Citrus tristeza virus: evolution of complex and varied genotypic groups

S J Harper

doi:10.3389/fmicb.2013.00093

Abstract

Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes.

Highlights

All organisms carry, in their genome, traces of their evolutionary history: past selective events, diversification, and recombination, all of which provide an insight into the adaptive landscape over which these organisms evolved
The existence of multiple strains exhibiting differences in infectivity, host range, transmission, or virulence is common amongst animal viruses, such as Hepatitis C virus (HCV) (Gray et al, 2011), Influenza A virus (Smith et al, 2009), and Simian immunodeficiency virus (Etienne et al, 2011), and in plant viruses, such as Cucumber mosaic virus (CMV) (Roossinck, 2001) and Plum pox virus (PPV) (Candresse and Cambra, 2006)
Citrus tristeza virus (CTV) is the exception, with at least six extant strains that exhibit a wide range phenotypic characteristics. These strains may have evolved through either a single introduction into citrus and subsequent radiation, or through multiple introductions followed by recombination; which scenario is more likely is obscured through subsequent evolution over time and the absence of extant protoclosterovirus sequences

Summary

Introduction

In their genome, traces of their evolutionary history: past selective events, diversification, and recombination, all of which provide an insight into the adaptive landscape over which these organisms evolved. Viral evolution and epidemiology are interdependent; the continued spread of a virus via vector species into new hosts relies on its ability to adapt (Pybus and Rambaut, 2009), both processes are subject to drift. One aspect of viral adaptation, of any given species, is the bifurcation of an ancestral sequence or population into two or more lineages that over time develop novel phenotypic characteristics, utilize novel vectors, and infect new host species. Members of a distinct phylogenetic lineage that possess a shared evolutionary history are, to all intents and purposes, strains. Amongst the Closteroviridae, the existence of multiple strains is a rarity, due in part to the limited host range of most species, phloem-specific tissue tropism, or lack of opportunity for spread due to absence of polyphagous vectors (Karasev, 2000), as well as a distinct lack of research on species infecting less economically important crops. With the possible exception of Grapevine leafroll virus (Bester et al, 2012), Citrus tristeza virus (CTV) is the only closterovirus species to possess multiple, phylogenetically distinct strains (Moreno et al, 2008)

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