The molecular diversity of Pelargonium flower break virus (PFBV) was assessed using a collection of isolates from different geographical origins, hosts, and collecting times. The genomic region examined was 1,828 nucleotides (nt) long and comprised the coding sequences for the movement (p7 and p12) and the coat (CP) proteins, as well as flanking segments including the entire 3 untranslated region (3 UTR). Some constraints limiting viral heterogeneity could be inferred from sequence analyses, such as the conservation of the amino acid sequences of p7 and of the shell domain of the CP, the maintenance of a leucine zipper motif in p12, and the preservation of a particular folding in the 3 UTR. A remarkable covariation, involving five specific amino acid sites, was found in the CP of isolates largely propagated in the local lesion host Chenopodium quinoa and in the progeny of a PFBV variant subjected to serial passages in this host. Concomitant with this covariation, up to 30 nucleotide substitutions in a 1,428-nt region of the viral RNA could be attributable to C. quinoa-specific adaptation, representing one of the most outstanding cases of host-driven genome variation for a plant virus. Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels.It is commonly believed that the high mutation rates characteristic of RNA viruses, together with their short replication times and large populations, favor their rapid adaptation to changing situations (12, 13). Despite the high potential for genetic variation of these pathogens, a considerable number of studies on the diversity of plant virus populations have found a remarkable genetic stability (reviewed in reference 21). This stability is usually considered to be the result of selective pressures inherently imposed by genome replication and expression strategies and by virus-vector and virus-host interactions. In addition, random genetic drift due to bottlenecks associated with transmission or colonization events may also limit the eventual accumulation of variation (21,23,47). Investigating the factors affecting the diversity levels of viral populations can undoubtedly provide significant clues for the development of efficient and stable control strategies for viral pathogens (22,27,49).Pelargonium flower break virus (PFBV) is one of the most prevalent viruses infecting geraniums (Pelargonium spp.) throughout the world (1, 3, 6, 19, 41, 52). Its most conspicuous symptoms are white flower streaking, chlorotic spotting of leaves, and growth reduction causing significant losses in crop production. PFBV is mainly transmitted by vegetative propagation and mechanical inoculation, although transmissions by irrigation systems and by the western flower thrips Frankiniella occidentalis may also occur (30).PFBV is a member of the genus Carmovirus (family Tombusviridae) and, like all the species in the group, produces icosahe...