Characterization of tulip streak virus, a novel virus associated with the family Phenuiviridae

First complete genome sequence of tulip mild mottle mosaic virus (Ophiovirus tulipae)

Tulip mild mottle mosaic disease, caused by tulip mild mottle mosaic virus (TMMMV, species Ophiovirus tulipae), was first reported in Japan in 1979. TMMMV has a negative-sense ssRNA genome and is closely related to ophioviruses such as Mirafiori lettuce big vein virus (MLBVV, Ophiovirus mirafioriense). However, its complete nucleotide sequence has not yet been reported. Therefore, in this study, we determined the complete nucleotide sequences of all four TMMMV segments. The 5'-terminal tetranucleotide sequences were highly conserved, and the five bases at the 5' end were identical in all segments. Nucleotide sequence comparisons of the four segments showed the highest sequence identity to those of MLBVV (70-76% for the genomic RNA sequences and 81-87% for the amino acid sequences of each ORF, except for ORF2). The amino acid sequences of the coat proteins of TMMMV and MLBVV were found to be 83.1% identical, which is below the 85% threshold for assignment to the same species, indicating that these viruses belong to different species in the same genus.

Identification of two missing genome segments of tulip streak virus

Complete sequences of RNA1 and RNA2 of tulip streak virus (TuSV) were already reported, but other segments were not yet. In this study, we reported RNA3 and RNA4 of TuSV, which shared around 69% nucleotide identity with those of closely related virus, suggesting that these are additional RNA segments.

Natural Populations from the Phytophthora palustris Complex Show a High Diversity and Abundance of ssRNA and dsRNA Viruses

We explored the virome of the "Phytophthora palustris complex", a group of aquatic specialists geographically limited to Southeast and East Asia, the native origin of many destructive invasive forest Phytophthora spp. Based on high-throughput sequencing (RNAseq) of 112 isolates of "P. palustris" collected from rivers, mangroves, and ponds, and natural forests in subtropical and tropical areas in Indonesia, Taiwan, and Japan, 52 putative viruses were identified, which, to varying degrees, were phylogenetically related to the families Botybirnaviridae, Narnaviridae, Tombusviridae, and Totiviridae, and the order Bunyavirales. The prevalence of all viruses in their hosts was investigated and confirmed by RT-PCR. The rich virus composition, high abundance, and distribution discovered in our study indicate that viruses are naturally infecting taxa from the "P. palustris complex" in their natural niche, and that they are predominant members of the host cellular environment. Certain Indonesian localities are the viruses' hotspots and particular "P. palustris" isolates show complex multiviral infections. This study defines the first bi-segmented bunya-like virus together with the first tombus-like and botybirna-like viruses in the genus Phytophthora and provides insights into the spread and evolution of RNA viruses in the natural populations of an oomycete species.

The Bunyavirales: The Plant-Infecting Counterparts

Negative-strand (-) RNA viruses (NSVs) comprise a large and diverse group of viruses that are generally divided in those with non-segmented and those with segmented genomes. Whereas most NSVs infect animals and humans, the smaller group of the plant-infecting counterparts is expanding, with many causing devastating diseases worldwide, affecting a large number of major bulk and high-value food crops. In 2018, the taxonomy of segmented NSVs faced a major reorganization with the establishment of the order Bunyavirales. This article overviews the major plant viruses that are part of the order, i.e., orthospoviruses (Tospoviridae), tenuiviruses (Phenuiviridae), and emaraviruses (Fimoviridae), and provides updates on the more recent ongoing research. Features shared with the animal-infecting counterparts are mentioned, however, special attention is given to their adaptation to plant hosts and vector transmission, including intra/intercellular trafficking and viral counter defense to antiviral RNAi.