Diversity of the virome associated with alfalfa (Medicago sativa L.) in the U.S. Pacific Northwest

Authors: Nemchinov, Lev; Irish, Brian; Grinstead, Sam; Shao, Jonathan; Vieira, Paulo

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2022
Publication Date: 5/24/2022
Citation: Nemchinov, L.G., Irish, B.M., Grinstead, S.C., Shao, J.Y., Vieira, P. 2022. Diversity of the virome associated with alfalfa (Medicago sativa L.) in the U.S. Pacific Northwest. Scientific Reports. 12:8726. https://doi.org/10.1038/s41598-022-12802-4.
DOI: https://doi.org/10.1038/s41598-022-12802-4

Interpretive Summary: Alfalfa is one of the most extensively cultivated forage legumes in the world. It is currently the third most valuable field crop in the United States with an estimated worth of over $9.3 billion. Alfalfa productivity is limited by various infectious diseases that can reduce forage yield and quality and shorten stand life. The crop is frequently infected with a diverse array of pathogens that have distinct life cycles, biology, and mode of action. Among them are many co-infecting viruses that greatly contribute to the heterogeneity of within-host pathogenic communities, representing a ubiquitous and abundant background for all other host-pathogen interactions. Regrettably, an impact of viral diseases, their role in alfalfa health and involvement in the severity of complex infections involving multiple pathogens are often underestimated. In this work, we characterized a diversity of viral populations in several commercial alfalfa production fields located in western US states of Idaho and Washington. It is expected that this study will be of interest to a wide range of scientists involved in research on alfalfa health and development in academia and government organizations.

Technical Abstract: The following conclusions could be drawn based on the outcome of this work: 1. The prevailing viral pathogens infecting alfalfa in the surveyed areas included both well-known as well as emerging, newly discovered viruses, with the potential to increase in incidence. In the first group were alfalfa mosaic virus, pea streak virus, alfalfa latent virus, and bean leafroll virus, while the second group contained viruses that were only recently reported in the host and in this country: alfalfa virus S, lucerne transient streak virus, partitiviruses and amalgavirus. 2. Alfalfa may potentially be a host for viruses that were not previously reported to infect the plant, such as alfalfa strain of cherry virus Trakiya (CVT-A). While detection of CVT-A strain is most likely due to the presence of authentic infection, occurrence of hop latent virus (HLV) and potato virus X (PVX), despite confirmative RT-PCRs, could be a result of external contamination of alfalfa plants via aphids (HLV) or contaminated machinery (PVX). Negative results of N. benthamiana inoculation with alfalfa samples containing PVX reads support this hypothesis. It is noteworthy however, that PVX, among other viruses, was believed to infect clovers and alfalfa in Illinois, according to the plant disease report from the University of Illinois. 3. Several conceivably novel viruses were identified in the survey, including three different rhabdoviruses, a toti-like virus, two picorna-like viruses, and a deltapartitivirus. Their exact origin and importance for alfalfa health remains to be clarified. Rhabdoviruses, such as alfalfa dwarf virus, can cause a severe disease in alfalfa. 4. Each tested sample was co-infected with a cluster of different viruses. Occurrence of multiple viral infections can affect within-plant virulence, disease dynamics, host-pathogen interactions, and as a result trigger epidemiological implications. 5. In many cases, virus-infected samples carried non-viral pathogens as well, such as bacteria and fungi, suggesting that viruses represent a ubiquitous and abundant background for all other host-pathogen interactions. This sophisticated multi-pathogenic habitat involving viruses as an essential part of the disease complexes can affect behavior of all co-infecting agents, their intra-host accumulation, and transmission rates. Consequently, host fitness may be altered triggering susceptibility, expanding disease damage to the plant and, potentially, disease epidemiology.