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Abstract
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 RdRp (PB1) gene segment of a divergent negative-sense RNA virus, denoted Lauta virus (LTAV), in a native Australian gecko (Gehyra lauta). The presence of this virus was confirmed by PCR and Sanger sequencing. Phylogenetic analysis revealed that Lauta virus likely represents a newly described genus within the family Amnoonviridae, order Articulavirales, that is most closely related to the fish virus Tilapia tilapinevirus (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 Articulavirales.
Highlights
The development of next-generation sequencing (NGS) technologies, including total RNA sequencing, has revolutionized studies of virome diversity and evolution [1,2,3].Despite this, the discovery of highly divergent viruses remains challenging because of the often limited primary sequence similarity between putative novel viruses and those for which genome sequences are already available [4,5,6]
Library preparation and sequencing was performed by the Australian Genome Research Facility (AGRF), generating a total of 22,394,787 paired end reads for the pooled liver RNA library
Matches to known viral structures were identified. These included a single match to the RNA-dependent RNA polymerase (RdRp) of a vertebrate-associated virus, and the queried contig was selected for downstream analyses
Summary
The development of next-generation sequencing (NGS) technologies, including total RNA sequencing (meta-transcriptomics), has revolutionized studies of virome diversity and evolution [1,2,3]. The RdRp exhibits the highest level of sequence similarity ( still limited) among RNA viruses, and is expected to contain relatively well conserved protein structures. TiLV was initially classified as a putative orthomyxo-like virus based on weak sequence resemblance (~17% amino acid identity) in the PB1 segment that contains the RdRp, as well as the presence of conserved 50 and 30 termini [17]. While both the Orthomyxoviridae and Amnoonviridae have negative-sense, segmented genomes, the genomic organization of the Amnoonviridae comprises. Our work suggests that this Gecko virus likely represents a novel genus within the Amnoonviridae
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