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The discovery of highly divergent RNA viruses is compromised by their limited sequence similarity to known viruses. Evolutionary information obtained from protein structural modelling offers a powerful approach to detect distantly related viruses based on the conservation of tertiary structures in key proteins such as the RNA-dependent RNA polymerase (RdRp). We utilised a template-based approach for protein structure prediction from amino acid sequences to identify distant evolutionary relationships among viruses detected in meta-transcriptomic sequencing data from Australian wildlife. The best predicted protein structural model was compared with the results of similarity searches against protein databases. Using this combination of meta-transcriptomics and protein structure prediction we identified the <i>RdRp</i> (PB1) gene segment of a divergent negative-sense RNA virus, denoted <i>Lauta virus</i> (LTAV), in a native Australian gecko (<i>Gehyra lauta</i>). The presence of this virus was confirmed by PCR and Sanger sequencing. Phylogenetic analysis revealed that <i>Lauta virus</i> likely represents a newly described genus within the family <i>Amnoonviridae,</i> order <i>Articulavirales</i>, that is most closely related to the fish virus <i>Tilapia tilapinevirus</i> (TiLV). These findings provide important insights into the evolution of negative-sense RNA viruses and structural conservation of the viral replicase among members of the order <i>Articulavirales</i>.