This record contains nucleotide sequences of CsRV1 virus amplified from blue crabs (Callinectes sapidus) across the study region. RNA from crabs identified as infected using a sensitive Rt-qPCR assay was amplified using primers specific to segment and segment 9 of the virus genome. A subset of CsRV1-positive RNA preparations were amplified using a full-genome amplification set of primers to amplify the entire CsRV1 genome. (http://primal.zibraproject.org; Quick et al. 2017). The segment-specific data: seg9 (960 nt amplicon) and seg8 (807 nt amplicon) were trimmed and used to create maximum likelihood trees. Similarly, the full genome sequences were used for a maximum likelihood tree. In total, 22 complete or near-complete genomes, 42 seg8 ORF sequences, and 96 seg9 ORF sequences of CsRV1 were collected from 15 geographic locations along the US Atlantic coast, Gulf of Mexico, Caribbean Sea and S. America between 2006 – 2021. Sequence generation and tree building was accomplished by Mingli Zhao with input from coauthors Plough and Kough. Pairwise analyses and ML trees can be found in the Supplemental Materials of results publication Zhao et al. (2023). The sequences generated in this study are deposited in NCBI GenBank, with accession numbers OP067244-OP067635 and are accessible under BioProject PRJNA939818.

Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Supplemental Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

Location: 
Coastal waters and estuaries N. America and S. America, including the Caribbean and Gulf of Mexico. Collections from trapping, dredging, and netting by commercial and recreational fishers, and scientific collections by resource managers.

Methods & Sampling:
Crabs were obtained by collaborating partners in the Caribbean and South America using mixed methods of baited traps and line, nets, and dredges.

DNA sequencing was conducted using both Sanger sequencing (Big Dye terminator) of PCR amplicons at the BioAnalytical Lab in IMET (https://www.umces.edu/baslab).

Illumina-based sequencing of full virus genome amplifications used Illumina MiSeq platform at GENEWIZ (South Plainfield, NJ, USA) with a MiSeq Reagent kit v3 (Illumina, San Diego, CA, USA).

Instruments:
No lab-specific environmental equipment was used to record metadata at the time of crab collection.

For sequence analysis, equipment was 3130 XL Genetic Analyzer from Life Technologies at IMET and contracted  Illumina MiSeq platform at GENEWIZ (South Plainfield, NJ, USA) with a MiSeq Reagent kit v3 (Illumina, San Diego, CA, USA).

Taxonomic identifiers:
blue crabs, Callinectes sapidus, urn:lsid:marinespecies.org:taxname:107379

BCO-DMO dataset processing notes:
* lat lons formatted as decimal degrees (W and S are negative)
* empty depth column removed
* upon request from the submitter all "host" values filled in as Callinectes sapidus.  And VA site coordinates were corrected from 38.0214,-76.3524 to 37.1477,-76.1573

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Coverage: Atlantic coast of north and south America from Massachusetts to Southern Brazil, Caribbean

NSF Award Abstract:

Marine invertebrates use an array of strategies to survive, move, and reproduce across diverse and dynamic environmental conditions. This project investigates the intersection of these strategies and how they facilitate the persistence of blue crabs and a pathogenic virus along the Atlantic coast of North and South America. The widespread distribution of this crab-virus system makes it useful for investigating host-pathogen interactions. Blue crabs can reduce their activity level and induce winter dormancy in colder climates, but it is unclear how this alters progression and transmission of the pathogen. Conversely, year-round growth and reproduction of tropical blue crabs may be offset by higher pathogen abundance and activity. This project will use a combination of field and laboratory studies to reveal how crab life history and pathogen dynamics interact and adapt at the extremes of their range. Genetic sequencing, crab movement tracking and oceanographic models will be used to understand how crab-disease dynamics vary across temperate and tropical latitudes. The blue crab is an ecologically and economically important species and knowledge generated in this project will help provide management guidance to support sustainable fisheries. Best practices to avoid and limit disease will be communicated to commercial and artisanal harvesters through partnerships and workshops. Local high school and undergraduate students from underrepresented groups will be engaged through a variety of formal and informal educational programs. Public outreach will be implemented through a museum partnership with the Shedd Aquarium and will include the training of a science communication intern.

This collaborative project will combine empirical field and laboratory experiments, population genomics, and biophysical modeling to explore the consequences of latitude-driven changes in life history and oceanic connectivity on a trans-hemispheric pathosystem comprised of the blue crab, Callinectes sapidus, and the pathogenic virus, CsRV1. The virulence of the CsRV1 virus from tropical and temperate latitudes and the impact of overwintering will be studied by experimental virus challenges of crabs transplanted between high and low latitudes. The impact of infection and virulence on crab movement will be investigated in laboratory raceway experiments of healthy and infected crabs and in the field with acoustically tagged crabs deployed in temperate and tropical locations. Population genetic studies using thousands of genome-wide RAD sequencing markers for crabs and whole-genome sequencing for the virus will define genetic connectivity of crab and virus populations across their range, and will investigate the possible latitudinal, seascape, and life history-driven changes in blue crab and virus genomes. The two population genomic data sets are expected to provide different inferences and scales of connectivity because CsRV1 virus genotypes are transmitted only among post-larval crabs while blue crab genotypes also move by a potentially long-range dispersive larval stage. Finally, integrated biophysical models will be used to investigate the relative contributions of adult and larval dispersal on the population structure of the crab and the pathogen across a broad swath of habitat between New England and Argentina with a decade of simulations. An open-source Lagrangian stochastic model will estimate pelagic larval transport, and spatially explicit biased-correlated random walk models will estimate adult movement. Models will be informed by experimentally-derived movement and behavior data, as well as information on crab larval and adult behavior and overwintering duration available in the published literature. Under a series of scenarios in which crab behavior is affected by latitude and virus infection, statistical comparisons will be made between biophysical model-based predictions of connectivity and genetic estimates of connectivity. These analyses will advance our understanding of the physical, environmental, and biological factors that shape the dynamics of the blue crab CsRV1 pathosystem.