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Non-invasive surveys of mammalian viruses using environmental DNA

Citation

Alfano, Niccolò et al. (2021), Non-invasive surveys of mammalian viruses using environmental DNA, Dryad, Dataset, https://doi.org/10.5061/dryad.2v6wwpznc

Abstract

This dataset provides supplemental information to interpret the data published in Alfano & Dayaram et al. 2021. The study investigates how environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) can be used to characterize the yet largely unknown virome present in mammalian wildlife. Environmental DNA and iDNA are used to survey biodiversity non-invasively to mitigate difficulties in obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA were used to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent. To detect and identify known and novel mammalian viruses from eDNA/iDNA, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing. We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes. Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.

Usage Notes

This dataset contains several supplementary files that support the findings of Alfano N, Dayaram A, et al. 2021 (https://doi.org/10.1111/2041-210X.13661). It contains phylogenetic trees of the different virus families, assembly plots of the viral sequencing reads and other supportive information.

The readme file contains an explanation of each of the variables in the supplemental tables (Suppl._Tab._1 - Suppl._Tab._5). NA denotes not available information. For detailed information on how data was processed please see the method section in the above publication (Alfano, N. & Dayaram, A., et al. (2021)).

  • Supplemental_material_Info.pdf:
    It contains additional information on the check for potentail suid DNA contaminations, phylogenetic trees of the different virus families and assembly plots of the viral sequencing reads.
  • Suppl._Tab._1_noSRA.xlsx:
    Read counts for leech and waterhole samples.
  • Suppl._Tab._2.xlsx:
    Primers used and amplification results obtained for the leech viral contigs confirmation PCRs.
  • Suppl._Tab._3.xlsx:
    Leech and vertebrate species genomes used in BLAST searches to identify potential endogenous viral elements among the viral sequences generated in this study.
  • Suppl._Tab._4.xlsx:
    Best BLAST hit for each viral contig identified in leech and waterhole samples.
  • Suppl._Tab._5.xlsx:
    Viral enrichment achieved by capture for each sample.

Funding

Bundesministerium für Bildung und Forschung, Award: BMBF FKZ: 01LN1301A

Leibniz-Gemeinschaft, Award: SAW-2015-IZW-1 440