Superinfection Exclusion Is an Active Virus-Controlled Function That Requires a Specific Viral Protein

Abstract

Superinfection exclusion, a phenomenon in which a preexisting viral infection prevents a secondary infection with the same or a closely related virus, has been described for various viruses, including important pathogens of humans, animals, and plants. The phenomenon was initially used to test the relatedness of plant viruses. Subsequently, purposeful infection with a mild isolate has been implemented as a protective measure against virus isolates that cause severe disease. In the medical and veterinary fields, superinfection exclusion was found to interfere with repeated applications of virus-based vaccines to individuals with persistent infections and with the introduction of multicomponent vaccines. In spite of its significance, our understanding of this phenomenon is surprisingly incomplete. Recently, it was demonstrated that superinfection exclusion of Citrus tristeza virus (CTV), a positive-sense RNA closterovirus, occurs only between isolates of the same strain, but not between isolates of different strains of the virus. In this study, I show that superinfection exclusion by CTV requires production of a specific viral protein, the p33 protein. Lack of the functional p33 protein completely eliminated the ability of the virus to exclude superinfection by the same or a closely related virus. Remarkably, the protein appeared to function only in a homology-dependent manner. A cognate protein from a heterologous strain failed to confer the exclusion, suggesting the existence of precise interactions of the p33 protein with other factors involved in this complex phenomenon. Superinfection exclusion or homologous interference is defined as the ability of an established virus infection to interfere with a secondary infection by the same or a closely related virus. The phenomenon has been described for various virus-host systems, including viruses that cause serious diseases in humans, animals, and plants (2, 9, 10, 11, 14, 19-21, 23, 28, 29, 31, 35, 37, 38, 55, 61-64, 74-77). From an evolutionary standpoint, superinfection exclusion can be a powerful strategy that determines the genetic structure of the virus population. Superinfection exclusion protects the virus from a related competing secondary virus targeting the cell that has been successfully infected by the primary virus. Besides elimination of competition for host resources, the phenomenon could function as a means to maintain the stability of viral sequences because it prevents replication of two or more viral genomes in the same cell, thus reducing the likelihood of the recombination or reassortment of viral genes, with the latter event of particular importance for the evolution of segmented viruses (18,27). From a practical standpoint, superinfection exclusion can have both positive and negative attributes. Referred to as cross-protection, this phenomenon has been implemented as an agricultural practice in which purposeful infection with a mild isolate was used as a protective measure against isolates of the virus that cause severe disease (reviewed in...

Generation of an Attenuated, Cross-Protective Pepino mosaic virus Variant Through Alignment-Guided Mutagenesis of the Viral Capsid Protein

“…Alternatively, competition for certain unknown factors of the plant host could also contribute (38). Finally, recently published results suggest that cross protection might be caused by certain virus-encoded functions (6,7). Although it remains to be determined which mechanism is at play for mutant KD-mediated cross-protection against PepMV, we showed that the superinfected WT PepMV was undetectable in plants preinoculated with KD, thus suggesting a near complete exclusion of the former.…”

Comparison of multiple viral population characterization methods on a candidate cross-protection Citrus tristeza virus (CTV) source

“…Amplicon templates however only allow conclusions limited to the specific gene fragment amplified, and no information on whether recombination took place in any other region of the virus genome and hence if the gene sequenced is representative of the entire genome. While it is not known whether the p33 gene is the only gene playing a role in cross-protection, it does appear as though it is responsible for the genotype specificity of super-infection exclusion (Folimonova, 2012). This makes it particularly important to characterize this gene region of circulating CTV strains to identify potential crossprotection sources, as was done in this study.…”

“…Since recombination is common within the CTV genome Rubio et al, 2001;Vives et al, 2005), targeting only a specific region may provide distorted identification of the genotype as recombination events that occurred elsewhere in the genome would not be detected. This approach is however warranted when targeting a gene important for a specific biological function (Cook et al, 2015) for example the p33 gene which has been shown to be involved in the genotype specificity of the super-infection exclusion mechanism of CTV (Folimonova, 2012). While useful for the specific goal of identifying the genotypic variation within that specific gene, conclusions can only be inferred regarding that gene and not the actual genotype variation, which would require the sequence determination of the entire genome.…”

Genotyping WSSV isolates from northwestern Mexican shrimp farms affected by white spot disease outbreaks in 2010-2012

“…It should also be noted that this is the first report which includes cases of double WSSV infections based on the complete nucleotide sequence of ORF 125 (Table 8). This means that for the case of WSSV, the possible occurrence of viral superinfection cannot be excluded, especially since this phenomenon has been described for other viruses (Folimonova 2012, Campbell et al 2014.…”