scholarly journals Evolutionary origins of epidemic potential among human RNA viruses

2019 ◽  
Author(s):  
Lu Lu ◽  
Liam Brierley ◽  
Gail Robertson ◽  
Feifei Zhang ◽  
Samantha Lycett ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Virus Genome ◽  
Human Populations ◽  
Infective Virus ◽  
Genome Sequences ◽  
Evolutionary Origins ◽  
Virus Diversity ◽  
Human Viruses ◽  
Do So

AbstractTo have epidemic potential, a pathogen must be able to spread in human populations, but of human-infective RNA viruses only a minority can do so. We investigated the evolution of human transmissibility through parallel analyses of 1755 virus genome sequences from 39 RNA virus genera. We identified 57 lineages containing human-transmissible species and estimated that at least 74% of these lineages have evolved directly from non-human viruses in other mammals or birds, a public health threat recently designated “Disease X”. Human-transmissible viruses rarely evolve from virus lineages that can infect but not transmit between humans. This result cautions against focussing surveillance and mitigation efforts narrowly on currently known human-infective virus lineages and supports calls for a better understanding of RNA virus diversity in non-human hosts.

scholarly journals Activation of viral transcription by stepwise largescale folding of an RNA virus genome

2020 ◽  
Vol 48 (16) ◽  
pp. 9285-9300
Author(s):  
Tamari Chkuaseli ◽  
K Andrew White
Keyword(s):  
Rna Structure ◽  
Rna Viruses ◽  
Rna Virus ◽  
Initial Step ◽  
Binding Pocket ◽  
Regulatory Elements ◽  
Virus Genome ◽  
Genomic Rna ◽  
Stem Loop ◽  
Rna Complex

Abstract The genomes of RNA viruses contain regulatory elements of varying complexity. Many plus-strand RNA viruses employ largescale intra-genomic RNA-RNA interactions as a means to control viral processes. Here, we describe an elaborate RNA structure formed by multiple distant regions in a tombusvirus genome that activates transcription of a viral subgenomic mRNA. The initial step in assembly of this intramolecular RNA complex involves the folding of a large viral RNA domain, which generates a discontinuous binding pocket. Next, a distally-located protracted stem-loop RNA structure docks, via base-pairing, into the binding site and acts as a linchpin that stabilizes the RNA complex and activates transcription. A multi-step RNA folding pathway is proposed in which rate-limiting steps contribute to a delay in transcription of the capsid protein-encoding viral subgenomic mRNA. This study provides an exceptional example of the complexity of genome-scale viral regulation and offers new insights into the assembly schemes utilized by large intra-genomic RNA structures.

scholarly journals Plant Virus Genome Is Shaped by Specific Dinucleotide Restrictions That Influence Viral Infection

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Alfonso González de Prádena ◽  
Adrián Sánchez Jimenez ◽  
David San León ◽  
Peter Simmonds ◽  
Juan Antonio García ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
High Throughput Sequencing ◽  
Rna Viruses ◽  
Rna Virus ◽  
Virus Genome ◽  
Viral Fitness ◽  
Plum Pox Virus ◽  
Dependent Manner ◽  
Viral Restriction ◽  
Rna Accumulation

ABSTRACT The presence of CpG and UpA dinucleotides is restricted in the genomes of animal RNA viruses to avoid specific host defenses. We wondered whether a similar phenomenon exists in nonanimal RNA viruses. Here, we show that these two dinucleotides, especially UpA, are underrepresented in the family Potyviridae, the most important group of plant RNA viruses. Using plum pox virus (PPV; Potyviridae family) as a model, we show that an increase in UpA frequency strongly diminishes virus accumulation. Remarkably, unlike previous observations in animal viruses, PPV variants harboring CpG-rich fragments display just faint (or no) attenuation. The anticorrelation between UpA frequency and viral fitness additionally demonstrates the relevance of this particular dinucleotide: UpA-high mutants are attenuated in a dose-dependent manner, whereas a UpA-low variant displays better fitness than its parental control. Using high-throughput sequencing, we also show that UpA-rich PPV variants are genetically stable, without apparent changes in sequence that revert and/or compensate for the dinucleotide modification despite its attenuation. In addition, we also demonstrate here that the PPV restriction of UpA-rich variants works independently of the classical RNA silencing pathway. Finally, we show that the anticorrelation between UpA frequency and RNA accumulation applies to mRNA-like fragments produced by the host RNA polymerase II. Together, our results inform us about a dinucleotide-based system in plant cells that controls diverse RNAs, including RNA viruses. IMPORTANCE Dinucleotides (combinations of two consecutive nucleotides) are not randomly present in RNA viruses; in fact, the presence of CpG and UpA is significantly repressed in their genomes. Although the meaning of this phenomenon remains obscure, recent studies with animal-infecting viruses have revealed that their low CpG/UpA frequency prevents virus restriction via a host antiviral system that recognizes, and promotes the degradation of, CpG/UpA-rich RNAs. Whether similar systems act in organisms from other life kingdoms has been unknown. To fill this gap in our knowledge, we built several synthetic variants of a plant RNA virus with deoptimized dinucleotide frequencies and analyzed their viral fitness and genome adaptation. In brief, our results inform us for the first time about an effective dinucleotide-based system that acts in plants against viruses. Remarkably, this viral restriction in plants is reminiscent of, but not identical to, the equivalent antiviral response in animals.

scholarly journals Marine RNA Virus Quasispecies Are Distributed throughout the Oceans

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Marli Vlok ◽  
Andrew S. Lang ◽  
Curtis A. Suttle
Keyword(s):  
Amino Acid ◽  
Rna Viruses ◽  
Rna Virus ◽  
Purifying Selection ◽  
Amino Acid Sequences ◽  
Metagenomic Data ◽  
Spatial And Temporal Patterns ◽  
Data Set ◽  
Virus Diversity ◽  
Virus Genomes

ABSTRACTRNA viruses, particularly genetically diverse members of thePicornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, andHeterosigma akashiwoRNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans.IMPORTANCEVery little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, theMarnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.

scholarly journals Viromes in Marine Ecosystems Reveal Remarkable Invertebrate RNA Virus Diversity

2021 ◽  
Author(s):  
Yu-Yi Zhang ◽  
Yicong Chen ◽  
Xiaoman Wei ◽  
Jie Cui
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Marine Invertebrate ◽  
Ecological Factors ◽  
Virus Evolution ◽  
Marine Ecosystems ◽  
Invertebrate Species ◽  
Virus Diversity ◽  
First Time ◽  
Special Notice

AbstractOcean viromes remain poorly understood and little is known about the ecological factors driving aquatic RNA virus evolution. In this study, we used a meta-transcriptomic approach to characterize the viromes of 58 marine invertebrate species across three seas. This revealed the presence of 315 newly identified RNA viruses in nine viral families or orders (Durnavirales, Totiviridae, Bunyavirales, Hantaviridae, Picornavirales, Flaviviridae, Hepelivirales, Solemoviridae and Tombusviridae), with most of them are sufficiently divergent to the documented viruses. With special notice that we first time revealed an ocean virus rooting to mammalian hantaviruses. We also found evidence for possible host sharing and switch events during virus evolution. In sum, we demonstrated the hidden diversity of marine invertebrate RNA viruses.

scholarly journals A Genotype-to-Phenotype Modeling Framework to Predict Human Pathogenicity of Novel Coronaviruses

2021 ◽  
Author(s):  
Phillip Davis ◽  
Joseph A Russell
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Human Pathogens ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Modeling Framework ◽  
Strong Argument ◽  
Genomic Epidemiology ◽  
Phenotype Model ◽  
Level Information

Leveraging prior viral genome sequencing data to make predictions on whether an unknown, emergent virus harbors a phenotype-of-concern has been a long-sought goal of genomic epidemiology. A predictive phenotype model built from nucleotide-level information alone has previously been considered un-tenable with respect to RNA viruses due to the ultra-high intra-sequence variance of their genomes, even within closely related clades. Building from our prior work developing a degenerate k-mer method to accommodate this high intra-sequence variation of RNA virus genomes for modeling frameworks, and leveraging a taxonomic group-shuffle-split paradigm on complete coronavirus assemblies from prior to October 2018, we trained multiple regularized logistic regression classifiers at the nucleotide k-mer level capable of accurately predicting withheld SARS-CoV-2 genome sequences as human pathogens and accurately predicting withheld Swine Acute Diarrhea Syndrome coronavirus (SADS-CoV) genome sequences as non-human pathogens. LASSO feature selection identified several degenerate nucleotide predictor motifs with high model coefficients for the human pathogen class that were present across widely disparate classes of coronaviruses. However, these motifs differed in which genes they were present in, what specific codons were used to encode them, and what the translated amino acid motif was. This emphasizes the importance of a phenetic view of emerging pathogenic RNA viruses, as opposed to the canonical phylogenetic interpretations most-commonly used to track and manage viral zoonoses. Applying our model to more recent Orthocoronavirinae genomes deposited since October 2018 yields a novel contextual view of pathogen-potential across bat-related, canine-related, porcine-related, and rodent-related coronaviruses and critical adaptations which may have contributed to the emergence of the pandemic SARS-CoV-2 virus. Finally, we discuss the utility of these predictive models (and their associated predictor motifs) to novel biosurveillance protocols that substantially increase the pound-for-pound information content of field-collected sequencing data and make a strong argument for the necessity of routine collection and sequencing of zoonotic viruses.

scholarly journals Application of a sequence-based taxonomic classification method to uncultured and unclassified marine single-stranded RNA viruses in the order Picornavirales

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Marli Vlok ◽  
Andrew S Lang ◽  
Curtis A Suttle
Keyword(s):  
Rna Viruses ◽  
Sequence Data ◽  
Rna Virus ◽  
Taxonomic Classification ◽  
Sound Classification ◽  
Virus Diversity ◽  
Species Demarcation Threshold ◽  
The Family ◽  
Genetic Features ◽  
Taxonomic Framework

Abstract Metagenomics has altered our understanding of microbial diversity and ecology. This includes its applications to viruses in marine environments that have demonstrated their enormous diversity. Within these are RNA viruses, many of which share genetic features with members of the order Picornavirales; yet, very few of these have been taxonomically classified. The only recognized family of marine RNA viruses is the Marnaviridae, which was founded based on discovery and characterization of the species Heterosigma akashiwo RNA virus. Two additional genera of marine RNA viruses, Labyrnavirus (one species) and Bacillarnavirus (three species), were subsequently defined within the order Picornavirales but not assigned to a family. We have defined a sequence-based framework for taxonomic classification of twenty marine RNA viruses into the family Marnaviridae. Using RNA-dependent RNA polymerase (RdRp) phylogeny and distance-based analyses, we assigned the genera Labyrnavirus and Bacillarnavirus to the family Marnaviridae and created four additional genera in the family: Locarnavirus (four species), Kusarnavirus (one species), Salisharnavirus (four species) and Sogarnavirus (six species). We used pairwise capsid protein comparisons to delineate species within families, with 75 per cent identity as the species demarcation threshold. The family displays high sequence diversities and Jukes–Cantor distances for both the RdRp and capsid genes, suggesting that the classified viruses are not representative of all of the virus diversity within the family and that there are many more extant taxa. Our proposed taxonomic framework provides a sound classification system for this group of viruses that will have broadly applicable principles for other viral groups. It is based on sequence data alone and provides a robust taxonomic framework to include viruses discovered via metagenomic studies, thereby greatly expanding the realm of viruses subject to taxonomic classification.

scholarly journals Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams

2021 ◽  
Vol 12 ◽  
Author(s):  
Patrice Bonny ◽  
Julien Schaeffer ◽  
Alban Besnard ◽  
Marion Desdouits ◽  
Jean Justin Essia Ngang ◽  
...  
Keyword(s):  
De Novo ◽  
Hepatitis A Virus ◽  
Rna Viruses ◽  
Rna Virus ◽  
Zoonotic Transmission ◽  
Taxonomic Assignment ◽  
Virus Diversity ◽  
Health Authorities ◽  
Viral Contaminants ◽  
Quality Filtering

Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.

scholarly journals Meta-transcriptomic comparison of the RNA viromes of the mosquito vectors Culex pipiens and Culex torrentium in northern Europe

2019 ◽  
Author(s):  
John H.-O. Pettersson ◽  
Mang Shi ◽  
John-Sebastian Eden ◽  
Edward C. Holmes ◽  
Jenny C. Hesson
Keyword(s):  
Culex Pipiens ◽  
Rna Viruses ◽  
Rna Virus ◽  
Mosquito Species ◽  
Animal Health ◽  
Northern Europe ◽  
Mosquito Vector ◽  
Tropical Regions ◽  
South Central ◽  
Virus Diversity

AbstractThere is mounting evidence that mosquitoes harbour an extensive diversity of ‘insect-specific’ RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes there is a major knowledge gap on the genetic diversity, evolutionary history, and spread of RNA viruses sampled from mosquitoes in northern latitudes. Here, we determined and compared the RNA virome of two common northern Culex mosquito species, Cx. pipiens and Cx. torrentium, known vectors of West Nile virus and Sindbis virus, respectively, collected in south-central Sweden. Following bulk RNA-sequencing (meta-transcriptomics) of 12 libraries, comprising 120 specimens of Cx. pipiens and 150 specimens of Cx. torrentium, we identified 40 viruses (representing 14 virus families) of which 28 were novel based on phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) protein. Hence, we found similar levels of virome diversity as in mosquitoes sampled from the more biodiverse lower latitudes. Four libraries, all from Cx. torrentium, had a significantly higher abundance of viral reads, spanning ∼7– 36% of the total amount of reads. Many of these viruses were also related to those sampled on other continents, indicative of widespread global movement and/or long host-virus co-evolution. Importantly, although the two mosquito species investigated have overlapping geographical distributions and share many viruses, approximately one quarter of the viruses were only found at a specific location, such that geography must play an important role in shaping the diversity of RNA viruses in Culex mosquitoes.ImportanceRNA viruses are found in all domains of life and all global habitats. However, the factors that determine virome composition and structure within and between organisms are largely unknown. Herein, we characterised RNA virus diversity in two common mosquito vector species, Culex pipiens and Culex torrentium, sampled from northern Europe. Our analysis revealed extensive viral diversity, including 28 novel viruses, and was comparable to the levels of diversity found in other temperate and tropical regions globally. Importantly, as well as harbouring RNA viruses that are closely related to other mosquito-derived viruses sampled in diverse global locations, we also described a number of viruses that are unique to specific sampling locations in Sweden. Hence, these data showed that geographical factors can play an important role in shaping virome structure even at local scales.

scholarly journals A new lineage of segmented RNA viruses infecting animals

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Darren J Obbard ◽  
Mang Shi ◽  
Katherine E Roberts ◽  
Ben Longdon ◽  
Alice B Dennis
Keyword(s):  
Small Rnas ◽  
Rna Viruses ◽  
Rna Virus ◽  
Close Relative ◽  
Metagenomic Sequencing ◽  
Reading Frame ◽  
Virus Identification ◽  
Conserved Sequence ◽  
Virus Diversity ◽  
Close Relatives

Abstract Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.

scholarly journals Revealing RNA virus diversity and evolution in unicellular algae transcriptomes

2021 ◽  
Author(s):  
Justine Charon ◽  
Shauna Murray ◽  
Edward C Holmes
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Virus Species ◽  
Sequencing Project ◽  
Virus Diversity ◽  
Microbial Eukaryotes ◽  
Unicellular Algae ◽  
Positive Sense

Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified 30 new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA Partitiviridae, as well as a single negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.

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