Incidence, distribution, transmission, and genetic diversity of the novel waikavirus, sweetbriar rose curly top associated virus

This study describes a broad survey of sweetbriar rose curly-top associated virus (SRCTaV; sp. Waikavirus rosae) in Aotearoa New Zealand and the United Kingdom. A total of 37 out of 1,116 Rosaceae samples tested positive for the presence of SRCTaV by both real-time and conventional RT-PCR. A 574 bp fragment located in the RNA-dependent RNA Polymerase domain was obtained by end-point RT-PCR from each sample and Sanger sequenced. The resulting phylogenetic analysis showed no significant correlation between host species or geographical location. Four additional complete SRCTaV genome sequences were obtained from this pool of samples by high-throughput sequencing and shown to contain evidence of a conserved open reading frame (ORF) +1 to the main single ORF1, consistent with all other recognized waikaviruses. A broader search mining for the presence of SRCTaV in 248 Rosaceae BioProject Sequence Read Archive records did not identify any new sequences. Hypothetical transmission routes via seeds or commonly found aphids (Macrosiphum rosae and Chaetosiphon tetrarhodum) were not demonstrated experimentally. In light of these results, the possible origins for SRCTaV are discussed.