UC Riverside

Viroids are RNA-based infectious agents that are single-stranded, covalently closed circular, non-coding and naked. For a successful systemic infection, viroid must replicate in a cell, move systemically in whole-plant. The high genetic diversity observed at the cellular level for Citrus exocortis viroid (CEVd) might be due to the absence of proof-reading activity of the host RNA polymerases and the bottlenecks, associated with systemic movement of the virus, played an important role in the observed low genetic diversity at the plant level.

Study of molecular and biological properties of in vivo generated CEVd mutants has been approached by characterizing a single sequence variant and testing for its replication in citrus protoplasts, systemic accumulation in citron seedlings, biological properties in different experimental hosts and intra-population profile of progeny viroid within a single-host. In vivo generated CEVd mutant infection in a single plant resulted in a progeny population with distinct but closely related sequences composing a quasi-species. The study revealed the effects of mutation, selection, and genetic drift on the adaptation and extinction of CEVd RNA. The stability of the 62A+, U129A and U278A variants in their respective progeny populations indicates the phenomenon of genetic drift and fixation of a mutation in the population. Genetic structure and diversity of CEVd progeny population altered significantly with replication in different hosts and understanding these interactions may facilitate the prediction and prevention of emerging virulent strains.

The nucleotide sequence of Dweet mottle virus (DMV) was determined and compared to sequences of Citrus leaf blotch virus (CLBV) and other members of the family Alpha and Beta-flexiviridae. The DMV genome has 8747 nt excluding the poly(A) tail at the 3' end of the genome. DMV genomic RNA contains three putative open reading frames (ORFs) and untranslated regions of 73 nt at the 5' and 541 nt at 3' termini. ORF1 potentially encoding a 227.48 kDa polyprotein, which has methyltransferase, oxygenase, endo-peptidase, helicase, and RNA-dependent RNA polymerase (RdRP) domains. ORF2 encodes a movement protein of 40.25 kDa while ORF3 is the coat protein of 40.69 kDa. Phylogenetic analysis, based on RdRP core domain revealed that DMV and CLBV are closely related.