Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing

In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray-finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups. Collectively, our results revealed reliable and sufficient information within metatranscriptomics sequencing to characterize not only RNA viruses, but also DNA and retro-transcribing viruses, and therefore established a key methodology that will help us to understand the composition and evolution of the total “infectome” within a diverse range of vertebrate hosts.

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Mutation bias implicates RNA editing in a wide range of mammalian RNA viruses

10.1101/2021.02.09.430395 ◽

2021 ◽

Author(s):

Peter Simmonds ◽

M. Azim Ansari

Keyword(s):

Rna Editing ◽

Rna Viruses ◽

Rna Virus ◽

Structural Parameters ◽

Rapid Evolution ◽

Sequence Variability ◽

Diverse Range ◽

Mouth Disease Virus ◽

Wide Range ◽

Virus Sequence

ABSTRACTThe rapid evolution of RNA viruses has been long considered to result from a combination of high copying error frequencies during RNA replication, short generation times and the consequent extensive fixation of neutral or adaptive changes over short periods. While both the identities and sites of mutations are typically modelled as being random, recent investigations of sequence diversity of SARS coronavirus 2 (SARS-CoV-2) have identified a preponderance of C->U transitions, potentially driven by an APOBEC-like RNA editing process. The current study investigated whether this phenomenon could be observed in the more genetically diverse datasets of other RNA viruses. Using a 5% divergence filter to infer directionality, 18 from 32 datasets of aligned coding region sequences from a diverse range of mammalian RNA viruses (including Picornaviridae, Flaviviridae, Matonaviridae, Caliciviridae and Coronaviridae) showed a >2-fold base composition normalised excess of C->U transitions compared to U->C (range 2.1x–7.5x). C->U transitions showed a favoured 5’ U upstream context consistent with previous analyses of APOBEC-mediated RNA targeting. Amongst several genomic compositional and structural parameters, the presence of genome scale RNA secondary structure (GORS) was associated with C->U/U->C transition asymmetries (p < 0.001), potentially reflecting the documented structure dependence of APOBEC-mediated RNA editing. Using the association index metric, C->U changes were specifically over-represented at phylogenetically uninformative sites, consistent with extensive homoplasy documented in SARS-CoV-2. Excess C->U substitutions accounted for 15-20% of standing sequence variability of HCV and other RNA viruses; RNA editing may therefore represent a potent driver of RNA virus sequence diversification and longer term evolution.Author SummaryThe rapid evolution of RNA viruses is thought to arise from high mutation frequencies during replication and the rapid accumulation of genetic changes over time in response to its changing environments. This study describes an additional potent factor that contributes to the evolution of RNA infecting mammals, the deliberate mutation of the viral genome by host antiviral pathways active within the cell when it becomes infected. This so called “genome editing” by one or more APOBEC enzymes leads to characteristic C->U mutations that damage the virus’s ability to replicate. While this pathway is well characterised as an antiviral defence against HIV and other retroviruses, this study provides evidence for its activity against a wide range of human and veterinary viruses, including HCV and foot and mouth disease virus. APOBEC-driven mutations accounted for 15-20% of standing sequence variability of RNA virus groups, representing a potent driver of RNA virus sequence diversification.

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Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

BMC Genomics ◽

10.1186/s12864-020-07060-5 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Xiaofeng Xu ◽

Jinlong Bei ◽

Yibo Xuan ◽

Jiayuan Chen ◽

Defu Chen ◽

...

Keyword(s):

Rna Sequencing ◽

Genome Sequence ◽

Small Rna ◽

Rna Viruses ◽

Rna Virus ◽

Full Length ◽

Small Rna Sequencing ◽

Sequencing Data ◽

Geographical Regions ◽

Full Length Genome

Abstract Background In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)—evolutionarily related to MGTV—were reported. Results In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China’s Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. Conclusions To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.

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High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia

Journal of Virology ◽

10.1128/jvi.00680-17 ◽

2017 ◽

Vol 91 (17) ◽

Cited By ~ 62

Author(s):

Mang Shi ◽

Peter Neville ◽

Jay Nicholson ◽

John-Sebastian Eden ◽

Allison Imrie ◽

...

Keyword(s):

Western Australia ◽

Rna Viruses ◽

Rna Virus ◽

Geographic Location ◽

Striking Difference ◽

Sampling Location ◽

Virus Species ◽

Diverse Range ◽

Content Type ◽

Virus Diversity

ABSTRACT Mosquitoes harbor a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a metatranscriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described. Comparisons of viromes revealed a striking difference between the two mosquito genera, with viromes of mosquitoes of the Aedes genus exhibiting substantially less diversity and lower abundances than those of mosquitoes of the Culex genus, within which the viral abundance reached 16.87% of the total non-rRNA. In addition, there was little overlap in viral diversity between the two genera, although the viromes were very similar among the three Culex species studied, suggesting that the host taxon plays a major role in structuring virus diversity. In contrast, we found no evidence that geographic location played a major role in shaping RNA virus diversity, and several viruses discovered here exhibited high similarity (95 to 98% nucleotide identity) to those from Indonesia and China. Finally, using abundance-level and phylogenetic relationships, we were able to distinguish potential mosquito viruses from those present in coinfecting bacteria, fungi, and protists. In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses. IMPORTANCE Studies of virus ecology have generally focused on individual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus diversity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. Our results show that RNA viruses are some of the most important components of the mosquito transcriptome, and we identified 19 new virus species from a diverse set of virus families. A key result was that host genetic background plays a more important role in shaping virus diversity than sampling location, with Culex species harboring more viruses at higher abundance than those from Aedes mosquitoes.

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Novel RNA viruses associated with avian haemosporidian parasites

10.1101/2021.11.22.469476 ◽

2021 ◽

Author(s):

Jose Roberto Rodrigues ◽

Scott W Roy ◽

Ravinder N Sehgal

Keyword(s):

Rna Viruses ◽

Rna Virus ◽

Bird Species ◽

Amino Acid Identity ◽

Rna Dependent Rna Polymerase ◽

Haemosporidian Parasites ◽

Local Sequence ◽

Avian Haemosporidians ◽

Vertebrate Hosts ◽

Human Plasmodium

Avian haemosporidian parasites can cause malaria-like symptoms in their hosts and have been implicated in the demise of some bird species. The newly described Matryoshka RNA viruses (MaRNAV1 and MaRNAV2) infect parasites that in turn infect their vertebrate hosts. MaRNAV2 was the first RNA virus discovered associated with parasites of the genus Leucocytozoon. By analyzing metatranscriptomes from the NCBI SRA database with local sequence alignment tools, we detected two novel RNA viruses; we describe them as MaRNAV3 associated with Leucocytozoon and MaRNAV4 associated with Parahaemoproteus. These had ~40-60% amino acid identity to the RNA-dependent RNA-polymerase (RdRp) of MaRNAV1 and 2, respectively. These findings lead us to hypothesize that MaRNAV_like viruses are widespread and tightly associated with the order Haemosporida since they have been described in human Plasmodium vivax, and now two genera of avian haemosporidians.

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Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae

10.1101/2021.03.22.436364 ◽

2021 ◽

Author(s):

Allison K. Miller ◽

Jonathon C.O. Mifsud ◽

Vincenzo A. Costa ◽

Rebecca M. Grimwood ◽

Jane Kitson ◽

...

Keyword(s):

Rna Sequencing ◽

Rna Virus ◽

Bony Fish ◽

Sequencing Data ◽

History Of ◽

Entire History ◽

Vertebrate Hosts ◽

Patterns And Processes ◽

Jawless Fish

The Nidovirales comprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the Coronaviridae, in a range of aquatic hosts including fish, amphibians and reptiles. We sought to identify additional members of the Coronaviridae in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data, and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of divergent viruses that fell within the Letovirinae subfamily of the Coronaviridae, including those in a jawless fish - the pouched lamprey. By mining fish transcriptome data we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across the Coronaviridae, but formed a distinct and diverse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationships of viruses within the Letovirinae does not mirror that of their hosts. For example, the coronavirus found in the pouched lamprey fell within the phylogenetic diversity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.

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The Oxford Handbook of Endangered Languages

10.1093/oxfordhb/9780190610029.001.0001 ◽

2018 ◽

Cited By ~ 7

Keyword(s):

Language Revitalization ◽

Biocultural Diversity ◽

Endangered Languages ◽

Language Documentation ◽

Comprehensive Overview ◽

Diverse Range ◽

Language Endangerment ◽

Reference Volume ◽

New Findings ◽

Comprehensive Reference

The Oxford Handbook of Endangered Languages, in thirty-nine chapters, provides a comprehensive overview of the efforts that are being undertaken to deal with this crisis. Its purposes are (1) to provide a reasonably comprehensive reference volume, with the scope of the volume as a whole representing the breadth of the field; (2) to highlight both the range of thinking about language endangerment and the variety of responses to it; and (3) to broaden understanding of language endangerment, language documentation, and language revitalization, and, in so doing, to encourage and contribute to fresh thinking and new findings in support of endangered languages. The handbook is organized into five parts. Part I, Endangered Languages, addresses some of the fundamental issues that are essential to understanding the nature of the endangered languages crisis. Part II, Language Documentation provides an overview of the issues and activities of concern to linguists and others in their efforts to record and document endangered languages. Part III, Language Revitalization encompasses a diverse range of topics, including approaches, practices, and strategies for revitalizing endangered and sleeping (“dormant”) languages. Part IV, Endangered Languages and Biocultural Diversity, extends the discussion of language endangerment beyond its conventional boundaries to consider the interrelationship of language, culture, and environment. Part V, Looking to the Future, addresses a variety of topics that are certain to be of consequence in future efforts to document and revitalize endangered languages.

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Structure Unveils Relationships between RNA Virus Polymerases

Viruses ◽

10.3390/v13020313 ◽

2021 ◽

Vol 13 (2) ◽

pp. 313

Author(s):

Heli A. M. Mönttinen ◽

Janne J. Ravantti ◽

Minna M. Poranen

Keyword(s):

Phylogenetic Tree ◽

Rna Viruses ◽

Rna Virus ◽

Sequence Similarity ◽

Protein Structures ◽

Structural Similarity ◽

Functional Differentiation ◽

Comparison Method ◽

Homologous Structure ◽

Biological Entities

RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.

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Single-Cell RNA Sequencing in Parkinson’s Disease

Biomedicines ◽

10.3390/biomedicines9040368 ◽

2021 ◽

Vol 9 (4) ◽

pp. 368

Author(s):

Shi-Xun Ma ◽

Su Bin Lim

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Single Cell ◽

Rna Sequencing ◽

Rna Degradation ◽

Postmortem Brain ◽

Cell Type ◽

New Findings ◽

Postmortem Brain Tissue ◽

Technical Challenges

Single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) technologies have enhanced the understanding of the molecular pathogenesis of neurodegenerative disorders, including Parkinson’s disease (PD). Nonetheless, their application in PD has been limited due mainly to the technical challenges resulting from the scarcity of postmortem brain tissue and low quality associated with RNA degradation. Despite such challenges, recent advances in animals and human in vitro models that recapitulate features of PD along with sequencing assays have fueled studies aiming to obtain an unbiased and global view of cellular composition and phenotype of PD at the single-cell resolution. Here, we reviewed recent sc/snRNA-seq efforts that have successfully characterized diverse cell-type populations and identified cell type-specific disease associations in PD. We also examined how these studies have employed computational and analytical tools to analyze and interpret the rich information derived from sc/snRNA-seq. Finally, we highlighted important limitations and emerging technologies for addressing key technical challenges currently limiting the integration of new findings into clinical practice.

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Essential role of IPS-1 in innate immune responses against RNA viruses

Journal of Experimental Medicine ◽

10.1084/jem.20060792 ◽

2006 ◽

Vol 203 (7) ◽

pp. 1795-1803 ◽

Cited By ~ 345

Author(s):

Himanshu Kumar ◽

Taro Kawai ◽

Hiroki Kato ◽

Shintaro Sato ◽

Ken Takahashi ◽

...

Keyword(s):

Rna Viruses ◽

Rna Virus ◽

Critical Role ◽

Nuclear Factor Κb ◽

Type I ◽

Innate Immune Responses ◽

Antiviral Responses ◽

Deficient Mice

IFN-β promoter stimulator (IPS)-1 was recently identified as an adapter for retinoic acid–inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (Mda5), which recognize distinct RNA viruses. Here we show the critical role of IPS-1 in antiviral responses in vivo. IPS-1–deficient mice showed severe defects in both RIG-I– and Mda5-mediated induction of type I interferon and inflammatory cytokines and were susceptible to RNA virus infection. RNA virus–induced interferon regulatory factor-3 and nuclear factor κB activation was also impaired in IPS-1–deficient cells. IPS-1, however, was not essential for the responses to either DNA virus or double-stranded B-DNA. Thus, IPS-1 is the sole adapter in both RIG-I and Mda5 signaling that mediates effective responses against a variety of RNA viruses.

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RNA viruses and the mitogenic Raf/MEK/ERK signal transduction cascade

Biological Chemistry ◽

10.1515/bc.2008.145 ◽

2008 ◽

Vol 389 (10) ◽

Cited By ~ 64

Author(s):

Stephan Pleschka

Keyword(s):

Signal Transduction ◽

Rna Viruses ◽

Rna Virus ◽

Cell Metabolism ◽

Mitogen Activated Protein Kinase ◽

Erk Signaling ◽

Control Center ◽

Signal Transduction Cascade ◽

Host Interaction ◽

Differentiation And Proliferation

AbstractThe Raf/MEK/ERK signal transduction cascade belongs to the mitogen-activated protein kinase (MAPK) cascades. Raf/MEK/ERK signaling leads to stimulus-specific changes in gene expression, alterations in cell metabolism or induction of programmed cell death (apoptosis), and thus controls cell differentiation and proliferation. It is induced by extracellular agents, including pathogens such as RNA viruses. Many DNA viruses are known to induce cellular signaling via this pathway. As these pathogens partly use the DNA synthesis machinery for their replication, they aim to drive cells into a proliferative state. In contrast, the consequences of RNA virus-induced Raf/MEK/ERK signaling were less clear for a long time, but since the turn of the century the number of publications on this topic has rapidly increased. Research on this virus/host-interaction will broaden our understanding of its relevance in viral replication. This important control center of cellular responses is differently employed to support the replication of several important human pathogenic RNA viruses including influenza, Ebola, hepatitis C and SARS corona viruses.

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