# Novel RNA Viruses Discovered in Weeds in Rice Fields
## 3 Results
### Characterization of Positive-Sense RNA Viruses
The phylogenetic analysis showed that SNV was located outside the members of the genera _Alphanodavirus_ and _Betanodavirus_, while it formed a single cluster with Hubei noda-like virus 20 and Hubei noda-like virus 19 (Figure S6A). **(vii) _Yymoviruses_. ** The family _Yymoviridae_ contains three genera: _Marafivirus_, _Macalavirus_ and _Yymovirus_. Viruses in the family _Tymoviridae_ have a wide range of hosts [40]. The genomes of the members of the genera _Manafivirus_ and _Yymovirus_ each contained a 16-nt conserved sequence at the 3' end of ORF1, namely \"marafikov\" (CA(G/A)GGUGAAUUGCUUC) and \"tymobox\" (GAGUCUGAAUUGCUUC), respectively [41]. We characterized Guiyang Paspalum distichtum yromo-like virus 1 (GPdTV1) and classified it as a novel member of the family _Tymoviridae_. GPdTV1 has genome length of 6725 bp, and shares 45.3% aa identity with the closest related virus (Table S2). The genome of GPTV1 has a conserved sequence that is highly similar to \"marafibox\" (Figure S7A). GPdTV1 has a high abundance of 0.019, suggesting that _Paspulum distichtum_ is a possible host of GPdTV1. The phylogenetic analysis showed that GPdTV1 was located between the genera _Marafivirus_ and _Macalvirus_, and it was closely related to Citrus virus C (Figure S7B). GPdTV1 has a genome structure closely matching Citrus virus C, and it contains a putative movement protein for virus infection [42]. Together, these results indicate that GPdTV1 is a new member of the genus _Marafivirus_. **(viii) _Virgaviridae_** includes seven genera. Viruses in the family _Virgaviridae_ are plant viruses with rod-shaped virions, an ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein typical of alpha-like viruses [43]. Here, we identified a novel virus, Hangzhou virga-like virus (HVIV) in the weed _Lindernia procumbens_ acquired in Hangzhou. The genome size of HVIV was 2918 bp, and HVIV shared 53.4% aa identity with the closest related virus (Table S2). Phylogenetic analysis showed that HVIV clustered within the clade of the Luckshill virus and is closely related to the family _Virgaviridae_ (Figure S6B). **(ix) _Closteroviruses_**. The members of the family _Closteroviridae_ have a mono-, bi- or tripartite positive-sense RNA genomes, which are 13 kb to 19 kb in size and non-enveloped [44]. One virus was detected in the weed _Alternanthera philoseroides_ in Hangzhou, with a genome length of 8823 bp. This virus shared 99.7% aa similarity with _Sedum samnetosum crinivirus_ (SSCV) (GenBank no. MN814305) and has a high abundance of 0.028 (Table S2). SSCV was previously detected in plant, _Sedum samnetosum_ and was classified into the genus _Crinivirus_ of the family _Closteroviridae_ (Figure S6C) [44]. SSCV-HZ was annotated as a variant of SSCV. The members of the genus _Crinivirus_ could infect plants and cause diseases [45]. Such a close phylogenetic position suggests that SSCV-HZ may also infect plants and cause disease. **(x) _Botourmiaviruses_, _Mitoviruses_, _Narnaviruses_, _Fusarivirus_. Mycovviruses detected in this study include the families, _Botourmiaviridae_, _Mitoviridae_, _Narnaviridae_ and _Fusariviridae_. The members of the family _Botourmiaviridae_ can infect plants and filamentous fungi, containing a mono- or multi-segmented positive-sense, and an ssRNA genome. The family _Botourmiaviridae_ consists of four genera: _Ourniavirus_ (plant viruses), _Bototulivirus_, _Magoulivirus_ and _Scleroulivirus_ (mycoviruses). The members of the genera _Bototulivirus_, _Magoulivirus_ and _Scleroulivirus_ have positive-sense RNA genomes of 2 to 3 kb in size, while the genus _Ourniavirus_ has three segments of 2.8, 1.1 and 0.97 kb [46]. A total of 41 botourmiaviruses, including 35 novel viruses and 6 known viruses, were identified from 14 weed samples. The novel viruses were Guiyang botourmia-like virus (GBIV) 1 to 3 in Guiyang, Hangzhou botourmia-like virus (HBIV) 1 to 6 in Hangzhou, Sanya botourmia-like virus (SBoIV) 1 to 21 in Sanya and Xiaogan botourmia-like virus (XBIV) 1 to 5 in Xiaogan.