scholarly journals Description of a Novel Monopartite Geminivirus and Its Defective Subviral Genome in Grapevine

2017 ◽  
Vol 107 (2) ◽  
pp. 240-251 ◽  
Author(s):  
Maher Al Rwahnih ◽  
Olufemi J. Alabi ◽  
Nathaniel M. Westrick ◽  
Deborah Golino ◽  
Adib Rowhani
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
The Novel ◽  
The Family ◽  
Circular Ssdna ◽  
Novel Virus ◽  
Full Length Genome ◽  
Nonanucleotide Sequence ◽  
Complementary Sense ◽  
Viral Genomic Sequence

A novel virus was detected in grapevines by Illumina sequencing during the screening of two table grape (Vitis vinifera) accessions, cultivars Black Beet and Nagano Purple, from South Korea. The monopartite circular ssDNA genome sequence was subsequently confirmed by rolling cycle amplification, cloning and Sanger sequencing. The complete viral genomic sequence from both accessions ranged from 2,903 to 2,907 nucleotides in length and contained the conserved nonanucleotide sequence TAATATT↓AC and other sequence features typical of the family Geminiviridae, including two predicted sense and four complementary-sense open reading frames. Phylogenetic analysis placed the novel virus in a unique taxon within the family Geminiviridae. A naturally occurring defective subviral DNA was also discovered. This defective DNA molecule carried a deletion of approximately 46% of the full-length genome. Both the genomic and defective DNA molecules were graft-transmissible although no disease is yet correlated with their occurrence in Vitis spp. The tentative names Grapevine geminivirus A (GGVA) and GGVA defective DNA (GGVA D-DNA) are proposed. PCR assays developed using primers designed in the coat protein gene led to the detection of GGVA in 1.74% of 1,262 vines derived from 15 grapevine cultivars from six countries across three continents.

scholarly journals A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Thomas W. Allain ◽  
Grant D. Stentiford ◽  
David Bass ◽  
Donald C. Behringer ◽  
Jamie Bojko
Keyword(s):  
Penaeus Monodon ◽  
Penaeid Shrimp ◽  
Open Reading Frames ◽  
The Novel ◽  
Dna Viruses ◽  
Gene Synteny ◽  
Double Stranded Dna ◽  
The Family ◽  
Novel Virus ◽  
Dikerogammarus Haemobaphes

Abstract The Nudiviridae are a family of large double-stranded DNA viruses that infects the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus (Nudiviridae).

scholarly journals Tomato leaf curl Gujarat virus, a New Begomovirus Species Causing a Severe Leaf Curl Disease of Tomato in Varanasi, India

2003 ◽  
Vol 93 (12) ◽  
pp. 1485-1495 ◽  
Author(s):  
S. Chakraborty ◽  
P. K. Pandey ◽  
M. K. Banerjee ◽  
G. Kalloo ◽  
C. M. Fauquet
Keyword(s):  
Tomato Leaf ◽  
Open Reading Frames ◽  
New Delhi ◽  
Tomato Plants ◽  
The Family ◽  
Infected Tomato ◽  
Tomato Leaf Curl ◽  
Full Length Genome ◽  
Severe Leaf ◽  
Leaf Curl

The biological and molecular properties of Tomato leaf curl Gujarat virus from Varanasi, India (ToLCGV-[Var]) were characterized. ToLCGV-[Var] could be transmitted by grafting and through whitefly transmission in a persistent manner. The full-length genome of DNA-A and DNA-B of ToLCGV-[Var] was cloned in pUC18. Sequence analysis revealed that DNA-A (AY190290) is 2,757 bp and DNA-B (AY190291) is 2,688 bp in length. ToLCGV-[Var] could infect and cause symptoms in tomato, pepper, Nicotiana benthamiana, and N. tabacum when partial tandem dimeric constructs of DNA-A and DNA-B were co-inoculated by particle bombardment. DNA-A alone also is infectious, but symptoms were milder and took longer to develop. ToLCGV-Var virus can be transmitted through sap inoculation from infected tomato plants to the above-mentioned hosts causing the same symptoms. Open reading frames (ORFs) in both DNA-A and DNA-B are organized similarly to those in other begomoviruses. DNA-A and DNA-B share a common region of 155 bp with only 60% sequence identity. DNA-B of ToLCGV-[Var] shares overall 80% identity with DNA-B of Tomato leaf curl New Delhi virus-Severe (ToLCNDV-Svr) and 75% with ToLCNDV-[Lucknow] (ToLCNDV-[Luc]). Comparison of DNA-A sequence with different begomoviruses indicates that ToLCGV-[Var] shares 84% identity with Tomato leaf curl Karnataka virus (ToLCKV) and 66% with ToLCNDV-Svr. ToLCGV-[Var] shares a maximum of 98% identity with another isolate of the same region (ToLCGV-[Mir]; AF449999) and 97% identity with one isolate from Gujarat (ToLCGV-[Vad]; AF413671). All three viruses belong to the same species that is distinct from all the other geminivirus species described so far in the genus Begomovirus of the family Geminiviridae. The name Tomato leaf curl Gujarat virus is proposed because the first sequence was taken from an isolate of Gujarat, India.

scholarly journals Use of hydroxychloroquine for novel corona virus infection in India: is it ethically justifiable?

2020 ◽  
Vol 7 (6) ◽  
pp. 2426
Author(s):  
Ramesh Verma ◽  
Vinod Chayal ◽  
Meenakshi Kalhan ◽  
Rohit Dhaka ◽  
Ginni Agrawal ◽  
...  
Keyword(s):  
Public Health ◽  
Public Health Emergency ◽  
World Health ◽  
The Novel ◽  
Wuhan City ◽  
First Case ◽  
The Family ◽  
Novel Virus ◽  
Health Organization ◽  
Corona Viruses

Coronavirus disease is caused by a novel virus belonging to the family of corona viruses similar to severe acute respiratory syndrome (SARS) and  name given to the novel virus as SARS Coronavirus- 2 (SARS-CoV-2) and the disease was named as COVID-19 on 11th February 2020 by World Health Organization (WHO). First case of this infection was reported in December 2019 in Wuhan city of China and after that it spread globally.3 On 30th January 2020, WHO declared this disease as Public Health Emergency of International Concern (PHEIC) and on 11th March 2020, WHO declared it as a pandemic when the infection was reported from all six WHO regions.

scholarly journals Complete Genome Sequence of Macrobrachium rosenbergii Golda Virus (MrGV) from China

Animals ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 27
Author(s):  
Fanzeng Meng ◽  
Yiting Wang ◽  
Guohao Wang ◽  
Tao Hu ◽  
La Xu ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Genomic Sequence ◽  
Clinical Signs ◽  
Macrobrachium Rosenbergii ◽  
Open Reading Frames ◽  
Freshwater Prawn ◽  
Ribosomal Frameshift ◽  
Giant Freshwater Prawn ◽  
The Family ◽  
Reading Frames

In a meta-transcriptome study of the giant freshwater prawn Macrobrachium rosenbergii sampled in 2018 from a hatchery, we identified a variant of Macrobrachium rosenbergii golda virus (MrGV) in postlarvae without clinical signs. The virus belongs to the family Roniviridae, and the genome of this MrGV variant, Mr-18, consisted of 28,957 nucleotides, including 4 open reading frames (ORFs): (1) ORF1a, encoding a 3C-like protein (3CLP) (4933 aa); (2) ORF1b, encoding a replicase polyprotein (2877 aa); (3) ORF2, encoding a hypothetical nucleocapsid protein (125 aa); and (4) ORF3, encoding a glycoprotein (1503 aa). ORF1a overlaps with ORF1b with 40 nucleotides, where a −1 ribosomal frameshift with slippage sequence 5′-G14925GGUUUU14931-3′ produces the pp1ab polyprotein. The genomic sequence of Mr-18 shared 97.80% identity with MrGV LH1-2018 discovered in Bangladesh. The amino acid sequence identities between them were 99.30% (ORF1a), 99.60% (ORF1b), 100.00% (ORF2), and 99.80% (ORF3), respectively. Phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) proteins revealed that they clustered together and formed a separate cluster from the genus Okavirus. The finding of MrGV in China warrants further studies to determine its pathogenicity and prevalence within the region.

scholarly journals Genomic Sequence of Spodoptera frugiperda Ascovirus 1a, an Enveloped, Double-Stranded DNA Insect Virus That Manipulates Apoptosis for Viral Reproduction

2006 ◽  
Vol 80 (23) ◽  
pp. 11791-11805 ◽  
Author(s):  
Dennis K. Bideshi ◽  
Marie-Véronique Demattei ◽  
Florence Rouleux-Bonnin ◽  
Karine Stasiak ◽  
Yeping Tan ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
Genomic Sequence ◽  
Open Reading Frames ◽  
The Novel ◽  
Fatty Acid Elongase ◽  
Dna Viruses ◽  
Origin And Evolution ◽  
Iridescent Virus ◽  
Double Stranded Dna ◽  
New Hosts

ABSTRACT Ascoviruses (family Ascoviridae) are double-stranded DNA viruses with circular genomes that attack lepidopterans, where they produce large, enveloped virions, 150 by 400 nm, and cause a chronic, fatal disease with a cytopathology resembling that of apoptosis. After infection, host cell DNA is degraded, the nucleus fragments, and the cell then cleaves into large virion-containing vesicles. These vesicles and virions circulate in the hemolymph, where they are acquired by parasitic wasps during oviposition and subsequently transmitted to new hosts. To develop a better understanding of ascovirus biology, we sequenced the genome of the type species Spodoptera frugiperda ascovirus 1a (SfAV-1a). The genome consisted of 156,922 bp, with a G+C ratio of 49.2%, and contained 123 putative open reading frames coding for a variety of enzymes and virion structural proteins, of which tentative functions were assigned to 44. Among the most interesting enzymes, due to their potential role in apoptosis and viral vesicle formation, were a caspase, a cathepsin B, several kinases, E3 ubiquitin ligases, and especially several enzymes involved in lipid metabolism, including a fatty acid elongase, a sphingomyelinase, a phosphate acyltransferase, and a patatin-like phospholipase. Comparison of SfAV-1a proteins with those of other viruses showed that 10% were orthologs of Chilo iridescent virus proteins, the highest correspondence with any virus, providing further evidence that ascoviruses evolved from a lepidopteran iridovirus. The SfAV-1a genome sequence will facilitate the determination of how ascoviruses manipulate apoptosis to generate the novel virion-containing vesicles characteristic of these viruses and enable study of their origin and evolution.

scholarly journals Molecular Characterization of A Novel Victorivirus Infecting Corynespora Cassiicola

2021 ◽  
Author(s):  
Mingming Liu ◽  
Yunxia Ni ◽  
Hui Zhao ◽  
Xintao Liu ◽  
Min Jia ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Corynespora Cassiicola ◽  
Rna Dependent Rna Polymerase ◽  
The Family ◽  
Fungal Viruses ◽  
Reading Frames

Abstract One victorivirus was detected in the isolate of Corynespora cassiicola strains 20180909-03, which was named Corynespora cassiicola victorivirus 1 (CcVV1). The whole-genome sequence of the virus was sequenced and identified. The CcVV1 genome is 5140 nt and contains 56.87%GC with two large open reading frames (ORFs) overlapping at the tetranucleotide AUGA. The two ORFs were predicted to encode coat protein (CP) and RNA-dependent RNA polymerase (RdRp) respectively, which were conservative in dsRNA fungal viruses of the family Totiviridae. Conservative domains comparison and phylogenetic analysis of the deduced amino acid sequence of RdRp and CP showed that CcVV1 was a new virus of the Victorivirus genus. As far as we know, it is the first report of a genomic sequence of the genus Victorivirus infecting Corynespora cassiicola.

scholarly journals Complete Genomic Sequence of Bacteriophage φEcoM-GJ1, a Novel Phage That Has Myovirus Morphology and a Podovirus-Like RNA Polymerase

2007 ◽  
Vol 74 (2) ◽  
pp. 516-525 ◽  
Author(s):  
Nidham Jamalludeen ◽  
Andrew M. Kropinski ◽  
Roger P. Johnson ◽  
Erika Lingohr ◽  
Josée Harel ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Genomic Sequence ◽  
Open Reading Frames ◽  
Lytic Phage ◽  
E Coli ◽  
The Family ◽  
Contractile Tail ◽  
Single Subunit ◽  
Reading Frames ◽  
Tail Fibers

ABSTRACT The complete genome of φEcoM-GJ1, a lytic phage that attacks porcine enterotoxigenic Escherichia coli of serotype O149:H10:F4, was sequenced and analyzed. The morphology of the phage and the identity of the structural proteins were also determined. The genome consisted of 52,975 bp with a G+C content of 44% and was terminally redundant and circularly permuted. Seventy-five potential open reading frames (ORFs) were identified and annotated, but only 29 possessed homologs. The proteins of five ORFs showed homology with proteins of phages of the family Myoviridae, nine with proteins of phages of the family Podoviridae, and six with proteins of phages of the family Siphoviridae. ORF 1 encoded a T7-like single-subunit RNA polymerase and was preceded by a putative E. coli σ70-like promoter. Nine putative phage promoters were detected throughout the genome. The genome included a tRNA gene of 95 bp that had a putative 18-bp intron. The phage morphology was typical of phages of the family Myoviridae, with an icosahedral head, a neck, and a long contractile tail with tail fibers. The analysis shows that φEcoM-GJ1 is unique, having the morphology of the Myoviridae, a gene for RNA polymerase, which is characteristic of phages of the T7 group of the Podoviridae, and several genes that encode proteins with homology to proteins of phages of the family Siphoviridae.

scholarly journals Molecular Characterization of the Complete Coding Sequence of Olive Leaf Yellowing-Associated Virus

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1272
Author(s):  
Ana Belén Ruiz-García ◽  
Thierry Candresse ◽  
Celia Canales ◽  
Félix Morán ◽  
Carlos Machado de Oliveira ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Olive Tree ◽  
Open Reading Frames ◽  
Olive Leaf ◽  
Coding Sequence ◽  
The Family ◽  
Leaf Yellowing ◽  
Yellowing Disease

Genome organization and phylogenetic relationships of olive leaf yellowing-associated virus (OLYaV) with other members of the Closteroviridae family were determined. The complete coding sequence of OLYaV was obtained by high throughput sequencing of total RNA from a 35-year-old olive tree (cv. Zarzaleña) from Brazil, showing olive leaf yellowing disease and deformations in the wood. This represents the first report of OLYaV in this country. A genomic sequence of 16,700 nt containing 11 open reading frames (ORFs) was recovered, representing the complete virus coding capacity. The knowledge of the nucleotide sequence of the genome including the gene that codes the coat protein will facilitate the development of diagnostic tests, which are limited so far to PCR-based methods targeting the HSP70h gene. Interestingly, a thaumatin-like protein (ORF2), previously reported in other unassigned viruses in the Closteroviridae family, persimmon virus B and actidinia virus 1, was identified in the OLYaV genome. Phylogenetic analysis of shared proteins (ORF1a, ORF1b, HSP70h, HSP90h and CP) with all members of the Closteroviridae family provides new insight into the taxonomic position of these three closteroviruses and suggests they could represent a new genus in the family.

scholarly journals Identification and genomic characterization of a novel human torque teno virus of 3.2 kb

2007 ◽  
Vol 88 (7) ◽  
pp. 1939-1944 ◽  
Author(s):  
Masashi Ninomiya ◽  
Tsutomu Nishizawa ◽  
Masaharu Takahashi ◽  
Felipe R. Lorenzo ◽  
Tooru Shimosegawa ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Torque Teno Virus ◽  
The Novel ◽  
Entire Genome ◽  
Human Sera ◽  
Genomic Characterization ◽  
Novel Virus ◽  
Entire Genomic Sequence ◽  
Genomic Length

In the process of searching for the recently described small anelloviruses 1 and 2 (SAVs) with the genomic DNA length of 2.2 or 2.6 kb in human sera, we isolated a novel virus with its genomic organization resembling those of torque teno virus (TTV) of 3.8–3.9 kb and torque teno mini virus (TTMV) of 2.8–2.9 kb. The entire genomic sequence of three isolates (MD1-032, MD1-073 and MD2-013), which comprised 3242–3253 bases and exhibited 76–99 % identities with the SAVs within the overlapping sequence, was determined. Although the MD1-032, MD1-073 and MD2-013 isolates differed by 10–28 % from each other over the entire genome, they segregated into the same cluster and were phylogenetically distinguishable from all reported TTVs and TTMVs. These results suggest that SAVs are deletion mutants of the novel virus with intermediate genomic length between those of TTV and TTMV and that the novel virus can be classified into a third group of the genus Anellovirus.

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