Virus Evolution最新文献

{"title":"Comparative Analysis of Multiple Consensus Genomes of the Same Strain of Marek’s Disease Virus Reveals Intrastrain Variation","authors":"Alejandro Ortigas-Vasquez, Utsav Pandey, Daniel Renner, Chris D Bowen, Susan J Baigent, John Dunn, Hans Cheng, Yongxiu Yao, Andrew F Read, Venugopal Nair, Dave A Kennedy, Moriah L Szpara","doi":"10.1093/ve/veae047","DOIUrl":"https://doi.org/10.1093/ve/veae047","url":null,"abstract":"Current strategies to understand the molecular basis of Marek’s disease virus (MDV) virulence primarily consist of cataloguing divergent nucleotides between strains with different phenotypes. However, most comparative genomic studies of MDV rely on previously published consensus genomes despite the confirmed existence of MDV strains as mixed viral populations. To assess the reliability of interstrain genomic comparisons relying on published consensus genomes of MDV, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform 3-way comparisons between multiple consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). In contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Notably, we were able to identify 3 SNPs in the Unique Long region and 16 SNPs in the Unique Short (US) region of CVI988GenBank.BAC that were not present in either CVI988Pirbright.lab or CVI988USDA.PA.field. Recombination analyses of field strains previously described as natural recombinants of CVI988 yielded no evidence of crossover events in the US region when either CVI988Pirbright.lab or CVI988USDA.PA.field were used to represent CVI988 instead of CVI988GenBank.BAC. We were also able to confirm that both CVI988 and Md5 populations were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. However, we did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988GenBank.BAC. Taken together, our findings suggest that continued reliance on the same published consensus genome of CVI988 may have led to an overestimation of genomic divergence between CVI988 and virulent strains, and that multiple consensus genomes per strain may be necessary to ensure the accuracy of interstrain genomic comparisons.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141509282","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}

{"title":"Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin.","authors":"Tongyu Liu, William K Reiser, Timothy J C Tan, Huibin Lv, Joel Rivera-Cardona, Kyle Heimburger, Nicholas C Wu, Christopher B Brooke","doi":"10.1093/ve/veae046","DOIUrl":"10.1093/ve/veae046","url":null,"abstract":"<p><p>The antigenic evolution of the influenza A virus hemagglutinin (HA) gene poses a major challenge for the development of vaccines capable of eliciting long-term protection. Prior efforts to understand the mechanisms that govern viral antigenic evolution mainly focus on HA in isolation, ignoring the fact that HA must act in concert with the viral neuraminidase (NA) during replication and spread. Numerous studies have demonstrated that the degree to which the receptor-binding avidity of HA and receptor-cleaving activity of NA are balanced with each other influences overall viral fitness. We recently showed that changes in NA activity can significantly alter the mutational fitness landscape of HA in the context of a lab-adapted virus strain. Here, we test whether natural variation in relative NA activity can influence the evolutionary potential of HA in the context of the seasonal H1N1 lineage (pdmH1N1) that has circulated in humans since the 2009 pandemic. We observed substantial variation in the relative activities of NA proteins encoded by a panel of H1N1 vaccine strains isolated between 2009 and 2019. We comprehensively assessed the effect of NA background on the HA mutational fitness landscape in the circulating pdmH1N1 lineage using deep mutational scanning and observed pronounced epistasis between NA and residues in or near the receptor-binding site of HA. To determine whether NA variation could influence the antigenic evolution of HA, we performed neutralizing antibody selection experiments using a panel of monoclonal antibodies targeting different HA epitopes. We found that the specific antibody escape profiles of HA were highly contingent upon NA background. Overall, our results indicate that natural variation in NA activity plays a significant role in governing the evolutionary potential of HA in the currently circulating pdmH1N1 lineage.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae046"},"PeriodicalIF":5.5,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11196192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447687","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":"Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks","authors":"Michael A Martin, Nick Berg, Katia Koelle","doi":"10.1093/ve/veae042","DOIUrl":"https://doi.org/10.1093/ve/veae042","url":null,"abstract":"Influenza infections result in considerable public health and economic impacts each year. One of the contributing factors to the high annual incidence of human influenza is the virus’s ability to evade acquired immunity through continual antigenic evolution. Understanding the evolutionary forces that act within and between hosts is therefore critical to interpreting past trends in influenza virus evolution and in predicting future ones. Several studies have analyzed longitudinal patterns of influenza A virus genetic diversity in natural human infections to assess the relative contributions of selection and genetic drift on within-host evolution. However, in these natural infections, within-host viral populations harbor very few single nucleotide variants, limiting our resolution in understanding the forces acting on these populations in vivo. Further, low levels of within host viral genetic diversity limit the ability to infer the extent of drift across transmission events. Here, we propose to use influenza virus genomic diversity as an alternative signal to better understand within and between host patterns of viral evolution. Specifically, we focus on the dynamics of defective viral genomes (DVGs) which harbor large internal deletions in one or more of influenza virus’s eight gene segments. Our longitudinal analyses of DVGs show that influenza A virus populations are highly dynamic within hosts, corroborating previous findings based on viral genetic diversity that point towards the importance of genetic drift in driving within-host viral evolution. Further, our analysis of DVG populations across transmission pairs indicate that DVGs rarely appeared to be shared, consistent with previous findings indicating the presence of tight transmission bottlenecks. Our analyses demonstrate that viral genomic diversity can be used to complement analyses based on viral genetic diversity to reveal processes that drive viral evolution within and between hosts.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"22 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141191273","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}

{"title":"Comparative genome analysis reveals driving forces behind Monkeypox virus evolution and sheds light on the role of ATC trinucleotide motif","authors":"Preeti Agarwal, Nityendra Shukla, Ajay Bhatia, Sahil Mahfooz, Jitendra Narayan","doi":"10.1093/ve/veae043","DOIUrl":"https://doi.org/10.1093/ve/veae043","url":null,"abstract":"Monkeypox (MPOX), a zoonotic disease originating in Western and Central Africa in 1970, has seen a recent surge in outbreaks across 100+ countries. A comparative analysis of 404 Monkeypox virus (MPXV) genomes revealed notable changes in microsatellite abundance and density, especially within Clades I, IIa, and IIb. Each clade exhibited unique microsatellite motifs, with twenty-six conserved loci specific to MPXV, suggesting their potential as molecular markers in diagnostics. Additionally, nine genes in the MPXV genome featured ten variable hotspot microsatellite regions associated with surface protein synthesis and host control. Notably, gene OPG153, especially at the SSR locus ‘(ATC)n’, exhibited the most pronounced variations among lineages over time and plays a role in virus pathogenesis within the host cell. These findings not only enhance our understanding of MPXV unique molecular profile but also offer valuable insights into potential pathogenic and evolutionary implications.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"83 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141191420","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}

{"title":"The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat","authors":"Jackie E Mahar, Michelle Wille, Erin Harvey, Craig C Moritz, Edward C Holmes","doi":"10.1093/ve/veae044","DOIUrl":"https://doi.org/10.1093/ve/veae044","url":null,"abstract":"Lizards have diverse ecologies and evolutionary histories, and represent a promising group to explore how hosts shape virome structure and virus evolution. Yet little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than 30 novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as the Flaviviridae, Picornaviridae, Bornaviridae, Iridoviridae and Rhabdoviridae. Members of the Flaviviridae were particularly abundant across species sampled here, largely belonging to the genus Hepacivirus: 14 novel hepaciviruses were identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness in the animals sampled here was shaped by host taxonomy, and habitat. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"64 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141168881","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}

{"title":"Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations-Application to HIV-1 quasispecies.","authors":"","doi":"10.1093/ve/veae038","DOIUrl":"https://doi.org/10.1093/ve/veae038","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ve/veae019.].</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae038"},"PeriodicalIF":5.3,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11099541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141066403","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":"Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals","authors":"Danae Stephens, Zahra Faghihi, Mohammad Moniruzzaman","doi":"10.1093/ve/veae039","DOIUrl":"https://doi.org/10.1093/ve/veae039","url":null,"abstract":": Stony corals (Order Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for ‘endogenous’ viruses. Our study uncovered a remarkable number of integrated viral elements recognized as ‘Polintoviruses’ (Class Polintoviricetes) in 30 Scleractinia genomes; with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony coral genomes, alongside presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, along with paralogous expansions, shaped stony coral genomes. Re-analysis of existing gene expression data reveals all polintovirus structural and non-structural hallmark genes are expressed, providing support for free virion production from polintoviruses. Our results, revealing a significant diversity of polintovirus across the Scleractinia order, open a new research avenue into polintovirus and their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"23 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140932564","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}

{"title":"A Parasite Odyssey: An RNA virus concealed in Toxoplasma gondii","authors":"Purav Gupta, Aiden Hiller, Jawad Chowdhury, Declan Lim, Dillon Yee Lim, Jeroen P J Saeij, Artem Babaian, Felipe Rodriguez, Luke Pereira, Alex Morales","doi":"10.1093/ve/veae040","DOIUrl":"https://doi.org/10.1093/ve/veae040","url":null,"abstract":"We are entering a “Platinum Age of Virus Discovery”, an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally-assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health. From a computational viral screen of human neuronal datasets, we identified a novel narnavirus Apocryptovirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically-proximal viruses to Ao and discovered 19 Apocryptovirus species, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While samples containing this genus of narnaviruses are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic Apicomplexa nucleic acid co-occurrence, supporting that Apocryptovirus is a genus of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"66 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140932749","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}

{"title":"Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York","authors":"Fabiana Gambaro, Ralf Duerr, Dacia Dimartino, Christian Marier, Eduardo Iturrate, Mark J Mulligan, Adriana Heguy, Simon Dellicour","doi":"10.1093/ve/veae035","DOIUrl":"https://doi.org/10.1093/ve/veae035","url":null,"abstract":"The recombinant SARS-CoV-2 Omicron XBB.1.5 variant was first detected in New York City (NYC) and rapidly became the predominant variant in the area by early 2023. The increased occurrence of circulating variants within the SARS-CoV-2 XBB-sublineage prompted the modification of COVID-19 mRNA vaccines by Moderna and Pfizer-BioNTech. This update, implemented in mid-September 2023, involved the incorporation of a monovalent XBB.1.5 component. Considering that NYC probably played a central role in the emergence of the XBB.1.5 variant, we conducted phylogeographic analysis to investigate the emergence and spread of this variant in the metropolitan area. Our analysis confirms that XBB.1.5 emerged within or near the NYC area and indicates that XBB.1.5 had a diffusion velocity similar to that of the variant Alpha in the same study area. Additionally, the analysis of 2,392 genomes collected in the context of the genomic surveillance program at NYU Langone Health system (NYULH) showed that there was no increased proportion of XBB.1.5, relative to all cocirculating variants, in the boosted compared to unvaccinated individuals. This study provides a comprehensive description of the emergence and dissemination of XBB.1.5.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"36 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140932492","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}

{"title":"Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae)","authors":"Danyil Grybchuk, Arnau Galan, Donnamae Klocek, Diego H Macedo, Yuri I Wolf, Jan Votýpka, Anzhelika Butenko, Julius Lukeš, Uri Neri, Kristína Záhonová, Alexei Yu Kostygov, Eugene V Koonin, Vyacheslav Yurchenko","doi":"10.1093/ve/veae037","DOIUrl":"https://doi.org/10.1093/ve/veae037","url":null,"abstract":"Trypanosomatids (Euglenozoa) are a diverse group of unicellular flagellates predominately infecting insects (monoxenous species) or circulating between insects and vertebrates or plants (dixenous species). Monoxenous trypanosomatids harbor a wide range of RNA viruses belonging to the families Narnaviridae, Totiviridae, and Qinviridae, a putative group of tombus-like viruses. Here, we focus on the subfamily Blastocrithidiinae, a previously unexplored divergent group of monoxenous trypanosomatids comprising two related genera: Obscuromonas and Blastocrithidia. Members of the genus Blastocrithidia employ a unique genetic code, in which all three stop-codons are repurposed to encode amino acids, with TAA also used to terminate translation. Obscuromonas isolates studied here bear viruses of three families: Narnaviridae, Qinviridae, and Mitoviridae. The latter viral group is documented in trypanosomatid flagellates for the first time. While other known mitoviruses replicate in the mitochondria, those of trypanosomatids appear to reside in the cytoplasm. Although no RNA viruses were detected in Blastocrithidia spp. we identified an endogenous viral element in the genome of B. triatomae indicating its past encounter(s) with tombus-like viruses.","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"18 1","pages":""},"PeriodicalIF":5.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140886049","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}