Superinfection exclusion by complex virus populations: the ‘rule’ is in effect

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Understanding SIE in populations of Citrus tristeza virus

Written by María Bergua, Sung-Hwan Kang and Svetlana Y. Folimonova

Superinfection exclusion (SIE) is a phenomenon in which a viral infection prevents a subsequent infection with the same or closely related virus. Although SIE has many practical applications for reduction of pathogenic infections, our understanding of the phenomenon is largely incomplete. We are studying SIE using a unique Citrus species/Citrus tristeza virus (CTV) pathosystem. Previously, using CTV isolates each containing a single virus genotype, our lab has found that SIE operates by the following ‘rule’: the exclusion occurs only between isolates of the same genotype, but not between isolates of different genotypes (Folimonova et al., 2010). In the field, however, citrus trees are usually infected with mixtures of phylogenetically distinct genotypes of CTV. Thus, the main goal of this study was to examine how SIE works in the context of complex virus populations produced in different citrus varieties.

Our earlier work on the elucidation of the CTV SIE mechanism was done using “pure culture” isolates that contained only a single genotype of the virus. The idea of the present study came up with the need to translate our basic knowledge into practical applications that would allow protection of citrus trees in the field from aggressive CTV isolates. To model the situation in citrus orchards, we created mixed populations of single or multiple genotypes of CTV in several different citrus hosts. First, we examined how these populations were formed and how they were maintained over time within plants. We found that the multi-genotype populations reached equilibrium soon after inoculation and remained stable. Remarkably, in each combination, the population intra-host structure was uniform throughout the host plant. With that, the ratios between CTV genotypes in different citrus varieties significantly differed. That was exciting as such differences in the population profiles allowed us to assess the importance of a genotype level in the primary population for effective exclusion of an incoming virus variant. The results of our study showed that exclusion of a secondary infection by a CTV variant was determined by pre-existence of another variant of the same genotype in the primary population, even when the latter accumulated to a very low level, and was not affected by co-occurrence of additional heterologous genotypes. The same rule appeared to be in effect when SIE by mixed populations was assessed in a series of different citrus varieties.


Image legend

Observation of red fluorescent protein (RFP) fluorescence in phloem-associated cells on the internal surface of bark tissue from different citrus varieties (Swingle citrumelo, sour orange, Madam Vinous sweet orange, and Duncan grapefruit) infected with CTV populations at 16 weeks after the challenge with RFP-tagged CTV (T36-RFP) using a dissecting fluorescence microscope.

Introducing the authors


From left to right: María Bergua, University of California, Department of Plant Pathology, Davis, CA, USA; Sung-Hwan Kang, University of Florida, Department of Plant Pathology, Gainesville, FL, USA; Svetlana Y. Folimonova, University of Florida, Department of Plant Pathology, Gainesville, FL, USA.

About the research

Understanding superinfection exclusion by complex populations of Citrus tristeza virus
María Bergua, Sung-Hwan Kang, Svetlana Y. Folimonova
Virology, Volume 499, December 2016, Pages 331–339