Jemma Geoghegan
@jemmageoghegan.bsky.social
Professor at University of Otago, NZ; Webster Chair in Virology; Rutherford Discovery Fellow. I like viruses and evolution.
Read about this Genomics Aotearoa funded project to understand and help the rarest penguin in the world theconversation.com/why-the-race...
Why the race to save these cherished penguins just became more urgent
Researchers found the endangered yellow-eyed penguin is made up of three distinct subspecies, with the mainland lineage at greatest risk.
theconversation.com
New paper out today with @josephguhlin.bsky.social where we did penguin GWAS to better understand disease risk and found that these penguins represent three deep evolutionary lineages www.nature.com/articles/s41...
Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome - Nature Ecology & Evolution
Whole-genome data from 249 yellow-eyed penguins (hoiho) identify three lineages with high geographical and genomic divergence, and candidate gene variants associated with differential susceptibility t...
nature.com
New paper! 🐧 We sequenced 249 hoiho / yellow-eyed penguins across mainland Aotearoa New Zealand and the sub-Antarctic to understand their history and why a deadly chick disease is hitting the mainland population so hard. #Science #Conservation #Genomics #NZWildlife www.nature.com/articles/s41...
Photographer Richard Robinson & I spent the spring documenting the toughest time of year for Kaikōura's fur seals. In the last 2 years they've faced starvation and a new virus -- now, as bird flu looms, what will this breeding season hold? nzgeo.com/stories/silent-spring 🧪🦭 @nzgeo.bsky.social
Silent Spring
Last year, they were hit with a deadly virus. The year before that, starvation. What will this breeding season bring for the thousands of fur seals hauled up on our coasts?
nzgeo.com
Foraging ecology drives viral community structure in New Zealand's aquatic birds www.biorxiv.org/content/10.6...
Foraging ecology drives viral community structure in New Zealand's aquatic birds
Wild migratory birds play a major role in the global spread of viruses, yet the diversity, host range and transmission patterns of viruses harboured by migratory species in Aotearoa/New Zealand remain...
biorxiv.org
Sad day for the folks who staked their reputations on lab leak conspiracy theories. www.telegraph.co.uk/global-healt...
🐧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
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
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...
biorxiv.org
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...
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...
biorxiv.org
Our latest preprint on the genomic epidemiology of flu over 10 years in NZ www.researchsquare.com/article/rs-7...
A decade of genomic surveillance tracks the disappearance and reintroduction of seasonal influenza virus in Aotearoa New Zealand
Seasonal influenza virus circulation was eliminated in Aotearoa (New Zealand) from 2020 to 2022, following the nation's stringent public health response to the COVID-19 pandemic. Here, we generate nea...
researchsquare.com
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
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 ...
doi.org
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🧵
medRxivpreprint@medrxivpreprint.bsky.social · last yr.Anthropozoonotic spillovers reveal sustained long-term cryptic circulation of SARS-CoV-2 within and between Lithuanian mink farms https://www.medrxiv.org/content/10.1101/2025.07.15.25331253v1
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/...
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 ...
journals.asm.org
Phylogenetic insights into the transmission dynamics of arthropod-borne viruses www.nature.com/articles/s41... Great work by Verity Hill and team
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...
nature.com
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...
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...
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...
cell.com
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:
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.
otago.ac.nz
Recombination between positive-sense and negative-sense RNA viruses: journals.plos.org/plospathogen...
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...
journals.plos.org
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
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/...
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,...
meridian.allenpress.com
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. 🧵
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.
newsroom.co.nz
Preparing for the next pandemic: insights from Aotearoa New Zealand’s Covid-19 response www.sciencedirect.com/science/arti...
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…
sciencedirect.com
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...
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...
biorxiv.org
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/...
📰 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 👇
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.
gov.uk
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...
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.
nature.com