Chantelle Hooper

New preprint alert! 📣

We use Logan, a new database of SRA-wide genome assemblies, to look for an emerging virus in prawns. If you've ever spent too long trying to track down a known sequence in SRA data, this database is a real game changer.

lnkd.in/e9S5GhPc

We hope this study demonstrates that with careful application of this approach, alongside improvements in metadata quality and accessibility, it could be used to uncover critical insights into pathogen biology, transmission and control.

🌳 Phylogenetics: We assemble 30 new MrGV genomes that have clear geographic structuring in phylogenetic analysis.

🧬 Genomic variation: Most SNPs don't result in amino acid changes, but those that do require further study to determine change if they change MrGV virulence.

⏱️ Temporal signal: In developmental datasets, MrGV abundance spikes at 5–10 days post-hatch, coinciding with zoea III–VII stages. MrGV is also present in all stages of embryonic development.

Key findings are detailed in the below thread ⬇️

🌏 Geographic spread: MrGV was detected in M. rosenbergii from China (3 provinces), Thailand, India, and Bangladesh.

🦐 Life-stage association: Strong enrichment in larvae, with 61% of larval datasets containing MrGV sequences.

New preprint alert! 📣

We use Logan, a new database of SRA-wide genome assemblies, to look for an emerging virus in prawns. If you've ever spent too long trying to track down a known sequence in SRA data, this database is a real game changer.

lnkd.in/e9S5GhPc

I am incredibly honoured to have received the Mauro E. Martignoni Award from the Society for Invertebrate Pathology for my work describing a novel iridovirus, voted for unanimously by the committee

A fun week in Puerto Varas, Chile taking in the breathtaking Andes scenery and talking about viruses!

📢 New preprint describing a novel iridovirus infecting cockles!

For the first time, we provide the full genome for a bivalve-infecting iridovirus and characterise it infecting the haemocytes of moribund cockles in the UK.

Follow the link below to find out more ⬇️

www.biorxiv.org/content/10.1...

The manuscripts that both mine and @annatidy.bsky.social’s posters describe have just been submitted for peer review, so watch this space!

Last week I was at the HM Treasury funded Shared Outcomes Fund, Coastal Health, Livelihoods and Environment programme symposium.

It was exciting to see how our cockle pathogen work fits into the wider aims of the programme to improve our understanding of the health of coastal ecosystems 🌊🐚

We are excited to announce that we will be running the Genomics of Fish Pathogens Workshop at the 22nd European Association of Fish Pathologist (EAFP) Conference in Heraklion 2025! 🧬🐟🦪

Details of costs and how to sign up are linked below ⬇
eafp2025.org/bioinformati...

The workshop is tailored for early career researchers (ECRs) who are attending the EAFP main conference, and is designed for those with little to no experience in bioinformatics, providing a hands-on opportunity to work with genomics data. @aquagenomics.bsky.social

We are excited to announce that we will be running the Genomics of Fish Pathogens Workshop at the 22nd European Association of Fish Pathologist (EAFP) Conference in Heraklion 2025! 🧬🐟🦪

Details of costs and how to sign up are linked below ⬇
eafp2025.org/bioinformati...

@annatidy.bsky.social

Are you interested in bivalves and/or emerging pathogens? If you are, Anna Tidy's 1st first author paper is now available to read as a preprint! 🎉

The paper describes a novel genotype of Marteilia cocosarum infecting cockles in The Wash estuary, UK.

doi.org/10.1101/2025...

Last week I was at Cefas’s PhD Student Conference presenting some of the work from my PhD and was humbled to win best presentation in my session and best overall presentation! A huge thanks to Daniel Zeichner MP for taking time out of a busy schedule to present the prizes!

A massive thanks to Sustainable Aquaculture Innovation Centre (SAIC) for funding the workshop and to The Roslin Institute for hosting us. @aquagenomics.bsky.social

We had a great turnout for the European Association of Fish Pathologists (EAFP) fish pathogen genomics workshop earlier this week! The participants went from command line basics to identifying and characterising a bacterial species causing disease in fish from a whole genome sequencing dataset.