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Erik Karlsson

@eakarlsson.bsky.social
2.3K followers 243 following 120 posts

Emerging/endemic infectious diseases, mostly viruses. Pandemic Prevention. Early Warning. One Health. Science outside-the-box. Views my own. 🦠🧪🔬🐓🦇

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Erik Karlsson @eakarlsson.bsky.social · 09/10/2026
@duckswabber.bsky.social @whofluccmelb.bsky.social @fla-medic.bsky.social @thijskuiken.bsky.social @jsiegers.bsky.social @who.int @fao.org
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Erik Karlsson @eakarlsson.bsky.social · 09/10/2026
Thanks to colleagues and the laboratories generating and sharing the sequences behind it. Shared nomenclature helps us compare findings across borders and animal and human health. 🐓🦠🧪😷🥼💉
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Erik Karlsson @eakarlsson.bsky.social · 09/10/2026
One caveat matters: an HA clade describes the ancestry of ONE gene. It doesn’t describe the entire #genome, capture the virus’s #reassortment history, or automatically tell you its #pandemic potential. The name is useful. You still need to understand the virus #genotype. 🐓🦠🧪😷🥼💉
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Erik Karlsson @eakarlsson.bsky.social · 09/10/2026
What changes? 12 H5 hemagglutinin (HA) clade designations are expanded and formalized: Within the former 2.3.2.1c grouping: 2.3.2.1d, e, f, and g. Within 2.3.4.4: 2.3.4.4a, b, c, d, e, f, g, and h. 🐓🦠🧪😷🥼💉
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Erik Karlsson @eakarlsson.bsky.social · 09/10/2026
Glad to see the WHO/WOAH/FAO #H5 Evolution Working Group nomenclature update finally in print. We’ve used these names for a while. Now there’s a published reference: onlinelibrary.wiley.com/doi/10.1111/... 🐓🦠🧪😷🥼💉
onlinelibrary.wiley.com
Nomenclature Updates to the Hemagglutinin Gene Clade Designations Resulting From the Continued Evolution of High Pathogenicity Avian Influenza A(H5) Virus Clades 2.3.2.1c and 2.3.4.4
Background and Methods The evolutionary divergence of the A(H5) hemagglutinin (HA) gene of high pathogenicity avian influenza (HPAI) viruses (A/goose/Guangdong/96 lineage) was analyzed by phylogenet...
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Erik Karlsson @eakarlsson.bsky.social · 21/09/2026
#COVID-19 didn’t make avian #influenza disappear. But among #Cambodian #poultry workers, #PPE use, awareness, and training all fell as incomes tightened. The hopeful part? This is fixable: affordable PPE, training, and advice from people workers trust. onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Impact of the COVID‐19 Pandemic on Knowledge, Attitudes, and Practices Related to Avian Influenza Among Poultry Workers in Cambodia
Background Live bird markets (LBMs) are high-risk environments for the amplification and transmission of avian influenza viruses (AIVs). In Cambodia, limited data exist on knowledge, attitudes, and ...
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Erik Karlsson @eakarlsson.bsky.social · 21/09/2026
A wild animal does not become biologically neutral because someone puts a fence around it. Our new review compares #zoonotic risks in farmed vs wild-caught #wildlife sold for food. The inconvenient answer: origin alone is not risk assessment. www.sciencedirect.com/science/arti... #OneHealth
sciencedirect.com
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Erik Karlsson @eakarlsson.bsky.social · 21/09/2026
#Influenza viruses have 8 genome segments. When 2 infect the same host, evolution can shuffle the deck. Our new EID Perspective examines reassortment and #H5N1 spillover in Asia and why surveillance must detect what viruses have become. wwwnc.cdc.gov/eid/article/...
wwwnc.cdc.gov
Reassortment of Highly Pathogenic Avian Influenza as a Driver for Zoonotic Spillover, Asia
Reassortment of HPAI as Driver for Spillover
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Erik Karlsson @eakarlsson.bsky.social · 23/04/2026
Read more: www.khmertimeskh.com/501884589/go...
khmertimeskh.com
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Mike Coston @fla-medic.bsky.social · 22/04/2026
AFD Blog `Cambodian MOH Announces 4th Human #H5N1 Case of 2026' h/t @eakarlsson.bsky.social afludiary.blogspot.com/2026/04/camb...
afludiary.blogspot.com
Cambodian MOH Announces 4th Human H5N1 Case of 2026
#19,125 With thanks for the head's up from  @E_A_Karlsson , we have the following announcement from Cambodia's Ministry of Health on their...
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Erik Karlsson @eakarlsson.bsky.social · 22/04/2026
@duckswabber.bsky.social @thijskuiken.bsky.social @marionkoopmans.bsky.social @angelarasmussen.bsky.social @jsiegers.bsky.social @fla-medic.bsky.social @who.int @fao.org
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Erik Karlsson @eakarlsson.bsky.social · 22/04/2026
4th human #H5N1 case of 2026 in #Cambodia A 66-year-old woman from Svay Rieng province, currently hospitalized and receiving treatment. 2026: 4 cases, 0 deaths Since 2023: 38 cases, 15 deaths (CFR 39.5%) Since 2004: 94 cases, 52 deaths (CFR 55.3%) 🧪🦠💉🥼🔬😷🐓
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Erik Karlsson @eakarlsson.bsky.social · 01/04/2026
Read more in the news: cambodianess.com/article/camb...
cambodianess.com
Cambodia Reports Third H5N1 Case This Year as Resurgent Virus Gains Ground
PHNOM PENH — Cambodia has confirmed a new human case of H5N1 in a three-year-old boy in Oddar Meanchey, the country’s third infection this year, ...
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Mike Coston @fla-medic.bsky.social · 31/03/2026
AFD Blog `Cambodian MOH Announces 3rd Human #H5N1 Case of 2026' h/t @eakarlsson.bsky.social afludiary.blogspot.com/2026/03/camb...
afludiary.blogspot.com
Cambodian MOH Announces 3rd Human H5N1 Case of 2026
#19,102 With thanks for the head's up from   @E_A_Karlsson , we have the following announcement from Cambodia's Ministry of Health on thei...
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Erik Karlsson @eakarlsson.bsky.social · 31/03/2026
Apologies, find the corrected Press Release here
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Erik Karlsson @eakarlsson.bsky.social · 31/03/2026
@angierasmussen.bsky.social @marionkoopmans.bsky.social @jsiegers.bsky.social @fao.org @who.int @fla-medic.bsky.social @duckswabber.bsky.social
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Erik Karlsson @eakarlsson.bsky.social · 31/03/2026
Since re-emergence, Cambodia has been detecting a reassortant #H5N1 virus circulating in poultry with periodic spillover into humans, often linked to close household exposure. Read more: www.nejm.org/doi/full/10....
nejm.org
Resurgence of Zoonotic Highly Pathogenic Avian Influenza A(H5N1) Virus in Cambodia | NEJM
In this report from Cambodia, 16 human cases of highly pathogenic avian influenza A(H5N1) virus infection that occurred from February 2023 through August 2024 are described.
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Erik Karlsson @eakarlsson.bsky.social · 31/03/2026
Exposure context: reports of sick & dead chickens/ducks in the village. The child had played around poultry at home, including birds that were sick or had died. 🦠🐓😷🔬🧪💉🥼
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Erik Karlsson @eakarlsson.bsky.social · 31/03/2026
3rd human #H5N1 case of 2026 in #Cambodia A 3-year-old boy from Oddar Meanchey province, currently hospitalized and receiving treatment. 🔬🧪😷🐓🦠🥼💉 2026: 3 cases, 0 deaths Since 2023: 37 cases, 15 deaths (CFR 40.5%) Since 2004: 93 cases, 52 deaths (CFR 55.9%)
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Erik Karlsson @eakarlsson.bsky.social · 15/03/2026
@avianbiology.bsky.social @who.int @fao.org @fla-medic.bsky.social @angierasmussen.bsky.social @thijskuiken.bsky.social @avianinfluenza.bsky.social
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Erik Karlsson @eakarlsson.bsky.social · 15/03/2026
Cambodia confirms 2nd human #H5N1 case of 2026 in a 45-year-old woman from Banteay Meanchey province. Patient hospitalized and under treatment. 🥼🦠😷🔬🐓🧪💉 2026: 2 cases, 0 deaths Since 2023: 36 cases, 15 deaths (CFR 41.7%) Since 2004: 92 cases, 52 deaths (CFR 56.5%) #AvianInfluenza #BirdFlu
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Erik Karlsson @eakarlsson.bsky.social · 07/03/2026
There are limited #travel #scholarships available for participants from low- and lower-middle-income countries. If you’re an early-career #scientist working on respiratory viruses, or know someone who is, consider applying. 🦠🐓🧪😷🥼💉🔬
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Erik Karlsson @eakarlsson.bsky.social · 07/03/2026
This five-day intensive program brings together early-career scientists and postgraduate students studying #influenza, #coronaviruses, #RSV, and other respiratory viruses. 🦠🐓🧪😷🥼💉🔬
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Erik Karlsson @eakarlsson.bsky.social · 07/03/2026
Applications are now open for the 7th ISRV School of Respiratory Viruses, hosted by the School of Public Health at The University of Hong Kong. Program details: isrv.eventsair.com/7th-isrv-sch... Apply here: isrv.eventsair.com/Presentation... Applications close: 30 April (UTC+8) 🦠🐓🧪😷🥼💉🔬
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Erik Karlsson @eakarlsson.bsky.social · 19/02/2026
👋
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Erik Karlsson @eakarlsson.bsky.social · 14/02/2026
@michaelisonmd.bsky.social @mtosterholm.bsky.social @marionkoopmans.bsky.social @angierasmussen.bsky.social @jsiegers.bsky.social @filip-ectad.bsky.social @fao.org @who.int @duckswabber.bsky.social @fla-medic.bsky.social @thijskuiken.bsky.social
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Erik Karlsson @eakarlsson.bsky.social · 14/02/2026
This is the first case this year (1 case, 0 deaths in 2026). Since 2023 re-emergence: 35 cases, 15 deaths (CFR 42.9%) Overall since 2004: 91 cases, 52 deaths (CFR 57.1%) 🔬🧪🐓💉🥼🦠😷
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Erik Karlsson @eakarlsson.bsky.social · 14/02/2026
First human #H5N1 case of 2026 in #Cambodia: a 30-year-old man from Kampot province. Sequencing, virus isolation & animal investigations ongoing. Dead chicken at home before onset. Patient has since recovered. 🦠💉😷🐓🥼🔬🧪 Sequencing, contact tracing, and poultry investigations ongoing.
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Metagenomic Virus Discovery workshop @virus-metagenomics.bsky.social · 16/01/2026
Planning is underway for the 2026 Metagenomic Virus Discovery workshop. Last years workshop was a great success with 22 participants representing 11 countries. If you would like to know more, get in contact with our organising committee at mvdworkshop2025@gmail.com
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Erik Karlsson @eakarlsson.bsky.social · 14/01/2026
This isn’t about replacing classic #surveillance. It’s about upgrading it. Find smarter, safer ways to see what’s coming. Sometimes the first signal of risk isn’t inside the bird. It’s already in the air.
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Erik Karlsson @eakarlsson.bsky.social · 14/01/2026
Traditional sampling is time-consuming, expensive, and carries real #biosafety and animal health risks. Environmental sampling, especially #air, can reduce handling, broaden detection, and act as an early warning system in one of the most critical human–animal interfaces.
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Erik Karlsson @eakarlsson.bsky.social · 14/01/2026
Perhaps most important: Environmental sampling outperformed poultry swabs for detecting highly pathogenic #H5N1, including clades 2.3.4.4b and 2.3.2.1c. Translation: the market environment was positive for H5N1 on days when the birds we swabbed were “negative.”
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Erik Karlsson @eakarlsson.bsky.social · 14/01/2026
What we learned: - Environmental samples detected a wide diversity of viruses - Air was the MVP: greatest diversity of poultry viruses. - When we compared, the environment is highly similar to what we saw in poultry
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Erik Karlsson @eakarlsson.bsky.social · 14/01/2026
Here’s the problem: markets are not static. They’re more like airport terminals for #poultry. Constant arrivals, constant departures, constant mixing. Swabbing a few birds is a snapshot. So we tried something obvious in hindsight: Stop interrogating individual birds. Start listening to the room.
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Erik Karlsson @eakarlsson.bsky.social · 14/01/2026
In our recent @nature.com Communications study, we compared traditional #poultry swabs with environmental #metagenomics, sampling #air, cage surfaces, carcass wash water, and drinking water in two Cambodian live bird markets. 🦠😷🔬🧪🐓🥼 www.nature.com/articles/s41...
nature.com
Client Challenge
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Erik Karlsson @eakarlsson.bsky.social · 26/11/2025
The takeaway: H5 #avianflu isn’t slowing down. It’s accelerating. And each new clade is a reminder that surveillance, sequencing, and real cross-sector coordination aren’t optional, they’re the only way to keep up. 🦠🥼😷🔬🐓🧪 #H5N1 #influenza #avianinfluenza #birdflu
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Erik Karlsson @eakarlsson.bsky.social · 26/11/2025
The WHO/WOAH/FAO H5 Evolution Working Group just released a major nomenclature update: 12 new H5 clades across 2.3.2.1 and 2.3.4.4, the result of a decade of relentless viral evolution stretching from Asia to Africa, the Americas, and even Antarctica. 🥼🔬🧪🦠🐓😷 www.biorxiv.org/content/10.1...
biorxiv.org
Nomenclature updates to the hemagglutinin gene clade designations resulting from the continued evolution of high pathogenicity avian influenza A(H5) virus clades 2.3.2.1c and 2.3.4.4
The evolutionary divergence of the A(H5) hemagglutinin (HA) gene of high pathogenicity avian influenza (HPAI) viruses (A/goose/Guangdong/96 lineage) was analyzed by phylogenetic and average pairwise d...
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Pretzel @krispyhajkowicz.bsky.social · 19/11/2025
Go @eakarlsson.bsky.social knocking it out of the park at the @virus-metagenomics.bsky.social workshop at CERI in Stellenbosch.
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Metagenomic Virus Discovery workshop @virus-metagenomics.bsky.social · 18/11/2025
Tomorrow evening we have our keynote lecture session from 16:00 in the Neelsie Cinema, Stellenbosch University. Dr Maja Vukovikj will be speaking about Africas ancient disease landscape and Dr Erik Karlsson will talk about metagenomics and high-risk interfaces tinyurl.com/ytj3sppm
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Erik Karlsson @eakarlsson.bsky.social · 25/10/2025
Grateful to the team led by Benjamin Larsen, Cameron Myhrvold, and @ajtevelthuis.bsky.social, and proud that @jsiegers.bsky.social and the IPC Virology Unit could contribute. Sometimes evolution whispers. You just have to be listening fast enough to hear it.
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Erik Karlsson @eakarlsson.bsky.social · 25/10/2025
When those shifts happen, like the PB2-E627K mutation we’ve seen in human #H5N1 cases in #Cambodia, the clock starts ticking. Speed matters. #Surveillance only works if it moves fast enough to turn data into action. www.nejm.org/doi/full/10....
nejm.org
Resurgence of Zoonotic Highly Pathogenic Avian Influenza A(H5N1) Virus in Cambodia | NEJM
In this report from Cambodia, 16 human cases of highly pathogenic avian influenza A(H5N1) virus infection that occurred from February 2023 through August 2024 are described.
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Erik Karlsson @eakarlsson.bsky.social · 25/10/2025
Proud to be part of this new Nature Biotechnology paper, “RNA structure modulates Cas13 activity and enables mismatch detection.” Detecting single-nucleotide mutations in #influenza or SARS-CoV-2 is how you know, fast, when a virus is playing by different rules. www.nature.com/articles/s41...
nature.com
RNA structure modulates Cas13 activity and enables mismatch detection - Nature Biotechnology
An effective CRISPR RNA occlusion strategy enhances mismatch detection when using Cas13.
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Erik Karlsson @eakarlsson.bsky.social · 23/10/2025
@jsiegers.bsky.social @duckswabber.bsky.social @angierasmussen.bsky.social @fla-medic.bsky.social @cidrap.bsky.social @avianinfluenza.bsky.social @whofluccmelb.bsky.social @who.int @fao.org @marionkoopmans.bsky.social
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Erik Karlsson @eakarlsson.bsky.social · 23/10/2025
Genomics show no human-to-human transmission but evolution’s been busy. A local clade quietly swapped genes with others, creating a new reassortant now spreading across the Greater Mekong.
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Erik Karlsson @eakarlsson.bsky.social · 23/10/2025
Now out in @nejm.org : Between 2023–2024: Sixteen human infections with A/H5N1 in Cambodia. Six deaths. Most in children. All exposed to sick or dead poultry. www.nejm.org/doi/full/10....
nejm.org
Resurgence of Zoonotic Highly Pathogenic Avian Influenza A(H5N1) Virus in Cambodia | NEJM
In this report from Cambodia, 16 human cases of highly pathogenic avian influenza A(H5N1) virus infection that occurred from February 2023 through August 2024 are described.
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Erik Karlsson @eakarlsson.bsky.social · 07/08/2025
Time’s running out! We’re hiring 1 Scientist + 2 Postdocs at @PasteurCambodia’s #Virology Unit to work on emerging viruses & #zoonoses. If you want to do real-time science that matters—this is your chance. Apply now. Start soon. 🦠🔬🧪🐓💉🦇😷🥼 #academicjobs #OneHealth #Virology
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Erik Karlsson @eakarlsson.bsky.social · 06/08/2025
@angierasmussen.bsky.social @marionkoopmans.bsky.social @fao.org @who.int @jsiegers.bsky.social @peaseroland.bsky.social
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Erik Karlsson @eakarlsson.bsky.social · 06/08/2025
Cambodia has confirmed its 15th human case of #H5N1 in 2025. That brings the year’s total to 15 cases and 7 deaths (CFR: 46.6%). Since 2005: 87 cases, 50 deaths (CFR: 57.5%). 🧪🧬🥼🦠🔬😷🐓💉 #AvianInfluenza #Zoonoses #BirdFlu #Spillover
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Erik Karlsson @eakarlsson.bsky.social · 29/07/2025
‪Read more here: cambodianess.com/article/siem... ‬
cambodianess.com
Siem Reap Man in ICU as Cambodia Confirms 14th H5N1 Case
PHNOM PENH — A 26-year-old man from Siem Reap has tested positive for the H5N1 strain of avian influenza, bringing Cambodia’s total number of hum...
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Erik Karlsson @eakarlsson.bsky.social · 29/07/2025
@duckswabber.bsky.social @jsiegers.bsky.social @marionkoopmans.bsky.social @angierasmussen.bsky.social @cidrap.bsky.social @mtosterholm.bsky.social @michaelisonmd.bsky.social @peaseroland.bsky.social @fao.org @who.int
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