# Novel RNA Viruses Discovered in Weeds in Rice Fields
## 3 Results
### Characterization of Positive-Sense RNA Viruses
These variants shared 92.2% to 99.3% aa identities with the closely related viruses. Analysis of genome structures showed that all the novel viruses contain a conserved RdRp domain, with some containing a reversed ORF (Figure S10A). The phylogenetic analysis showed the novel viruses were divided into two groups (group 1 and group 2), 10 narnaviruses were located in group 1, which was related to the genus _Narnavirus_, and 7 narnaviruses grouped into group 2 (Figure S10B). Importantly, group 2 was clearly distinct from group 1 in the evolutionary relationship. Thus, group 2 may be a new genus of the family _Narnaviridae_. The family _Fusarioviridae_ is a newly established viral family, which has not yet been included in ICTV [51]. The genome of viruses in the family _Fusarioviridae_ can range from 6 kb to more than 10 kb and contain one to four ORFs [51; 52]. We identified Sanya fusari-like virus 1 (SFIV1) in weed _Leersia hexandra_ in Sanya, with a genome size of 6647 bp, and this virus clustered within the family _Fusarioviridae_ (Table S2). Phylogenetic analysis showed that SFIV1 formed a monophyletic clade with Pleospora typhicola fusarivirus 1, Erysiphe necator-associated fusarivirus 2, Setosphaeria turcica fusarivirus 1, Plasmopara viticola lesion-associated fusarivirus 3, Plasmopara viticola lesion-associated fusarivirus 1 and Erysiphe necator-associated fusarivirus 1, and they shared high sequence similarities (83.0% to 87.0%, aa identities) (Figure S11). **(xi) RNA bacteriophages. ** Bacteriophages have been integrated into one class (_Levivivricetes_) and two orders (_Norzivirales_ and _Timlovirales_). The order _Norzivirales_ includes four families: _Atkinsviridae_, _Duinvriidae_, _Fiersviridae_ and _Solspiviridae_. The order _Timlovirales_ contains two families: _Blumevriidae_ and _Steitzviridae_. They all belong to the phylum _Lenarviriota_[53]. In this study, 79 viruses were classified into the phylum _Levivivricetes_ including 78 novel viruses and 1 known virus (Table S2). These novel viruses have genome lengths between 2098 and 4340 bp and displayed 29.5% to 77.8% aa identities with the closely related viruses. We also detected one known virus, and it shared 91.2% aa identity with the virus ssRNA phage SRR696079 10 (GenBank no. BK014060). The phylogenetic analysis showed that 3 novel viruses clustered within the family _Aikinsviridae_, 1 novel virus was classified into the family _Duinvriidae_, 64 novel viruses clustered within the family _Fiersviridae_ and 5 novel viruses clustered within the family _Solspiviridae_, while the other 6 new viruses belong to the family _Steitzviridae_ (Figure S12). The genome lengths of these novel viruses ranged from 2098 to 4340 bp, and shared 29.5% to 77.8% aa identities with the closely related viruses (Table S2). Importantly, of the 79 bacteriophages, 72 were detected in Sanya, accounting for 91% of the identified bacteriophages, and indicating that RNA bacteriophages showed obvious geographical preference. All the RNA bacteriophages were identified with low abundance (Table S2), indicating that these bacteriophages may be derived from endophytic bacteria. Thus, endophytic bacteria may be rich in weeds in paddy fields in Sanya.