Sequence and phylogenetic analyses

Sequences were analyzed and assembled using Vector NTI 11.5, then submitted to the GenBank database in NCBI using the software Sequin. The reconstructed genome was subjected to standard sequence analyses: (I) prediction of ORFs using the ORF Finder program in NCBI (http://www.ncbi.nlm.nih.gov/projects/gorf/); (II) identification of conserved and functional domains of the predicted proteins in WCLaV-1 and WCLaV-2 using the Conserved Domain Database (CDD) in NCBI (https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) (Marchler-Bauer et al., 2015) and the SMART tool (http://smart.embl-heidelberg.de/) (Letunic et al., 2015); analyses of the core RdRp and NP domains in other (-ss) RNA viruses using the CDD; (III) multiple sequence alignment of the core motifs in RdRp and the conserved nucleotide sequence at the 5′- and 3′-end by CLC Genomics Workbench 9.5; (IV) identity analyses using the needle program in WebLab (http://weblab.cbi.pku.edu.cn/); (V) multiple sequence alignments first using the Clustal W method and then MEGA 6.0 (Tamura et al., 2013) for phylogenetic tree construction using the neighbor-joining method with 1,000 bootstrap replicates, the Poisson model and pairwise gap deletion options. Abbreviations and accession numbers of viruses used in this study are listed in Table S5.