Comparison of the 5′ and 3′ termini of tomato ringspot virus RNA1 and RNA2: Evidence for RNA recombination

Rott, Michael; Tremaine, J. H.; Rochon, D’Ann

doi:10.1016/0042-6822(91)90801-h

Cited by 60 publications

(32 citation statements)

References 18 publications

(3 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The ORF1/2 boundary region is highly conserved in NoV GII/4, as shown previously by very low scores of Shannon entropy within the reported GII/4 sequences (38). This and our present findings on the presence of the putative parent GII/4 sequences of the mosaic genomes suggest that the ORF1/2 mosaic genomes we identified were generated by homologous recombination, as seen in other single-stranded, positive-sense RNA viruses, including poliovirus (20), foot-and-mouth disease virus (36), brome mosaic virus (9, 39), turnip crinkle virus (70), and tomato ringspot virus (52). If this were the case, the intersubtype recombination at the ORF1/2 boundary region would occur and generate variable recombinant viruses in vivo more frequently than the intergenotype and intergenogroup recombination would, because the boundary region and neighboring sequences are more similar within the NoV subtype than within the genotype and genogroup.…”

Section: Discussionsupporting

confidence: 66%

Divergent Evolution of Norovirus GII/4 by Genome Recombination from May 2006 to February 2009 in Japan

Motomura

Yokoyama

Ode

et al. 2010

J Virol

View full text Add to dashboard Cite

Norovirus GII/4 is a leading cause of acute viral gastroenteritis in humans. We examined here how the GII/4 virus evolves to generate and sustain new epidemics in humans, using 199 near-full-length GII/4 genome sequences and 11 genome segment clones from human stool specimens collected at 19 sites in Japan between May 2006 and February 2009. Phylogenetic studies demonstrated outbreaks of 7 monophyletic GII/4 subtypes, among which a single subtype, termed 2006b, had continually predominated. Phylogenetic-tree, bootscanningplot, and informative-site analyses revealed that 4 of the 7 GII/4 subtypes were mosaics of recently prevalent GII/4 subtypes and 1 was made up of the GII/4 and GII/12 genotypes. Notably, single putative recombination breakpoints with the highest statistical significance were constantly located around the border of open reading frame 1 (ORF1) and ORF2 (P < 0.000001), suggesting outgrowth of specific recombinant viruses in the outbreaks. The GII/4 subtypes had many unique amino acids at the time of their outbreaks, especially in the N-term, 3A-like, and capsid proteins. Unique amino acids in the capsids were preferentially positioned on the outer surface loops of the protruding P2 domain and more abundant in the dominant subtypes. These findings suggest that intersubtype genome recombination at the ORF1/2 boundary region is a common mechanism that realizes independent and concurrent changes on the virion surface and in viral replication proteins for the persistence of norovirus GII/4 in human populations.

show abstract

Section: Discussionsupporting

confidence: 66%

Divergent Evolution of Norovirus GII/4 by Genome Recombination from May 2006 to February 2009 in Japan

Motomura

Yokoyama

Ode

et al. 2010

J Virol

View full text Add to dashboard Cite

show abstract

Section: Cherry Leaf Roll Virus (Clrv) Was First Described In 1955 Bymentioning

confidence: 99%

“…They are characterized by a large, separately encapsidated RNA-2 with a long (1.2 to 1.6 kb) 3Ј noncoding region which is identical or almost identical to that of RNA-1 (2). It has been speculated that this very high conservation of the 3Ј NCR between the two genomic RNAs could be the result of an RNA recombination mechanism acting as part of the RNA-2 replication process of these viruses (37,39,23).To date, very little information is available on the molecular or serological variability of CLRV isolates, but many isolates of CLRV are known and have been distinguished by virulence on experimental hosts, by differences in reactivity with polyclonal antisera in agarose gel immunodiffusion analyses (9,16,17,19,20,41) or by nucleic acid hybridization analyses (26). The isolates or strains of CLRV that have been most studied include the type (cherry) strain, the elm mosaic strain, the rhubarb strain, the golden elderberry strain, the red elder ringspot strain, the dogwood ringspot strain, the birch strain, the walnut ringspot and walnut yellow vein strains, and the blackberry and red raspberry strains (18).…”

mentioning

confidence: 99%

Host Species-Dependent Population Structure of a Pollen-Borne Plant Virus, Cherry Leaf Roll Virus

Rebenstorf

Candresse²,

Dulucq³

et al. 2006

J Virol

View full text Add to dashboard Cite

Cherry leaf roll virus (CLRV) belongs to the Nepovirus genus within the family Comoviridae. It has a host range which includes a number of wild tree and shrub species. The serological and molecular diversity of CLRV was assessed using a collection of isolates and samples recovered from woody and herbaceous host plants from different geographical origins. Molecular diversity was assessed by sequencing a short (375-bp) region of the 3 noncoding region (NCR) of the genomic RNAs while serological diversity was assessed using a panel of seven monoclonal antibodies raised initially against a walnut isolate of CLRV. The genomic region analyzed was shown to exhibit a significant degree of molecular variability with an average pairwise divergence of 8.5% (nucleotide identity). Similarly, serological variability proved to be high, with no single monoclonal antibody being able to recognize all isolates analyzed. Serological and molecular phylogenetic reconstructions showed a strong correlation. Remarkably, the diversity of CLRV populations is to a large extent defined by the host plant from which the viral samples are originally obtained. There are relatively few reports of plant viruses for which the genetic diversity is structured by the host plant. In the case of CLRV, we hypothesize that this situation may reflect the exclusive mode of transmission in natural plant populations by pollen and by seeds. These modes of transmission are likely to impose barriers to host change by the virus, leading to rapid biological and genetic separation of CLRV variants coevolving with different plant host species. Cherry leaf roll virus (CLRV) was first described in 1955 byPosnette and Cropley as causing a disease of sweet cherry (Prunus avium L.) in England (7). Since then it has been shown to exhibit a wide natural host range including a variety of herbaceous and woody plants. Some of the most common natural hosts of CLRV are common birch (Betula pendula Roth), black elderberry (Sambucus nigra L.), English walnut (Juglans regia L.), and sweet cherry. The virus is widely distributed and has been detected throughout Europe, the former U.S.S.R., North America, Chile (13), New Zealand, Australia, China (18), and Japan. CLRV is naturally transmitted through seeds and pollen (1, 18). It is a member of the genus Nepovirus (46) but, unlike the majority of other members of this genus, CLRV is not considered to be transmitted by soil-borne nematodes (45).CLRV has a bipartite single-stranded positive-sense RNA genome estimated to be about 15 kb total, with RNA-1 and RNA-2 sizes estimated at about 8.2 and 6.8 kb, respectively (29). Both RNAs are separately encapsidated in isometric particles (18). The genomic RNAs have a genome-encoded protein (VPg) covalently linked at their 5Ј terminus and are polyadenylated at their 3Ј terminus (4,12).CLRV belongs to the subgroup C nepoviruses. They are characterized by a large, separately encapsidated RNA-2 with a long (1.2 to 1.6 kb) 3Ј noncoding region which is identical or almost identical to that of RNA-...

show abstract

“…Whereas most currently recognised nepoviruses (including ArMV) are in one subgroup, cherry leaf roll nepovirus (CLRV; with tomato ringspot) is in another subgroup (Scott et al 1993). At the 3' termini, RNA-1 and RNA-2 for any isolate of these viruses are almost identical over c. 1.5 kb (Rott et al 1988(Rott et al , 1991Scott et al 1992). Furthermore, within the 3' terminal region, substantial homology (c. 0.7 kb) exists between two serologically distinguishable (Jones 1976;Massalski & Cooper 1981) CLRV isolates.…”

Section: Introductionmentioning

confidence: 99%

Transgenic resistance genes from nepoviruses: Efficacy and other properties

Cooper

Edwards

Rosenwasser

et al. 1994

New Zealand Journal of Crop and Horticultural Science

View full text Add to dashboard Cite

Evidence of RNA-RNA recombination or transcapsidation was sought in transgenic tobacco (Nicotiana tabacum L. 'Xanthi-nc') containing the 3'-non coding sequence (1.3 kb) from a birch isolate of cherry leaf roll nepovirus (CLRV). Following mechanical inoculation with a rhubarb isolate of the virus, no evidence of recombination was obtained using polymerase chain reactions whether the transgenic gene produced transcripts in the sense or the antisense orientation. Transgenic tobacco containing the CLRV-derived sequence (in either orientation) did not lessen the pathological effects of the rhubarb isolate of the virus althdugh there was amelioration of the disease caused by the birch isolate. When expressed as a transgenic gene in tobacco, the capsid coding sequence of arabis mosaic nepovirus (ArMV) lessened infectibility by nematodes carrying that virus. This construct did not influence the pathogenicity of potato virus Y o (PVY 0 ), tobacco rattle tobravirus (PRN), alfalfa mosaic ilarvirus (A1MV), or CLRV, did not alter the levels of their accumulation and did not render their virions more or less prone to recognition by ArMVspecific antibodies. Uninoculated tobacco expressing the ArMV capsid protein contained ArMV-like particles which co-purified with RNA that hybridised with cDNA to tobacco mRNA and to DNA complementary to the capsid coding sequence.

show abstract

Comparison of the 5′ and 3′ termini of tomato ringspot virus RNA1 and RNA2: Evidence for RNA recombination

Cited by 60 publications

References 18 publications

Divergent Evolution of Norovirus GII/4 by Genome Recombination from May 2006 to February 2009 in Japan

Divergent Evolution of Norovirus GII/4 by Genome Recombination from May 2006 to February 2009 in Japan

Host Species-Dependent Population Structure of a Pollen-Borne Plant Virus, Cherry Leaf Roll Virus

Transgenic resistance genes from nepoviruses: Efficacy and other properties

Contact Info

Product

Resources

About