Maize lethal necrosis viruses and other maize viruses in Rwanda

Authors: ASIIMWE, T - Rwanda Agriculture Board (RAB); Stewart, Lucy; Willie, Kristen; MASSAWE, DEOGRACIOUS - The Ohio State University; KAMATANESI, JOVIA - Rwanda Agriculture Board (RAB); Redinbaugh, Margaret

Submitted to: Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/4/2019
Publication Date: 12/17/2019
Citation: Asiimwe, T., Stewart, L.R., Willie, K.J., Massawe, D., Kamatanesi, J., Redinbaugh, M.G. 2019. Maize lethal necrosis viruses and other maize viruses in Rwanda. Journal of Plant Pathology. 69(3):585-597. https://doi.org/10.1111/ppa.13134.
DOI: https://doi.org/10.1111/ppa.13134

Interpretive Summary: Maize lethal necrosis (MLN) emergence in East Africa has been reported since 2011. Corn is a staple crop in East Africa, and MLN causes up to 100% losses. MLN is caused by synergistic co-infection of endemic potyviruses with emerging maize chlorotic mottle virus (MCMV). In order to effectively manage MLN, the distribution and variability of the viruses that cause it is essential for diagnostics and control. In this study, we examined the distribution of viruses in corn in Rwanda, using serological and amplification-based traditional diagnostics for MCMV and the most common potyvirus in East Africa, sugarcane mosaic virus (SCMV). We also used next generation RNA sequencing (RNASeq) to identify all virus sequences in samples from across the country. Our results identified MCMV and SCMV across all regions of Rwanda, compared detection techniques, and compared sequences of isolates identified. Other viruses were also identified in Rwanda, including sequences of viruses for which pathology or disease association in corn is not yet known. These data inform diagnostics for MLN, and data on locations in Rwanda where MLN is most and least pervasive.

Technical Abstract: Maize lethal necrosis (MLN) is emergent in East Africa, first reported in 2011 in Kenya, and is devastating to maize production in the region. MLN is caused by co-infection of maize with the emergent maize chlorotic mottle virus (MCMV) and any of several maize-infecting potyviruses endemic in East Africa and found worldwide. Here, we examine the distribution of MCMV and sugarcane mosaic virus (SCMV), the major viruses contributing to MLN in Rwanda. In addition, viruses and virus populations in maize across Rwanda were characterized by deep sequencing. Potyviruses including SCMV were prevalent across the country, while MCMV was found frequently in the north, west and south, but not in the east where rates of MLN were relatively low. When identified, MCMV had very high titers in infected plants and minimal sequence variability, whereas SCMV showed moderate titers and high sequence variability. MCMV and SCMV were detected in non-maize alternative hosts (Napier grass, sugarcane and sorghum), sometimes in co-infection, indicating that non-maize virus reservoirs may be important for management of MLN in mixed farming systems characteristic of Sub-Saharan Africa. Deep sequencing also identified maize streak virus and other maize-associated viruses, including a previously described polerovirus, maize-associated totiviruses, and a pteridovirus, which were confirmed in maize by reverse transcription polymerase chain reaction. Whether the totiviruses and pteridovirus infect maize and if these and the polerovirus contribute to disease is not known.