Seungwon Kim, Godfrey Kigozi, Michael A Martin, Ronald M Galiwango, Thomas C Quinn, Andrew D Redd, Robert Ssekubugu, David Bonsall, Deogratius Ssemwanga, Andrew Rambaut, Joshua T Herbeck, Steven J Reynolds, Brian Foley, Lucie Abeler-Dörner, Christophe Fraser, Oliver Ratmann, Joseph Kagaayi, Oliver Laeyendecker, M Kate Grabowski
{"title":"Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study","authors":"Seungwon Kim, Godfrey Kigozi, Michael A Martin, Ronald M Galiwango, Thomas C Quinn, Andrew D Redd, Robert Ssekubugu, David Bonsall, Deogratius Ssemwanga, Andrew Rambaut, Joshua T Herbeck, Steven J Reynolds, Brian Foley, Lucie Abeler-Dörner, Christophe Fraser, Oliver Ratmann, Joseph Kagaayi, Oliver Laeyendecker, M Kate Grabowski","doi":"10.1093/ve/veae065","DOIUrl":"https://doi.org/10.1093/ve/veae065","url":null,"abstract":"There is limited data on HIV evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-four-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from persons living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994 to 2018) and four hyperendemic Lake Victoria fishing communities (2011 to 2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population sub-groups, including by migration status. 9,931 HIV sequences were available from 4,999 PLHIV, including 3,060 and 1,939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (p<0.001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (p<0.001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population sub-groups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"8 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ulad Litvin, Eddie C.Y Wang, Richard J Stanton, Ceri A Fielding, Joseph Hughes
{"title":"Evolution of the Cytomegalovirus RL11 Gene Family in Old World monkeys and Great Apes","authors":"Ulad Litvin, Eddie C.Y Wang, Richard J Stanton, Ceri A Fielding, Joseph Hughes","doi":"10.1093/ve/veae066","DOIUrl":"https://doi.org/10.1093/ve/veae066","url":null,"abstract":"Cytomegalovirus is a genus of herpesviruses, members of which share a long history of co-evolution with their primate hosts including Great Apes, Old and New World monkeys. These viruses are ubiquitous within their host populations and establish lifelong infection in most individuals. Although asymptomatic in healthy individuals, infection poses a significant risk to individuals with a weakened or underdeveloped immune system. The genome of human cytomegalovirus is the largest among human-infecting viruses, and comprises at least fifteen separate gene families, which may have arisen by gene duplication. Within human cytomegalovirus, the RL11 gene family is the largest. RL11 genes are non-essential in vitro but have immune evasion roles that are likely critical to persistence in vivo. These genes demonstrate an extreme level of inter-species and intra-strain sequence diversity, that makes it challenging to deduce the evolutionary relationships within this gene family. Understanding the evolutionary relationships of these genes, especially accurate ortholog identification, is essential for reconstructing ancestral genomes, deciphering gene repertoire and order, and enabling reliable functional analyses across the Cytomegalovirus species, thereby offering insights into evolutionary processes, genetic diversity, and the functional significance of genes. In this work, we combined in silico genome screening with sequence-based and structure-guided phylogenetic analysis to reconstruct the evolutionary history of the RL11 gene family. We confirmed that RL11 genes are unique to cytomegaloviruses of Old World monkeys and Great Apes, showing that this gene family was formed by multiple early duplication events and later lineage-specific losses. We identified four main clades of RL11 genes and showed that their expansions were mainly lineage-specific and happened independently in cytomegaloviruses of Great Apes, African Old World monkeys and Asian Old World monkeys. We also identified groups of orthologous genes across the Cytomegalovirus tree showing that some human cytomegalovirus-specific RL11 genes emerged before the divergence of human and chimpanzee cytomegaloviruses but were subsequently lost in the latter. The extensive and dynamic species-specific evolution of this gene family suggests their functions target elements of host immunity that have similarly co-evolved during speciation.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"29 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Virus EvolutionPub Date : 2024-08-22eCollection Date: 2024-01-01DOI: 10.1093/ve/veae062
Chenxi Li, Yazhou Hu, Yuhang Liu, Nan Li, Le Yi, Changchun Tu, Biao He
{"title":"The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses.","authors":"Chenxi Li, Yazhou Hu, Yuhang Liu, Nan Li, Le Yi, Changchun Tu, Biao He","doi":"10.1093/ve/veae062","DOIUrl":"10.1093/ve/veae062","url":null,"abstract":"<p><p>Amphibians are an essential class in the maintenance of global ecosystem equilibrium, but they face serious extinction risks driven by climate change and infectious diseases. Unfortunately, the virus diversity harbored by these creatures has been rarely investigated. By profiling the virus flora residing in different tissues of 100 farmed black-spotted frogs (<i>Rana nigromaculata</i>) using a combination of DNA and RNA viromic methods, we captured 28 high-quality viral sequences covering at least 11 viral families. Most of these sequences were remarkably divergent, adding at least 10 new species and 4 new genera within the families <i>Orthomyxoviridae, Adenoviridae, Nodaviridae, Phenuiviridae</i>, and <i>Picornaviridae</i>. We recovered five orthomyxovirus segments, with three distantly neighboring two Chinese fish-related viruses. The recombination event of frog virus 3 occurred among the frog and turtle strains. The relative abundance and molecular detection revealed different tissue tropisms of these viruses, with the orthomyxovirus and adenoviruses being enteric and probably also neurotropic, but the new astrovirus and picornavirus being hepatophilic. These results expand the spectrum of viruses harbored by anurans, highlighting the necessity to continuously monitor these viruses and to investigate the virus diversity in a broader area with more diverse amphibian species.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae062"},"PeriodicalIF":5.5,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11341201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037837","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}
Virus EvolutionPub Date : 2024-08-17eCollection Date: 2024-01-01DOI: 10.1093/ve/veae064
Art F Y Poon
{"title":"Prospects for a sequence-based taxonomy of influenza A virus subtypes.","authors":"Art F Y Poon","doi":"10.1093/ve/veae064","DOIUrl":"10.1093/ve/veae064","url":null,"abstract":"<p><p>Hemagglutinin (HA) and neuraminidase (NA) proteins are the primary antigenic targets of influenza A virus (IAV) infections. IAV infections are generally classified into subtypes of HA and NA proteins, e.g. H3N2. Most of the known subtypes were originally defined by a lack of antibody cross-reactivity. However, genetic sequencing has played an increasingly important role in characterizing the evolving diversity of IAV. Novel subtypes have recently been described solely by their genetic sequences, and IAV infections are routinely subtyped by molecular assays, or the comparison of sequences to references. In this study, I carry out a comparative analysis of all available IAV protein sequences in the Genbank database (over 1.1 million, reduced to 272,292 unique sequences prior to phylogenetic reconstruction) to determine whether the serologically defined subtypes can be reproduced with sequence-based criteria. I show that a robust genetic taxonomy of HA and NA subtypes can be obtained using a simple clustering method, namely, by progressively partitioning the phylogeny on its longest internal branches. However, this taxonomy also requires some amendments to the current nomenclature. For example, two IAV isolates from bats previously characterized as a divergent lineage of H9N2 should be separated into their own subtype. With the exception of these small and highly divergent lineages, the phylogenies relating each of the other six genomic segments do not support partitions into major subtypes.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae064"},"PeriodicalIF":5.5,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11378807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142157200","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":"GALV-KoRV-related retroviruses in diverse Australian and African rodent species.","authors":"Joshua A Hayward, Shuoshuo Tian, Gilda Tachedjian","doi":"10.1093/ve/veae061","DOIUrl":"https://doi.org/10.1093/ve/veae061","url":null,"abstract":"The enigmatic origins and transmission events of the gibbon ape leukemia virus (GALV) and its close relative, the koala retrovirus (KoRV) have been a source of enduring debate. Bats and rodents are each proposed as major reservoirs of interspecies transmission, with ongoing efforts to identify additional animal hosts of GALV-KoRV-related retroviruses. In this study, we identified nine rodent species as novel hosts of GALV-KoRV-related retroviruses. Included among these hosts are two African rodents, revealing the first appearance of this clade beyond the Australian and Southeast Asian region. One of these African rodents, Mastomys natalensis, carries an endogenous GALV-KoRV-related retrovirus that is fully intact and potentially still infectious. Our findings support the hypothesis that rodents are the major carriers of GALV-KoRV-related retroviruses.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"16 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Megan E Golding, Guanghui Wu, Rebekah Wilkie, Evelyne Picard-Meyer, Alexandre Servat, Denise A Marston, James N Aegerter, Daniel L Horton, Lorraine M McElhinney
{"title":"Investigating the emergence of a zoonotic virus: phylogenetic analysis of European bat lyssavirus 1 in the UK","authors":"Megan E Golding, Guanghui Wu, Rebekah Wilkie, Evelyne Picard-Meyer, Alexandre Servat, Denise A Marston, James N Aegerter, Daniel L Horton, Lorraine M McElhinney","doi":"10.1093/ve/veae060","DOIUrl":"https://doi.org/10.1093/ve/veae060","url":null,"abstract":"European bat lyssavirus 1 (EBLV-1, Lyssavirus hamburg) is predominantly detected in serotine bats (Eptesicus serotinus) and is responsible for the majority of bat rabies cases in mainland Europe. A passive bat rabies surveillance scheme detected the virus in a serotine bat in the UK for the first time in October 2018. As of May 2024, 34 cases have been reported, 20 of which involved contact with an animal and 5 reported human contact. We investigated the emergence of EBLV-1 by undertaking comprehensive sequence analysis and Bayesian phylogenetics, based on complete virus genomes of 33 UK sequences and 108 sequences covering six countries in mainland Europe (1968 to 2023), including 21 French EBLV-1 positive RNA samples sequenced for this study. Sequence analysis revealed extreme similarity among UK EBLV-1 sequences (99.9-100%), implying a single source of introduction rather than multiple independent introductions. Bayesian analysis revealed the UK EBLV-1 sequences shared their most recent common ancestor with an EBLV-1 sequence from a serotine bat detected in Brittany, France in 2001, with an estimated date of divergence of 1997. Within the UK sequences, the earliest divergence was estimated to occur in 2007. This study provides valuable insights into the molecular epidemiology of an emerging zoonotic pathogen, and improved understanding of the risks posed to public and animal health.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"22 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141863987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Morgane Chesnais, Erika Bujaki, Typhaine Filhol, Vincent Caval, Marie-Line Joffret, Javier Martin, Nolwenn Jouvenet, Maël Bessaud
{"title":"Opening a 60-year time capsule: sequences of historical poliovirus cold variants shed a new light on a contemporary strain.","authors":"Morgane Chesnais, Erika Bujaki, Typhaine Filhol, Vincent Caval, Marie-Line Joffret, Javier Martin, Nolwenn Jouvenet, Maël Bessaud","doi":"10.1093/ve/veae063","DOIUrl":"https://doi.org/10.1093/ve/veae063","url":null,"abstract":"Polioviruses (PVs) are positive strand RNA viruses responsible for poliomyelitis. Many PVs have been isolated and phenotypically characterized in the 1940s-50s for the purpose of identifying attenuated strains that could be used as vaccine strains. Among these historical PVs, only few are genetically characterized. We report here the sequencing of four PV strains stored for more than 60 years in a sealed box. These PVs are cold variants that were selected by Albert Sabin based on their capacity to multiply at relatively low temperatures. Inoculation of permissive cells at 25°C showed that two of the four historical virus stocks still contained infectious particles. Both viruses reached titres that were higher at 25°C than at 37°C, thus demonstrating that they were genuine cold variants. We obtained sequences that span virtually all the genome for three out of the four strains; a short sequence that partly covers the 5ʹ untranslated region was recovered for the last one. Unexpectedly, the genome of one historical cold variant (which derived from PV-3 Glenn) displayed a very high nucleotide identity (above 95%) with that of a PV strain (PV-3 strain WIV14) sampled in China in 2014 and then classified as a highly evolved vaccine-derived PV. Our analyses made this hypothesis very unlikely and strongly suggested that Glenn and WIV14 share a very recent common ancestor with one another. Some strains used to produce the inactivated polio vaccine were also very close to Glenn and WIV14 in the capsid-encoding region, but they had not been sequenced beyond the capsid. We therefore sequenced one of these strains, Saukett A, which was available in our collection. Saukett A and WIV14 featured an identity higher than 99% at the nucleotide level. This work provides original data on cold variants that were produced and studied decades ago. It also highlights that sequences of historical PV strains could be crucial to reliably characterize contemporary PVs in case of release from a natural reservoir or from a facility, which is of highest importance for the PV eradication program.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"49 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141864004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Virus EvolutionPub Date : 2024-07-26eCollection Date: 2024-01-01DOI: 10.1093/ve/veae057
{"title":"Correction to: Cell type-specific adaptation of the SARS-CoV-2 spike.","authors":"","doi":"10.1093/ve/veae057","DOIUrl":"https://doi.org/10.1093/ve/veae057","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ve/veae032.].</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae057"},"PeriodicalIF":5.5,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287204/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857264","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}
Foo Hou Tan, Asif Sukri, Nuryana Idris, Kien Chai Ong, Jie Ping Schee, Chong Tin Tan, Soon Hao Tan, Kum Thong Wong, Li Ping Wong, Kok Keng Tee, Li-Yen Chang
{"title":"A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development","authors":"Foo Hou Tan, Asif Sukri, Nuryana Idris, Kien Chai Ong, Jie Ping Schee, Chong Tin Tan, Soon Hao Tan, Kum Thong Wong, Li Ping Wong, Kok Keng Tee, Li-Yen Chang","doi":"10.1093/ve/veae048","DOIUrl":"https://doi.org/10.1093/ve/veae048","url":null,"abstract":"Nipah virus (NiV) is an emerging pathogen that causes encephalitis and a high mortality rate in infected subjects. This systematic review aimed to comprehensively analyze the global epidemiology and research advancements of NiV to identify key knowledge gaps in the literature. Articles searched using literature databases, namely PubMed, Scopus, Web of Science, and Science Direct yielded 5596 articles. After article screening, 97 articles were included in this systematic review, comprising 41 epidemiological studies and 56 research developments on NiV. The majority of the NiV epidemiological studies were conducted in Bangladesh, reflecting the country’s significant burden of NiV outbreaks. The initial NiV outbreak was identified in Malaysia in 1998 in Malaysia, with subsequent outbreaks reported in Bangladesh, India, and the Philippines. Transmission routes vary by country, primarily through pigs in Malaysia, consumption of date palm juice in Bangladesh, and human-to-human in India. However, the availability of NiV genome sequences remains limited, particularly from Malaysia and India. Mortality rates also vary according to the country, exceeding 70% in Bangladesh, India, and the Philippines, and less than 40% in Malaysia. Understanding these differences in mortality rate among countries is crucial for informing NiV epidemiology and enhancing outbreak prevention and management strategies. In terms of research developments, the majority of studies focused on vaccine development, followed by phylogenetic analysis and antiviral research. While many vaccines and antivirals have demonstrated complete protection in animal models, only two vaccines have progressed to clinical trials. Phylogenetic analyses have revealed distinct clades between NiV Malaysia, NiV Bangladesh and NiV India, with proposals to classify NiV India as a separate strain from NiV Bangladesh. Taken together, comprehensive OneHealth approaches integrating disease surveillance and research are imperative for future NiV studies. Expanding the dataset of NiV genome sequences, particularly from Malaysia, Bangladesh and India will be pivotal. These research efforts are essential for advancing our understanding of NiV pathogenicity and for developing robust diagnostic assays, vaccines and therapeutics necessary for effective preparedness and response to future NiV outbreaks.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"59 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141770466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zhongshuai Tian, Tao Hu, Edward C Holmes, Jingkai Ji, Weifeng Shi
{"title":"Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system","authors":"Zhongshuai Tian, Tao Hu, Edward C Holmes, Jingkai Ji, Weifeng Shi","doi":"10.1093/ve/veae059","DOIUrl":"https://doi.org/10.1093/ve/veae059","url":null,"abstract":"RNA viruses are characterized by a broad host range and high levels of genetic diversity. Despite a recent expansion in the known virosphere following metagenomic sequencing, our knowledge of the species-rank genetic diversity of RNA viruses, and how often they are misassigned and misclassified, is limited. We performed a clustering analysis of 7,801 RNA-directed RNA polymerase (RdRp) sequences representing 1,897 established RNA virus species. From this, we identified substantial genetic divergence within some virus species and inconsistency in RNA virus assignment between the GenBank database and The International Committee on Taxonomy of Viruses (ICTV). In particular, 27.57% virus species were comprised of multiple virus operational taxonomic units (vOTUs), including Alphainfluenzavirus influenzae, Mammarenavirus lassaense, Apple stem pitting virus, and Rotavirus A, with each having over 100 vOTUs. In addition, the distribution of average amino acid identity between vOTUs within single assigned species showed a relatively low threshold: &lt;90%, and sometimes &lt;50%. However, when only exemplar sequences from virus species were analyzed, 1,889 of the ICTV-designated RNA virus species (99.58%) were clustered into a single vOTU. Clustering of RdRp sequences from different virus species also revealed that 17 vOTUs contained two distinct virus species. These potential misassignments were confirmed by phylogenetic analysis. A further analysis of ANI (Average Nucleotide Identity) values ranging from 70% to 97.5% revealed that at ANI of 82.5%, 1559 (82.18%) of the 1,897 virus species could be correctly clustered into one single vOTU. However, at ANI values greater than 82.5%, an increasing number of species were clustered into two or more vOTUs. In sum, we have identified some inconsistency and misassignment of RNA virus species based on the analysis of RdRp sequences alone which has important implications for the development of an automated RNA virus classification system.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"101 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141770467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}