Variations in Two Gene Sequences of Citrus Tristeza Virus after Host Passage

Ayllón, Marı́a A.; Rubio, Luís; Sentandreu, Vicente; Moya, Andrés; Guerri, José; Moreno, Pedro

doi:10.1007/s11262-005-6866-4

Cited by 31 publications

(26 citation statements)

References 56 publications

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“…This has been studied for GRLaV-1 (Alabi et al, 2011), GRLaV-3 (Turturo et al, 2005; Esteves et al, 2012), CYSDV (Rubio et al, 1999, 2001a), ToCV (Lozano et al, 2009), GRLaV-2 (Bertazzon et al, 2010b; Jarugula et al, 2010), and CTV (Ayllón et al, 1999b, 2006; d'Urso et al, 2000; Kong et al, 2000; Rubio et al, 2001b; Davino et al, 2005; Hilf et al, 2005; Melzer et al, 2005; Silva et al, 2007; Gomes et al, 2008; Iglesias et al, 2008; Černi et al, 2009; Oliveros-Garay et al, 2009; Matos et al, 2013; Wu et al, 2013). Analysis of nucleotide sequences or molecular markers such as single-strand conformation polymorphism (Rubio et al, 1996) of a certain number of clones obtained from RT-PCR products showed that most viral isolates had populations composed of a predominant sequence variant and different one- or two-nucleotide mutants in a very low frequency.…”

Section: Discussionmentioning

confidence: 99%

Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

2013

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RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. (I) A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. (2) Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. (3) Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. (4) Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. (5) Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation) or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process.

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Section: Discussionmentioning

confidence: 99%

Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

2013

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“…Similarly, isolates containing mixed infection of mild and severe strains in the same tree was previously reported in different citrus growing regions (Harper et al, 2009; Sentandreu et al, 2006). Particularly one Spanish isolate contain both mild and severe strains which were separated by aphid transmission and host passage and characterized in detail (Ayllon et al, 2006; Sentandreu et al, 2006). Similarly, some CTV isolates from New Zealand were sequenced and genomes of different strains were obtained from the same isolates (Harper et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

The First Identified Citrus tristeza virus Isolate of Turkey Contains a Mixture of Mild and Severe Strains

Çevik

Yardımcı

Korkmaz

2013

The Plant Pathology Journal

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The presence of Citrus tristeza virus (CTV) has previously been reported in citrus growing regions of Turkey. All serologically and biologically characterized isolates including Iğdır, which was the first identified CTV isolates from Turkey, were considered mild isolates. In this study, molecular characteristics of the Iğdır isolate were determined by different methods. Analysis of the Iğdır isolate by western blot and BD-RT-PCR assays showed the presence of MCA13 epitope, predominantly found in severe isolates, in the Iğdır isolate revealing that it contains a severe component. For further characterization, the coat protein (CP) and the RNA-dependent RNA polymerase (RdRp) genes representing the 3′ and 5′ half of CTV genome, respectively, were amplified from dsRNA by RT-PCR. Both genes were cloned separately and two clones for each gene were sequenced. Comparisons of nucleotide and deduced amino acid sequences showed that while two CP gene sequences were identical, two RdRp clones showed only 90% and 91% sequence identity in their nucleotide and amino acid sequences, respectively, suggesting a mixed infection with different strains. Phylogenetic analyses of the CP and RdRp genes of Iğdır isolate with previously characterized CTV isolates from different citrus growing regions showed that the CP gene was clustered with NZRB-TH30, a resistance breaking isolate from New Zealand, clearly showing the presence of severe component. Furthermore, two different clones of the RdRp gene were clustered separately with different CTV isolates with a diverse biological activity. While the RdRp-1 was clustered with T30 and T385, two well-characterized mild isolates from Florida and Spain, respectively, the RdRp-2 was most closely related to NZRB-G90 and NZRB-TH30, two well-characterized resistance breaking and stem pitting (SP) isolates from New Zealand confirming the mixed infection. These results clearly demonstrated that the Iğdır isolate, which was previously described as biologically a mild isolate, actually contains a mixture of mild and severe strains.

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“…The molecular mechanisms involved in symptom expression are still unknown. As for other RNA viruses, genetic variation has been observed in CTV isolates resulting from the error-prone nature of RNA polymerases and selection pressures (Domingo & Holland, 1994), superinfection of field trees with divergent CTV variants (Rubio et al, 2001), genetic drift after transmission to new hosts (Albiach-Martí et al, 2000a;D'Urso et al, 2000;Aylló n et al, 2006) or recombination (Rubio et al, 2001;Vives et al, 2005). Characterization of the genetic structure of viral populations and factors contributing to their evolution may help in the understanding of important features like the outbreak of new epidemics or virulence changes in current isolates (Fernández-Cuartero et al, 1994;Escriu et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

Contribution of recombination and selection to molecular evolution of Citrus tristeza virus

Martin

Sambade

Rubio

et al. 2009

Journal of General Virology

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The genetic variation of Citrus tristeza virus (CTV) was analysed by comparing the predominant sequence variants in seven genomic regions (p33, p65, p61, p18, p13, p20 and p23) of 18 pathogenically distinct isolates from seven different countries. Analyses of the selective constraints acting on each codon suggest that most regions were under purifying selection. Phylogenetic analysis shows diverse patterns of molecular evolution for different genomic regions. A first clade composed of isolates that are genetically close to the reference mild isolates T385 or T30 was inferred from all genomic regions. A second clade, mostly comprising virulent isolates, was defined from regions p33, p65, p13 and p23. For regions p65, p61, p18, p13 and p23, a third clade that mostly included South American isolates could not be related to any reference genotype. Phylogenetic relationships among isolates did not reflect their geographical origin, suggesting significant gene flow between geographically distant areas. Incongruent phylogenetic trees for different genomic regions suggested recombination events, an extreme that was supported by several recombination-detecting methods. A phylogenetic network incorporating the effect of recombination showed an explosive radiation pattern for the evolution of some isolates and also grouped isolates by virulence. Taken together, the above results suggest that negative selection, gene flow, sequence recombination and virulence may be important factors driving CTV evolution.

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Variations in Two Gene Sequences of Citrus Tristeza Virus after Host Passage

Cited by 31 publications

References 56 publications

Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

The First Identified Citrus tristeza virus Isolate of Turkey Contains a Mixture of Mild and Severe Strains

Contribution of recombination and selection to molecular evolution of Citrus tristeza virus

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