Is There a “Biological Desert” With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses

Abstract

High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

“…We used this framework to review how the 45 new viruses discovered in tomato, both through HTS and through other methods, were characterized. The same approach was recently employed for fruit tree infecting viruses (Hou et al, 2020), where fulfillment of 14 characterization categories were reviewed. We analyzed 53 publications on novel tomato viruses (41 reporting viruses for the first time and 12 follow-up studies) from the 2011-2020 period contributing to characterization of newly discovered viruses associated with tomato, reviewing the fulfillment of 14 characterization categories (Figure 2A; for details, see Supplementary Table 1).…”

“…In the first part of this review, we discuss the discovery of 45 novel virus species in tomato within the 2011-2020 period and contextualize the role of HTS in these findings. Moreover, a postdiscovery characterization of new viruses represents an important step toward understanding their biological and/or economical relevance (Massart et al, 2017;Hou et al, 2020); thus, we also systematically reviewed to which extent such characterization have been performed for newly discovered viruses associated with tomato. Beyond discovering and detecting viruses in tomato, HTS can enable a broader look into the virome of tomato on a defined geographical scale, a virome of surrounding plants and vectors, and possible exchanges among those communities.…”

The Viral Capsid As Novel Nanomaterials for Drug Delivery

“…The primary goal of the virus is to transfer its genome to the target cell through the host. The virus genome then encodes the capsid protein subunits and several specific viral proteins [ 13 , 14 ]. The genome encodes only for a few structural proteins (in addition to nonstructural regulatory proteins involved in virus replication) and is constrained in its size.…”

Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems

“…The need for a current review about forest viruses is further strengthened by the fact that advances in plant virology are traditionally restricted in crop or fruit tree pathogenic viruses. This becomes apparent when considering the latest reviews [ 24 , 25 ] resuming viral discoveries using deep sequencing techniques in fruit trees, where virus discoveries in the forest ecosystem are not included. It is true that few groups worldwide focus their plant pathology research on forest ecosystems, which may be partially attributed to the difficulties in quantitatively estimating the importance of forest ecosystems and the economic impact due to viral epidemics.…”