Identification and Characterization of Viruses Associated with the Atlantic Blue Crab, Callinectes sapidus, Across Its United States Geographic Range

Abstract

Across two hemispheres, including in the United States, the Atlantic blue crab, Callinectes sapidus, supports a multi-million dollar fishery and plays critical roles in benthic food webs. Recent blue crab population declines in the Mid-Atlantic highlight the need to better understand potential threats to the fishery, including infectious diseases. Viruses can cause disease outbreaks and mortality yet remain relatively understudied compared to other microbial pathogens of marine shellfish. Movement of harvested blue crabs between states may pose a threat of unknown magnitude to the health of wild crabs in the receiving location. To gain a preliminary understanding of the viral communities associated with the blue crab, we performed a virus-enrichment protocol on specimens collected from six U.S. states, from New York to Texas along the U.S. Atlantic and Gulf Coasts. Enrichment was followed by RNA extraction, cDNA synthesis, and high-throughput sequencing. Bioinformatic tools were used to identify and characterize putative virus genomes in gill collections. We discovered a total of 97 putative viral sequences, of which 29 were high-quality genomes with a k-mer coverage >10. Positive-sense RNA viruses were especially prominent, with provisional Picornavirales members constituting 19 of the 29 genomes. Beyond the Picornavirales, seven other positive-sense, two negative-sense, and one double-stranded RNA virus were identified. Finally, this survey yielded potential insights into viral geographic distributions. This research expands our current knowledge of viruses associated with the blue crab across multiple U.S. states. Similar to several prior studies of crustacean viruses, this study identified a large number of entities that putatively belong to viruses of the Picornavirales. Future work will investigate whether the observation of regionally-restricted virus genomes is confirmed when additional crabs are screened using specific PCR assays. The knowledge generated here will enable investigation of the pathogenicity of novel blue crab viruses, which is especially relevant in the face of climate change and the interstate transport of marine resources. Ultimately, such research can help monitor and mitigate the spread of shellfish pathogens.