Emergence and phylodynamics of Citrus tristeza virus in Sicily, Italy.

Salvatore Davino,Stefano Panno,Anouk Willemsen,Santiago F Elena,Luis Rubio,Mario Davino,Antonino Catara,Dhanasekaran Vijaykrishna

doi:10.1371/journal.pone.0066700

Abstract

Citrus tristeza virus (CTV) outbreaks were detected in Sicily island, Italy for the first time in 2002. To gain insight into the evolutionary forces driving the emergence and phylogeography of these CTV populations, we determined and analyzed the nucleotide sequences of the p20 gene from 108 CTV isolates collected from 2002 to 2009. Bayesian phylogenetic analysis revealed that mild and severe CTV isolates belonging to five different clades (lineages) were introduced in Sicily in 2002. Phylogeographic analysis showed that four lineages co-circulated in the main citrus growing area located in Eastern Sicily. However, only one lineage (composed of mild isolates) spread to distant areas of Sicily and was detected after 2007. No correlation was found between genetic variation and citrus host, indicating that citrus cultivars did not exert differential selective pressures on the virus. The genetic variation of CTV was not structured according to geographical location or sampling time, likely due to the multiple introduction events and a complex migration pattern with intense co- and re-circulation of different lineages in the same area. The phylogenetic structure, statistical tests of neutrality and comparison of synonymous and nonsynonymous substitution rates suggest that weak negative selection and genetic drift following a rapid expansion may be the main causes of the CTV variability observed today in Sicily. Nonetheless, three adjacent amino acids at the p20 N-terminal region were found to be under positive selection, likely resulting from adaptation events.

Highlights

Viruses, in particular those with RNA genomes, are the most abundant parasites infecting animals, plants, and bacteria
The prevalence of Citrus tristeza virus (CTV) increased from 2002 reaching a maximum peak of about 50% in Syracuse in 2005 and in Catania in 2007, followed by a moderate decrease in Catania until 37.4% whereas in Syracuse plummeted to about 10% (Fig. 1)
In the South, CTV was only found in Ragusa in 2006 and 2007 with a prevalence around 10% whereas it was never detected in the western provinces of Trapani, Agrigento and Caltanissetta

Summary

Introduction

In particular those with RNA genomes, are the most abundant parasites infecting animals, plants, and bacteria. RNA viruses have a great potential for rapid evolution due to the high mutation rates, large population sizes and short generation times [1]. This rapid evolution means that epidemiological and evolutionary processes occur on a similar time scale of a few years and that they may interact conditioning the spatiotemporal incidence and phylogenetic patterns. Many studies on the phylogeography or phylodynamics of human and animal viruses on different geographical scales have been performed [4,5,6,7,8,9] but these studies are still scarce for plant viruses and are mostly restricted to viruses infecting annual crops [10,11,12,13]. To our knowledge, phylodynamics associated with the colonization of a new geographical area by a plant virus has not been addressed

Methods

Results

Conclusion