Viral Profiles in Aquaculture Fish from Kazakhstan: A Metagenomic Survey

Viral diversity in aquaculture fish from Kazakhstan remains poorly characterized. This study investigated candidate virus-associated sequences in ten pooled tissue libraries representing four commercially important fish groups: silver carp, grass carp, sturgeon, and rainbow trout. RNA-enriched libraries were sequenced using an Illumina MiSeq platform, and viral assignments were evaluated through a metagenomic analysis pipeline. Of 21 initially identified taxonomic bins, eight were retained for fish-focused analyses. The most prominent finding was an Orthoreovirus-like sequence signal concentrated in two rainbow trout libraries from the Almaty region. A 2356-nt partial L1-region sequence showed 99.96% nucleotide identity to a previously reported piscine orthoreovirus 3 (PRV-3) reference, and phylogenetic analysis supported its placement among PRV-3 sequences. Candidate viral taxonomic profiles differed between the sampled sturgeon and rainbow trout libraries (PERMANOVA R2 = 0.455, exact p = 0.0286), although host species, sampling location, and tissue type were confounded. Taxonomic filtering also substantially influenced the observed diversity estimates. These findings provide preliminary evidence of candidate viral diversity in Kazakhstan’s aquaculture fish and identify PRV-3-like sequences in rainbow trout as a priority for further investigation. Broader sampling, targeted molecular confirmation, and additional genomic characterization are needed to clarify the distribution and potential clinical significance of these viruses.