Erik Karlsson

👋

@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

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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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.

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

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.

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.

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.”

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

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.

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...

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

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...

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...

Go @eakarlsson.bsky.social knocking it out of the park at the @virus-metagenomics.bsky.social workshop at CERI in Stellenbosch.

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

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.

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.

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....

RNA structure modulates Cas13 activity and enables mismatch detection - Nature Biotechnology An effective CRISPR RNA occlusion strategy enhances mismatch detection when using Cas13.

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...

@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

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.

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.

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....

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.
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#academicjobs #OneHealth #Virology

@angierasmussen.bsky.social @marionkoopmans.bsky.social @fao.org @who.int @jsiegers.bsky.social @peaseroland.bsky.social

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%).
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#AvianInfluenza #Zoonoses #BirdFlu #Spillover

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...

‪Read more here: cambodianess.com/article/siem... ‬

@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

Cambodia continues to lead a coordinated #OneHealth response — linking human, animal, and environmental health. Early #detection, rapid #diagnostics, and cross-sector #collaboration are essential to prevent and respond to current and future spillover events.

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#GlobalHealth #H5N1

Emergence of a Novel Reassortant Clade 2.3.2.1c Avian Influenza A/H5N1 Virus Associated with Human Cases in Cambodia After nearly a decade without reported human A/H5N1 infections, Cambodia faced a sudden resurgence with 16 cases between February 2023 and August 2024, all caused by A/H5 clade 2.3.2.1c viruses. Fourt...

All cases have been linked to #poultry exposure, with no evidence of human-to-human transmission.

The virus remains the #reassortant strain that emerged in 2023, a reminder of the continued #zoonotic risk.

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🔗 medrxiv.org/content/10.1...

Cambodia has confirmed its 14th human case of avian influenza A/H5N1 in 2025 : a 26-year-old man from Siem Reap.

So far in 2025: 14 cases, 7 deaths — a case fatality rate (CFR) of 50%

Since 2005: 86 cases, 50 deaths (CFR: 58.1%)

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Read more here: www.khmertimeskh.com/501722452/ca... 🧪🦠🧬🔬💉🥼😷🐓🐔🐤🐣🐥