Characterisation and Distribution of Karaka Ōkahu Purepure Virus—A Novel Emaravirus Likely to Be Endemic to New Zealand

Abstract

We report the first emaravirus on an endemic plant of Aotearoa New Zealand that is, to the best of our knowledge, the country’s first endemic virus characterised associated with an indigenous plant. The new-to-science virus was identified in the endemic karaka tree (Corynocarpus laevigatus), and is associated with chlorotic leaf spots, and possible feeding sites of the monophagous endemic karaka gall mite. Of the five negative-sense RNA genomic segments that were fully sequenced, four (RNA 1–4) had similarity to other emaraviruses while RNA 5 had no similarity with other viral proteins. A detection assay developed to amplify any of the five RNAs in a single assay was used to determine the distribution of the virus. The virus is widespread in the Auckland area, particularly in mature trees at Ōkahu Bay, with only occasional reports elsewhere in the North Island. Phylogenetic analysis revealed that its closest relatives are pear chlorotic leaf spot-associated virus and chrysanthemum mosaic-associated virus, which form a unique clade within the genus Emaravirus. Based on the genome structure, we propose this virus to be part of the family Emaravirus, but with less than 50% amino acid similarity to the closest relatives in the most conserved RNA 1, it clearly is a novel species. In consultation with mana whenua (indigenous Māori authority over a territory and its associated treasures), we propose the name Karaka Ōkahu purepure virus in te reo Māori (the Māori language) to reflect the tree from which it was isolated (karaka), a place where the virus is prevalent (Ōkahu), and the spotted symptom (purepure, pronounced pooray pooray) that this endemic virus appears to cause.

Mixed infection of an emaravirus, a crinivirus, and a begomovirus in Pueraria lobata (Willd) Ohwi

“…In contrast with RNA1-4, from which the putative proteins derived included recognizable functional domains, RNA5 encodes a protein of unknown function. It was not unusual in other emaraviruses that the role of P5 with a similar molecular weight but no sequence homology with each other is still to be determined (Buzkan et al, 2019 ; Wang et al, 2020 ; Fan et al, 2021 ; Rabbidge et al, 2021 ).…”

New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand

“…Records of plant viruses increased from around 100 species in the 1990s [ 14 , 15 , 16 , 17 ] to 258 species in 2021 [ 18 ] ( Figure 2 ). Most plant virus records in NZ are from economically important plants including horticultural, ornamental, and unwanted invasive plant species (the latter acting as virus reservoirs) [ 14 , 16 , 18 ]; however, it is probable that some of these new viruses are endemic to NZ [ 14 , 18 , 19 ]. The increase in the cumulative total number of viruses reflects not only new incursions but also changing technologies and our ability to detect and identify viruses.…”

“…The use of high-throughput sequencing (HTS) in plant diagnostics has accelerated the discovery of new viruses in native plants in recent years [ 18 , 19 , 20 ], including potential endemic viruses from the Emaravirus genus [ 18 ], such as the recently identified and characterized Karaka Ōkahu purepure virus [ 19 ]. There are still limited data available on the true extent of virus diseases in native ecosystems in NZ with information available from only five of the ten largest plant families [ 14 ].…”

The Complex World of Emaraviruses – Challenges, Insights and Prospects

“…In Turkey, PiVB was identified in pistachio [30]. From Oceania, FMV [118], HPWMoV [98], karaka Okahu purepure virus (KOPV) [70] and ARaV [65] have all been reported.…”

“…karaka Okahu purepure virus In New Zealand, KOPV was detected in karaka trees (Corynocarpus laevigatus) showing chlorotic spots. KOPV contains five genome segments and is closely related to clade D emaraviruses [70].…”