scholarly journals Molecular Characterization of a Novel Wheat-infecting Virus in Family Betaflexiviridae

2021 ◽  
Author(s):  
Jianxiang Wu ◽  
Shuai Fu ◽  
Mengzhu He ◽  
Bingjian Sun ◽  
Xueping Zhou
Keyword(s):  
Triple Gene Block ◽  
International Committee ◽  
Open Reading Frames ◽  
Yellow Mosaic Virus ◽  
Wheat Yellow Mosaic Virus ◽  
Gene Block ◽  
Transmission Electron ◽  
The Family ◽  
Novel Virus

Abstract Wheat plants showing yellow mosaic in leaves and stunting were observed and collected from wheat fields in the Henan Province, China. Analyses of these plants through transmission electron microscopy showed that these plants contained two filamentous virus-like particles of 200–500 nm and 1000–1300 nm long, respectively. RNA-seq result unveiled a co-infection of wheat yellow mosaic virus (WYMV) and an unknown wheat-infecting virus. The complete genome sequence of the unknown virus is 8,410 nucleotide long, excluding its 3’ end poly (A) tail. This unknown virus has six open reading frames (ORFs). The ORF1 encodes a putative viral replication-associated protein, and the ORF2, 3 and 4 encode the triple gene block (TGB) proteins. The ORF5 and 6 encode the capsid protein (CP) and a protein with unknown function, respectively. Phylogenetic relationship analyses showed that this novel virus is evolutionarily related to viruses in the subfamily Quinvirinae, family Betaflexiviridae. It is, however, distinctly different from the viruses in other genera. Based on the species and genus demarcation criteria set by the International Committee on Taxonomy of Viruses (ICTV), we tentatively name this novel virus as wheat yellow stunt-associated betaflexivirus (WYSaBV). We also propose WYSaBV as a new member in a new genus in the family Betaflexiviridae.

scholarly journals A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

2018 ◽  
Author(s):  
Thanuja Thekke-Veetil ◽  
Thien Ho ◽  
Joseph D. Postman ◽  
Robert R. Martin ◽  
Ioannis E. Tzanetakis
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Methyl Transferase ◽  
Gene Block ◽  
New Family ◽  
Molecular Features ◽  
Genome Features ◽  
Novel Virus

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus tentatively named as blackcurrant virus A (BCVA) has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase and RNA dependent RNA polymerase (RdRp) domains. The other four putative proteins exhibit no significant homology to other virus proteins. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement. Phylogenetic analysis using replicase conserved motifs loosely placed BCVA within the Betaflexiviridae whereas it was evolutionarily distant to existing members of the family when using the putative TGBp 1-like and coat protein sequences. Our analysis strongly suggests that BCVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family in the order Tymovirales.

scholarly journals ICTV Virus Taxonomy Profile: Alphaflexiviridae

2020 ◽  
Vol 101 (7) ◽  
pp. 699-700 ◽  
Author(s):  
Jan F. Kreuze ◽  
Anna Maria Vaira ◽  
Wulf Menzel ◽  
Thierry Candresse ◽  
Sergey K. Zavriev ◽  
...  
Keyword(s):  
Triple Gene Block ◽  
International Committee ◽  
Replication Proteins ◽  
Virus Taxonomy ◽  
Long Distance ◽  
Gene Block ◽  
The Family ◽  
Single Exception ◽  
Distinct Lineage ◽  
Long Distance Movement

The family Alphaflexiviridae includes viruses with flexuous filamentous virions that are 470–800 nm in length and 12–13 nm in diameter. Alphaflexiviruses have a single-stranded, positive-sense RNA genome of 5.5–9 kb. They infect plants and plant-infecting fungi. They share a distinct lineage of alphavirus-like replication proteins that is unusual in lacking any recognized protease domain. With a single exception, cell-to-cell and long-distance movement is facilitated by triple gene block proteins in plant-infecting genera. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Alphaflexiviridae, which is available at www.ictv.global/report/alphaflexiviridae.

Occurrence and distribution of Actinidia viruses in Shaanxi Province of China

Plant Disease ◽  
2020 ◽  
Author(s):  
Zhao Lei ◽  
Mengji Cao ◽  
Qianru Huang ◽  
Yicheng Wang ◽  
Jiaxiu Sun ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Virus Detection ◽  
International Committee ◽  
Shaanxi Province ◽  
Transmission Electron ◽  
Viral Particles ◽  
The Family ◽  
Novel Virus ◽  
Actinidia Spp ◽  
Yellowing Virus

Kiwifruit (Actinidia spp.) is an economically important fruit crop globally. China is the largest kiwifruit-growing country in the world, and Shaanxi Province is the major kiwifruit-growing region in China. A systematic survey detected various symptoms in kiwifruit plants grown in a commercial kiwifruit field in Shaanxi Province. Samples were collected from kiwifruit plants showing symptoms and used for virus detection by high-throughput sequencing. In addition to ten known kiwifruit viruses, three new viruses were detected and tentatively named Actinidia yellowing ringspot virus (AYRSpV), Actinidia yellowing virus 1 (AcYV1) and Actinidia yellowing virus 2 (AcYV2). The genome sequences of the three new viruses and four known viruses were determined. Based on the demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV), AYRSpV might be a new member of the genus Ilarvirus in the family Bromoviridae, AcYV1 might be a new virus of the genus Waikavirus in the family Secoviridae, and AcYV2 might be a novel virus in the family Tombusviridae. Spherical viral particles were found in the samples infected with AYRSpV, AcYV1 and AcYV2 by transmission electron microscopy. Further analysis showed that all thirteen viruses can infect both A. deliciosa and A. chinensis, but the incidences of these infections vary among different kiwifruit cultivars in different regions. These results provide valuable information for understanding the viriome of kiwifruit in China.

scholarly journals A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 406 ◽  
Author(s):  
Thanuja Thekke-Veetil ◽  
Thien Ho ◽  
Joseph Postman ◽  
Robert Martin ◽  
Ioannis Tzanetakis
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Methyl Transferase ◽  
Gene Block ◽  
New Family ◽  
Molecular Features ◽  
Genome Features ◽  
Novel Virus

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.

scholarly journals Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing

Plants ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 167 ◽  
Author(s):  
Gonçalo Silva ◽  
Moritz Bömer ◽  
Ajith I. Rathnayake ◽  
Steven O. Sewe ◽  
Paul Visendi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Virus Species ◽  
Gene Block ◽  
Full Diversity ◽  
Putative Coat Protein ◽  
The Family ◽  
International Distribution

To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus “yam virus Y” (YVY). Twenty-three of the samples in which YVY was detected showed mosaic and chlorotic leaf symptoms, but Yam mosaic virus was also detected in these samples. Complete genome sequences of two YVY viral isolates were assembled and found to contain five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further work is needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production.

Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

2021 ◽  
Author(s):  
Yang Sun ◽  
Yan qiong Li ◽  
Wen han Dong ◽  
Ai li Sun ◽  
Ning wei Chen ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Rna Virus ◽  
Dsrna Virus ◽  
Open Reading Frames ◽  
The Family ◽  
Significant Amino Acid Sequence ◽  
Overlapping Open Reading Frames ◽  
Significant Amino Acid ◽  
Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

scholarly journals The Potato Virus X TGBp2 Protein Plays Dual Functional Roles in Viral Replication and Movement

2018 ◽  
Vol 93 (5) ◽  
Author(s):  
Xiaoyun Wu ◽  
Jiahui Liu ◽  
Mengzhu Chai ◽  
Jinhui Wang ◽  
Dalong Li ◽  
...  
Keyword(s):  
Triple Gene Block ◽  
Potato Virus X ◽  
Plant Viruses ◽  
Open Reading Frames ◽  
Movement Proteins ◽  
Gene Block ◽  
Functional Roles ◽  
Viral Rdrp ◽  
Dual Functional ◽  
Intercellular Movement

ABSTRACTPlant viruses usually encode one or more movement proteins (MP) to accomplish their intercellular movement. A group of positive-strand RNA plant viruses requires three viral proteins (TGBp1, TGBp2, and TGBp3) that are encoded by an evolutionarily conserved genetic module of three partially overlapping open reading frames (ORFs), termed the triple gene block (TGB). However, how these three viral movement proteins function cooperatively in viral intercellular movement is still elusive. Using a novelin vivodouble-stranded RNA (dsRNA) labeling system, we showed that the dsRNAs generated by potato virus X (PVX) RNA-dependent RNA polymerase (RdRp) are colocalized with viral RdRp, which are further tightly covered by “chain mail”-like TGBp2 aggregates and localizes alongside TGBp3 aggregates. We also discovered that TGBp2 interacts with the C-terminal domain of PVX RdRp, and this interaction is required for the localization of TGBp3 and itself to the RdRp/dsRNA bodies. Moreover, we reveal that the central and C-terminal hydrophilic domains of TGBp2 are required to interact with viral RdRp. Finally, we demonstrate that knockout of the entire TGBp2 or the domain involved in interacting with viral RdRp attenuates both PVX replication and movement. Collectively, these findings suggest that TGBp2 plays dual functional roles in PVX replication and intercellular movement.IMPORTANCEMany plant viruses contain three partially overlapping open reading frames (ORFs), termed the triple gene block (TGB), for intercellular movement. However, how the corresponding three proteins coordinate their functions remains obscure. In the present study, we provided multiple lines of evidence supporting the notion that PVX TGBp2 functions as the molecular adaptor bridging the interaction between the RdRp/dsRNA body and TGBp3 by forming “chain mail”-like structures in the RdRp/dsRNA body, which can also enhance viral replication. Taken together, our results provide new insights into the replication and movement of PVX and possibly also other TGB-containing plant viruses.

Characterization of the Q.Ymym region on wheat chromosome 2D associated with wheat yellow mosaic virus resistance

2019 ◽  
Vol 139 (1) ◽  
pp. 93-106 ◽  
Author(s):  
Fuminori Kobayashi ◽  
Hisayo Kojima ◽  
Tsuyoshi Tanaka ◽  
Mika Saito ◽  
Chikako Kiribuchi‐Otobe ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Virus Resistance ◽  
Wheat Chromosome ◽  
Yellow Mosaic Virus ◽  
Wheat Yellow Mosaic Virus

scholarly journals Genomic Analyses of Cherry Rusty Mottle Group and Cherry Twisted Leaf-Associated Viruses Reveal a Possible New Genus Within the FamilyBetaflexiviridae

2015 ◽  
Vol 105 (3) ◽  
pp. 399-408 ◽  
Author(s):  
D. E. V. Villamor ◽  
J. Susaimuthu ◽  
K. C. Eastwell
Keyword(s):  
New Genus ◽  
High Throughput Sequencing ◽  
Prunus Avium ◽  
Triple Gene Block ◽  
Mottle Virus ◽  
Virus Species ◽  
Gene Block ◽  
Green Ring ◽  
The Family ◽  
Prunus Spp

It is demonstrated that closely related viruses within the family Betaflexiviridae are associated with a number of diseases that affect sweet cherry (Prunus avium) and other Prunus spp. Cherry rusty mottle-associated virus (CRMaV) is correlated with the appearance of cherry rusty mottle disease (CRMD), and Cherry twisted leaf-associated virus (CTLaV) is linked to cherry twisted leaf disease (CTLD) and apricot ringpox disease (ARPD). Comprehensive analysis of previously reported full genomic sequences plus those determined in this study representing isolates of CTLaV, CRMaV, Cherry green ring mottle virus, and Cherry necrotic rusty mottle virus revealed segregation of sequences into four clades corresponding to distinct virus species. High-throughput sequencing of RNA from representative source trees for CRMD, CTLD, and ARPD did not reveal additional unique virus sequences that might be associated with these diseases, thereby further substantiating the association of CRMaV and CTLaV with CRMD and CTLD or ARPD, respectively. Based on comparison of the nucleotide and amino acid sequence identity values, phylogenetic relationships with other triple-gene block-coding viruses within the family Betaflexiviridae, genome organization, and natural host range, a new genus (Robigovirus) is suggested.

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