Genetic Diversity, Reassortment, and Recombination inAlfalfa mosaic virusPopulation in Spain

Abstract

The variability and genetic structure of Alfalfa mosaic virus (AMV) in Spain was evaluated through the molecular characterization of 60 isolates collected from different hosts and different geographic areas. Analysis of nucleotide sequences in four coding regions--P1, P2, movement protein (MP), and coat protein (CP)--revealed a low genetic diversity and different restrictions to variation operating on each coding region. Phylogenetic analysis of Spanish isolates along with previously reported AMV sequences showed consistent clustering into types I and II for P1 and types I, IIA, and IIB for MP and CP regions. No clustering was observed for the P2 region. According to restriction fragment length polymorphism analysis, the Spanish AMV population consisted of seven haplotypes, including two haplotypes generated by reassortment and one involving recombination. The most frequent haplotypes (types for P1, MP, and CP regions, respectively) were I-I-I (37%), II-IIB-IIB (30%), and one of the reassortants, II-I-I (17%). Distribution of haplotypes was not uniform, indicating that AMV population was structured according to the geographic origin of isolates. Our results suggest that agroecological factors are involved in the maintenance of AMV genetic types, including the reassortant one, and in their geographic distribution.

Diversity of Plant Virus Populations: A Valuable Tool for Epidemiological Studies

“…It has been shown that selection against heterologous gen combinations increases as host colonization progresses along the infection cycle of Cucumber mosaic virus [32], affecting the frequency of genetic exchange. This explains that recombinants and reassortants are often found at low frequencies [33,34], although the frequency of particular combinations may be dependent on agro-ecological factors [17,19], and support the hypothesis of co-adaptation of gene complexes within the viral genomes [32,35].…”

“…Analysis of their sequences indicates that both mechanisms contribute significantly to the generation of variability in the evolution and diversification of certain taxonomic groups [11][12][13][14][15][16]. Recombination and reassortment events may involve members of the same plant virus species [17][18][19], members of different species [20][21][22][23][24] or even genus [25]. Genetic exchange by recombination or reassortment may have important epidemiological implications of practical relevance, even more than mutation, as it has been associated to host jumps, host range expansion, changes in virulence, breaking of host resistance and finally, the emergence of new viral plant diseases.…”

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing

“…It provides evidence for two distinct PNRSV phylo-groupings for each of RNA1 and RNA2, which were observed for similar gene regions of RNA1 and RNA2 of the Bromoviridae family members Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV; genus Cucumovirus ) [52, 53]. Phylogenetic analysis of CP sequence variants from the 53 plant samples diverged into the three already defined PNRSV RNA3 phylo-groups [26, 27, 30, 32], even though a smaller portion of the genome was used.…”

Biological and Molecular Characterization of Alfalfa Mosaic Virus Infecting Trumpet Creeper (Campsis radicans) in Iran

“…Furthermore, Bergua et al. () showed that agroecological factors including the reassortant one are involved in survival and in their geographical distribution of AMV genetic types. To date, new genetic type IIB is exclusively composed of several Spanish isolates and two isolates from New Zealand.…”

“…Similarly, type IIA mostly contains isolates from Europe (Bergua et al. ). Our phylogenetic relationship analysis using 21 AMV isolates (Table S1) is in accordance with previous genetic studies based on sequences of the CP gene (Parrella et al.…”