First report of Turnip yellows virus in cabbage in the Philippines

Abstract

In March 2017, 52 dried-leaf samples of brassicaceous plants from the Philippine Highlands, one of which was a sample of cabbage (Brassica oleracea var. capitata; Fig. 1), were submitted to Fera Science Ltd., via the Centre for Agriculture and Bioscience International (CABI). The plants were all displaying virus-like, yellowing symptoms (Reeder et al., 2017). Initially, samples were bulked together and tested by ELISA for the presence of viruses known to occur in the Brassicaceae including Cucumber mosaic virus (CMV) (Agdia, USA), Turnip mosaic virus (TuMV) and Turnip yellows virus (TuYV) (Loewe, Germany). All the bulked samples gave negative results for CMV, TuMV and TuYV, and the samples were also tested individually for the presence of Turnip yellow mosaic virus (TYMV) (DSMZ, Germany). All Chinese cabbage (Brassica rapa subsp. pekinensis) samples were positive for TYMV as described by Reeder et al. (2017). However, the Brassica oleracea var. capitata sample tested negative for TYMV and was therefore screened for virus infection using an Illumina MiSeq as described by Adams et al. (2014). A total of 857,018 reads were obtained from the sample, 924 were assembled to yield the complete coding sequence of a polerovirus (GenBank Accession No. MW537050). The average sequencing depth of this contig was 31. Comparison at the whole genome level initially suggested that the isolate was either Brassica yellows virus or TuYV with significant nucleotide identity (>94%) to examples of both viruses. Recombination analysis using RDP 4 (Martin et al., 2015) for both TuYV (NC003743) and BrYV (NC016038) type isolates suggested that this isolate has a small recombination event in the P3-P5 region. Filardo et al. (2021) have proposed that TuYV and BrYV are the same species and describe isolates with a similar P3-P5 recombination as within a clade (group 2) of their unified TuYV species. Therefore, this isolate has been identified as containing a group 2 TuYV. A specific real-time RT-PCR primer/probe set was designed based on both TuYV and BrYV sequences. The primer/probe sequences are as follows TuYV-F2: 5′-GCCGCYTGTTTCTCAGTTCTG-3′; TuYV-R2: 5′-RACTAACCACGAGTAAAGAAGCTCAA-3′; TuYV-P2 (probe): [FAM] 5′-ACGAGTTGCGGCAYGATCCAGC[BHQ1] -3′. Testing the Brassica oleracea var. capitata sample by the real-time RT-PCR assay yielded a positive result, whereas the sample had tested negative by ELISA, suggesting the ELISA does not detect all strains of TuYV. TuYV is widespread in cruciferous plants across mainland China, South Korea and Japan (Zhang et al., 2016) but this is the first report of TuYV in the Philippines. Further work is needed to determine the prevalence of TuYV in cruciferous plants in the Philippines and identify the key aphid vectors. This information could then be used to inform future management strategies. This testing was partially funded through the Defra-Fera Long Term Service Agreement. The authors would like to thank CABI for their support.