scholarly journals Variability of the coat protein gene of Grapevine leafroll-associated virus 3 in Brazil

2007 ◽  
Vol 32 (4) ◽  
pp. 335-340 ◽  
Author(s):  
Thor V.M. Fajardo ◽  
Érico C. Dianese ◽  
Marcelo Eiras ◽  
Daniela M. Cerqueira ◽  
Daniela B. Lopes ◽  
...  
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Coat Protein Gene ◽  
North American ◽  
Protein Gene ◽  
Sequence Data ◽  
Geographic Origin ◽  
Coat Protein Sequence ◽  
Northeastern Brazil ◽  
Complete Coat Protein

Leafroll is an economically important disease affecting grapevines (Vitis spp.). Nine serologically distinct viruses, Grapevine leafroll-associated virus-1 through 9, are associated with this disease. The present study describes the coat protein gene sequence of four GLRaV-3 isolates occurring in the São Francisco River basin, Northeastern Brazil. The viral RNA was extracted from GLRaV-3 ELISA-positive plants and the complete coat protein gene was amplified by RT-PCR. Sequences were generated automatically and compared to the complete coat protein sequence from North American (NY1) and Chinese (Dawanhong Nº2 and SL10) GLRaV-3 isolates. The four studied isolates, named Pet-1 through 4, showed deduced amino acid identities of 98-100% (Pet-1 through 3) and 95% (Pet-4) with North American and Chinese isolates. A total of seventeen amino acid substitutions was detected among the four characterized isolates in comparison to the NY1, Dawanhong No.2 and SL10 sequences. The results indicated the existence of natural variation among GLRaV-3 isolates from grapevines, also demonstrating a lack of correlation between sequence data and geographic origin. This variability should be considered when selecting regions of the viral genome targeted for reliable and consistent virus molecular detection.

scholarly journals Sequence variability in the coat protein gene of Cowpea severe mosaic virus isolates from northeastern Brazil

2011 ◽  
Vol 36 (2) ◽  
pp. 121-124 ◽  
Author(s):  
José Evando A. Beserra Jr. ◽  
Eduardo C. Andrade ◽  
Rosa F.R. Araújo Camarço ◽  
Aline K.Q. Nascimento ◽  
José Albérsio A. Lima
Keyword(s):  
Coat Protein ◽  
Mosaic Virus ◽  
Coat Protein Gene ◽  
Protein Gene ◽  
Northeastern Brazil ◽  
Sequence Variability ◽  
Virus Isolates

scholarly journals First Report of Raspberry bushy dwarf virus in Rubus multibracteatus from China

Plant Disease ◽  
2003 ◽  
Vol 87 (5) ◽  
pp. 603-603 ◽  
Author(s):  
C. J. Chamberlain ◽  
J. Kraus ◽  
P. D. Kohnen ◽  
C. E. Finn ◽  
R. R. Martin
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Coat Protein Gene ◽  
Protein Gene ◽  
Dwarf Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Black Raspberry ◽  
First Report ◽  
Raspberry Bushy Dwarf Virus ◽  
Plant Pathol

Raspberry bushy dwarf virus (RBDV), genus Idaeovirus, has been reported in commercial Rubus spp. from North and South America, Europe, Australia, New Zealand, and South Africa. Infection can cause reduced vigor and drupelet abortion leading to crumbly fruit and reduced yields (3,4). In recent years, Rubus germplasm in the form of seed, was obtained on several collection trips to The People's Republic of China to increase the diversity of Rubus spp. in the USDA-ARS National Clonal Germplasm Repository, (Corvallis, OR). Before planting in the field, seedlings were tested for the presence of RBDV, Tomato ringspot virus, and Tobacco streak virus using triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) (antiserum produced by R. R. Martin). One symptomless plant of R. multibracteatus H. Lev. & Vaniot (PI 618457 in USDA-ARS GRIN database), from Guizhou province in China, tested positive for RBDV (RBDV-China). After mechanical transmission on Chenopodium quinoa Willd., this isolate produced typical symptoms of RBDV (3). To determine if RBDV-China was a contaminant during the handling of the plants, or if the source was a seedborne virus, the coat protein gene was sequenced and compared to published sequences of RBDV. RNA was extracted from leaves of R. multibracteatus and subjected to reverse transcription-polymerase chain reaction (RT-PCR) using primers that flank the coat protein gene. Products from four separate PCR reactions were sequenced directly or were cloned into the plasmid vector pCR 2.1 (Invitrogen, Carlsbad, CA) and then sequenced. The coding sequence of the coat protein gene of RBDV-China was 87.5% (722/825) identical to that isolated from black raspberry (Genbank Accession No. s55890). The predicted amino acid sequences were 91.6% (251/274) identical. Previously, a maximum of five amino acid differences had been observed in the coat proteins of different RBDV strains (1). The 23 differences observed between RBDV-China and the isolate from black raspberry (s55890) confirm that the RBDV in R. multibracteatus is not a greenhouse contaminant but is indeed a unique strain of RBDV. In addition, monoclonal antibodies (MAbs) to RBDV (2) were tested against RBDV-China. In these tests, MAb D1 did not detect RBDV-China, whereas MAb R2 and R5 were able to detect the strain. This is the first strain of RBDV that has been clearly differentiated by MAbs using standard TAS-ELISA tests. Although RBDV is common in commercial Rubus spp. worldwide, to our knowledge, this is the first report of RBDV in R. multibracteatus, and the first report of RBDV from China. The effects of this new strain of RBDV could be more or less severe, or have a different host range than previously studied strains. It is more divergent from the type isolate than any other strain that has been studied to date. Phylogenetic analysis of coat protein genes of RBDV may be useful in understanding the evolution and spread of this virus. References: (1) A. T. Jones et al. Eur. J. Plant Pathol. 106:623, 2000. (2) R. R. Martin. Can. J. Plant. Pathol. 6:264, 1984. (3) A. F. Murant. Raspberry Bushy Dwarf. Page 229 in: Virus Diseases of Small Fruits. R. H. Converse, ed. U.S. Dep. Agric. Agric. Handb. 631, 1987. (4) B. Strik and R. R. Martin. Plant Dis. 87:294, 2003.

scholarly journals Biological, Pathological, and Molecular Characteristics of a New Potyvirus, Dendrobium Chlorotic Mosaic Virus, Infecting Dendrobium Orchid

Plant Disease ◽  
2019 ◽  
Vol 103 (7) ◽  
pp. 1605-1612 ◽  
Author(s):  
Chih-Hung Huang ◽  
Chia-Hsing Tai ◽  
Ruey-Song Lin ◽  
Chung-Jan Chang ◽  
Fuh-Jyh Jan
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Coat Protein ◽  
Amino Acid Sequence ◽  
Mosaic Virus ◽  
Coat Protein Gene ◽  
Nucleotide Sequence Identity ◽  
Amino Acid Sequence Identity ◽  
Protein Gene ◽  
Sequence Identity

Dendrobium smillieae is one of the popular orchids in Taiwan. This report describes a new potyvirus tentatively named Dendrobium chlorotic mosaic virus (DeCMV) causing chlorotic and mosaic symptoms in D. smillieae. Enzyme-linked immunosorbent assay (ELISA) tests using six antisera against orchid-infecting viruses revealed that only a monoclonal antibody against the potyvirus group reacted positively with crude saps prepared from a symptomatic dendrobium orchid. Potyvirus-like, flexuous, filamentous particles were observed under an electron microscope, measuring approximately 700 to 800 nm in length and 11 to 12 nm in diameter. Sequence analyses revealed that DeCMV coat protein gene shared 59.6 to 66.0% nucleotide sequence identity and 57.6 to 66.0% amino acid sequence identity, whereas the DeCMV complete genome shared 54.1 to 57.3% nucleotide sequence identity and 43.7 to 49.5% amino acid sequence identity with those other known potyviruses. These similarity levels were much lower than the criteria set for species demarcation in potyviruses. Thus, DeCMV can be considered a new potyvirus. The whole DeCMV genome contains 10,041 nucleotides (GenBank accession no. MK241979) and encodes a polyprotein that is predicted to produce 10 proteins by proteolytic cleavage. In a pathogenicity test, results of inoculation assays demonstrated that DeCMV can be transmitted to dendrobium orchids by grafting and mechanical inoculation, as verified by ELISA and western blot analyses using the DeCMV polyclonal antiserum and by reverse transcription polymerase chain reaction using the coat protein gene-specific primers. The inoculated orchids developed similar chlorotic and mosaic symptoms. In conclusion, DeCMV is a novel orchid-infecting potyvirus, and this is the first report of a new potyvirus that infects dendrobium orchids in Taiwan.

scholarly journals Sequence diversity in the coat protein gene of Lettuce big-vein associated virus and Mirafiori lettuce big-vein virus infecting lettuce in Brazil

2008 ◽  
Vol 34 (2) ◽  
pp. 175-177 ◽  
Author(s):  
Márcio Martinello Sanches ◽  
Renate Krause-Sakate ◽  
Marcelo Agenor Pavan
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Amino Acid Sequence ◽  
Coat Protein Gene ◽  
Amino Acid Sequence Identity ◽  
Restriction Site ◽  
Protein Gene ◽  
Sequence Identity ◽  
Disease Analysis ◽  
Vein Disease

Lettuce big vein associated virus (LBVaV) and Mirafiori lettuce big vein virus (MLBVV) have been found in mixed infection in Brazil causing the lettuce big vein disease. Analysis of part of the coat protein (CP) gene of Brazilian isolates of LBVaV collected from lettuce, showed at least 93% amino acid sequence identity with other LBVaV isolates. Genetic diversity among MLBVV CP sequences was higher when compared to LBVaV CP sequences, with amino acid sequence identity ranging between 91% to 100%. Brazilian isolates of MLBVV belong to subgroup A, with one RsaI restriction site on the coat protein gene. There is no indication for a possible geografical origin for the Brazilian isolates of LBVaV and MLBVV.

scholarly journals PENGKLONAN DAN PERUNUTAN NUKLEOTIDA GEN SELUBUNG PROTEIN DAN 3’UTR (untranslated region) PEANUT STRIPE VIRUS

2001 ◽  
Vol 1 (1) ◽  
pp. 1-6
Author(s):  
Hasriadi Mat Akin
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Coat Protein Gene ◽  
Cleavage Site ◽  
Untranslated Region ◽  
Protein Gene ◽  
Start Codon ◽  
Genomic Rna ◽  
Cp Gene ◽  
Peanut Stripe Virus

Cloning and sequencing of coat protein gene and 3’UTR (untranslated region) of peanut stripe virus. The cDNA of 3' terminal of peanut stripe virus genomic RNA was cloned and sequenced. The cDNA was ligated with plasmid vector pGEM-T Easy and transformed to competent cells of Escherichia coli. The 3' terminal of PstV genomic RNA contained 1195 nucleotides (nts).  The region included the nucleotide sequences of NIb (nuclear inclusion body) (129 nts), CP gene (coat protein gene) (861 nts), and 3'UTR (untranslated region) (205 nts). The nucleotide sequence of a CP gene contained one long uninterrupted open reading frame (ORF) without a start codon, which ended a UAG stop codon. The 287 amino acid residues of PStV coat protein were predicted from the CP gene.  The amino acid was analyzed for the presence of consensus polyprotein cleavage site for maturation of potyvirus polyprotein.  A putative cleavage site was found at position 43 (Q/S) following the Valine (V) residue at -4 position.  This isolate of PstV can be expected to be aphid transmissible because the coat protein contained a DAG triplet at position 53-55.

scholarly journals Sequence analysis of the capsid protein gene of an isolate of Apple stem grooving virus, and its survey in Southern Brazil

2001 ◽  
Vol 26 (3) ◽  
pp. 655-659 ◽  
Author(s):  
OSMAR NICKEL ◽  
THOR V.M. FAJARDO ◽  
WILHELM JELKMANN ◽  
GILMAR B. KUHN
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Coat Protein Gene ◽  
Large Scale ◽  
Protein Gene ◽  
Amino Acid Sequences ◽  
Close Relative ◽  
Apple Stem Grooving Virus ◽  
Apple Stem ◽  
High Amino Acid

Apple stem grooving virus (ASGV) is one of the most important viruses infecting fruit trees. This study aimed at the molecular characterization of ASGV infecting apple (Malus domestica) plants in Santa Catarina (SC). RNA extracted from plants infected with isolate UV01 was used as a template for RT-PCR using specific primers. An amplified DNA fragment of 755 bp was sequenced. The coat protein gene of ASGV isolate UV01 contains 714 nucleotides, coding for a protein of 237 amino acids with a predicted Mr of approximately 27 kDa. The nucleotide and the deduced amino acid sequences of the coat protein gene showed identities of 90.9% and 97.9%, respectively, with a Japanese isolate of ASGV. Very high amino acid homologies (98.7%) were also found with Citrus tatter leaf capillovirus (CTLV), a very close relative of ASGV. These results indicate low coat protein gene variability among Capillovirus isolates from distinct regions. In a restricted survey, mother stocks in orchards and plants introduced into the country for large scale fruit production were indexed and shown to be infected by ASGV (20%), usually in a complex with other (latent) apple viruses (80%).

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