# Novel RNA Viruses Discovered in Weeds in Rice Fields
## 3 Results
### Characterization of Positive-Sense RNA Viruses
These botourmiaviruses have genome lengths ranging from 2061 to 3202 bp, and share 31.2% to 82.5% aa identities with the closest related viruses. In addition to these novel viruses, we also detected seven known viruses. They shared 91.8% to 98.0% aa identities with the already-described viruses Erysiphe necator-associated ourmia-like virus 2, Magnaporthe oryzae botourmiavirus 5, Magnaporthe oryzae botourmia-like virus 4, Erysiphe necator-associated ourmia-like virus 97 and Plasmopara viticola lesion-associated ourmia-like virus 50. Importantly, the six known viruses were previously identified from fungal pathogens, such as _Erysiphe reactor_, _Magnaporthe oryzae_ and _Plasmopara viticola. Magnaporthe oryzae_ is the causal agent of rice blast, the most destructive disease of rice that causes great yield losses annually [47]. Phylogenetic analysis indicated that 7 viruses clustered within the genus _Botoulivirus_, 2 viruses clustered within the genus _Penoulivirus_, 11 viruses were grouped within the genus _Magoulivirus_, 12 viruses clustered within the genus _Scleroulivirus_ and 3 viruses clustered within the genus _Ourmiavirus_ (Figure S8). Further analysis showed that there were two obvious branches within the genus _Scleroulivirus_ (group 1 and group 2). Interestingly, nine novel botourmiaviruses clustered within group 2 with Pyriculara oryzae ourmia-like virus 2. Viruses in the family _Mitovirdae_ are non-encapsulated and have small positive-sense ssRNA genomes that are 2.2 to 3.0 kb in size, with a single ORF encoding a viral RNA-dependent RNA polymerase (RdRp) [48]. Mitoviruses are the only viruses that can infect eukaryotic mitochondria [49]. A total of 26 novel mitoviruses were detected in eight weed samples. Of the identified mitoviruses, 20 viruses, Guiyang mito-like virus (GMIV) 1 to 19 and Guiyang Paspalum thunbergii mito-like virus 1 (GPtMV1) were detected in Guiyang, with genome lengths between 2238 and 4342 bp. Two viruses, Hangzhou mito-like virus (HMIV) 1 to 2, were detected in Hangzhou, and have genome lengths between 2441 and 2513 bp. Three viruses, Sanya mito-like virus (SMIV) 1 to 3, were detected in Sanya, and the three viruses have RNA genomes between 2189 and 2796 bp in size. One virus, Xiaogan mito-like virus 1 (XMIV1), was identified in Xiaogan, with a genome length of 2279 bp (Table S2). All the novel mitoviruses in this study displayed 34.0% to 81.9% aa identities with the closely related viruses (Table S2). GMIV1 was identified in seven different weed species in Guiyang; SMIV1 was detected in two different weed species in Sanya (Table S2). In addition, GPtMV1 has a high abundance of 0.402, suggesting that _Paspalum thunbergii_ is a possible host of GPtMV1. Phylogenetic analysis showed that these viruses fell within the family _Mitovirdae_ (Figure S9). The members of the family _Narnaviridae_ contain the simplest genomes ranging from 2.3 kb to 3.6 kb in size and encoding only a single polypeptide that has an RNA-dependent RNA polymerase domain [50]. Here, we identified 14 viruses as new members of the family _Narnaviridae_, including Guiyang narma-like virus (GNIV) 1 to 4, Guiyang Paspalum thunbergii narma-like virus 1 (GPtNV1), Hangzhou narma-like virus (HNIV) and Sanya narma-like virus (SNIV) 1 to 8. All these novel viruses in the family _Narnaviridae_ have genome lengths ranging from 1837 to 3356 bp and share 26.5% to 74.6% aa identities with the closely related viruses (Table S2). GPtNV1 displayed a high abundance of 0.814, suggesting that _Paspalum thunbergii_ was the possible host of GPtNV1. In addition to these novel viruses, we identified three variants of the already-described Plasmopara viticola lesion-associated narnavirus 2 (PVaN 2) (GenBank no. MN539819), Erysiphe necator-associated narnavirus 6 (EnNV6) (GenBank no. MN605419) and Plasmopara viticola lesion-associated narnavirus 15 (PVA1 15) (GenBank no. MN539832), respectively. PVAN 2-SY was annotated as a variant of PVAN 2, EnNV6-HZ was annotated as a variant of FnNV6 and PVAN 15-SY was annotated as a variant of PVAN 15.