Mutation, recombination, and ensuing phenotypic modifications in response to selective pressures can be readily observed and quantitated with RNA viruses both in cell culture and in vivo within modest time periods. This has rendered viruses suitable experimental systems for studies of basic Darwinian processes of genetic modification, competition, and selection or random drift as agents of genome diversification and biological adaptation (reviewed in references
1,
8, and
12). However, some major evolutionary transitions such as RNA genome segmentation have never been observed in the laboratory, yet they have probably occurred, given the hundreds of animal, plant, bacterial, and fungal viruses with segmented RNA genomes that have been described, including picornavirus-like plant RNA viruses (
43). We have carried out extensive studies on the population dynamics of the important animal picornavirus foot-and-mouth disease virus (FMDV), including that of phenotypic evolution upon long-term serial cytopathic infections of BHK-21 cells (
2). Unexpectedly, after more than 200 serial infections of viral population C-S8c1 of FMDV (a clone of serotype C [reviewed in reference
33]), defective genomes became dominant in the population. Defective interfering (DI) particles are frequently produced upon passage of RNA viruses at a high multiplicity of infection (MOI). DI particles are deletion mutants that require the presence of helper virus for replication and can interfere with the replication of the standard infectious virus (
14-
16,
29,
32,
35). The results described here show that defective genomes which individually could not cause cytopathology could nevertheless complement each other to produce progeny and kill cells in the absence of standard virus. The results provide, to our knowledge, the first description of defective RNA genomes occurring during viral replication that can be stably maintained by complementation upon passage at a high MOI in the absence of standard infectious virus. Therefore, the results provide experimental evidence of the initial step of an evolutionary transition towards genome segmentation of an unsegmented RNA virus.
DISCUSSION
Defective viral genomes requiring a helper virus for replication are frequently generated upon serial high MOI passage of RNA viruses (
14-
16,
29,
32,
35). Deletions in most picornavirus DI genomes are located in the 5′ portion of the viral RNA in the capsid protein-coding region (
20,
26), and they ranged between 4 and 16% of the genomic residues (
21). Packaging constraints dictate the approximate size limits of genome deletions that can be accommodated by viral encapsidation mechanisms (
14,
35). In the case of FMDV, defective Δ417 RNA-lacking 417 nucleotides of the L region-was shown to be packaged and to contribute capsid proteins to the particles of the helper virus (
6). Engineered FMDV RNA lacking the complete open reading frame of protein Lb produced infectious virus upon transfection of BHK-21 cells (
30). O
1K FMDV RNA transcripts lacking Lb- and capsid-coding regions were replication competent but their
trans encapsidation upon superinfection with homologous virus was inefficient (
22). The difference between this O
1K-based replicon and the defective RNAs described here in their capacities to produce cytopathology may be influenced by nucleotide sequence context, the nature of the deletions, or a longer time required for cytopathology in transfections with C-S8c1 cDNA transcripts than with O
1K cDNA transcripts (Table
3). The observed complementation between FMDV-defective genomes lacking the L protease and some capsid proteins is in agreement with the
trans-acting properties of these proteins (
22,
23,
30,
39).
Engineered RNAs encoding nonstructural or structural proteins of Sindbis virus could function to produce infectious particles with copackaged bipartite RNA (
13). DI RNAs of mouse hepatitis virus could complement engineered RNAs expressing the missing proteins (
18). In the DNA virus simian virus 40, a defective DNA encoding mostly early functions could complement another defective DNA encoding late functions to produce infectivity (
27). Both DNAs contained iterated replication origins that could contribute to their stability and infectivity.
In the present study we have documented that FMDV can evolve to produce defective genomes that can replicate and kill cells in the absence of wild-type virus. This has been shown by independent procedures such as the presence of defective genomes in individual viral plaques, infection by transcripts of the defective genomes, and two-hit kinetics for cell killing.
What could trigger the evolutionary transition from a high fitness, replication-competent standard FMDV genome toward two RNA forms with deletions that become dominant and are infectious by complementation? Theoretical studies have led to two main proposals for the driving force for genome segmentation. One proposal is that genome segmentation evolved in response to high mutation rates to provide multicomponent reproduction as a form of sex to attenuate the effect of deleterious mutations (
5,
31). In this respect, it has been recently reported that genomes of nucleopolyhedrovirus with deletions can work with full-length partners to mutual benefit, possibly through complementation (
19). Another proposal is that segmentation could result from selection of shorter RNA molecules that replicate faster than the corresponding parental genome, favored at high MOIs to ensure efficient complementation (
25,
40). Deleted forms of viral RNAs have indeed been shown to have a selective replicative advantage over parental full-length genomes in vitro (
24,
34). A difference of replication capacity or of tolerance to mutations is now amenable to direct experimental testing with the segmented-unsegmented FMDV genome system, and such experiments are currently in progress.
Nucleotide sequence analyses (unpublished data) suggest that a recombination event within the VP4-coding region could be involved in the transition from the segmented to the unsegmented FMDV genome, a transition which is strongly selected at low MOIs.
It is not possible to know the relevance of these observations in cell culture for the natural evolution of RNA genomes or whether in nature segmented RNA genomes evolved from or preceded unsegmented forms. What our results show, however, is that RNA genomes have an evolutionary potential to evolve towards genome segmentation within infected cells, provided a strong selective pressure to favor complementation (high MOI) is present. A number of plant RNA viruses have segmented genomes encapsidated into separate particles (multipartite genomes) (
43). The FMDV provides an experimental system with which to compare possible advantages of segmentation in ways that have not been possible until now because segmented and unsegmented cognate forms can be compared. It will be also intriguing to examine further the evolution of the system dominated by defective RNAs at high MOI passage and to analyze whether additional divergence and functional specialization of the two segments occur. These studies may be relevant for probing the advantage of sex in genetic systems.