Virus Evolution最新文献

{"title":"The virome of the panglobal, wide host-range plant pathogen <i>Phytophthora cinnamomi</i>: phylogeography and evolutionary insights.","authors":"Leticia Botella, Ondřej Hejna, Tomáš Kudláček, Kateřina Kovačiková, Michael Rost, Marco Forgia, Milica Raco, Ivan Milenković, Tamara Corcobado, Cristiana Maia, Bruno Scanu, André Drenth, David I Guest, Edward C Y Liew, Nguyen Minh Chi, Pham Quang Thu, Tun-Tschu Chang, Chuen-Hsu Fu, Koji Kageyama, Ayaka Hieno, Hayato Masuja, Seiji Uematsu, Álvaro Durán, Marthin Tarigan, Muhammad Junaid, Nasri Nasri, Eugenio Sanfuentes, Vladislav Čurn, Joan F Webber, Clive M Brasier, Marília Horta Jung, Thomas Jung","doi":"10.1093/ve/veaf020","DOIUrl":"https://doi.org/10.1093/ve/veaf020","url":null,"abstract":"<p><p><i>Phytophthora cinnamomi</i> stands out as one of the most devastating plant pathogens worldwide, rapidly expanding its range and impacting a wide range of host species. In this study, we investigated the virome of <i>P. cinnamomi</i> across 222 isolates from Africa, Asia, Europe, Oceania, and the Americas using stranded total RNA sequencing, reverse transcription polymerase chain reaction screening, and Sanger sequencing of selected isolates. Our analysis revealed that virus infections were prevalent across all sampled populations, including RNA viruses associated with the orders <i>Ghabrivirales, Martellivirales</i>, and <i>Tolivirales</i>, and the classes <i>Amabiliviricetes, Bunyaviricetes</i>, and the recently proposed <i>Orpoviricetes</i>. Viruses were mainly found in East and Southeast Asian populations, within the geographic origin of <i>P. cinnamomi</i> but have also spread to new regions where the pathogen has emerged as a clonal destructive pathogen. Among the identified viruses, eight species, including two bunya-like viruses, one narna-like virus, and five ormycoviruses, exhibit a global distribution with some genetic divergence between continents. The interaction between <i>P. cinnamomi</i> and its virome indicates a dynamic coevolution across diverse geographic regions. Indonesia is indicated to be the viral epicentre of <i>P. cinnamomi</i>, with the highest intra- and interspecies diversity of viruses. Viral diversity is significantly enhanced in regions where sexual recombination of <i>P. cinnamomi</i> occurs, while regions with predominantly asexual reproduction harbour fewer viral species. Interestingly, only the partially self-fertile mating type (MAT) A2, associated with the global pandemic, facilitates the spread of viruses across different biogeographic regions, whereas viruses are absent in the self-sterile MAT A1 in its areas of introduction like Australia and South Africa. Intriguingly, the presence of a plant tombusvirus suggests a potential cross-kingdom infection among Chilean isolates and a plant host. This study sheds further light on the geographical origin of <i>P. cinnamomi</i> from a novel virome perspective.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf020"},"PeriodicalIF":5.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018711","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 variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis.","authors":"Bangyao Sun, Meng Xu, Lijia Jia, Haizhou Liu, Aixin Li, Lixia Hui, Zhitao Wang, Di Liu, Yi Yan","doi":"10.1093/ve/veaf013","DOIUrl":"10.1093/ve/veaf013","url":null,"abstract":"<p><p>Since its first academic record in 1978, dengue epidemics have occurred in all provinces of China, except Xizang. The epidemiological and molecular features of the whole genome of dengue virus (DENV) have not yet been completely elucidated, interfering with prevention and control strategies for dengue fever in China. Here, we obtained 553 complete genomes of the four serotypes of DENV (DENV1-4) isolated in China from the GenBank database to analyze the phylogeny, recombination, genomic variants, and selection pressure and to estimate the substitution rates of DENV genomes. Phylogenetic analyses indicated that DENV sequences from China did not cluster together and were genetically closer to those from Southeast Asian countries in the maximum likelihood trees, indicating that DENV was not endemic in China. Thirty intra-serotype recombinant sequences were identified for DENV1-4, with the highest frequency in DENV4. Selection pressure analyses revealed that 13 codons under positive selection were located in the C, NS1, NS2A, NS3, and NS5 proteins. For DENV1 to DENV3, the substitution rates evaluated in this study were 9.23 × 10^-4, 7.59 × 10^-4, and 7.06 × 10^-4 substitutions per site per year, respectively. These findings improve our understanding of the evolution of DENV in China.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf013"},"PeriodicalIF":5.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712277","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":"Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein.","authors":"Miguel Álvarez-Herrera, Paula Ruiz-Rodriguez, Beatriz Navarro-Domínguez, Joao Zulaica, Brayan Grau, María Alma Bracho, Manuel Guerreiro, Cristóbal Aguilar-Gallardo, Fernando González-Candelas, Iñaki Comas, Ron Geller, Mireia Coscollá","doi":"10.1093/ve/veaf015","DOIUrl":"https://doi.org/10.1093/ve/veaf015","url":null,"abstract":"<p><p>Mutations within the N-terminal domain (NTD) of the spike (S) protein are critical for the emergence of successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral lineages. The NTD has been repeatedly impacted by deletions, often exhibiting complex and dynamic patterns, such as the recurrent emergence and disappearance of deletions in dominant variants. This study investigates the influence of repair of NTD lineage-defining deletions found in the BA.1 lineage (Omicron variant) on viral success. We performed comparative genomic analyses of >10 million SARS-CoV-2 genomes from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCov database to evaluate the detection of viruses lacking S:ΔH69/V70, S:ΔV143/Y145, or both. These findings were contrasted against a screening of publicly available raw sequencing data, revealing substantial discrepancies between data repositories, suggesting that spurious deletion repair observations in GISAID may result from systematic artifacts. Specifically, deletion repair events were approximately an order of magnitude less frequent in the read-run survey. Our results suggest that deletion repair events are rare, isolated events with limited direct influence on SARS-CoV-2 evolution or transmission. Nevertheless, such events could facilitate the emergence of fitness-enhancing mutations. To explore potential drivers of NTD deletion repair patterns, we characterized the viral phenotype of such markers in a surrogate <i>in vitro</i> system. Repair of the S:ΔH69/V70 deletion reduced viral infectivity, while simultaneous repair with S:ΔV143/Y145 led to lower fusogenicity. In contrast, individual S:ΔV143/Y145 repair enhanced both fusogenicity and susceptibility to neutralization by sera from vaccinated individuals. This work underscores the complex genotype-phenotype landscape of the spike NTD in SARS-CoV-2, which impacts viral biology, transmission efficiency, and immune escape potential, offering insights with direct relevance to public health, viral surveillance, and the adaptive mechanisms driving emerging variants.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf015"},"PeriodicalIF":5.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12041916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144059307","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":"Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark.","authors":"Sophie George, Pia Ryt-Hansen, Anders Gorm Pedersen, Klara M Anker, Jakob N Nissen, Jesper S Krog, Charlotte K Hjulsager, Ramona Trebbien, Lars E Larsen","doi":"10.1093/ve/veaf014","DOIUrl":"https://doi.org/10.1093/ve/veaf014","url":null,"abstract":"<p><p>Transmission of influenza A viruses (IAVs) between pigs and humans can trigger pandemics but more often cease as isolated infections without further spread in the new host species population. In Denmark, a major pig-producing country, the first two detections of human infections with swine-like IAVs were reported in 2021. These zoonotic IAVs were reassortants of the H1N1 pandemic 2009 lineage (\"H1N1pdm09,\" H1 lineage 1A, clade 1A.3.3.2) introduced to swine farms in Denmark through humans approximately 11 years prior. However, predicting the likelihood and outcome of such IAV spillovers is challenging without a better understanding of the viral determinants. This study traced the evolution of H1N1pdm09 from 207 sequenced genomes as the virus propagated across Danish swine farms over a decade. H1N1pdm09 diverged into several genetically distinct viral populations, largely prompted by reassortments with neuraminidase (NA) segments from other enzootic IAV lineages. The genomic segments encoding the viral envelope glycoproteins, hemagglutinin (HA) and NA, evolved at the fastest rates, while the M and NS genomic segments were among the lowest evolutionary rates. The two zoonotic IAVs emerged from separate viral populations and shared the highest number of amino acid mutations in the PB2 and HA proteins. Acquisition of additional predicted glycosylation sites on the HA proteins of the zoonotic IAVs may have facilitated infection of the human patients. Ultimately, the analysis provides a foundation from which to further explore viral genetic indicators of host adaptation and zoonotic risk.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf014"},"PeriodicalIF":5.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11997423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056380","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":"FluMut: a tool for mutation surveillance in highly pathogenic H5N1 genomes.","authors":"Edoardo Giussani, Alessandro Sartori, Angela Salomoni, Lara Cavicchio, Cristian de Battisti, Ambra Pastori, Maria Varotto, Bianca Zecchin, Joseph Hughes, Isabella Monne, Alice Fusaro","doi":"10.1093/ve/veaf011","DOIUrl":"10.1093/ve/veaf011","url":null,"abstract":"<p><p>Over the past century, Influenza A virus (IAV) has caused four of the five reported pandemics, all of which originated from viruses possessing genome segments of avian origin. The recent spread of highly pathogenic avian influenza (HPAI) viruses, particularly the clade 2.3.4.4b A(H5N1) subtype, has led to an alarming increase in mammalian infections, raising concerns about the potential for future pandemics. In response to this, we developed FluMut, an open-source, cross-platform tool designed to identify molecular markers with potential impacts on H5N1 virus phenotypes. FluMut leverages an up-to-date database, FluMutDB, to rapidly analyze thousands of nucleotide sequences, identifying mutations associated with host adaptation, increased virulence, and antiviral resistance. The tool is available both as a command-line interface and a user-friendly graphical interface, making it accessible to researchers with varying levels of computational expertise. FluMut provides comprehensive outputs, including tables of detected markers, their biological effects, and corresponding literature references. This tool fills a critical gap in the genomic surveillance of HPAI H5N1, facilitating real-time monitoring of viral evolution and aiding in the identification of mutations that may signal increased pandemic potential. Future updates will extend FluMut's capabilities to other influenza subtypes.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf011"},"PeriodicalIF":5.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652132","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":"Multiple, diverse endogenous giant virus elements within the genome of a brown alga.","authors":"Dean Mckeown, Alexandre Cormier, Declan Schroeder, Arnaud Couloux, Nachida Tadrent, J Mark Cock, Erwan Corre","doi":"10.1093/ve/veaf009","DOIUrl":"10.1093/ve/veaf009","url":null,"abstract":"<p><p>Endogenous viral elements (EVEs) have been found in diverse eukaryotic genomes. These elements are particularly frequent in the genomes of brown algae (Phaeophyceae) because these seaweeds are infected by viruses (<i>Phaeovirus</i>) of the phylum <i>Nucleocytoviricota</i> (NCV) that are capable of inserting into their host's genome as part of their infective cycle. A search for inserted viral sequences in the genome of the freshwater brown alga <i>Porterinema fluviatile</i> identified seven large EVEs, including four complete or near-complete proviruses. The EVEs, which all appear to have been derived from independent insertion events, correspond to phylogenetically diverse members of the <i>Phaeovirus</i> genus and include members of both the A and B subgroups of this genus. This latter observation is surprising because the two subgroups were thought to have different evolutionary strategies and were therefore not expected to be found in the same host. The EVEs contain a number of novel genes including a H4 histone-like sequence but only one of the EVEs possesses a full set of NCV core genes, indicating that the other six probably correspond to nonfunctional, degenerated viral genomes. The majority of the genes within the EVEs were transcriptionally silent and most of the small number of genes that showed some transcriptional activity were of unknown function. However, the existence of some transcriptionally active genes and several genes containing introns in some EVEs suggests that these elements may be undergoing some degree of endogenization within the host genome over time.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf009"},"PeriodicalIF":5.5,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11890097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588350","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":"Sequence analysis of the hepatitis D virus across genotypes reveals highly conserved regions amidst evidence of recombination.","authors":"Shruti Chowdhury, Carina Jacobsen, Daniel P Depledge, Heiner Wedemeyer, Lisa Sandmann, Helenie Kefalakes","doi":"10.1093/ve/veaf012","DOIUrl":"10.1093/ve/veaf012","url":null,"abstract":"<p><p>Sequence diversity of the hepatitis D virus (HDV) may impact viral clearance, contributing to the development of chronic infection. T-Cell-induced selection pressure and viral recombination can induce diversity throughout the viral genome including coding and noncoding regions, with the former potentially impacting viral pathogenicity and the latter exerting regulatory functions. Here, we aim to assess sequence variations of the HDV genome within and across HDV genotypes. Sequences from 721 complete HDV genomes and 793 large hepatitis D antigen (L-HDAg) regions belonging to all eight genotypes and published through December 2023 were compiled. Most retrieved sequences belonged to Genotype 1, whereas for Genotype 8, the fewest sequences were available. Alignments were conducted using Clustal Omega and Multiple Alignment using Fast Fourier Transform. Phylogeny was analysed using SplitsTree4, and recombination sites were inspected using Recombination Detection Program 4. All reported sequences were aligned per genotype to retrieve consensus and reference sequences based on the highest similarity to consensus per genotype. L-HDAg alignments of the proposed reference sequences showed that not only conserved but also highly variable positions exist, which was also reflected in the epitope variability across HDV genotypes. Importantly, <i>in silico</i> binding prediction analysis showed that CD8⁺ T-cell epitopes mapped for Genotype 1 may not bind to major histocompatibility complex class I when examining their corresponding sequence in other genotypes. Phylogenetic analysis showed evidence of recombinant genomes within each individual genotype as well as between two different HDV genotypes, enabling the identification of common recombination sites. The identification of conserved regions within the L-HDAg allows their exploitation for genotype-independent diagnostic and therapeutic strategies, while the harmonized use of the proposed reference sequences may facilitate efforts to achieve HDV control.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf012"},"PeriodicalIF":5.5,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694449","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":"Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived.","authors":"Jonathan E Pekar, Niema Moshiri, Philippe Lemey, Alexander Crits-Christoph, Florence Débarre, Stephen A Goldstein, Zach Hensel, Andrew Rambaut, Michael Worobey, Edward C Holmes, Joel O Wertheim","doi":"10.1093/ve/veaf008","DOIUrl":"10.1093/ve/veaf008","url":null,"abstract":"<p><p>Understanding the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the outset of the coronavirus disease 2019 pandemic can provide insight into the circumstances leading to its emergence. Early SARS-CoV-2 genomic diversity has been classified into two distinct viral lineages, denoted \"A\" and \"B,\" which we hypothesized were separately introduced into humans. Recently published data contain two genomes with a haplotype suggested to be an evolutionary intermediate to these two lineages, known as \"T/T.\" We used a phylodynamic approach to analyze SARS-CoV-2 genomes from early 2020 to determine whether these two T/T genomes represent an evolutionarily intermediate haplotype between lineages A and B, or if they are a later descendent of either of these two lineages. We find that these two recently published T/T genomes do not represent an evolutionarily intermediate haplotype and were, instead, derived from either lineage A or lineage B. However, we cannot conclusively determine from which lineage they were derived. After including additional data from the start of the pandemic, including these two T/T genomes, we again find a discrepancy in the molecular clock when inferring the ancestral haplotype of SARS-CoV-2, corroborating existing evidence for the separate introductions of SARS-CoV-2 lineages A and B into the human population in late 2019.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf008"},"PeriodicalIF":5.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143558861","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":"Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza.","authors":"Albert Perlas, Tim Reska, Guillaume Croville, Ferran Tarrés-Freixas, Jean-Luc Guérin, Natàlia Majó, Lara Urban","doi":"10.1093/ve/veaf010","DOIUrl":"10.1093/ve/veaf010","url":null,"abstract":"<p><p>Avian influenza virus (AIV) currently causes a panzootic with extensive mortality in wild birds, poultry, and wild mammals, thus posing a major threat to global health and underscoring the need for efficient monitoring of its distribution and evolution. We here utilized a well-defined AIV strain to systematically investigate AIV genetic characterization through rapid, portable nanopore sequencing by comparing the latest DNA and RNA nanopore sequencing approaches and various computational pipelines for viral consensus sequence generation and phylogenetic analysis. We show that the latest direct RNA nanopore sequencing updates improve consensus sequence generation, but that the application of the latest DNA nanopore chemistry after reverse transcription and amplification outperforms, such native viral RNA sequencing by achieving higher sequencing accuracy and throughput. We additionally leveraged the direct RNA nanopore sequencing data for the detection of RNA modifications, such as <i>N</i> ⁶-methyladenosine and pseudouridine, which play a role in viral immune evasion. Finally, we applied these sequencing approaches together with portable AIV diagnosis and quantification tools to environmental samples from a poultry farm, demonstrating the feasibility of nanopore sequencing for on-site non-invasive AIV monitoring in real-world outbreak scenarios.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf010"},"PeriodicalIF":5.5,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143598163","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 surveillance and evolution of Getah virus.","authors":"Jiaqi Shen, Shaogui Liu, Shiqiang Liu, Shiyi Shen, Mingkai Lei, Qian Xu, Wentao Li, Qigai He, Xiaojuan Xu, Xuwang Cai","doi":"10.1093/ve/veaf007","DOIUrl":"10.1093/ve/veaf007","url":null,"abstract":"<p><p>Getah virus (GETV), a member of the <i>Alphaviruses</i>, has spread widely and is expanding its host range worldwide, posing a serious threat to public health safety and the farming industry. However, genetic monitoring of GETV is inadequate, and its evolution and transmission remain unclear. This study employed reverse transcription-polymerase chain reaction to screen pig tissue samples for the presence of GETV. Subsequent steps included DNA sequencing, phylogenetic analysis, and selection pressure assessments to elucidate the evolutionary history and transmission patterns of the virus. A total of 1382 samples were examined, with a positivity rate of 4.12% (95% confidence interval: 3.07%-5.17%) from 2022 to 2023. Subsequently, seven GETV strains were isolated and identified. A phylogenetic tree was constructed, which showed that all seven strains belonged to Group III. Phylodynamic analysis revealed that GETV evolved rapidly. Additionally, eight amino acid sites within the GETV E2 protein were identified as being under positive selection. These data provide insight into the epidemiology and evolution of GETV.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf007"},"PeriodicalIF":5.5,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484764","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}