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United States Department of Agriculture

Agricultural Research Service

Title: Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity.

item Weng, Ziming
item Barthelson, Roger
item Gowda, Siddarame
item Hilf, Mark
item Dawson, W. O.
item Galbraith, D. W.
item Xiong, Z.

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2007
Publication Date: 9/18/2007
Citation: Weng, Z., Barthelson, R., Gowda, S., Hilf, M.E., Dawson, W., Galbraith, D., Xiong, Z. 2007. Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity.. PLoS One. 2(a):e917.doi:10.1371/journal.pone.0000917.

Interpretive Summary: Citrus tristeza virus is an important pathogen of citrus in many of the world's citrus growing areas. Within the global CTV population there is great genetic and biological diversity. Many genetically different strains of CTV can simultaneously infect a single citrus tree. A sequencing microarray was developed to rapidly analyze CTV genetic diversity and was applied to analyze the genetic diversity found in a single isolate of CTV from a specific infected sweet orange tree in Florida. The microarray determined that this one isolate was composed of three genetically distinct strains of CTV and numerous genetic recombinants derived from these three strains. The recombinant progeny viruses could have characteristics which are biologically distinct from the parent strains, such as different symptoms or different host ranges. The microarray is a rapid and sensitive method for analyzing CTV populations and can provide a tool to recognize potentially new and damaging strains of CTV.

Technical Abstract: Recombination and reassortment of viral genomes are major processes contributing to emerging viruses. These processes are especially significant in long-term persistent infections where multiple viral genotypes co-replicate in a single host, generating abundant genotypic variants, some of which may possess novel host-colonizing and pathogenicity traits. In some plants, vegetative propagation allows for viral populations to increase in complexity for hundreds of years allowing co-replication and subsequent recombination of the multiple viral genotypes. Here we examined a persistent infection by a Citrus tristeza virus (CTV) complex on citrus, a vegetatively propagated fruit plant, using a resequencing microarray, and found that the complex comprised three major and a number of minor genotypes. Subsequent deep sequencing analysis of the viral population confirmed the presence of the three major CTV genotypes and, in addition, revealed that the minor genotypes consisted of an extraordinarily large number of genetic variants generated by promiscuous recombination between the major genotypes. Further analysis provided evidence that some of the recombinants underwent subsequent divergence, further increasing the genotypic complexity. These data demonstrate that persistent infection of multiple viral genotypes within a host organism is sufficient to drive the large-scale production of viral genetic variants that may evolve into new and emerging viruses.

Last Modified: 09/18/2017
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