# Novel RNA Viruses Discovered in Weeds in Rice Fields
## 3 Results
### Characterization of Positive-Sense RNA Viruses  
A total of 196 ssRNA (+) viruses were identified from the collected weeds. Among these viruses, 12 belong to the phylum _Pisuvriciota_, which includes the families _Dicistro-viridae_ (\(n=5\)), _Solemoviridae_ (\(n=2\)), _Astroviidae_ (\(n=1\)) and _Marnaviridae_ (\(n=4\)). Twenty clustered within the Phylum _Kitrinovivriciota_, which includes the families _Tombusviridae_ (\(n=16\)), _Nodaviridae_ (\(n=1\)), _Tymoviridae_ (\(n=1\)), _Closteroviridae_ (\(n=1\)) and _Virgaviridae_ (\(n=1\)), Eighty-five ssRNA(+) viruses belong to the families of mycoviruses (Table S3), including _Botourmiavidae_ (\(n=41\)), _Mitoviridae_ (\(n=26\)), _Narnaviridae_ (\(n=17\)) and _Fusaviridae_ (\(n=1\)). Seventy-nine are bacteriophages (_Leviviricetes_, \(n=79\)) and belong to the Phylum _Lenarviricota_ (Table S4). Figure 2: Phylogenetic diversity of RNA viruses identified in this study. Phylogenetic trees were constructed using the aligned sequences of RdRp. The name of each tree is shown to the top left of each phylogeny. Within each tree, the names of new viruses discovered in this study are marked with a red square, the names of known viruses discovered in this study are marked with a blue square and the families and genera of viruses (and branches in minimized trees) obtained in this study are marked in bold. Potential new families or genera are indicated with orange box. **(i) _Dicistroviruses_. The family _Dicistroviridae_ includes three genera, _Apvaravirus_, _Criavirus_ and _Triatovirus_, with positive-sense genomes ranging from 8 kb to 10 kb [24]. Here, four new dicistroviruses, Sanya dicistro-like virus (SDiV) 1 to 3 and Guizhou dicistro-like virus (GDiV) 1, were detected in weeds. These new dicistroviruses have genome lengths between 7275 and 9272 bp, and share 28.5% to 40.9% of their amino acid (aa) identities with the closely related viruses. In Sanya, SDiV1 was discovered in weed species _Leersia hexandra_, _Leptachloa chinensis_, _Eleocharis dulcis_, _Monochoria vaginalis_ and _Cleverus diffornis_; SDiV2 was identified in weed _Leersia hexandra_, and SDiV3 was identified in weed _Cleverus diffornis_ and _Monochoria vaginalis_. However, GDiV1 was identified in the weed _Paspulum distchum_ in Guiyang (Table S2). In addition to these novel dicistroviruses, we also identified a variant of the already-described Beihai picorna-like virus 77 (BPIV77) (GenBank non. NC_032551.1) [13]. BPIV77-HN was annotated as a variant of BPIV77, and sequence similarity analysis showed that the predicted RdRp protein of BPIV77-HN was 99.8% identical to BPIV77 (Table S2). Phylogenetic analysis showed that the four novel dicistroviruses were not classified into the well-defined genus in the family _Dicistroviridae_ (Figure S2). SDiV1 and GDiV1 formed a separate branch, SDiV2 clustered within the Human blood-associated dicistrovirus clade, while SDiV3 was located between Shahe picorna-like virus 9 and Changjiang picorna-like virus 11, which were previously identified in invertebrate species [13]. **(ii) _Selemoviruses_. The family _Selemoviridae_ includes four genera: _Sobemovirus_, _Polerovirus_, _Enamovirus_ and _Polerovirus_. The genomes of the members contain 4 to 10 open reading frames (ORFs) with a positive-sense RNA molecule of 4 kb to 6 kb without a 3\({}^{\prime}\)-poly(A) tail [25]. The family includes important plant pathogens with high economic impact, with rice yellow mottle virus, potato leafroll virus and sugarcane yellow leaf virus (ScYLV) being some of the most devastating [26; 27; 28]. Here, we identified two novel solemoviruses: Guiyang Paspulum distichum solemo-like virus 1 (GPDV1) and Xiaogan Aeschynomene indica solemo-like virus 1 (XAISV1). GPDV1 has a genome of 5786 bp in size and was identified in the weed _Paspulum distichum_ in Guiyang. XASV1 has a genome of 5689 bp in size and was detected in the weed _Aeschynomene indica_ in Xiaogan.