Novel positive-sense single-stranded RNA virus related to alphavirus-like viruses from Fusarium graminearum

2019 ◽  
Vol 165 (2) ◽  
pp. 487-490
Author(s):  
Xing Zhang ◽  
Haotian Zhang ◽  
Dongfang Ma ◽  
Huaigu Chen ◽  
Wei Li
Keyword(s):  
Fusarium Graminearum ◽  
Rna Virus ◽  
Positive Sense

scholarly journals Origins and Evolution of the Global RNA Virome

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Yuri I. Wolf ◽  
Darius Kazlauskas ◽  
Jaime Iranzo ◽  
Adriana Lucía-Sanz ◽  
Jens H. Kuhn ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Rna Viruses ◽  
Rna Virus ◽  
Phylogenomic Analysis ◽  
Rna Helicases ◽  
Sequence Alignments ◽  
Recent Advances ◽  
Wide Range ◽  
Positive Sense ◽  
Dsrna Viruses

ABSTRACTViruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas −RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.IMPORTANCEThe majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.

scholarly journals Novel RNA Virus Genome Discovered in Ghost Ants (Tapinoma melanocephalum) from Hawaii

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Laura E. Brettell ◽  
Gideon J. Mordecai ◽  
Purnima Pachori ◽  
Stephen J. Martin
Keyword(s):  
Amino Acids ◽  
Genome Sequence ◽  
Rna Virus ◽  
Virus Genome ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Tapinoma Melanocephalum ◽  
Positive Sense

ABSTRACT Here, we report the full-genome sequence of Milolii virus, a novel single-stranded (positive-sense) RNA virus discovered from Tapinoma melanocephalum ants in Hawaii. The genome is 10,475 nucleotides long, encoding a polyprotein of 3,304 amino acids.

scholarly journals NOVEL CORONAVIRUS (2019-nCoV): DISEASE BRIEFINGS

2020 ◽  
pp. 22-27
Author(s):  
KANAAN AL-TAMEEMI ◽  
RAIAAN KABAKLI
Keyword(s):  
Public Health ◽  
Potential Risk ◽  
Rna Virus ◽  
Viral Pneumonia ◽  
The Novel ◽  
Strategic Objectives ◽  
Positive Sense ◽  
Novel Coronavirus

Coronavirus (CoV) (2019‐nCoV) is a large, enveloped, positive-sense, single-stranded RNA virus. The abnormal outbreak of 2019‐nCoV in Wuhan warns of the risk of CoV (2019‐nCoV) to public health which causes viral pneumonia outbreak. In our review, we will discuss the biology of CoVs and the potential risk of the novel CoV (2019‐nCoV) and guide us to strategic objectives for controlling the virus.

scholarly journals Autophagy is involved in assisting the replication of Bamboo mosaic virus in Nicotiana benthamiana

2019 ◽  
Vol 70 (18) ◽  
pp. 4657-4670 ◽  
Author(s):  
Ying-Ping Huang ◽  
Ying-Wen Huang ◽  
Yung-Jen Hsiao ◽  
Siou-Cen Li ◽  
Yau-Huei Hsu ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Fluorescent Protein ◽  
Rna Virus ◽  
Critical Role ◽  
Viral Rna ◽  
Autophagosome Formation ◽  
Orange Fluorescent Protein ◽  
Positive Sense ◽  
Trigger Cell Death

Abstract Autophagy plays a critical role in plants under biotic stress, including the response to pathogen infection. We investigated whether autophagy-related genes (ATGs) are involved in infection with Bamboo mosaic virus (BaMV), a single-stranded positive-sense RNA virus. Initially, we observed that BaMV infection in Nicotiana benthamiana leaves upregulated the expression of ATGs but did not trigger cell death. The induction of ATGs, which possibly triggers autophagy, increased rather than diminished BaMV accumulation in the leaves, as revealed by gene knockdown and transient expression experiments. Furthermore, the inhibitor 3-methyladenine blocked autophagosome formation and the autophagy inducer rapamycin, which negatively and positively affected BaMV accumulation, respectively. Pull-down experiments with an antibody against orange fluorescent protein (OFP)-NbATG8f, an autophagosome marker protein, showed that both plus- and minus-sense BaMV RNAs could associate with NbATG8f. Confocal microscopy revealed that ATG8f-enriched vesicles possibly derived from chloroplasts contained both the BaMV viral RNA and its replicase. Thus, BaMV infection may induce the expression of ATGs possibly via autophagy to selectively engulf a portion of viral RNA-containing chloroplast. Virus-induced vesicles enriched with ATG8f could provide an alternative site for viral RNA replication or a shelter from the host silencing mechanism.

scholarly journals Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements

2017 ◽  
Vol 46 (5) ◽  
pp. 2573-2584 ◽  
Author(s):  
Kyle E Watters ◽  
Krishna Choudhary ◽  
Sharon Aviran ◽  
Julius B Lucks ◽  
Keith L Perry ◽  
...  
Keyword(s):  
Rna Virus ◽  
Structural Elements ◽  
Rna Structures ◽  
Selection Pressures ◽  
Positive Sense

scholarly journals Complete Genome Sequence of a Fusarium graminearum Double-Stranded RNA Virus in a Newly Proposed Family, Alternaviridae

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
Hao He ◽  
Xiaoguang Chen ◽  
Pengfei Li ◽  
Dewen Qiu ◽  
Lihua Guo
Keyword(s):  
Phylogenetic Analysis ◽  
Fusarium Graminearum ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Phytopathogenic Fungus ◽  
Double Stranded Rna ◽  
First Report ◽  
The Family

ABSTRACT We describe here a double-stranded RNA mycovirus, termed Fusarium graminearum alternavirus 1 (FgAV1/AH11), from the isolate AH11 of the phytopathogenic fungus F. graminearum . Phylogenetic analysis showed that FgAV1/AH11 belongs to a newly proposed family, Alternaviridae . This is the first report of a mycovirus in the family Alternaviridae that infects F. graminearum .

scholarly journals Activation of CXCL-8 Transcription by Hepatitis E Virus ORF-1 via AP-1

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Zhubing Li ◽  
Lu Chen ◽  
Qiang Liu
Keyword(s):  
Transcriptional Activation ◽  
Promoter Activity ◽  
Hepatitis E Virus ◽  
Rna Virus ◽  
Ectopic Expression ◽  
Hepatitis E ◽  
Genomic Rna ◽  
Host Interactions ◽  
Positive Sense ◽  
Binding Sequence

Hepatitis E virus (HEV) is a small nonenveloped single-stranded positive-sense RNA virus and is one of the major causes for acute hepatitis worldwide. CXCL-8 is a small multifunctional proinflammatory chemokine. It was reported recently that HEV infection significantly upregulates CXCL-8 gene expression. In this study, we investigated the mechanism of HEV-induced CXCL-8 transcriptional activation. Using CXCL-8 promoter reporters of different lengths ranging from −1400 to −173, we showed that −173 promoter has the highest promoter activity in the presence of HEV genomic RNA, indicating that the −173 promoter contains sequences responsible for CXCL-8 activation by HEV. Ectopic expression of the ORF-1 protein can upregulate the −173 CXCL-8 promoter activity. In contrast, expression of the ORF-2 protein suppresses the CXCL-8 promoter activity and expression of the ORF-3 protein has no effect on the CXCL-8 promoter activity. We further showed that AP-1 is required for CXCL-8 activation because neither HEV genomic RNA nor the ORF-1 protein can upregulate the −173 CXCL-8 promoter in the absence of the AP-1 binding sequence. Taken together, our results showed that HEV and HEV ORF-1 protein activate the CXCL-8 promoter via AP-1. This novel function of HEV ORF-1 protein should contribute to our understanding of HEV-host interactions and HEV-associated pathogenesis.

scholarly journals QUASISPECIES FEATURE IN SARS-CoV-2

2021 ◽  
Vol 9 (5) ◽  
pp. 591-597
Author(s):  
Bramhadev Pattnaik ◽  
◽  
Kuralayanapalya Puttahonnappa Suresh ◽  
Rajangam Sridevi ◽  
Mahendra P. Yadav ◽  
...  
Keyword(s):  
Genetic Heterogeneity ◽  
Viral Genome ◽  
Neutralizing Antibodies ◽  
Human Population ◽  
Rna Virus ◽  
Base Population ◽  
Virus Population ◽  
Control Programs ◽  
Positive Sense ◽  
Selection Of

Since the identification of the SARS-CoV-2, genus Beta- Coronavirus, in January 2020, the virus quickly spread in less than 3 months to all continents with a susceptible human population of about a 7.9billion, and still in active circulation. In the process, it has accumulated mutations leading to genetic diversity. Regular emergence of variants of concern/significance in different ecology shows genetic heterogeneity in the base population of SARS-CoV-2 that is continuously expanding with the passage of the virus in the vast susceptible human population. Natural selection of mutant occurs frequently in a positive sense (+) single-stranded (ss) RNA virus upon replication in the host. The Pressure of sub-optimal levels of virus-neutralizing antibodies and also innate immunity influence the process of genetic/ antigenic selection. The fittest of the mutants, that could be more than one, propagate and emerge as variants. The existence of different lineages, clades, and strains, as well as genetic heterogeneity of plaque purified virus population, justifies SARS-CoV-2 as ‘Quasispecies’ that refers to swarms of mutant sequences generated during replication of the viral genome, and all mutant sequences may not lead to virion. Viruses having a quasispecies nature may end up with progressive antigenic changes leading to antigenic plurality that is driven by ecology, and this phenomenon challenges vaccination-based control programs.

scholarly journals Molecular Characterization of a Novel Virga-like Virus Isolated From Wheat

2021 ◽  
Author(s):  
Hua Li ◽  
Jun Guo ◽  
ZhongHua Zhao ◽  
Zhuangxin Ye ◽  
Jianping Chen ◽  
...  
Keyword(s):  
Rna Virus ◽  
Open Reading Frames ◽  
Polya Tail ◽  
Rna Dependent Rna Polymerase ◽  
Future Studies ◽  
Putative Protein ◽  
Host Growth ◽  
Positive Sense ◽  
Reading Frames

Abstract In this work, we report the isolation of a novel positive-sense single strand RNA virus from wheat, tentatively named Triticum aestivum-associated virga-like virus 1 (TaAVLV1). Further characterization revealed that the complete genome of TaAVLV1 was divided into two segments, RNA1 and RNA2, which were 3530 and 3466 nt long, excluding the polyA tail. These segments contained two open reading frames (ORFs). The ORF in RNA1 encoded an RNA-dependent RNA polymerase (RdRp), while the ORF in RNA2 encoded a putative protein carrying MET and HEL domains. Phylogenetic analysis based on the RdRp protein of each representative genus of Virgaviridae placed TaAVLV1 in the unclassified Virgaviridae clade of the Virgaviridae family. To our knowledge, this is the first report of virga-like virus isolated from wheat. Future studies will be conducted to examine its effect on host growth and development.

scholarly journals Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

2020 ◽  
Author(s):  
Nicholas C. Huston ◽  
Han Wan ◽  
Rafael de Cesaris Araujo Tavares ◽  
Craig Wilen ◽  
Anna Marie Pyle
Keyword(s):  
Secondary Structure ◽  
Rna Virus ◽  
Genomic Structure ◽  
Structural Features ◽  
Evolutionary Analysis ◽  
Rna Structures ◽  
Genomic Context ◽  
Positive Sense ◽  
Folded Rna

SummarySARS-CoV-2 is the positive-sense RNA virus that causes COVID-19, a disease that has triggered a major human health and economic crisis. The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form stable RNA structures and yet, as much as 97% of its 30 kilobases have not been structurally explored in the context of a viral infection. Our limited knowledge of SARS-CoV-2 genomic architecture is a fundamental limitation to both our mechanistic understanding of coronavirus life cycle and the development of COVID-19 RNA-based therapeutics. Here, we apply a novel long amplicon strategy to determine for the first time the secondary structure of the SARS-CoV-2 RNA genome probed in infected cells. In addition to the conserved structural motifs at the viral termini, we report new structural features like a conformationally flexible programmed ribosomal frameshifting pseudoknot, and a host of novel RNA structures, each of which highlights the importance of studying viral structures in their native genomic context. Our in-depth structural analysis reveals extensive networks of well-folded RNA structures throughout Orf1ab and reveals new aspects of SARS-CoV-2 genome architecture that distinguish it from other single-stranded, positive-sense RNA viruses. Evolutionary analysis of RNA structures in SARS-CoV-2 shows that several features of its genomic structure are conserved across beta coronaviruses and we pinpoint individual regions of well-folded RNA structure that merit downstream functional analysis. The native, complete secondary structure of SAR-CoV-2 presented here is a roadmap that will facilitate focused studies on mechanisms of replication, translation and packaging, and guide the identification of new RNA drug targets against COVID-19.

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