Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil

Abstract

Citrus sudden death-associated virus (CSDaV) is a monopartite positive-sense single-stranded RNA virus that was suggested to be associated with citrus sudden death (CSD) disease in Brazil. Here, we report the first study of the genetic structure and molecular variability among 31 CSDaV isolates collected from both symptomatic and asymptomatic trees in CSD-affected areas. Analyses of partial nucleotide sequences of five domains of the CSDaV genomic RNA, including those encoding for the methyltransferase, the multi-domain region (MDR), the helicase, the RNA-dependent RNA polymerase and the coat protein, showed that the MDR coding region was the most diverse region assessed here, and a possible association between this region and virus adaption to different host or plant tissues is considered. Overall, the nucleotide diversity (π) was low for CSDaV isolates, but the phylogenetic analyses revealed the predominance of two main groups, one of which showed a higher association with CSD-symptomatic plants. Isolates obtained from CSD-symptomatic plants, compared to those obtained from asymptomatic plants, showed higher nucleotide diversity, nonsynonymous and synonymous substitution rates and number of amino acid changes on the coding regions located closer to the 5’ end region of the genomic RNA. This work provides new insights into the genetic diversity of the CSDaV, giving support for further epidemiological studies.

Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses

“…CSDaV could be this other virus and involved with CSD. Interestingly, the CSDaV consensus sequence obtained from libraries constructed from the symptomatic plants (CSDaV_SPBR_01) showed to be phylogenetically distant from the CSDaV consensus sequence extracted from the asymptomatic libraries (CSDaV_SPBR_02), showing at about 13% nucleotide diversity between them, which is consistent with our previous work on the CSDaV genetic diversity [33]. Furthermore, a remarkable 29 times higher average coverage was found in mapping reads from symptomatic libraries on the CSDaV_SPBR_01 consensus sequence, compared to mapping reads from asymptomatic libraries.…”

Characterization of a new apple luteovirus identified by high-throughput sequencing

“…The eight apple cultivars propagated on MM106 rootstock showed graft union necrosis and tree decline. Similar diseases such as citrus tristeza quick decline disease (T-QD) [ 20 ] and citrus sudden death (CSD) have described in citrus trees [ 21 ]. T-QD destroyed millions of sweet citrus trees ( Citrus sinensis L.…”

“…RAD is only observed on apple trees grafted on certain dwarf rootstock cultivars such as M9. Both T-QD and CSD also occurred only on sweet orange grafted on certain rootstock [ 20 , 21 ]. T-QD was controlled by replacement of the sour orange rootstock with CTV-tolerant rootstock such as Rangpur lime and Volkamer lemon.When examined by RT-PCR assay, ALV-1 was detected by RT-PCR in trees from the RAD-affected orchard (Tables 1 and 2 ).…”

“…This study suggested the symptoms on the trunk develop gradually in affected trees. Citrus trees infected with CSDaV have an incubation period of at least two years before symptoms of sudden death are observed [ 21 ]. Similarly, apple trees may remain functional and healthy in early infection before appearance of the tree decline and trunk symptoms such cracks and cankers, which could be caused by secondary fungal/bacterial infection on the trees weaken by the virus infection.…”

“…Therefore, M9 may be susceptible to ALV-1. Occurrence of AUND, T-QD and CSD had been associated with trees grafted on virus-susceptible rootstocks, respectively [ 19 – 21 ]. Replacement of the sour orange rootstock with CTV-tolerant rootstocks controlled T-QD [ 20 ].…”