Characterisation of the association of apple stem pitting virus (ASPV) with pear stony pit disease

Apple stem pitting virus (ASPV) is believed to be closely associated with pear stony pit disease (PSPD), however this has not been proven conclusively. It is also speculated that similar fruit damage can be caused by stink bugs. The objectives of this study were to survey pear orchards for PSPD, investigate the association between PSPD and ASPV, determine the genetic variation of ASPV and to develop a sensitive detection assay for ASPV.

Pear stony pit disease-like trees were visually identified. Samples were collected from symptomatic trees over two seasons to test for the presence of ASPV using an RT-PCR assay. A subsample of these samples was sent for high-throughput sequencing and data bioinformatically analysed to construct virome profiles of each sample. Based on all the sequence information available a new ASPV detection assay was developed and validated using the samples of the survey. Orchards were also surveyed for the presence of stink bugs. Stink bugs (Antestia) were collected and a lab colony established. A small stinkbug trail was conducted to attempt to prove or disprove the association between stinkbug presence and pear stony pit disease-like symptoms.

Pear stony pit disease-like trees were visually identified in 6 pear cultivars.

A new ASPV RT-PCR assay was designed and optimised.

ASPV was detected in 78% of pear stony pit disease-like samples.

High-throughput sequencing (HTS) analyses of pear stony pit disease-like samples identified citrus virus A (CiVA) and apple rubbery wood virus 2 (ARWV-2) for the first time in South African pear trees.

The stinkbug trial resulted in 37-44% pear damage in fruit clusters that were in mesh bags compared to 55-61% damage in fruit clusters that were left open for the season.

Two very similar but distinct symptoms were observed on fruit. One symptom had a 56% association with ASPV while the other had a 100% association with ASPV.

A positive association between the presence of ASPV and symptomatic fruit was observed, but the association was only 78%. However, after identifying two symptom categories, the defined pits on the surface with small deep penetrating dark shapes in the fruit’s flesh had a 100% association with the presence of ASPV. The high-throughput sequencing data allowed the observation of the high degree of diversity between ASPV accessions and as a result a new ASPV detection assay was designed and validated to be able to detect the ASPV variants present in South Africa. The contribution HTS can make to ensure virus free planting material was illustrated with the identification of two viruses not previously identified in pears in South Africa. The study identified both the virus and antestia feeding damage as potential contributing factors to pear stony pit disease-like symptoms. To date the best practice recommendation to prevent disease symptoms or disease-like feeding damage is to plant ASPV free plant material and to eliminate stink bugs from orchards.

The use of high-throughput sequencing can ensure virus free planting material with a higher degree of confidence.

A new ASPV detection assay was developed that can ensure ASPV free propagation and planting material for growers.

Both the virus and feeding damage were identified as potential contributing factors to pear stony pit symptoms and therefore the best practice recommendation to prevent symptoms is to plant ASPV free plant material and to eliminate stink bugs from orchards.