Dataset: Nucleotide sequences of CsRV1 virus amplified from blue crabs (Callinectes sapidus) from coastal waters and estuaries in North and South America, including the Caribbean and Gulf of Mexico from 2006 to 2020

Final no updates expectedDOI: 10.26008/1912/bco-dmo.890835.1Version 1 (2023-02-28)Dataset Type:Other Field Results

Principal Investigator: Eric Schott (University of Maryland Center for Environmental Science)

Co-Principal Investigator: Louis V. Plough (University of Maryland Center for Environmental Science)

Scientist: Mingli Zhao (University of Maryland at Baltimore)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)


Project: Collaborative research: Variation in life history and connectivity as drivers of pathogen-host dynamics and genetic structure in a trans-hemispheric pathosystem (Blue Crab Connectivity)


Abstract

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...

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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


Related Datasets

IsRelatedTo

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA939818
University of Maryland Center for Environmental Science. Callinectes sapidus reovirus 1. (2023). In: NCBI:BioProject: PRJNA939818. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA939818.

Related Publications

Results

Zhao, M., Plough, L. V., Behringer, D. C., Bojko, J., Kough, A. S., Alper, N. W., Xu, L., & Schott, E. J. (2023). Cross-Hemispheric Genetic Diversity and Spatial Genetic Structure of Callinectes sapidus Reovirus 1 (CsRV1). Viruses, 15(2), 563. https://doi.org/10.3390/v15020563
Results

Zhao, M., Xu, L., Bowers, H., & Schott, E. J. (2022). Characterization of Two Novel Toti-Like Viruses Co-infecting the Atlantic Blue Crab, Callinectes sapidus, in Its Northern Range of the United States. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.855750
Methods

Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., Burton, D. R., Lewis-Ximenez, L. L., de Jesus, J. G., Giovanetti, M., Hill, S. C., Black, A., Bedford, T., Carroll, M. W., Nunes, M., … Loman, N. J. (2017). Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature Protocols, 12(6), 1261–1276. https://doi.org/10.1038/nprot.2017.066