Going viral: understanding viral RNA diversity in sharks

The main goals of this project were to:

1.  Characterise the RNA diversity in Chondrichthyan hosts and identify a core virome in the group;
2.  Assess  possible  differences  in  viral  RNA  communities  among  major  Chondrichtyan lineages: 2 sharks, 2 rays and 2 chimaeras;
3.  Compare  the  viral  RNA  pathogens  of  Chondrichtyan  hosts  with  those  reported  for other aquatic animal taxa: similarities and phylogenetic relationships.

One of the sample species: a blue shark (prionace glauca). Photo © Sebastian Staines | Save Our Seas Foundation

Table showing samples taken for viral RNA extraction. Image © Fabiana Neves

Samples for viral RNA extraction

In total we extracted viral RNA  from several tissues and individuals from:

two ocean pelagic sharks

• 15 Prionace glauca individuals

13 Isurus oxyrinchus individuals

• two coastal benthic rays

11 Raja clavata individuals

5 Torpedo marmorata indiviiduals

• two  benthic  deepwater  chimaeras

4 Hydrolagus  affinis individuals

4 Chimaera monstrosa individuals.

One of the sample species: a marbled electric ray (Torpedo marmorata). Photo © aquapix | Shutterstock

The process of extracting viral RNA. Photos © Fabiana Neves

Methods for viral RNA sequencing and analysis

Samples were pooled by species and sequenced on  an  Illumina  Novaseq6000 at Macrogen

• 150PE libraries

Illumina Truseq stranded total RNA library Prep Kit with host  Ribo-depletion

• Bioinformatic pipeline​FastQC

Trimmomatic

Bowtie2

Megahit / Spades

​Diamond / Blastx

One of the sample species: a ghost shark (Chimaera monstrosa). Photo © Heine Jensen | Shutterstock

Illustration showing the methods for viral RNA sequencing and analysis. Image © Fabiana Neves

Results / Discussion

Despite the use of internal organs to ensure the detection of viruses, no viral hit was confirmed. This may be due to:

• Type of tissue used?​

Maybe in future studies we should focus on swabs (reducing the amounth od host contamination)

• Technical(extraction protocol)/analytical (bioinformatic pipeline) reasons?

other studies sucessfully used same methodology

• Health status of the species?​

These individuals were colected during scientific cruisers in their natural environment, and did not presented any signs of disease.

• Viral load amount?​

Even if present, if a virus presents a low viral load, may not be sequenced through Next-Generation sequencing. ​

Table showing results of the viral RNA analysis. Image © Fabiana Neves