Virus Evolution最新文献

{"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":"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":"https://doi.org/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}

{"title":"<i>Mamastrovirus</i> species are shaped by recombination and can be reliably distinguished in ORF1b genome region.","authors":"Yulia Aleshina, Alexander Lukashev","doi":"10.1093/ve/veaf006","DOIUrl":"10.1093/ve/veaf006","url":null,"abstract":"<p><p>Astroviruses are a diverse group of small non-enveloped positive sense single-stranded RNA viruses that infect animals and birds. More than half of all known genome sequences of mammalian astroviruses are not assigned to provisional species, and the biological mechanisms that could support segregation of astroviruses into species are not well understood. The systematic analysis of recombination in <i>Mamastrovirus</i> genomes available in GenBank was done to identify mechanisms providing genetic distinction between astroviruses. Recombination breakpoints were present in all <i>Mamastrovirus</i> genome regions, but occurred most commonly at the ORF1b/ORF2 junction. Recombination was ubiquitous within, but never between established and putative new species, and may be suggested as an additional species criterion. The current species criterion for the genus <i>Mamastrovirus</i> based on ORF2 amino acid sequence p-distances did not reliably distinguish several established species and was of limited use to identify distinct groups among unclassified astroviruses that were isolated recently, predominantly from cattle and pigs. A 17% nucleotide sequence distance cut-off in ORF1b fairly distinguished the established species and several groups among the unclassified viruses, providing better correspondence between phylogenetic grouping, reproductive isolation and the virus hosts. Sequence distance criteria (17% in nucleotide sequence of ORF1b and 25% in amino acid sequence of ORF2) and the recombination pattern corresponded fairly well as species criteria, but all had minor exclusions among mammalian astroviruses. A combination of these taxonomic criteria supported the established <i>Mamastrovirus</i> species and suggested redefining a few provisional species that were proposed earlier and introducing at least six novel species among recently submitted rat and bovine astroviruses.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf006"},"PeriodicalIF":5.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842974/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484715","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":"Correction to: Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda.","authors":"","doi":"10.1093/ve/veaf003","DOIUrl":"https://doi.org/10.1093/ve/veaf003","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ve/vead053.].</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf003"},"PeriodicalIF":5.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11769856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061179","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":"Dispersal dynamics and introduction patterns of SARS-CoV-2 lineages in Iran.","authors":"Emanuele C Gustani-Buss, Mostafa Salehi-Vaziri, Philippe Lemey, Marijn Thijssen, Zahra Fereydouni, Zahra Ahmadi, Marc Van Ranst, Piet Maes, Mahmoud Reza Pourkarim, Ali Maleki","doi":"10.1093/ve/veaf004","DOIUrl":"10.1093/ve/veaf004","url":null,"abstract":"<p><p>Understanding the dispersal patterns of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) lineages is crucial to public health decision-making, especially in countries with limited access to viral genomic sequencing. This study provides a comprehensive epidemiological and phylodynamic perspective on SARS-CoV-2 lineage dispersal in Iran from February 2020 to July 2022. We explored the genomic epidemiology of SARS-CoV-2 combining 1281 genome sequences with spatial data in a phylogeographic framework. Our analyses shed light on multiple international imports seeding subsequent waves and on domestic dispersal dynamics. Lineage B.4 was identified to have been circulating in Iran, 29 days (95% highest probability density interval: 21-47) before non-pharmaceutical interventions were implemented. The importation dynamics throughout subsequent waves were primarily driven from the country or region where the variant was first reported and gradually shifted to other regions. At the national level, Tehran was the main source of dissemination across the country. Our study highlights the crucial role of continuous genomic surveillance and international collaboration for future pandemic preparedness and efforts to control viral transmission.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veaf004"},"PeriodicalIF":5.5,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11803630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384172","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}