April 2015 – March 2018
FishGuard: a fast, cost-effective, user-friendly and in-field screening test
Viral hemorrhagic septicemia (VHSV) and infectious hematopoietic necrosis (IHNV) are highly contagious fish diseases that cause important losses in fish farms. Ensuring early detection of the responsible viruses is therefore important to improve biosecurity of the aquaculture industry. The aim of this project is to develop a rapid in-field immuno-assay-based screening test. This requires generating highly sensitive and specific antibodies against viral antigens.
In order to ensure high sensitivity and early-onset detection of the infection, we selected those viral proteins shown to be most abundant in early and late responses to infection. We also ensured that no homologous sequences to these proteins existed in Eukaryotes.
Then, using publicly-available protein sequences from isolates of the virus, we identified perfectly conserved and hydrophilic regions of at least 12 amino acids (aa) in peptides of 20aa-long.
Peptides containing repeats, post-translational modifications or on average hydrophobic were discarded. Remaining peptides were post-processed if they contained cysteins in their middle, as cysteins are used for carrier protein conjugation.
Keep remaining peptides if:
– they contain a strech of at least 12 consecutive amino acids perfectly conserved
across all virus isolates
– the conserved stretch is on average hydrophilic
– there are no homologous sequences in related viruses or species of interest
Peptides were then finally scored and ranked as potential epitopes using three CRITERIA:
- Epitope predictions (combination of 9 existing classifiers based on hierarchical clustering of their predictions)
- Predicted average solvent accessibility
- Average hydrophilicity of the conserved stretch.
Based on our predictions, 18 peptides were selected and used to conduct mouse immunization experiments. Generated antibodies are currently being characterized by our partners.
They were presented by Dr Aitana Neves and Prof. Carlos Peña
Poster at SIBDays
June 7-8, 2016
at the SIB Swiss Institute of Bioinformatics Days held in Biel (Switzerland).
Poster at InnovationSante
October 1st, 2015
at the CHUV (Lausanne) meeting of Health Engineering , innovation in the public health service.
Poster at [BC]2
June 7-10, 2015
at the Basel Computational Biology Conference held in Basel.