Identification and Characterization of a Novel Xi'an Ifla-like Virus Strain in Itch Mite (Sarcoptes scabiei)

Abstract

Objective: The goal of this study was to identify and characterize a novel Xi'an Ifla-like virus strain in Sarcoptes scabiei using information from the SRA dataset SRR19592729.

Materials and Methods: The viral genome, consisting of 7,388 nucleotides, encodes a polyprotein of 2,203 amino acids, shorter than the 2,612 amino acids in the closest known relative, the Xi’an Ifla-like virus (QPN36934.1). Codon usage analysis revealed the polyprotein is encoded in the 3'→5' frame, an atypical feature in positive-sense RNA viruses, suggesting distinct regulatory mechanisms. De novo sequencing produced 37,872 mapped reads.

Results: Despite 93.73% similarity at the protein level, the absence of the RNA-dependent RNA polymerase (RdRp) domain and multiple amino acid mismatches in conserved regions such as SF3 helicase and 3C protease support the classification of SRR19592729 as a new strain. De novo sequencing produced 37,872 mapped reads, revealing a 13.74% nucleotide divergence and frequent C→G and A→G substitutions. Phylogenetic analysis using the Neighbour-Joining method placed SRR19592729 within the Iflaviridae family but on a distinct branch from its closest relatives, with a node distance of 0.113.

Conclusion: These findings, including truncated genome features and structural variations, indicate that SRR19592729 represents a genetically divergent, possibly host-adapted viral strain. This sequence exhibits a hallmark characteristic of the Iflaviridae family having polyproteins such as capsid protein, SF3 helicase, as well as truncated protein sequence and missing RNA-dependent RNA polymerase. Therefore, continued surveillance and future functional studies are essential to understand its evolutionary origins, host specificity and potential implications for parasite-host-virus interactions.