Megan E Golding, Guanghui Wu, Rebekah Wilkie, Evelyne Picard-Meyer, Alexandre Servat, Denise A Marston, James N Aegerter, Daniel L Horton, Lorraine M McElhinney
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.
{"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
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.
{"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}
Pub Date : 2024-07-26eCollection Date: 2024-01-01DOI: 10.1093/ve/veae057
[This corrects the article DOI: 10.1093/ve/veae032.].
[此处更正了文章 DOI：10.1093/ve/veae032]。
{"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
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.
{"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
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: <90%, and sometimes <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.
{"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}
Yongtao Ye, Marcus H Shum, Isaac Wu, Carlos Chau, Ningqi Zhao, David K Smith, Joseph T Wu, Tommy T Lam
The unprecedentedly large size of the global SARS-CoV-2 phylogeny makes any computation on the tree difficult. Lineage identification (e.g. the PANGO nomenclature for SARS-CoV-2) and assignment are key to track the virus evolution. It requires annotating clade roots of lineages to unlabeled ancestral nodes in a phylogenetic tree. Then the lineage labels of descendant samples under these clade roots can be inferred to be the corresponding lineages. This is the ancestral lineage annotation problem, and matUtils (a package in pUShER) and PastML are commonly used methods. However, their computational tractability is a challenge and their accuracy needs further exploration in huge SARS-CoV-2 phylogenies. We have developed an efficient and accurate method, called ‘F1ALA’, that utilizes the F1-score to evaluate the confidence with which a specific ancestral node can be annotated as the clade root of a lineage, given the lineage labels of a set of taxa in a rooted tree. Compared to these methods, F1ALA achieved roughly an order of magnitude faster yet with ~12% of their memory usage when annotating 2,277 PANGO lineages in a phylogeny of 5.26 million taxa. F1ALA allows real-time lineage tracking be performed on a laptop computer. F1ALA outperformed matUtils (pUShER) with statistical significance, and had comparable accuracy to PastML in tests on empirical and simulated data. F1ALA enables a tree refinement by pruning taxa with inconsistent labels to their closest annotation nodes and re-inserting them back to the pruned tree to improve a SARS-CoV-2 phylogeny with both higher log-likelihood and lower parsimony score. Given the ultrafast speed and high accuracy, we anticipated that F1ALA will also be useful for large phylogenies of other viruses. Codes and benchmark datasets are publicly available at https://github.com/id-bioinfo/F1ALA.
{"title":"F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny","authors":"Yongtao Ye, Marcus H Shum, Isaac Wu, Carlos Chau, Ningqi Zhao, David K Smith, Joseph T Wu, Tommy T Lam","doi":"10.1093/ve/veae056","DOIUrl":"https://doi.org/10.1093/ve/veae056","url":null,"abstract":"The unprecedentedly large size of the global SARS-CoV-2 phylogeny makes any computation on the tree difficult. Lineage identification (e.g. the PANGO nomenclature for SARS-CoV-2) and assignment are key to track the virus evolution. It requires annotating clade roots of lineages to unlabeled ancestral nodes in a phylogenetic tree. Then the lineage labels of descendant samples under these clade roots can be inferred to be the corresponding lineages. This is the ancestral lineage annotation problem, and matUtils (a package in pUShER) and PastML are commonly used methods. However, their computational tractability is a challenge and their accuracy needs further exploration in huge SARS-CoV-2 phylogenies. We have developed an efficient and accurate method, called ‘F1ALA’, that utilizes the F1-score to evaluate the confidence with which a specific ancestral node can be annotated as the clade root of a lineage, given the lineage labels of a set of taxa in a rooted tree. Compared to these methods, F1ALA achieved roughly an order of magnitude faster yet with ~12% of their memory usage when annotating 2,277 PANGO lineages in a phylogeny of 5.26 million taxa. F1ALA allows real-time lineage tracking be performed on a laptop computer. F1ALA outperformed matUtils (pUShER) with statistical significance, and had comparable accuracy to PastML in tests on empirical and simulated data. F1ALA enables a tree refinement by pruning taxa with inconsistent labels to their closest annotation nodes and re-inserting them back to the pruned tree to improve a SARS-CoV-2 phylogeny with both higher log-likelihood and lower parsimony score. Given the ultrafast speed and high accuracy, we anticipated that F1ALA will also be useful for large phylogenies of other viruses. Codes and benchmark datasets are publicly available at https://github.com/id-bioinfo/F1ALA.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"34 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141770464","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}
Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including the influenza, Ebola and measles viruses. NSV genomes consist of one or multiple single-stranded RNA molecules that are encapsidated into one or more ribonucleoprotein (RNP) complexes. These RNPs consist of viral RNA, a viral RNA polymerase, and many copies of the viral nucleoprotein (NP). Current evolutionary relationships within the NSV phylum are based on alignment of conserved RNA-directed RNA polymerase (RdRp) domain amino acid sequences. However, the RdRp domain-based phylogeny does not address whether NP, the other core protein in the NSV genome, evolved along the same trajectory or whether several RdRp-NP pairs evolved through convergent evolution in the segmented and non-segmented NSV genomes architectures. Addressing how NP and the RdRp domain evolved may help us better understand NSV diversity. Since NP sequences are too short to infer robust phylogenetic relationships, we here used experimentally-obtained and AlphaFold 2.0-predicted NP structures to probe whether evolutionary relationships can be estimated using NSV NP sequences. Following flexible structure alignments of modeled structures, we find that the structural homology of the NSV NPs reveals phylogenetic clusters that are consistent with RdRp-based clustering. In addition, we were able to assign viruses for which RdRp sequences are currently missing to phylogenetic clusters based on the available NP sequence. Both our RdRp-based and NP-based relationships deviate from the current NSV classification of the segmented Naedrevirales, which cluster with the other segmented NSVs in our analysis. Overall, our results suggest that the NSV RdRp and NP genes largely evolved along similar trajectories and that even short pieces of genetic, protein-coding information can be used to infer evolutionary relationships, potentially making metagenomic analyses more valuable.
负感 RNA 病毒（NSV）包括一些对人类危害最大的病原体，如流感病毒、埃博拉病毒和麻疹病毒。NSV 基因组由一个或多个单链 RNA 分子组成，这些分子被封装成一个或多个核糖核蛋白（RNP）复合物。这些 RNP 由病毒 RNA、病毒 RNA 聚合酶和多个病毒核蛋白（NP）拷贝组成。目前，NSV 门内的进化关系是基于保守的 RNA 定向 RNA 聚合酶（RdRp）结构域氨基酸序列的比对。然而，基于 RdRp 结构域的系统发育并没有解决 NSV 基因组中的另一个核心蛋白 NP 是否沿着相同的轨迹进化，或者在分节和非分节的 NSV 基因组结构中，是否有几对 RdRp-NP 通过趋同进化而进化。解决 NP 和 RdRp 结构域如何进化的问题有助于我们更好地理解 NSV 的多样性。由于 NP 序列太短，无法推断出可靠的系统发育关系，因此我们在此使用实验获得的和 AlphaFold 2.0 预测的 NP 结构来探究是否可以使用 NSV NP 序列来估计进化关系。通过对模型结构进行灵活的结构比对，我们发现 NSV NP 的结构同源性揭示了与基于 RdRp 的聚类一致的系统发生群。此外，我们还能根据现有的 NP 序列将目前缺少 RdRp 序列的病毒归入系统发生群。基于 RdRp 和基于 NP 的关系都偏离了目前对分段 Naedrevirales 的 NSV 分类，在我们的分析中，Naedrevirales 与其他分段 NSV 聚类在一起。总之，我们的结果表明，NSV RdRp 和 NP 基因在很大程度上是沿着相似的轨迹进化的，即使是很短的基因、蛋白质编码信息也可以用来推断进化关系，从而可能使元基因组分析更有价值。
{"title":"Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships","authors":"Kimberly R Sabsay, te Velthuis Aartjan J.W","doi":"10.1093/ve/veae058","DOIUrl":"https://doi.org/10.1093/ve/veae058","url":null,"abstract":"Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including the influenza, Ebola and measles viruses. NSV genomes consist of one or multiple single-stranded RNA molecules that are encapsidated into one or more ribonucleoprotein (RNP) complexes. These RNPs consist of viral RNA, a viral RNA polymerase, and many copies of the viral nucleoprotein (NP). Current evolutionary relationships within the NSV phylum are based on alignment of conserved RNA-directed RNA polymerase (RdRp) domain amino acid sequences. However, the RdRp domain-based phylogeny does not address whether NP, the other core protein in the NSV genome, evolved along the same trajectory or whether several RdRp-NP pairs evolved through convergent evolution in the segmented and non-segmented NSV genomes architectures. Addressing how NP and the RdRp domain evolved may help us better understand NSV diversity. Since NP sequences are too short to infer robust phylogenetic relationships, we here used experimentally-obtained and AlphaFold 2.0-predicted NP structures to probe whether evolutionary relationships can be estimated using NSV NP sequences. Following flexible structure alignments of modeled structures, we find that the structural homology of the NSV NPs reveals phylogenetic clusters that are consistent with RdRp-based clustering. In addition, we were able to assign viruses for which RdRp sequences are currently missing to phylogenetic clusters based on the available NP sequence. Both our RdRp-based and NP-based relationships deviate from the current NSV classification of the segmented Naedrevirales, which cluster with the other segmented NSVs in our analysis. Overall, our results suggest that the NSV RdRp and NP genes largely evolved along similar trajectories and that even short pieces of genetic, protein-coding information can be used to infer evolutionary relationships, potentially making metagenomic analyses more valuable.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"20 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141770465","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}
Dongbin Park, Kwan Woo Kim, Young-Il Kim, Mark Anthony B Casel, Hyunwoo Jang, Woohyun Kwon, Kanghee Kim, Se-Mi Kim, Monford Paul Abishek N, Eun-Ha Kim, Hobin Jang, Suhee Hwang, Seok-Min Yun, Joo-Yeon Lee, Hye Won Jeong, Su-Jin Park, Young Ki Choi
The Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) poses a significant public health challenge in East Asia, necessitating a deeper understanding of its evolutionary dynamics to effectively manage its spread and pathogenicity. This study provides a comprehensive analysis of the genetic diversity, recombination patterns, and selection pressures across the SFTSV genome, utilizing an extensive dataset of 2,041 sequences from various hosts and regions up to November 2023. Employing Maximum Likelihood (ML) and Bayesian Evolutionary Analysis (BEAST), we elucidated the phylogenetic relationships among nine distinct SFTSV genotypes (A, B1, B2, B3, B4, C, D, E, and F), revealing intricate patterns of viral evolution and genotype distribution across China, South Korea, and Japan. Further, our analysis identified 34 potential reassortments, underscoring a dynamic genetic interplay among SFTSV strains. Genetic recombination was observed most frequently in the L segment and least in the S segment, with notable recombination hotspots characterized by stem-loop hairpin structures, indicative of a structural propensity for genetic recombination. Additionally, selection pressure analysis on critical viral genes indicated a predominant trend of negative selection, with specific sites within the RdRp and glycoprotein genes showing positive selection. These sites suggest evolutionary adaptations to host immune responses and environmental pressures. This study sheds light on the intricate evolutionary mechanisms shaping SFTSV, offering insights into its adaptive strategies and potential implications for vaccine development and therapeutic interventions.
严重发热伴血小板减少综合征病毒（SFTSV）对东亚地区的公共卫生构成了重大挑战，因此有必要深入了解其进化动态，以有效控制其传播和致病性。本研究利用截至2023年11月来自不同宿主和地区的2041个序列的广泛数据集，对SFTSV基因组的遗传多样性、重组模式和选择压力进行了全面分析。利用最大似然法（ML）和贝叶斯进化分析法（BEAST），我们阐明了九种不同的SFTSV基因型（A、B1、B2、B3、B4、C、D、E和F）之间的系统发育关系，揭示了病毒进化的复杂模式以及基因型在中国、韩国和日本的分布。此外，我们的分析还发现了 34 个潜在的基因重组，突显了 SFTSV 株系间动态的基因相互作用。基因重组在 L 段最常见，在 S 段最少，显著的重组热点以茎环发夹结构为特征，表明了基因重组的结构倾向。此外，对关键病毒基因的选择压力分析表明，主要趋势是负选择，RdRp 和糖蛋白基因中的特定位点显示出正选择。这些位点表明病毒在进化过程中适应了宿主的免疫反应和环境压力。这项研究揭示了形成 SFTSV 的复杂进化机制，有助于深入了解其适应策略以及对疫苗开发和治疗干预的潜在影响。
{"title":"Deciphering the Evolutionary Landscape of Severe Fever with Thrombocytopenia Syndrome Virus Across East Asia","authors":"Dongbin Park, Kwan Woo Kim, Young-Il Kim, Mark Anthony B Casel, Hyunwoo Jang, Woohyun Kwon, Kanghee Kim, Se-Mi Kim, Monford Paul Abishek N, Eun-Ha Kim, Hobin Jang, Suhee Hwang, Seok-Min Yun, Joo-Yeon Lee, Hye Won Jeong, Su-Jin Park, Young Ki Choi","doi":"10.1093/ve/veae054","DOIUrl":"https://doi.org/10.1093/ve/veae054","url":null,"abstract":"The Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) poses a significant public health challenge in East Asia, necessitating a deeper understanding of its evolutionary dynamics to effectively manage its spread and pathogenicity. This study provides a comprehensive analysis of the genetic diversity, recombination patterns, and selection pressures across the SFTSV genome, utilizing an extensive dataset of 2,041 sequences from various hosts and regions up to November 2023. Employing Maximum Likelihood (ML) and Bayesian Evolutionary Analysis (BEAST), we elucidated the phylogenetic relationships among nine distinct SFTSV genotypes (A, B1, B2, B3, B4, C, D, E, and F), revealing intricate patterns of viral evolution and genotype distribution across China, South Korea, and Japan. Further, our analysis identified 34 potential reassortments, underscoring a dynamic genetic interplay among SFTSV strains. Genetic recombination was observed most frequently in the L segment and least in the S segment, with notable recombination hotspots characterized by stem-loop hairpin structures, indicative of a structural propensity for genetic recombination. Additionally, selection pressure analysis on critical viral genes indicated a predominant trend of negative selection, with specific sites within the RdRp and glycoprotein genes showing positive selection. These sites suggest evolutionary adaptations to host immune responses and environmental pressures. This study sheds light on the intricate evolutionary mechanisms shaping SFTSV, offering insights into its adaptive strategies and potential implications for vaccine development and therapeutic interventions.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"93 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745154","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}
Pub Date : 2024-07-18eCollection Date: 2024-01-01DOI: 10.1093/ve/veae052
[This corrects the article DOI: 10.1093/ve/vead084.].
[此处更正了文章 DOI：10.1093/ve/vead084]。
{"title":"Correction to: Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants.","authors":"","doi":"10.1093/ve/veae052","DOIUrl":"https://doi.org/10.1093/ve/veae052","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ve/vead084.].</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae052"},"PeriodicalIF":5.5,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11259755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735787","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}
José L Carrasco, Silvia Ambrós, Pablo A Gutiérrez, Santiago F Elena
The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study, we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins in Arabidopsis thaliana that bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes, including cpr5-2 with constitutive expression of systemic acquired resistance. In contrast, mutation R118H specifically emerged in the jin1 mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPg’s interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection. We also discuss our findings in a broad virus evolution context.
{"title":"Adaptation of turnip mosaic virus to Arabidopsis thaliana involves rewiring of VPg - host proteome interactions","authors":"José L Carrasco, Silvia Ambrós, Pablo A Gutiérrez, Santiago F Elena","doi":"10.1093/ve/veae055","DOIUrl":"https://doi.org/10.1093/ve/veae055","url":null,"abstract":"The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study, we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins in Arabidopsis thaliana that bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes, including cpr5-2 with constitutive expression of systemic acquired resistance. In contrast, mutation R118H specifically emerged in the jin1 mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPg’s interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection. We also discuss our findings in a broad virus evolution context.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"61 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141718825","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}
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