During summer 2019, virus-like symptoms were observed in strawberry (Fragaria × ananassa) fields in Kurdistan Province, Iran. Total RNA was extracted from a sample (P1F) using Gene JET Plant RNA Purification Kit (Thermo Fisher Scientific) and sequencing libraries were prepared using Collibri Stranded RNA Library Prep Kit for Illumina Systems (Invitrogen). The library was sequenced using a NovaSeq 6000 instrument (Illumina) resulting in 80 million of 150b pair-end reads and CLC Genomics Workbench 9.5.1 (Qiagen) were used for de novo assembly. Blast analysis showed that twelve contigs (ranging from 340 to 7594 nt) shared 79–95% nucleotide (nt) identities with RNA1 of the isolate M1 of strawberry pallidosis-associated virus (SPaV; Closteroviridae, Crinivirus) (NC_005895) from Maryland, USA, and eight contigs (ranging from 426 to 3296 nt) shared 84–99% nt identities with the M1 RNA2 (NC_005896). The largest assembled contigs of RNA1 (7594 nt) and RNA2 (3296 nt) (OK042926 and OK042927) had 82.4% and 93.7% nt identity with isolate M1, respectively. To confirm the detection of SPaV, total RNA was isolated from P1F using a silica-capture method and RT-PCR was conducted with primers SPaV-CPf (5ʹ-ATCTTATCAGCTAGAACAAGGCA-3′) and SPaV-CPr (5ʹ-AGGAAAAGGGGATGGTTCCTC-3ʹ) designed on the RNA2 sequences. The expected 794 bp amplicon was amplified from P1F and 6 out of 12 additional strawberry samples. The amplicons from PM2 and SSA2, were cloned and sequenced (MZ130323 and MZ130324). The sequences of PM2 and SSA2 shared 92.7% nt identity together, 93.3–99.8% and 93.1–98.4% with the two corresponding RNA2 contigs from P1F, and 98.4–93.1% with the SPaV-M1 isolate, respectively. SPaV was first found in the USA (Tzanetakis et al. 2004) and has subsequently been found in other countries (Tzanetakis et al. 2013; Ding et al. 2017). To our knowledge, this is the first report of SPaV infecting strawberries in Iran.
