Diversity of Tomato Brown Rugose Fruit Virus in Canadian Greenhouses

Abstract

Tomato brown rugose fruit virus (ToBRFV) has been a serious threat to greenhouse tomato production worldwide since its emergence in 2014 in Israel and Jordan. A member of the Tobamovirus genus, ToBRFV’s ability to break the longstanding Tm-22 resistance gene and ease of mechanical transmission has allowed the virus to spread rapidly through greenhouses worldwide. Little is known regarding the extent and genomic diversity of ToBRFV in Canada, despite the major impacts of this virus on greenhouse tomato production. 15 new Canadian ToBRFV genomic sequences have been determined, combined with 5 additional Canadian ToBRFV isolates retrieved from GenBank, and 5 consensus sequences assembled from a Canadian metagenomics wastewater monitoring study. The 25 Canadian sequences were combined with 332 international ToBRFV isolates to create a global phylogeny. Most Canadian isolates grouped together with other North American isolates but, several isolates branched separately, suggesting multiple introductions of ToBRFV to Canadian greenhouse systems. Canadian isolates sequenced in 2019 and 2024 originating from three different greenhouses grouped together, suggesting transmission of ToBRFV between greenhouses in Canada, showing that biosecurity of greenhouses is vital for the control of ToBRFV. Focused analysis on individual viral ORFs show the p126 and movement protein (MP) are the most variable regions of the genome. Novel mutations unique to Canadian isolates of ToBRFV were identified in both the p126 and MP. In the p126, 5 mutations were found in an area previously shown to directly interact with the TM-1 protein. Three of these mutations were unique to Canadian ToBRFV isolates and may be novel Tm-1 breaking mutations. In the MP, four novel mutations were identified that do not appear to be associated with Tm-22 and are potentially involved in breaking resistance mediated by an unknown resistance gene. Additionally, 7 isolates from greenhouse 2 had mutations in both the p126 and the MP, suggesting the virus has acquired potential resistance breaking mutations for multiple resistance genes. Until more robust resistance is identified, ToBRFV will continue to be a major threat to greenhouse tomato production in Canada.