Crop age is the main driver affecting alfalfa mosaic virus: The predominant virus in the alfalfa virome

The alfalfa virome has been understudied. Existing research dealing with viral incidences within the crop primarily concentrate on local factors, rather than considering a broader perspective. In this comprehensive 2-year study, we define the alfalfa virome and the main local and landscape factors affecting the incidence and annual increase of the Alfalfa mosaic virus (AMV), the most prevalent virus in alfalfa. The study was conducted in commercial alfalfa fields located along the highly productive northeast region of the Iberian Peninsula. For the first time in Europe, next-generation sequencing revealed the presence of 14 different viruses representing the genera Cytorhabdovirus, Alphapartitivirus, Amalgavirus, Alfamovirus, Luteovirus, Enamovirus and Flavivirus. AMV was the most prevalent species, accounting for 89% of the identified viral contigs. Enzyme-linked immunosorbent assays showed that the incidence of AMV varied between fields, with the average incidence doubling from 34% in 2019 to 65% in 2020. To assess the effect of local and landscape characteristics on the incidence of AMV and the observed annual increase, we selected different local variables and recorded landscape structure at three different buffer radii (250, 500 and 1000 m) from the centre of each field. Both the incidence and annual increase in AMV were driven mainly by local characteristics. The incidence of AMV showed a significant relationship with crop age and field area, whereas the annual increase was mainly influenced by crop age and the cumulative number of alate morphs of the aphid Acyrthosiphon pisum. Only one landscape composition variable, the percentage of alfalfa, showed a significant relationship with AMV incidence at the 250-m scale. These results confirm the effect of local variables on the population structure of generalist viruses.