What does research in the era of COVID look like at the TAV?

… a little different. Work is undoubtedly a lot slower than the before times, but we’re still getting things done as best we can! Cornell restarted research labs in mid-summer 2020 after shutting down for nearly 3 months. To de-densify our building and ensure safety of all workers, each lab has a reactivation plan, which generally means only one person in each research space at a time (i.e. distancing), mask use, lots of hand hygiene, and moving all office work off-campus. Cornell also has a daily health check, and surveillance monitoring for COVID – a strategy which has been largely successful in keeping everyone safe and the case load on campus low, even with the resumption of in-person classes last autumn. For various reasons, the team hasn’t been in the lab much – and have been focused on computational analyses that can be done remotely – but we’ve also completed a bit of lab work in the last few weeks!

Last week, Chris was focused on trying out some new primers to examine aiFV diversity in sea cucumbers. Our new Flavivirus-oxygen-sea cucumber project is focused on this one group of viruses, which is a little different to our approach in the past (metagenomics). A grand challenge with this project is desigining PCR primers which encompass this groups of similar, but still very divergent viruses. At the beginning of January, Ian assembled all known aiFVs from work we’ve performed in the past, as well as more that were ‘mined’ from both host transcriptomes and viral metagenomes prepared by others and deposited in GenBank. This revealed a cluster of viral sequences – infecting molluscs (especially cephalopods), a shark, and several crustaceans (notably a portunid crab and amphipods). While these were somewhat similar in amino acid sequence and shared the same genome architecture, they were rather different in RNA sequence. Ian chose to look at the nonstructural gene 5 (NS5), which tends to be conserved in flaviviruses, and for which there was most similarity in these aiFVs – and performed a robust alignment. Fortunately, there were a few motifs within this region which had sufficient – though still quite different – sequence similarity so as to allow the design of degenerate (i.e. ambiguous base), nested PCR primers. Chris’ first attempt with these – applying them to old cDNA from sea cucumbers – was not successful. So, he extracted more RNA, reversely transcribed this, and tried a new annealing temperature spectrum. Work’s ongoing but it is promising- a primer set that targets the sea cucumber aiFV seemed to amplify a product of the predicted size – and there appears to be some very very weak amplification using the degenerate primer set. This week, he’ll try the nested amplification, tweaking annealing temperatures, and using a high-fidelity polymerase which permits a higher annealing temp. Fingers crossed!

If you squint, you can see something in mid-picture!

Meanwhile, Jordan’s been hard at work – on a completely different schedule to Chris so as to allow distancing in the lab – preparing RNA viral metagenomes from seagrass samples. We’ve been doing this in the lab for a number of years, but this is a first time for Jordan! We hope to sequence a few seagrass viromes in the next month or so. Jordan’s also been at work mining seagrass transcriptomes for other viruses and has come across some very intriguing plant viruses that were hitherto not known. We’re hoping to mesh with our collaborators at USF (Mya Breitbart and Karyna Rosario) to generate a clear picture of the seagrass virome. One thing we have already seen is that many of the viral families infecting seagrass are similar to terrestrial plant viruses – which are all vectored by arthropods. This leads to an interesting idea – do invertebrates inhabiting seagrass habitats vector plant viruses in a similar way as flying insects?

We have lots of seagrass samples that were preserved in RNALater and frozen… but converting these to viromes is a bit of a challenge right now!

Meanwhile Ian has been isolated at home since March 2020. Much of what he does – for research, which is one of many facets of faculty- on a daily basis involves computer work – including data mining and phylogenomics. Its frustrating not being able to get into the lab right now, but he’s coping – and at least the commute to work isn’t bad. He started teaching his marine diseases class last week – which continues until mid-May – and gave a seminar at the University of Minnesota on Friday. But he longs for the opportunity to do field work, which hopefully will happen this summer, pandemic-depending. In addition to guiding research in the lab remotely, he’s also been engaging with scientists in southeast Alaska to facilitate long-term monitoring of oxygen and chlorophyll – two important variables that we’re examining in context of flaviviruses. On that note, we are looking to partner with citizen scientists, schools, and other groups who may be interested in collaborating on monitoring sea cucumbers in Southeast Alaska (i.e. Ketchikan-Juneau-Sitka). Please get in touch if you’re interested in working together!

Well, at least the commute isn’t bad…

So… work continues – albeit a bit more slowly than usual. Stay tuned for exciting results!

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