Prevalence study of three pear tree viruses in Europe and biological characterization of Pyrus virus A

Abstract

Plant pathogens, including viruses, fungi, bacteria, or nematodes, can cause significant losses in pear fruit yield and quality. In the past, several disease-causing viruses were identified and further characterised in order to better understand the biology and mechanisms behind these infections. High-throughput sequencing (HTS) techniques make it possible, theoretically to detect any virus present in a sample, even in the absence of symptoms. These new technologies have changed how plant viruses can be detected without any prior information. Thanks to HTS technologies, a new virus, tentatively called Pyrus virus A (PyVA), was discovered in asymptomatic pear trees in the germplasm collection of the Walloon Agricultural Research Centre (CRA-W). The aim of this master’s thesis was to better characterise this new virus and to investigate the prevalence of two other recently discovered viruses, Citrus virus A (CiVA) and apple rubbery wood virus-1 (ARWV-1). In this study, a combination of bioinformatics, molecular (targeted RT-PCR), and biological methods were used to better characterise the beforementioned viruses by doing a field survey and grafting assays in greenhouse and in the field. To better characterise PyVA, bioinformatics analyses were carried out to obtain one PyVA genome and their comparison with neighbouring viral species. These analyses led to the conclusion that PyVA belongs to the Velarivirus genus. Its closest relative is Malus domestica virus A, according to their phylogenetic relationships. Among the different tissues tested for PyVA, the best tissue for sampling was the leaves, at the four cardinal points and at two different heights. Moreover, the presence of the three investigated viruses was tested in germplasm collections from three European countries: Slovenia (6 pear trees), Switzerland (9 pear trees), and Belgium (96 pear trees). The newly discovered PyVA was only found in Belgium at a prevalence of 4.2 %. CiVA was detected in all three countries, with a prevalence of 66.7 %, 44.4 %, and 51 %, in Slovenia, Switzerland, and Belgium, respectively. ARWV-1 was found in Switzerland and Belgium, with a prevalence of 11.1 % and 14.6 %, respectively. Regarding the grafting assay, which was carried out solely for analysis of PyVA, all the tests carried out were negative. These results suggest that PyVA has yet to be transmitted by grafting to the rootstocks and varieties tested after three months. Since, a virus transmission can take several months to develop, these results are not enough to draw a conclusion on transmissibility of PyVA by grafting and its potential host range. Finally, better knowledge of the genetic diversity of the three viruses could also be obtained thanks to partial sequences of the coat protein (PyVA and ARWV-1), and the movement protein (CiVA). In conclusion, overall, this master’s thesis has provided new information on the prevalence and geographical distribution of ARWV-1 and CiVA, and more knowledge on the biology of the novel virus PyVA such as prevalence, potential narrow host range and geographical distribution.