Identification and complete genome sequencing of alfalfa virus S diagnosed in alfalfa plants (Medicago sativa) from Washington State, U.S.A.
Alfalfa virus S (AVS) is a new species in the genus Allexivirus, family Alphaflexiviridae. It was recently identified in alfalfa (M. sativa) plants obtained from Sudan, Northern Africa. In 2019, the virus was also diagnosed in alfalfa samples acquired from China. Prior to this report, the virus has not been identified in the United States. Alfalfa plants used in this study originated from the Prosser (Washington) area. Leaves displaying chlorotic symptoms with a mosaic pattern were collected from 10 different plants and pooled together in two samples (three to five leaves in each). Based on the results of high-thoughput sequencing (HTS), the causal agent was confirmed as AVS. The identity of the viral genome was additionally confirmed by RT-PCR and phylogenetic analysis. HTS revealed that the alfalfa sample in which AVS was identified was coninfected with other pathogens including alfalfa mosaic virus, bean leafroll virus, pea streak virus, Medicago sativa alphapartitivirus, Medicago sativa amalgavirus, and Pseudomonas bacterial species. This once again demonstrated that viral coinfections are common in alfalfa and may constitute a substantial part of the disease complexes.