Complete genome sequence of a lettuce chlorosis virus isolate from China and genome recombination/rearrangement analysis

Epidemiology and control of emerging criniviruses in bean

During the last two decades, new criniviruses emerged in green bean crops in the south-east of Spain. Bean yellow disorder virus (BnYDV) was first detected in 2003 and caused major economic damage in crops grown in greenhouses. It was characterized as the first crinivirus to infect a member species of the Leguminosae family. Symptoms induced during BnYDV infection include interveinal chlorosis and yellowing on leaves, and reduced fruit yield and quality. Similar symptoms, although more severe, were observed in bean crops in the same region during the fall of 2011. From that moment on, BnYDV was not detected anymore in diseased plants, but instead lettuce chlorosis virus (LCV) was associated with the diseased plants. Previously, LCV was detected only in California, USA, infecting lettuce and sugarbeets. The host range and partial genomic sequences lead to the description of the new strain, LCV-SP. The complete sequence of its genome revealed the virus as a recombinant of BnYDV and LCV, in which the latter had lost two ORFs in the RNA1 of the bipartite genome and had acquired two homologue ORFs from BnYDV. Both viruses are transmitted by the whitefly Bemisia tabaci. When compared with other crinivirus pathosystems, the transmission efficiency of BnYDV to its primary host bean, is among the highest, and its persistence in the vector among the longest, up to 9 days. The host range of BnYDV s restricted to several crop species of the Leguminosae: common bean (Phaseolus vulgaris), pea (Pisum sativum), tirabeque (P. sativum subsp. sativum var. macrocarpon), lentil (Lens culinaris) and faba bean (Vicia faba). LCV-SP is also able to infect green bean plants but not lettuce, its original host, probably following its recombinant nature. Symptoms and epidemiology of the bean criniviruses are compared with similar pathosystems that occur in the same region and that involve cucurbit yellow stunting disorder virus and tomato chlorosis virus, infecting cucurbitaceous and solanaceous crops, respectively. Control of the criniviruses in bean crops will depend on efficient control of the vector. Physical control with greenhouses that prevent viruliferous whiteflies from gaining access to crops reduces BnYDV infection in plants and loss of production. Integrated pest management in beans would be preferred and the use of natural enemies to reduce secondary spread within greenhouses must be investigated.

Lettuce Chlorosis Virus Disease: A New Threat to Cannabis Production

In a survey conducted in Cannabis sativa L. (cannabis) authorized farms in Israel, plants showed disease symptoms characteristic of nutrition deprivation. Interveinal chlorosis, brittleness, and occasional necrosis were observed in older leaves. Next generation sequencing analysis of RNA extracted from symptomatic leaves revealed the presence of lettuce chlorosis virus (LCV), a crinivirus that belongs to the Closteroviridae family. The complete viral genome sequence was obtained using RT-PCR and Rapid Amplification of cDNA Ends (RACE) PCR followed by Sanger sequencing. The two LCV RNA genome segments shared 85-99% nucleotide sequence identity with LCV isolates from GenBank database. The whitefly Bemisia tabaci Middle Eastern Asia Minor1 (MEAM1) biotype transmitted the disease from symptomatic cannabis plants to un-infected 'healthy' cannabis, Lactuca sativa, and Catharanthus roseus plants. Shoots from symptomatic cannabis plants, used for plant propagation, constituted a primary inoculum of the disease. To the best of our knowledge, this is the first report of cannabis plant disease caused by LCV.

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

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.