In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses.Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations.RNA virus populations, including those within an individual virus-infected host or those in different host individuals, are heterogeneous in nature. For RNA viruses, this is often attributed to their large population sizes, short generation times, and high mutation rates from error-prone replication by the viral RNAdependent RNA polymerase (RdRp), which lacks a proofreading activity (9). Additional sources which can give rise to genetic variation include genome recombination and reassortment (39). The genetic diversity and structure of virus populations are limited and shaped by natural selection, genetic drift, and gene flow (37). The effects of these evolutionary mechanisms are also affected by the virus biology (e.g., host type and range, and means and extent of spread), the ecological environment, and population parameters (e.g., population size and history of population bottlenecks). Understanding the factors involved in the genetic diversity and structure of virus populations is fundamental for designing effective strategies for disease control or virus eradication (1).Like many animal viruses and bacteriophages, some RNA plant viruses have measurably evolving populations (11,20) whereas others evolve more slowly and have genetically stable populations (19). Two key aspects affecting virus evolution are the means of spread and host type. Plant viruses mostly utilize specific vectors for their plant-to-plant transmission (40). Plant-to-plant spread of viruses among herbaceous annual plants may be rapid and the life of the plant host is relatively short. Thus, these viruses are constantly infecting and adapting to new plant hosts. By contrast, the chronic infections in woody perennial plants can last for decades, with or without observable symptoms (44). In addition, most perennial crop plants are vegetatively propagated. If source plants used for propagation are virus infected, this provides opportunity for efficient transfer and mainten...

RNA and nucleotide sequence-based analyses were used to identify viruses in fig mosaic (FM)-affected fig (Ficus carica) trees. Nucleotide sequence analyses of 267 cloned cDNAs identified sequences corresponding to four viruses representing four distinct taxa from fig trees in California. Virus sequences corresponding to members of the family Closteroviridae were most common (55 sequences). We also found two sequences for an Umbravirus, one sequence corresponding to a Luteovirus-associated RNA, and two sequences that showed homology to European mountain ash ringspot-associated virus (EMARAV). Reverse transcription–polymerase chain reaction (RT-PCR) and northern hybridization analyses were used to confirm the presence of specific virus RNAs in fig trees. A survey of 184 fig trees from a germplasm collection, a commercial orchard, backyards, and feral fig trees showed that one virus was most common (detected in 96% of tested samples), while none of the other virus sequences were detected in more than 36% of the fig trees. Based on its association with FM-affected trees, nucleotide sequence-based phylogenetic association, and previous reported properties, we suggest the name of this virus as Fig mosaic-associated virus (FMaV).

Fig mosaic virus (FMV), a member of the newly described genus Emaravirus, has four negative-sense single-stranded genomic RNAs, and each codes for a single protein in the viral complementary RNA (vcRNA). In this study we show that FMV mRNAs for genome segments 2 and 3 contain short (12-18 nucleotides) heterogeneous nucleotide leader sequences at their 5' termini. Furthermore, by using the high affinity cap binding protein eIF4E(K119A), we also determined that a 5' cap is present on a population of the FMV positive-sense RNAs, presumably as a result of cap-snatching. Northern hybridization results showed that the 5' capped RNA3 segments are slightly smaller than the homologous vcRNA3 and are not polyadenylated. These data suggest that FMV generates 5' capped mRNAs via cap-snatching, similar to strategies used by other negative-sense multipartite ssRNA viruses.