Research Article: First natural crossover recombination between two distinct species of the family Closteroviridae leads to the emergence of a new disease

Date Published: September 13, 2018

Publisher: Public Library of Science

Author(s): Leticia Ruiz, Almudena Simón, Carmen García, Leonardo Velasco, Dirk Janssen, Satyanarayana Tatineni.


Lettuce chlorosis virus-SP (LCV-SP) (family Closteroviridae, genus Crinivirus), is a new strain of LCV which is able to infect green bean plants but not lettuce. In the present study, high-throughput and Sanger sequencing of RNA was used to obtain the LCV-SP full-length sequence. The LCV-SP genome comprises 8825 nt and 8672 nt long RNA1 and RNA2 respectively. RNA1 of LCV-SP contains four ORFs, the proteins encoded by the ORF1a and ORF1b are closely related to LCV RNA1 from California (FJ380118) whereas the 3´ end encodes proteins which share high amino acid sequence identity with RNA1 of Bean yellow disorder virus (BnYDV; EU191904). The genomic sequence of RNA2 consists of 8 ORFs, instead of 10 ORFs contained in LCV-California isolate. The distribution of vsiRNA (virus-derived small interfering RNA) along the LCV-SP genome suggested the presence of subgenomic RNAs corresponding with HSP70, P6.4 and P60. Results of the analysis using RDP4 and Simplot programs are the proof of the evidence that LCV-SP is the first recombinant of the family Closteroviridae by crossover recombination of intact ORFs, being the LCV RNA1 (FJ380118) and BnYDV RNA1 (EU191904) the origin of the new LCV strain. Genetic diversity values of virus isolates in the recombinant region obtained after sampling LCV-SP infected green bean between 2011 and 2017 might suggest that the recombinant virus event occurred in the area before this period. The presence of LCV-SP shows the role of recombination as a driving force of evolution within the genus Crinivirus, a globally distributed, emergent genus.

Partial Text

Lettuce chlorosis virus (LCV) belongs to the genus Crinivirus, family Closteroviridae. Viruses included in this family are the largest among the known plant viruses and present ssRNA, positive-sense genome [1]. Family Closteroviridae has been classified into three genera based on vector transmission and phylogenetic relationships: Closterovirus, Ampelovirus, and Crinivirus. Recently, a new genus named Velarivirus has been proposed [2]. All members of genus Crinivirus include segmented genomes, are whitefly-transmitted and limited to the phloem [3].

Members of genus Crinivirus represent worldwide emerging diseases as evidence of the increasing number of new species identified during the past 20 years [44–46, 9, 4]. Other members of the genus emerge, not as a new species, but as a new strain affecting a new host range [47]. New LCV isolates from China have been recently described affecting ornamental plants, tobacco and tomato crops [12,13,48]; but there is no information about the capability of these LCV isolates to infect lettuce crops. Primer walking method and deep sequencing of vsiRNA allowed the elucidation of the sequence and genome organization of the first recombinant closterovirus resulting after crossover recombination of intact ORFs. The 5´ from LCV-SP RNA1 includes the replication module (ORF 1a and 1b), which share high homology with the LCV type isolate (FJ380118); however, the 3´end, which encompass P26 and P6, shares high amino acid identity with the 3´end of BnYDV RNA1. These ORFs, are described to be expressed in LCV from 3´ coterminal subgenomic RNAs (sgRNAs), a typical strategy among closteroviruses [8,6,49] that increases the probability of recombination events [50]. The existence of this recombinant region in the genome of LCV-SP was confirmed by genome sequencing after primer walking, deep sequencing of vsiRNAs and dsRNA, and RT-PCR of genomic RNA from purified virion.




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