Jemma Geoghegan

The Telegraph Headline: New Covid virus found in wild Brazilian bats Subhed: The discovery of a ‘furin cleavage site’ suggests the mutation which helps the virus adapt to humans is naturally occurring

Sad day for the folks who staked their reputations on lab leak conspiracy theories.

www.telegraph.co.uk/global-healt...

Hoiho - the world’s rarest penguin, fewer than 150 mainland pairs left

🐧We researched one of the world’s rarest #penguins. The yellow‑eyed penguin (aka hoiho/takaraka) isn’t one homogeneous species after all!

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

#hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature

Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes ) are among the world’s rarest penguins and are regarded as a taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the N...

We did a penguin GWAS! Turns out that yellow-eyed penguins (or hoiho) are actually three very divergent groups, which we are calling subspecies www.biorxiv.org/content/10.1... @josephguhlin.bsky.social @peterkdearden.bsky.social @annasanture.bsky.social @cegrueber.bsky.social

Evaluating sampling strategies for the detection of avian influenza viruses in the environment Highly pathogenic avian influenza (HPAI) viruses threaten humans, livestock and wildlife, highlighting the urgent need for early warning surveillance. Environmental RNA (eRNA) monitoring provides a sa...

Our latest preprint evaluates sampling strategies for the detection of avian influenza virus from the environment @profgemmell.bsky.social @dwinter.bsky.social www.biorxiv.org/content/10.1...

Our latest preprint on the genomic epidemiology of flu over 10 years in NZ www.researchsquare.com/article/rs-7...

A Novel Crustavirus as a Candidate Aetiology of Tail Fan Necrosis in New Zealand Red Rock Lobsters, Jasus edwardsii Tail fan necrosis (TFN) is a shell disease affecting spiny lobsters' outer integument, with significant implications for the health and commercial viability of red rock lobsters (Jasus edwardsii) in ...

New publication from the Department of Microbiology and Immunology:

A Novel Crustavirus as a Candidate Aetiology of Tail Fan Necrosis in New Zealand Red Rock Lobsters, Jasus edwardsii

🔗 doi.org/10.1111/jfd....
#Microbiology #Virology #AquaticHealth #CrustaceanResearch #MarineBiology #Otago

This is quite late but our lab has a preprint out about a SARS-CoV-2 situation we had in mink in Lithuania back in 2021. It's a doozy with re-emergence of extinct lineages, a country-wide test of all mink farms in Lithuania & some interesting dynamics in mink. www.medrxiv.org/content/10.1... 1/5🧵

Metatranscriptomic detection of rabbit hemorrhagic disease virus 2 in karoro (southern black-backed gulls) | Journal of Virology Rabbit hemorrhagic disease virus 2 (RHDV2; species Lagovirus europaeus) is a highly pathogenic lagovirus (Caliciviridae) responsible for a lethal disease in rabbits and hares (1). First identified in ...

We found RHDV2 in gulls! While the virus is likely to be dietary in origin, this suggests that birds may act as mechanical vectors for virus spread. Work by Steph Waller, @dwinter.bsky.social @eddieholmes.bsky.social @mongoosekiwi.bsky.social et al. journals.asm.org/doi/10.1128/...

Phylogenetic insights into the transmission dynamics of arthropod-borne viruses - Nature Reviews Genetics Arthropod-borne viruses have a substantial impact on global health, with climate change and urbanization exacerbating their emergence. Integrating genomic surveillance and phylogenetic models with eco...

Phylogenetic insights into the transmission dynamics of arthropod-borne viruses

www.nature.com/articles/s41...

Great work by Verity Hill and team

Rhys and I found some weird influenza B viruses in fish a few years ago. For 2, the HA's bind a2,3 sialic acid ("bird type receptor"). The Siamese algae eater virus NA has a highly conserved structure and active site. No cross-reactive antibodies in human sera.
👉 biorxiv.org/content/10.1...

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...

Sooo happy to finally have this one published!! (3 years in the making… 👀) A comprehensive investigation into the recency and geographical origins of both SARS-CoVs that spilled to humans in the past few decades, now in @cp-cell.bsky.social www.cell.com/cell/fulltex...

Prime Minister’s prizes awarded to two Otago academics Work on managing anxiety and managing viruses has resulted in two Otago academics receiving Prime Minister’s Science Prizes.

Two Otago academics, Dr Olivia Harrison and Professor Jemma Geoghegan, have been awarded Prime Minister's Science Prizes for their outstanding work on managing viruses and managing anxiety. Ngā mihi nui! 👏

Read more here:

A positive-sense single-stranded RNA virus acquired a negative-sense open reading frame through recombination Author summary The discovery of brine shrimp virga-like virus 1 (BSVV1) challenges the conventional view that positive- and negative-sense RNA viruses are evolutionarily independent. Through genomic a...

Recombination between positive-sense and negative-sense RNA viruses: journals.plos.org/plospathogen...

We're looking for a PhD student to join us at Vilnius University in Lithuania. We work on RNA virus evolution computationally but we'd like to generate more mosquito RNA virus sequence data. Official ad: www.gmc.vu.lt/en/doctoral-.... Please share & continue reading if interested.

Just out "Making sense of the virome in light of evolution and ecology" doi.org/10.1098/rspb... from super ⭐ team @meganawallace.bsky.social @duckswabber.bsky.social @jemmageoghegan.bsky.social @ryanmimrie.bsky.social @eddieholmes.bsky.social @xavh.bsky.social in Proc B @royalsocietypublishing.org

A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode Abstract. Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions,...

One for the hepaci fans. We found a cool new hepacivirus (along with some other things) in kiwi with dermatitis meridian.allenpress.com/jwd/article/...

The next pandemic is coming. NZ isn't ready Special report: The island nation is less prepared for a pandemic than it was five years ago, even as new threats emerge overseas.

I spent about 30 hours over four weeks reading all 716 pages of the report of the Royal Commission into the Covid-19 response, then wrote two articles detailing its findings and recommendations.

With the paywall now lifted on both of those pieces, here's what I found. 🧵

Preparing for the next pandemic: insights from Aotearoa New Zealand’s Covid-19 response In 2020 Aotearoa New Zealand, like many other countries, faced the coronavirus pandemic armed with an influenza-based pandemic plan. The country adapt…

Preparing for the next pandemic: insights from Aotearoa New Zealand’s Covid-19 response www.sciencedirect.com/science/arti...

A novel crustavirus associated with tail fan necrosis in New Zealand red rock lobsters, Jasus edwardsii Tail fan necrosis (TFN) is a shell disease affecting spiny lobsters' outer integument, with significant implications for the health and commercial viability of red rock lobsters (Jasus edwardsii) in N...

We found a crustavirus that may or may not have something to do with tail fan necrosis in lobsters www.biorxiv.org/content/10.1...

Great walk through of all the knowns and unknowns of the current HPAI outbreak in US dairy cattle with a focus on both the cattle, but also human pandemic risk.
👉 journals.asm.org/doi/10.1128/...

Bird flu (avian influenza): latest situation in England Find out about the latest bird flu situation in England and guidance for bird keepers and the public.

📰 DEFRA avian Influenza update on 04 Mar 2025 #IDSky #IDEpi

🐔 Highly pathogenic avian influenza (HPAI) H5N1 confirmed in a commercial poultry premises near Kington, Herefordshire.

📊 25 cases of HPAI H5N1 in England in 2025

🔗 Avian influenza: latest situation in England 👇

Pathogens and planetary change - Nature Reviews Biodiversity This Review explores the relationship between emerging infectious diseases and biodiversity loss, and how both are connected to global environmental changes in the Anthropocene.

Couldn't ask for a better first Bluesky post! Our new paper, "Pathogens and planetary change," is out now in @natrevbiodiv.bsky.social. We discuss the linkages between biodiversity loss + pandemics and how we can address these interconnected crises 🧪😷

Give it a read: www.nature.com/articles/s44...

Bird Flu Is a National Embarrassment America should have more aggressively intervened almost a year ago.

Essential reading from @katherinejwu.com @theatlantic.com.

For months, we've passively watched H5N1 tear through animals. A year into the cattle outbreak & it remains out of control. H5N1 is everywhere.

If H5N1 causes a pandemic, it will be because we let it.
www.theatlantic.com/health/archi...

Lots of new viruses (and other known pathogens) here, especially in carnivores and rodents. Of most interest, a bi-segmented coronavirus sampled from diseased red (lesser) pandas (Ailurus fulgens) and that represents a new genus. Work led my Mang Shi and Shuo Su. www.biorxiv.org/content/10.1...

Thrilled to be co-leading these efforts with our colleagues at Scripps Research and UCSD.

As usual, Helen is first out of the gate with a great explanatory piece on the CDC's updated technical report on the H5N1 case in Louisiana, with quotes from me and @scottehensley.bsky.social. 👇

🎁 Early Xmas present from your friends at the MRC-University of Glasgow Centre for Virus Research @cvrinfo.bsky.social

We're thrilled to unwrap Viro3D - a comprehensive database of virus protein structures: >85,000 predicted structures from 4,400 human & animal viruses! 🦠

viro3d.cvr.gla.ac.uk

Oral and faecal viromes of New Zealand calves on pasture with an idiopathic ill-thrift syndrome Since 2015, an idiopathic ill-thrift syndrome featuring diarrhoea and, in some cases, gastrointestinal ulceration has been reported in weaned New Zealand dairy calves. Similar syndromes have been desc...

Our latest preprint investigates viruses in calves associated with an idiopathic ill-thrift syndrome www.biorxiv.org/content/10.1...

Fatal Case of Crimean-Congo Hemorrhagic Fever, Portugal, 2024 Fatal Crimean-Congo Hemorrhagic Fever, Portugal

Fatal Case of Crimean-Congo Hemorrhagic Fever, Portugal, 2024

#IDSky #EpiSky

Influenza-like viruses in basal chordates. Love it.