Longitudinal sampling of New Zealand cockles (Austrovenus stutchburyi) reveals high viral diversity and taxa-specific responses to environmental factors.

Bivalves bioaccumulate microorganisms and, therefore, serve as effective indicators of microbial activity in intertidal ecosystems. Monitoring bivalve-associated viruses can provide insight into circulating viral communities and their relationship with environmental change. The New Zealand cockle (Austrovenus stutchburyi) is culturally, ecologically, and economically important, yet little is known about the viruses it hosts, how these change over time, or whether cockles act as reservoirs for pathogenic viruses affecting bivalves or humans. We used a metatranscriptomic approach to characterise the cockle RNA virome over 12 months and assess whether environmental parameters influenced viral dynamics. Longitudinal sampling revealed a highly diverse RNA virome spanning 16 viral orders within the kingdom Orthornavirae. Phylogenetic analysis of RNA-dependent RNA polymerase sequences identified 358 viral transcripts representing 213 distinct viral species, of which 199 were likely novel, including several putative new virus families and three orders. No viruses known to be pathogenic to humans or bivalves were detected. While total virome composition showed no strong seasonal patterns, environmental parameters influenced virus abundance within specific viral orders, including the highly abundant Picornavirales, Wolframvirales, Bunyavirales, and Sobelivirales. Overall, New Zealand cockles harbour an exceptionally diverse RNA virome, with environmental drivers acting in a taxon-specific rather than community-wide manner.