Success! We think…

Another busy week in the lab has resulted in some success in studying sea cucumber aiFVs. Around 3 weeks ago we received our newly-designed, highly degenerate PCR primers to study aiFV diversity; this was a bit of a long-shot since the aiFV genomes that are known are very divergent – sharing only ~ 40 – 50 % amino acid identity. Trials of these proved rather unsuccessful against a wide range of samples – and so it was back to the drawing board. Ian redesigned primers to be a bit more constricted to the Apostichopus californicus flavivirus we found last year from samples collected in 2015 as well as a shark flavivirus and a nudibranch virus, which were the closest relatives. This past week, Chris tested these new primers out some Apostichopus samples from southeast Alaska, and there was some success. There are bands (amplicons) of the correct size across all 3 amplicons – but also a lot more. So next up, Jay will be cloning these, sequencing them, and then we’ll move on to optimizing thermocycling conditions to ensure we exclude anything that might be spuriously amplified. It’s a long process, but hopefully at its conclusion we’ll have a good assay to look at this interesting group of viruses!

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