":"Phylodynamic analyses reveal persistence and extensive intermixing of Usutu virus in the Netherlands.","authors":"Emmanuelle Münger, David F Nieuwenhuijse, Nnomzie C Atama, James Baxter, Lu Lu, Mandev S Gill, Henk P van der Jeugd, Judith M A van den Brand, Reina S Sikkema, Marion P G Koopmans, Fabiana Gámbaro, Bas B Oude Munnink, Simon Dellicour","doi":"10.1093/ve/veag041","DOIUrl":"10.1093/ve/veag041","url":null,"abstract":"<p><p>Mosquito-borne viruses are expanding their geographic range in Europe, increasingly affecting wildlife and human health. Usutu virus (USUV), a zoonotic mosquito-borne <i>Orthoflavivirus</i> with birds as amplifying hosts, has caused large-scale avian mortality in Europe, particularly among Eurasian Blackbirds (<i>Turdus merula</i>). 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag041"},"PeriodicalIF":3.8,"publicationDate":"2026-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13419076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148622652","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":"Genomic characterization and evolutionary dynamics of human adenovirus C (HAdV-C) in Beijing (2023-2024): insights into multiple recombination and adaptive evolution.","authors":"Changcheng Wu, Chen Mai, Zhihao Zhao, Shiyao Zhang, Lin Ma, Fei Ye, Weibang Huo, Yuda Chen, Meihui Luo, Xiaona Yang, Wenling Wang, Jiegang Huang, Wenjie Tan","doi":"10.1093/ve/veag040","DOIUrl":"10.1093/ve/veag040","url":null,"abstract":"<p><p>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 <i>E1a_26KD</i> exhibited elevated <i>dN/dS</i> 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag040"},"PeriodicalIF":3.8,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13390923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148563912","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":"Differences in codon usage between host-species-specific rabies virus clades are driven by non-GC3 nucleotide composition.","authors":"Rowan Durrant, Jonathan Dushoff, Matthew Arnold, Christina Cobbold, Katie Hampson","doi":"10.1093/ve/veag039","DOIUrl":"10.1093/ve/veag039","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag039"},"PeriodicalIF":3.8,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13403185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148610157","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":"Evolution of SARS-CoV-2 caused infection in farmed minks: continuous surveillance of an 11-month outbreak at the largest Latvian mink farm.","authors":"Ņikita Zrelovs, Edvīns Oļševskis, Jurijs Perevoščikovs, Ivars Silamiķelis, Alise Jakovele, Kristīne Lamberga, Aivars Bērziņš, Monta Brīvība, Jānis Kloviņš","doi":"10.1093/ve/veag038","DOIUrl":"10.1093/ve/veag038","url":null,"abstract":"<p><p>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 <i>in situ</i> 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag038"},"PeriodicalIF":3.8,"publicationDate":"2026-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13367582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148450537","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":"Experimental evolution of Rc-o319 sarbecovirus spike protein reveals limited ACE2 adaptability.","authors":"Jorge Moreno-García, Jérémy Dufloo, Rafael Sanjuán","doi":"10.1093/ve/veag035","DOIUrl":"10.1093/ve/veag035","url":null,"abstract":"<p><p>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, <i>Rhinolophus cornutus</i>, and to mouse ACE2 at low levels, but not to <i>R. sinicus</i>, 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag035"},"PeriodicalIF":3.8,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13340462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148407029","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":"Phylogenetic analysis of enteroviruses from non-human primates suggests two new species within the genus <i>Enterovirus</i> and inter-species recombination.","authors":"Corentin Aubé, Paulina Cruz de Casas, Matthieu Prot, Artem Baidaliuk, Marie-Claire Endegue Zanga, Etienne Simon-Lorière, Nolwenn Jouvenet, Serge A Sadeuh-Mba, Maël Bessaud","doi":"10.1093/ve/veag037","DOIUrl":"10.1093/ve/veag037","url":null,"abstract":"<p><p>To date, 15 species have been described within the genus <i>Enterovirus.</i> 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 <i>Enterovirus betacoxsackie</i> 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 <i>Enterovirus mbel</i>. 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 <i>Enterovirus jesimi</i>, some of which are relatively divergent from the others in the capsid and could belong to another species, tentatively named <i>Enterovirus noa</i>. 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 <i>Enterovirus alphacoxsackie</i> and <i>Enterovirus betacoxsackie</i> 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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag037"},"PeriodicalIF":3.8,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13390911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148563877","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":"Respiratory virus genomic epidemiology during post-pandemic re-emergence of influenza in Australia.","authors":"Rebecca J Rockett, Jessica E Agius, Shona Chandra, Winkie Fong, Ammar Aziz, Carl J E Suster, Kerri Basile, Connie Lam, Sharon C-A Chen, Dominic E Dwyer, Jen Kok, Sheena G Sullivan, Ian G Barr, Vitali Sintchenko, Tanya Golubchik","doi":"10.1093/ve/veag036","DOIUrl":"10.1093/ve/veag036","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag036"},"PeriodicalIF":3.8,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13356897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148431583","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}