Analysis of novel strawberry pallidosis-associated virus (SPaV) variants reveals intragenomic recombination

Strawberry pallidosis-associated virus (SPaV) contains a bipartite RNA genome and belongs to the family Closteroviridae, genus Crinivirus. SPaV is one of the primary viruses associated with strawberry decline, a disease that threatens strawberry production. Here, we detected the presence of the virus and then determined the complete genome sequence of three SPaV RNA1 segments and one RNA2 segment in a single strawberry field sample collected in Quebec, Canada. The plant was co-infected with strawberry mild yellow edge virus (SMYEV), strawberry mottle virus (SMoV) and strawberry vein banding virus (SVBV). Nucleotide sequence analysis indicates that the three SPaV RNA1 segments represent three different variants, and they were likely the types of the parental strains that created two additional SPaV RNA1 segments, AY488137 (a sequence from an isolate from the USA) and MN747001 (the sequence of an isolate previously found in China), through multiple RNA recombination events.