Phylodynamic of citrus leprosis virus C in the Americas: origin, diversification, and dispersion of the main causal agent of the citrus leprosis disease

Abstract

Citrus leprosis virus C (CiLV-C) is the prevalent viral species associated with citrus leprosis disease from Mexico to Argentina. CiLV-C, the type member of the genus Cilevirus, family Kitaviridae, has a genome composed of two (+)ssRNA molecules that encode six open reading frames (ORFs), two in the RNA1 (RdRp and p29); and four in the RNA2 (p15, p61, MP, and p24). Experimentally, CiLV-C infects plant species belonging to 28 families, but the range of natural hosts seems limited to only citrus (mainly sweet oranges), Commelina benghalensis and Swinglea glutinosa plants. CiLV-C is unable to move systemically in any of these hosts and is naturally transmitted by Brevipalpus sp. mites in a circulative manner, however, viral replication in the mite cells has not been confirmed. Two strains of CiLV-C have been described to date: CRD and SJP. Members of the SJP clade were firstly identified in 2015 and in silico analyses indicated that viruses from both clades were involved in putative natural recombination processes. Previous results indicated low genetic variability (nucleotide diversity À=0.07) of the CiLV-C population ranging from Mexico to Argentina, including isolates collected between 1932 and 2017. Co-existence of two well-defined clades with low molecular variability led us to propose two hypotheses: viruses of the two clades evolved either (i) independently, outside the citrus agroecosystem, or (ii) along with the non-permissive CL pathosystem (local infection, HR-like response, vector transmission), which prompted the stochastic fixation of divergent haplotypes through highly frequent bottlenecks. To test these and other hypotheses, the objective of this work is to provide evidence that supports the putative evolutionary history of CiLV-C in the Americas, inferring the most ancestral haplotype possible, its place of origin, dispersion and genetic diversification on a spatio-temporal scale. For this purpose, the characterization of the genomic sequence of CiLV-C from the Americas from the period of 1932-2019 will be performed. In addition, a deeper study of the genetic variability of the viral variants occurring in the Brazilian citrus belt from 2016-2019 will be carried out. With the dataset generated and through bioinformatic analyzes with evolutionary virologist who has previously been a CNPq Ciência sem fronteiras fellow who is based at the Biodesign Center for Fundamental and Applied Microbiomics (Biodesign Institute), Arizona State University, Tempe, USA, it is intended to determine the phylodynamics and phylogeography of CiLV-C epidemics across the Americas. The data from this may help us establish efficient control measures for citrus leprosis.