Partial Characterization of Artichoke Virus M

A virus with filamentous particles 697 nm in length was isolated from artichoke plants in Southern Italy and identified as a new possible member of Carlavirus group, for which the name artichoke virus M (AVM) is suggested. AVM could not be transmitted by sap inoculation to herbaceous hosts and was always present in artichoke in mixed infections with other viruses. Virus particles had a buoyant density in CsCl of 1.31 g × cm^?3 and contained a single species of nucleic acid with an apparent size of 7.5 Kb and a single coat protein species with a mol. wt of 31,000. The virus was distantly related serologically to carnation latent and poplar mosaic carlaviruses but not to other members of the group including the recently described artichoke latent S carlavirus. Cytological alterations consisted of complex cytoplasmic inclusions composed of deranged organelles, lipid droplets and accumulations of membranes.     

Nucleotide sequence analysis of the 3'-terminal region of two Korean isolates of lily symptomless Carlavirus and expression of the coat protein in E. coli.

The 3'-terminal regions of the genomic RNAs of two Korean isolates of the lily symptomless Carlavirus (LSV), LSV-Ko and LSV-KII, were cloned and their nucleotide sequences were determined. The nucleotide sequence analysis and protein analysis by the Western blot revealed that E. coli expressed a 32-kDa protein that is the viral coat protein (CP) for the LSV. The two Korean strains share 98.4% and 98.3% sequence identities at the nucleotide and amino acid levels, respectively. The CP gene of LSV-Ko showed 99.1% and 87.0% nucleotide sequence identities, and 99.0% and 96.6% amino acid sequence identities with those of the Netherlands and the Japanese LSV strains, respectively. A pairwise amino acid sequence comparison revealed a sequence similarity of 29.6% to 69.8% between LSV-Ko and other species of the carlavirus. The 16 kDa protein of LSV-Ko shares 17.6% to 42.7% amino acid similarity with those of 8 other the carlaviruses, and they are variable in the N-terminal region. The Cys repeated zinc finger nucleic acid binding domain was found in the 16 kDa protein for all of the LSV strains. Sequence comparisons of the 7 kDa protein of LSV in the strain level showed significant identities from 100.0% to 98.4%. LSV-Ko shares 21.9% to 42.2% amino acid similarity with those of 8 other carlaviruses, 4 members of the potexviruses, and a closterovirus. LSV is closely related to blueberry scorch virus (BISV) based upon the phylogenetic tree analyses of the three proteins, indicating LSV to be a quite distinct member of the genus Carlavirus.     

Genome organization and variation in the 3′-partial sequence of garlic latent virus in China

Ten different isolates of a carlavirus were detected by degenerate PCR from 12 garlic samples collected from 6 provinces in China, and the complete genome sequence of the Zhejiang isolate ZJ1 and 3′-terminal sequences of 9 other isolates were determined. The RNA genome of isolate ZJ1 consisted of 8363nts excluding the 3′-poly (A) tail, and the genome organization was similar to other carlaviruses with 6 open reading frames encoding a replicase, TGB1, TGB2, TGB3, CP and NABP respectively. Sequence comparisons showed that all 10 isolates were Garlic latent virus (GarLV). The variations in the TGB2, TGB3 and NABP were more significant than those in the CP. High homology was also detected between those isolates and Shallot latent virus (ShLV). Phylogenetic analysis suggested that GarLV isolates from garlic can be divided into 4 main groups and Chinese isolates belonged to each group. This is the first reported molecular analysis of members of the genus Carlavirus in China.     

Genome organization and variation in the 3′-partial sequence of garlic latent virus in China

Ten different isolates of a carlavirus were detected by degenerate PCR from 12 garlic samples collected from 6 provinces in China, and the complete genome sequence of the Zhejiang isolate ZJ1 and 3'-terminal sequences of 9 other isolates were determined. The RNA genome of isolate ZJ1 consisted of 8363nts excluding the 3'-poly (A) tail, and the genome organization was similar to other carlaviruses with 6 open reading frames encoding a replicase, TGB1, TGB2, TGB3, CP and NABP respectively. Sequence comparisons showed that all 10 isolates were Garlic latent virus (GarLV). The variations in the TGB2, TGB3 and NABP were more significant than those in the CP. High homology was also detected between those isolates and Shallot latent virus (ShLV). Phylogenetic analysis suggested that GarLV isolates from garlic can be divided into 4 main groups and Chinese isolates belonged to each group. This is the first reported molecular analysis of members of the genus Carlavirus in China.     

Occurrence of chloroplast ribosome recognition sites within conserved elements of the RNA genomes of carlaviruses

The nucleotide sequences upstream from the carlavirus open reading frames were examined for direct sequence homology. Blocks of homology were evident upstream from the 25 K ORFs of potato virus S (PVS), potato virus M (PVM) and lily symptomless virus (LSV), and upstream from the coat protein initiation codons of PVS, PVM, LSV, carnation latent virus and Helenium virus S. These blocks, which correspond to the 5′-terminal regions of the subgenomic RNAs, were shown to contain potential ribosome recognition sequences. The distances between the binding sites and initiation codons ranged from 20 to 40 nucleotides on the viral RNAs. Whilst the majority of chloroplasts mRNAs have a distance of 8 nucleotides between binding site and initiation codon, the remaining have a distance of 23 nucleotides which is similar to that reported here for the carlaviruses.     

Virus-like, double-stranded RNAs in the parasitic protozoan Cryptosporidium parvum

We have discovered and analysed two novel, linear extrachromosomal double-stranded RNAs (dsRNAs) within oocysts of major north Amercian isolates of Cryptosporidium parvum , a parasitic protozoan that infects the gastrointestinal tract of a variety of mammals, including humans. These dsRNAs were found to reside within the cytoplasm of sporozoites, and were not detected in other species of the genus. cDNAs representing both dsRNA genomes were cloned and sequenced, 1786 and 1374 nt, and each encoded one large open reading frame (ORF). The deduced protein sequence of the larger dsRNA (L-dsRNA) had homology with viral RNA-dependent RNA polymerases (RDRP), with more similarity to polymerases from fungi than those from other protozoa. The deduced protein sequence from the smaller dsRNA (S-dsRNA) had limited similarity with mitogen-activated c-June NH₂ terminal protein kinases (JNK) from mammalian cells. Attempts to visually identify or purify virus-like particles associated with the dsRNAs were unsuccessful. Sensitivity of the dsRNAs to RNase A also suggests that the dsRNAs may be unencapsidated. A RDRP activity was identified in crude extracts from C . parvum sporozoites and products of RNA polymerase activity derived in vitro were similar to the dsRNAs purified directly from the parasites.     

Cucumber mosaic virus, a model for RNA virus evolution

Taxonomic relationships: Cucumber mosaic virus (CMV) is the type member of the Cucumovirus genus, in the family Bromoviridae . Additional members of the genus are Peanut stunt virus (PSV) and Tomato aspermy virus (TAV). The RNAs 3 of all members of the genus can be exchanged and still yield a viable virus, while the RNAs 1 and 2 can only be exchanged within a species.
Physical properties: The virus particles are about 29 nm in diameter, and are composed of 180 subunits (T = 3 icosahedral symmetry). The particles sediment with an s value of approximately 98. The virions contain 18% RNA, and are highly labile, relying on RNA–protein interactions for their integrity. The three genomic RNAs, designated RNA 1 (3.3 kb in length), RNA 2 (3.0 kb) and RNA 3 (2.2 kb) are packaged in individual particles; a subgenomic RNA, RNA 4 (1.0 kb), is packaged with the genomic RNA 3, making all the particles roughly equivalent in composition. In some strains an additional subgenomic RNA, RNA 4A is also encapsidated at low levels. The genomic RNAs are single stranded, plus sense RNAs with 5' cap structures, and 3' conserved regions that can be folded into tRNA-like structures.
Satellite RNAs: CMV can harbour molecular parasites known as satellite RNAs (satRNAs) that can dramatically alter the symptom phenotype induced by the virus. The CMV satRNAs do not encode any proteins but rely on the RNA for their biological activity.
Hosts: CMV infects over 1000 species of hosts, including members of 85 plant families, making it the broadest host range virus known. The virus is transmitted from host to host by aphid vectors, in a nonpersistent manner.
Useful web sites: http://mmtsb.scripps.edu/viper/1f15.html (structure); http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/10040001.htm (general information)     

The nucleotide sequence of the S RNA of Impatiens necrotic spot virus, a novel tospovirus.

Impatiens necrotic spot virus (INSV) shares a number of properties with tomato spotted wilt virus (TSWV), the type species of the genus tospovirus within the family Bunyaviridae. INSV, however, differs from TSWV in plant host range and serology. In order to define the genomic structure and the taxonomic status of this TSWV-like virus, the nucleotide sequence of its genomic S RNA segment has been determined. The molecular data obtained demonstrate that, like TSWV, INSV has an ambisense S RNA molecule, encoding a non-structural protein in viral sense and the nucleocapsid protein in viral complementary sense. The level of nucleotide sequence homology between their S RNAs, as well as the divergence in amino acid sequence homology of their gene products, confirm previous conclusions from serological studies that INSV and TSWV represent distinct virus species within the newly created genus, tospovirus.     

Health Status (Virus) of Native North American Humulus lupulus in the Natural Habitat

Ninety-one native North American Humulus lupulus plants from natural habitats in seven western and mid-western states of the U.S.A. were tested by ELISA serology for presence of two ilarviruses and three carlaviruses common to cultivated hops. All plants in natural habitats were free of detectable viruses. Propagations of 14 such plants from earlier collections had become infected, particularly with two carlaviruses (hop latent virus, American hop latent virus) after exposure for 22 years tobreeding nurseries. ELISA tests of some 284 hop plants primarily from breeding nurseries in Oregon indicated the following infection rates: Prunus necrotic ringspot virus, 85/284, 30%; apple mosaic virus, 88/234, 38%; hop mosaic virus, 59/158, 37 %; hoplatent virus, 104/158, 66 %; and American hop latent virus, 79/158, 50 %. Inoculum reservoirs of AHLV were sought among 53 principally perennial non-Humulus plant species surrounding AHLV-infected hop yards and nurseries. AHLV was neither indigenous to native North American H. lupulus nor detectable in these selected non-Humulus plant species. Breeding nurseries and commercial hop yards, thus, were the only detectable inoculum reservoir for AHLV.     

菊花R病毒杭白菊分离株全基因组序列测定与分析

杭白菊作为著名的中药“浙八味”之一,种植规模和产区不断扩大,但其病毒病的发生也日益严重,对其产量和品质造成严重影响。本研究利用双链RNA（double stranded RNA,dsRNA）和非序列依赖PCR扩增（sequence independent amplification,SIA）等方法,对感病杭白菊病原物进行鉴定,为杭白菊病毒病原的检测构建一套快速和简便的方法。结果表明,感病杭白菊被菊花R病毒（Chrysanthemum virus R,CVR）侵染,将其命名为CVR-TX。通过对其全基因组进行序列扩增与分析,获得其全长基因组为8 872 bp,编码6个ORF,具有Carlavirus属病毒的典型特征。基于全基因组核酸序列以及复制酶、外壳蛋白氨基酸的序列比对发现,CVR-TX与CVR-BJ同源性最高,分别为85.5%、96.0%和96.3%;与Carlavirus属其他病毒同源性分别在48.2%～54.4%、46.9%～55.3%和36.8%～59.5%,因此CVR被确定为一种新的Carlavirus属病毒。系统进化分析表明,基于全长基因组、复制酶（replicase）基因和外壳蛋白（coat protein,CP）基因与CVR-BJ聚为一簇,亲缘性最近。本研究获得了CVR-TX的全长基因组,丰富了CVR的基因组信息,通过生物信息学分析明确其种属关系和区域变化情况,从而为建立CVR可靠灵敏的分子检测手段和有效的防控措施提供理论基础。     

Production and use of cDNA clones from arabis mosaic virus

Arabis mosaic virus (AMV) genomic RNAs were converted to dsDNA and cloned into bacterial plasmids. Insert sizes of cDNA clones ranged from 0·2 to 3·2 kbp. Restriction enzyme mapping identified clones representing at least 90% of the RNA-2 genome. A 0·9 kbp clone specific to RNA-1 was also identified. Northern blot hybridisations of AMV RNAs with clones from either RNA-1 or RNA-2 showed no cross reactions. The sensitivity of virus detection in dot hybridisation was 15 pg of purified genomic RNA and 40 pg of purified virus particles. The possibility of using cDNA clones for the detection of AMV in strawberry sap was demonstrated. Two AMV dsRNAs corresponding to genomic RNAs in size were isolated from infected cucumber plants and reacted in hybridisation experiments.     

Evidence that the Low Molecular Weight RNA Associated with Chicory Yellow Mottle Virus is a Satellite

Chicory yellow mottle virus, ringspot strain (CYMV-RS), supports the replication of a low molecular weight RNA (0.17 × 10⁶ daltons) associated with CYMV-T (type stain).
Competition hybridization experiments revealed lack or nucleotide sequence homology between 0.17 × 10⁶ mol. wt. RNA (Sat RNA) and CYMV-RS genomic RNAs, and partial homology (33 %) with CYMV-T genomic RNAs. However, such apparent partial homology can be due to contamination of CYMV-T genomic RNAs with a multimeric form of Sat RNA having a similar molecular weight. On this account the hypothesis that CYMV-T Sat RNA is a true satellite RNA becomes tenable.     

Molecular identification and phylogenetic analysis of a viral RNA associated with the Chinese tobacco bushy top disease complex

Tobacco bushy top disease is caused by a complex of the viruses tobacco bushy top virus (TBTV, a member of the genus Umbravirus) and tobacco vein distorting virus (TVDV, a member of the genus Polerovirus), which acts as a helper virus encapsidating the TBTV genomic RNA. RNA from purified virions is separated as five bands. The two largest (6.0 and 4.2 kb) were shown by Northern blot analysis to be the genomic RNAs of TVDV and TBTV, respectively. A band of about 3 kb was cloned and sequenced and shown to be the RNA of a previously undescribed virus with two open reading frames (ORFs), the second of which is an RNA‐dependent RNA polymerase (RdRp) and is probably expressed by readthrough of the ORF1a stop codon. BLAST and phylogenetic analyses of the RdRp show that it is related to two RNAs previously reported in association with the poleroviruses Beet western yellows virus and Carrot red leaf virus. These three RNAs appear to represent species of a new genus of plant viruses dependent upon a helper polerovirus for their transmission.     

菊花R病毒杭白菊分离株全基因组序列测定与分析

杭白菊作为著名的中药“浙八味”之一,种植规模和产区不断扩大,但其病毒病的发生也日益严重,对其产量和品质造成严重影响。本研究利用双链RNA（double stranded RNA,dsRNA）和非序列依赖PCR扩增（sequence independent amplification,SIA）等方法,对感病杭白菊病原物进行鉴定,为杭白菊病毒病原的检测构建一套快速和简便的方法。结果表明,感病杭白菊被菊花R病毒（Chrysanthemum virus R,CVR）侵染,将其命名为CVR-TX。通过对其全基因组进行序列扩增与分析,获得其全长基因组为8 872 bp,编码6个ORF,具有Carlavirus属病毒的典型特征。基于全基因组核酸序列以及复制酶、外壳蛋白氨基酸的序列比对发现,CVR-TX与CVR-BJ同源性最高,分别为85.5%、96.0%和96.3%;与Carlavirus属其他病毒同源性分别在48.2%～54.4%、46.9%～55.3%和36.8%～59.5%,因此CVR被确定为一种新的Carlavirus属病毒。系统进化分析表明,基于全长基因组、复制酶（replicase）基因和外壳蛋白（coat protein,CP）基因与CVR-BJ聚为一簇,亲缘性最近。本研究获得了CVR-TX的全长基因组,丰富了CVR的基因组信息,通过生物信息学分析明确其种属关系和区域变化情况,从而为建立CVR可靠灵敏的分子检测手段和有效的防控措施提供理论基础。     

Epstein-Barr virus RNA in Burkitt tumor tissue.

Analysis of the viral RNA in four Burkitt tumor biopsies indicates that tumor tissue contains RNA homologous to at least 3–6% of the DNA of Epstein-Barr virus (EBV). Most of these RNA species accumulate in the polyadenylated RNA fraction of Burkitt tumor tissue. Two approaches have been used to determine the location within the EBV genome of the DNA sequences which encode stable RNA in two Burkitt tumor biopsies, F and S, which contain 6–10 copies per cell of at least 80% of the EBV genome. With the first approach, ³²P-EBV DNA homologous to polyadenylated or nonpolyadenylated RNAs from the F, S or R tumors was hybridized to blots of fragments of EBV DNA. With the second approach, polyadenylated or nonpolyadenylated RNAs from the F or S tumors were hybridized to separated, labeled fragments of EBV DNA in solution. The results indicate that first, most of the viral RNA in Burkitt tumor tissue is encoded by approximately 20% of the Hsu I D fragment, 20% of the Eco RI A/Hsu I A double-cut fragment and 3% of the Hsu I B fragment of EBV DNA; second, an abundant RNA species in tumor tissue is homologous to the “additional DNA” present in the W91 and Jijoye/HR-I Burkitt tumor isolates of EBV and absent in the B95-8 virus, an isolate of EBV from outside the Burkitt endemic region; and third, there is little or no homology to other regions of the EBV genome.     

N‐terminal region of cysteine‐rich protein (CRP) in carlaviruses is involved in the determination of symptom types

Plant viruses in the genus Carlavirus include more than 65 members. Plants infected with carlaviruses exhibit various symptoms, including leaf malformation and plant stunting. Cysteine‐rich protein (CRP) encoded by carlaviruses has been reported to be a pathogenicity determinant. Carlavirus CRPs contain two motifs in their central part: a nuclear localization signal (NLS) and a zinc finger motif (ZF). In addition to these two conserved motifs, carlavirus CRPs possess highly divergent, N‐terminal, 34 amino acid residues with unknown function. In this study, to analyse the role of these distinct domains, we tested six carlavirus CRPs for their RNA silencing suppressor activity, ability to enhance the pathogenicity of a heterologous virus and effects on virus accumulation levels. Although all six tested carlavirus CRPs showed RNA silencing suppressor activity at similar levels, symptoms induced by the Potato virus X (PVX) heterogeneous system exhibited two different patterns: leaf malformation and whole‐plant stunting. The expression of each carlavirus CRP enhanced PVX accumulation levels, which were not correlated with symptom patterns. PVX‐expressing CRP with mutations in either NLS or ZF did not induce symptoms, suggesting that both motifs play critical roles in symptom expression. Further analysis using chimeric CRPs, in which the N‐terminal region was replaced with the corresponding region of another CRP, suggested that the N‐terminal region of carlavirus CRPs determined the exhibited symptom types. The up‐regulation of a plant gene upp‐L, which has been reported in a previous study, was also observed in this study; however, the expression level was not responsible for symptom types.