Preprint: Emergence of D1.1 Reassortant H5N1 Avian Influenza Viruses in North America

 

#19,003

As we discussed at some length last August in H5Nx: Reassort & Repeat, in the Northern hemisphere millions of migratory birds spend their summers in their high latitude breeding areas in Alaska, Canada, Siberia, and even the Arctic.

During their stay, they hatch a new generation of (flu naive) fledglings while mingling with other species, potentially sharing avian viruses picked up the previous spring (see 2016's Sci Repts.: Southward Autumn Migration Of Waterfowl Facilitates Transmission Of HPAI H5N1).

These factors can lead to the creation and spread of new reassortants (genetic hybrids). While most are genetic failures - and unable to compete with existing strains - every once in a while a `new and improved' virus appears.

In the fall of 2024, while most `flu watchers' were concentrating on the B3.13 `bovine' genotype infecting hundreds of U.S. dairy herds (and mildly infecting dairy workers), a new, genotype (D1.1) emerged in wild birds, and swiftly crossed the country from west to east.

Unlike the `bovine' version, however, it produced a few severe (and 2 fatal) illness among a handful of human infections (see map above).  

D1.1 was also joined last fall by two `lesser' reported emerging genotypes (D1.2 and D1.3), the former found in infected pigs in Oregon, and the latter infecting an ostrich farm in Canada and producing a human case in Ohio.

Not to be outdone by B3.13,  D1.1 also spilled over into cattle (twice) in early 2025, with a 3rd spillover reported in Wisconsin early this month. 

Since its arrival to North America in 2021, more than 100 new genotypes have been identified, with scores more circulating in Europe, Asia, and South America. As flu viruses are notoriously promiscuous, new genetic combinations are certain to emerge. 

Most will be less `biologically fit' than their competitors, and will fall by the wayside, but occasionally a new, better adapted, variant will emerge. Although B3.13 and D1.1 currently have the bulk of our attention, they are simply stepping stones to the `next' viral iteration. 

All of which brings us to a new preprint, released last week, which describes what we know about this emerging genotype, including the swapping out of its NA gene (Eurasian neuraminidase with a North American LPAI N1), and the remarkable continent-wide dispersal of this strain. 

While D1.1 may not be ready for prime time, it continues to hone its abilities - mostly outside of our view - and that should give us pause. 

Due to its length, I've just posted the Abstract and a few excerpts. Follow the link to read the paper in its entirety. 

Emergence of D1.1 reassortant H5N1 avian influenza viruses in North America
Alvin Crespo-Bellido, Nídia S. Trovão, Alexander Maksiaev, Guy Baele, Simon Dellicour, Martha I. Nelson
doi: https://doi.org/10.64898/2025.12.19.695329
This article is a preprint and has not been certified by peer review [what does this mean?].

Preview PDF

Summary

Since 2021, highly pathogenic avian influenza viruses (HPAIV) belonging to H5N1 clade 2.3.4.4b have caused high mortality in North American wild birds and poultry. In 2025, a new D1.1 genotype caused two human deaths and host-switched to dairy cattle. However, the evolutionary origins and dynamics of D1.1 have not been fully characterized.

Here, our phylogenetic analysis of 17,516 H5N1 genome sequences uncovers how D1.1 introduced a major shift in the antigenic diversity and ecology of the H5N1 epizootic in North America.

D1.1 is the first major H5N1 genotype to (a) emerge in the Pacific flyway and spread west-to-east faster than any prior genotype; (b) antigenically shift via reassortment with the North American N1 segment, displacing the previously fixed Eurasian N1; and (c) transmit to a broader range of host species than any H5N1 genotype to date, introducing mammalian adaptations 

(SNIP)

Thus far, Eurasia has been a major source of H5N1 viruses for North America, and there is little evidence of D1.1, B3.2, or other dominant North American genotypes migrating back to Europe or Asia. However, H5N1 is routinely changing patterns. Understanding the risk that major evolutionary changes in H5N1 in the Americas presents to the rest of the world is a central question going forward. 

(Continue . . . )

There's an old joke about a tourist asking a NYC cabbie, `What’s the best way to get to Carnegie Hall?” and the cabby replies, “Practice, practice, practice”.

In many ways, that applies to viruses. They usually get better (i.e. adapt) following repeated spillovers.  

And right now - in countless wild birds, poultry, cattle, pets, mammalian wildlife, and occasionally humans - it's getting a lot of practice. 

A Brief History of Influenza A in Canines & Canadian Report On A Recent Fatal H5N1 Dog Infection

 
Just one of many scenarios - Dogs as `mixing vessels' for Influenza 

#19,002

Until a little over 2 decades ago dogs and cats were thought to be poorly susceptible to influenza A viruses; but that all changed in 2004 when scores of captive cats (tiger, lions, etc.) in South East Asian zoos - fed on a diet of raw poultry - began dying from HPAI H5N1 (see 2006 WHO DON).

At roughly the same time dogs at a Florida racetrack unexpectedly began to fall ill from a variant of the equine H3N8 virus (see EID Journal article Influenza A Virus (H3N8) in Dogs with Respiratory Disease, Florida).

Three years later another flu virus (avian H3N2) jumped to dogs in South Korea (see Transmission of Avian Influenza Virus (H3N2) to Dogs). The HA and NA genes of the A/canine/Korea/01/2007 (H3N2) isolate were closely related to those identified in chickens and doves in South Korea in 2003.

After nearly a decade of spreading in  Asia, in 2015 canine H3N2 finally landed in North America (see CDC Statement On H3N2 Canine Influenza In Chicago Region) and quickly spread across the United States.

As a result, during the middle of the last decade the notion that dogs might serve as intermediate hosts - or even mixing vessels - for novel influenza began to gain traction.  A few, of many, reviews include:

Viruses Review: Potential Intermediates in the Cross-Species Transmission of Influenza A Virus to Humans

J. Virology: Zoonotic Risk, Pathogenesis, and Transmission of Canine H3N2

Study: Dogs As Potential `Mixing Vessels’ For Influenza

Admittedly, cats appear to be far more susceptible than dogs (see 2023's A Brief History Of Avian Influenza In Cats) - with hundreds more infections reported since - but as dogs tend to show fewer symptoms than cats, they may be less likely to be tested.

While rare, severe and even fatal canine infections with HPAI H5 have been reported, as we saw detailed in 2024's Microorganisms: Case Report On Symptomatic H5N1 Infection In A Dog - Poland, 2023, where the authors wrote:

The case described in our report confirms that on rare occasions the A/H5N1 virus can also induce a natural severe respiratory disease in dogs. While in some of them the infection remains asymptomatic, capable of shedding the virus [35], others exhibit mild symptoms such as transient fever [34], or even fatal disease [20].

In 2023, Canada reported a fatal H5N1 infection in a domestic dog in Ontario (see press release below), which renewed concerns, particularly for those with hunting dogs. 

Domestic dog tests positive for avian influenza in Canada

From: Canadian Food Inspection Agency

Statement

April 4, 2023 – Ottawa, Ontario

Today, the Canadian Food Inspection Agency and the Public Health Agency of Canada issued the following joint statement:

The Canadian Food Inspection Agency's (CFIA) National Centre for Foreign Animal Disease, confirmed on April 1, 2023, that a domestic dog in Oshawa, Ontario has tested positive for highly pathogenic avian influenza (HPAI).

The domestic dog was found to have been infected with avian influenza after chewing on a wild goose, and died after developing clinical signs. The necropsy was completed on April 3, 2023, and showed respiratory system involvement. Further testing is underway. It is the only case of its kind in Canada.

       (Continue . . . )

A year later, in EID Journal: Antibodies to Influenza A(H5N1) Virus in Hunting Dogs Retrieving Wild Fowl, Washington, USA, researchers reported finding a low - but significant - number of healthy hunting dogs with antibodies to H5N1 (tested over a 2 month period in 2023).

Spillovers into companion animals are particularly worrisome because of their potential for spreading the virus to other animals, or to humans (see JAVMA: Companion Animals and H5N1 Highly Pathogenic Avian Influenza: Cause for Concern?).

All of which brings us to the following memo from the Office of the Chief Provincial Veterinarian dated December 16, 2025, hosted on the Canadian Veterinary Medical Association (CVMA) website. 



While dog owners may be relieved by the relatively rare severe presentation of HPAI H5N1 in canines, as the following report indicates, that may present problems of its own. 

In 2023's Eurosurveillance: Asymptomatic infection with clade 2.3.4.4b HPAI A(H5N1) in carnivore pets, Italy, April 2023, the authors wrote:

Here we report a case of influenza A(H5N1) infection in a domestic cat and five dogs living on a rural backyard poultry farm where an HPAI H5N1 outbreak was notified; the infection in poultry was caused by an HPAI H5N1 virus strain belonging to the BB genotype that was characterised by the presence of a PB2 mutation related to mammalian adaptation.

In contrast, the affected pets in this report were completely asymptomatic, raising concerns over the possibility of subclinical infections with zoonotic viruses in animals in close contact with humans.

       (Continue . . . )

While the risks for the general public of contracting avian flu are currently very low, those who have pets that are allowed to roam outdoors may be at slightly greater risk, along with anyone who deals with animal rescue or rehoming operations (see California: San Mateo County Warns Residents After Stray Cat Found With H5N1).

The thing about risk, though, is it can change abruptly. And given the limits of surveillance and reporting, a specific risk may become elevated for days or even weeks before we ever learn about it.

While I dislike the phrase `the new normal', as long as HPAI H5 continues to circulate at high levels in our environment, we have to accept that this has become our `new reality'.

WHO Multi-country Outbreak of Mpox: External Situation Report #61

 #19,001

While based on limited reporting, the above graphic provides some valuable insight into how much progress the multiple strains of Mpox have made over the past 13 months in spreading both inside and outside of Africa.  

Four years ago, the global Mpox map was far more compact (see below), as Mpox (formerly Monkeypox) was only typically found inside of Africa (note: with a handful of exported cases reported each year).

Geographic Range of Monkeypox - Credit WHO  

In the spring of 2022, however, Mpox clade IIb emerged, and began its world tour. According to the CDC; The ongoing global outbreak of clade IIb monkeypox has caused more than 100,000 cases in 122 total countries, including 115 countries where monkeypox was not previously reported.

While that outbreak eventually slowed, it never really ended - and in the summer of 2024 the WHO declared a new emerging threat; Clade Ib (see WHO declared the Mpox outbreak in Central Africa to constitute a PHEIC ).

Although clade Ib has taken off slower than did clade IIb, it continues to make inroads around the world, with community transmission now being reported in a number of countries outside of Africa (see WHO DON: Broader Transmission of Mpox Due to clade Ib MPXV – Global situation). 

"Based on this, Italy, Malaysia, the Netherlands, Portugal, Spain, and the United States of America are now considered to be experiencing community transmission of clade Ib MPXV. In addition, travel-related cases continue to be reported in many countries."

Earlier this month, the UK also reported a New Recombinant Strain of Mpox Virus in a traveler returning from Asia.  Details remain scant, but this continues to validate the concerns expressed eleven years ago - in an EID Journal article Genomic Variability of Monkeypox Virus among Humans, Democratic Republic of the Congo - where the authors cautioned:

Small genetic changes could favor adaptation to a human host, and this potential is greatest for pathogens with moderate transmission rates (such as MPXV) (40). The ability to spread rapidly and efficiently from human to human could enhance spread by travelers to new regions.

In the decade since, 2 new clades (Ib and IIb) have emerged, with both (IIb and, to a lesser extent Ib) managing to spread internationally. Given this track record, new emerging variants and/or clades of the mpox virus are not totally unexpected.  

While we are in the midst of our annual holiday drought of infectious disease reporting, the WHO published their latest monthly Multi-Country Mpox report on the 22nd, which also includes a brief comment on the UK recombinant finding.  

A link, and a few excerpts from this 15-page report, follow.

Mpox

Multi-country external situation report no. 61, published 22 December 2025

Highlights

• All clades of monkeypox virus (MPXV) continue to circulate. Unless mpox outbreaks are rapidly contained and human-to-human transmission is interrupted, there is a risk of sustained community transmission.

• In November 2025, 48 countries across all WHO regions reported a total of 2150 new confirmed mpox cases, including five deaths (case fatality ratio [CFR] 0.2%). About 68% of these cases were reported in the African Region. Four regions observed a decline in confirmed cases in November, compared to October 2025, while the European and Western Pacific regions reported more cases than the previous month.

• Nineteen countries in Africa reported active transmission of mpox in the last six weeks (2 November– 14 December 2025), with 1435 confirmed cases, including seven deaths (CFR 0.5%). Countries reporting the highest number of cases in this period are the Democratic Republic of the Congo, Guinea, Liberia, Kenya and Ghana; while case reports in Liberia still show indications of a rise, weekly case counts in the other countries have been declining in recent weeks.

• Romania has reported detection of clade Ib MPXV for the first time, in a case confirmed in August 2025.

• Outside Africa, community transmission of clade Ib MPXV continues in Spain and in the Netherlands

.• In the Democratic Republic of the Congo, mpox transmission continues across multiple provinces with co-circulation of clades Ia and Ib MPXV, heterogeneous subnational trends and declining access to testing of suspected cases.

• The United Kingdom of Great Britain and Northern Ireland has reported a new travel-linked case of mpox with detection of a recombinant MPXV strain containing genetic elements of both clade Ib and clade IIb MPXV. The extent of circulation of the recombinant strain remains unknown.

• WHO assesses the ongoing public health risk to be moderate for men who have sex with men with new or multiple partners, sex workers and others with multiple partners who may be at risk, and low for the general population with no specific risk factors, continues close monitoring of the situation, and emphases the importance of maintaining surveillance and response capacity, including genomic sequencing notably in locations where multiple MPXV strains co-circulate.

(SNIP)

Recombinant strain of MPXV detected in the United Kingdom of Great Britain and Northern Ireland

On 2 December, WHO was notified by the United Kingdom of a single imported mpox case caused by a recombinant MPXV strain containing both clade Ib and clade IIb MPXV genetic elements in its genome. The case reported recent travel history to Asia, where exposure is likely to have occurred. The individual experienced mild illness and had atypical mpox presentation.

Recombination is a known natural process that can occur when an individual is infected with two related virus strains at the same time. Orthopoxviruses, including MPXV, are capable of recombination when co-infection occurs.Multiple MPXV strains are currently circulating in interconnected sexual networks across many countries and indifferent settings. In this case, the genomic analyses indicate that the virus acquired alternating fragments from both clade Ib and clade IIb MPXV, resulting in a replication-competent recombinant.

The information available for this one case is not sufficient to draw conclusions about the transmissibility or clinical severity of this recombinant strain, or the effectiveness of medical countermeasures against it. 

WHO, through its regional and country offices, is continuing to gather more information and closely monitor the situation. The WHO global risk assessment remains unchanged, with the risk considered moderate for men who have sex with men with new or multiple partners, for sex workers and for others with multiple partners who may beat risk, and low for the general population who have no specific risk factors for mpox.

WHO advises Member States to continue implementing the Standing recommendations currently extended to August 2026. Countries should maintain mpox surveillance, case management, infection prevention and control measures, and vaccination strategies, and prioritize genomic sequencing for new and unusual cases, particularly in key populations at risk and in settings where multiple MPXV strains are co-circulating, with timely sharing of sequence data to support close monitoring of viral evolution and transmission patterns.

       (Continue . . . )

Since the eradication of smallpox in the 1970s, there is a general feeling that poxviruses are a thing of the past; a near-forgotten relic of the 20th century. 

But a 2020 report in the Bulletin of the World Health Organization warned that our waning immunity to smallpox puts society at increasing risk of seeing new poxvirus epidemics (see WHO: Modelling Human-to-Human Transmission of Monkeypox).

The world basically ignored those warnings until the summer of 2022, when clade IIb Mpox burst unexpectedly on the world stage.  After about a year, that first epidemic lost its momentum, as did the world's attention. 

We are now on round two of Mpox, and due to its relatively glacial pace, many assume it will fizzle over time.  

But the emergence of 2 new clades (Ib & IIb) since 2020 - and a new recombinant in the UK - suggest that Mpox isn't near done reinventing itself, and we ignore its potential do to so at our considerable peril. 

South Korea: MAFRA Reports Increased Infectivity & Pathogenicity of This Year's Avian Flu Strains

#19,000

Last August we speculated over what kind of fall avian flu season we might see (H5Nx: Reassort & Repeat), following the previous year's introduction of a bovine B3.13 strain, and a new D1.1 genotype, both of which contributed to the 70+ human infections in the United States since March of 2024. 

Despite these recent developments, global avian flu activity had actually declined since the 2022-2023 season (see ECDC/EFSA chart below).  

While both the FAO and ECDC/EFSA data haven't been updated since November, we've already seen evidence that this year's wave of avian flu is the strongest in several years. 

We are less than 3 months into the 2025-2025 season, and already:

• Canada has reported almost 200 outbreaks, nearly matching the previous year's total in less than 90 days. 
• The UK has already reported 77 HPAI outbreaks, compared to just 87 over the previous 24 months. 
• And as of mid-November, Europe has reported (see graphic below) unprecedented surge in reports.  

Asia is also struggling with avian flu, with Japan reporting 10 outbreaks, and South Korea now reporting 22. China, however, almost never reports outbreaks, and reporting from other Asian nations can be spotty. 

Two days ago, in South Korean City (Naju) Orders Extraordinary Emergency Measures Due to HPAI, we looked at an unusually robust civic response to 2 outbreaks of HPAI in South Jeolla Province in recent days, which included the cancellation of outdoor holiday activities.

This followed previous reports of biosecurity failures on many South Korean farms this fall (see South Korea: MAFRA Identifies Biosecurity Breaches On HPAI Infected Poultry Farms), and South Korea's first report of 3 different subtypes of HPAI (H5N1, H5N5, H5N9) in wild birds. 

Overnight MAFRA released a lengthy report describing a sharp escalation in highly HPAI H5 activity this winter - along with test results showing increased infectivity and pathogenicity this year - which has prompted orders for greatly increased biosecurity. 

Normally I wouldn't post an entire report of this size, but since it is only available in Korean - and it is highly illuminating - I've posted the full translation.  For those who don't want to wade through the entire text, the short version is; they appear to be dealing with a much more challenging set of HPAI viruses this fall. 

Since we don't have uniform test results from all of the affected countries, it is difficult to make direct comparisons to what South Korea is reporting, and what is occurring globally. 

But compared to the past couple of seasons, globally this year's HPAI appears far more formidable. 

And while increased pathogenicity and/or infectivity in poultry doesn't necessarily translate to increased health risks to humans, it does increase the opportunities, intensity, and duration of exposure for those who must work with or are exposed to birds. 

First, the full (translated) report, after which I'll have a brief postscript. 

This winter, the highly pathogenic avian influenza virus is highly contagious, requiring further strengthening of quarantine management

2025.12.25 19:27:00 Avian Influenza Prevention Division, Quarantine Policy Bureau

The Central Disaster and Safety Countermeasures Headquarters for Highly Pathogenic Avian Influenza ( Chief: Song Mei-ryeong, Minister of Agriculture, Food and Rural Affairs , hereinafter referred to as the Central Disaster and Safety Countermeasures Headquarters ) announced that as the risk of additional outbreaks of highly pathogenic avian influenza (AI) has increased recently, an emergency quarantine meeting was held on Thursday, December 25 , chaired by Kim Jeong-wook, Director of the Agricultural Innovation Policy Office , to review the situation of highly pathogenic avian influenza outbreaks and quarantine measures and to further strengthen quarantine management .

1. Increased risk and occurrence situation

Today, an outbreak was confirmed at a laying hen farm in Pyeongtaek (the 22nd time ) , bringing the total number of highly pathogenic avian influenza cases to 22 in poultry farms and 21 in wild birds this winter ('25/'26 season ) .

* Poultry farm outbreak status ( total 22 cases ): Gyeonggi 9 cases ( Anseong 3, Paju 1, Hwaseong 2, Pyeongtaek 3), Chungbuk 4 cases ( Goesan 1, Yeongdong 1, Jincheon 1, Eumseong 1), Chungnam 3 cases ( Boryeong 1, Cheonan 2), Jeollabuk-do 2 cases ( Gochang 1, Namwon 1), Jeollanam-do 3 cases ( Naju 2, Yeongam 1), Gwangju Metropolitan City 1 case

** Status of wild bird detection ( total 21 cases ): Gyeonggi 1, Chungbuk 1, Chungnam 5, Jeonbuk 3, Jeonnam 4, Gyeongbuk 3, Gyeongnam 1, Busan 1, Gwangju 1, Seoul 1

This winter, for the first time in Korea, three types of viruses ( serotypes : H5N1, H5N6, H5N9) were detected in wild birds and poultry farms, raising the risk of further outbreaks .

In particular , the Animal and Plant Quarantine Agency conducted an evaluation of the infectivity and pathogenicity of the highly pathogenic avian influenza virus ( serotype H5N1) confirmed domestically this winter , and found that the infectivity was more than 10 times higher than in previous years .

This means that the disease can easily spread in poultry farms with a quantity of the virus that is more than 10 times smaller, so more thorough quarantine measures such as disinfection and access control are necessary than ever before .

* ( Infectious power ) The lethal dose ( LD50 : lethal dose, AI virus concentration when half of the infected chickens die ) this time is 103.3 , which is more than 10 times higher than 104.4 in the '23/'24 season and 104.6 in the '24/ '25 season .

* ( Pathogenic ) 100% mortality in case of natural infection in chickens , the average time from infection to death is 2.4 days this time, the shortest since the '20/'21 season (2.6 to 4.3 days )

In addition , looking at past outbreaks , highly pathogenic avian influenza has been occurring frequently * in December and January , and considering the current situation in various regions and with various livestock species ** , there is a risk of additional outbreaks in any region of the country, so more thorough quarantine management than ever is needed .

* 48.1% occurred in December and January ( 669 cases out of 1,389 cases since 2003 )

** Occurred in wild bird and poultry farms ( layer hens , meat breeders , native chickens , ducklings , meat ducks , quail, etc. ) in 30 cities and counties in 10 provinces and cities.

2. Results of epidemiological investigation and quarantine inspection of the outbreak farm

The Central Disaster and Safety Countermeasures Headquarters has confirmed that 16 poultry farms with confirmed outbreaks to date were not complying with basic quarantine guidelines through interim epidemiological investigations . Accordingly, the Central Disaster and Safety Countermeasures Headquarters plans to strictly enforce administrative sanctions, such as fines, and reductions in culling compensation , in accordance with the Livestock Infectious Disease Prevention Act, on farms that violate relevant regulations .

* According to the “ Standards for Payment and Reduction of Compensation in Appendix 2 of the Enforcement Decree of the Livestock Infectious Disease Prevention Act ,” the basic amount equivalent to 20/100 of the livestock appraisal value is reduced , and if any insufficient quarantine measures are identified, the compensation is additionally reduced for each applicable item.

During the special quarantine period for highly pathogenic avian influenza (AI), the Central Disaster and Safety Countermeasures Headquarters mobilized the on-site inspection team (20 teams, 40 people ) of the Animal and Plant Quarantine Agency to inspect violations of administrative orders ('25.10. 1 - 12. 22). As a result , a total of 43 farms were found to have violated the order and were issued with certificates. Of these , 30 farms (69.8%) were laying hen farms, accounting for more than two-thirds .

* 43 violating farms : 30 laying hens , 3 each of meat ducks , meat breeders , and broilers , 2 laying hens , 1 each of hatchery and livestock vehicle

The total number of violations was 58 ( including duplicates by farm ) , of which 23 cases (39.7%) were violations of administrative orders and public notices, such as insufficient disinfection of vehicles entering and exiting the farm and entry of illegal vehicles into the farm , followed by insufficient CCTV management with 11 cases ( 16.7 % ) .

* 14 cases of failure to perform level 2 disinfection of vehicles entering and exiting the farm , 9 cases of violation of farm entry by vehicles prohibited from entering ( egg transport , vaccination team , loading/unloading team )

In particular , the number of violations confirmed in laying hens (30 farms ) was 40 , and 19 cases * (40%) of them were found to be violations of the “ Administrative Order and Notice Details , ” and many violations of the ban on entry into farms by specific livestock vehicles , such as egg transport vehicles and vaccination team vehicles, were confirmed .

* 11 cases of non-implementation of two- stage disinfection (1st stage disinfection of vehicle with disinfectant → 2nd stage disinfection of vehicle wheels, etc. with high-pressure sprayer ) upon entry of livestock vehicles into farms, 8 cases of violation of prohibition of entry into farms by egg transport vehicles , vaccination team vehicles , and poultry loading/unloading crew personnel transport vehicles

In addition , as a result of an inspection of farms within the quarantine zone of Cheonan, South Chungcheong Province and Anseong , Gyeonggi Province ( within 10km ) , it was confirmed that five laying hen farms were in violation of the “ administrative order and public notice details ” and quarantine compliance matters .

* 1 case of failure to perform 2- stage disinfection when entering a livestock vehicle on the farm , 1 case of violation of the ban on entry of egg transport vehicles into the farm , 2 cases of failure to store CCTV ( closed-circuit television ) video records for more than 30 days , 1 case of failure to disinfect a forklift used for loading eggs

Accordingly , we plan to strictly enforce fines and penalties in accordance with relevant laws and regulations in cooperation with local governments , and reduce compensation for culling by up to 80% in the event of an outbreak of highly pathogenic avian influenza .

* In case of violation of quarantine -related administrative orders , imprisonment of up to 1 year or a fine of up to 10 million won is imposed , and in case of violation of public notices, a penalty of up to 10 million won is imposed.

The Central Disaster and Safety Countermeasures Headquarters plans to continue to inspect the quarantine status of poultry farms to prevent further spread of highly pathogenic avian influenza .

In particular, during this quarantine inspection, we will focus on cracking down on violations of the ban on entry into farms by specific livestock vehicles * , which were identified as major violations , and whether livestock vehicles that can enter farms are implementing the second- stage disinfection . We plan to strictly enforce the zero-tolerance principle and take administrative action not only against farms that violate related regulations but also against owners ( or drivers ) of vehicles entering livestock- related facilities . 

* ( No entry into the farm ) Livestock vehicles such as eggs , egg trays , animal medicine , loading and unloading trucks , and delivery vehicles

3. Strengthening quarantine measures

The Central Disaster and Safety Countermeasures Headquarters is implementing the following strengthened quarantine measures to prevent further outbreaks of highly pathogenic avian influenza .

First , from December 24, the Ministry of Agriculture, Food and Rural Affairs will form a “Special Response Team (TF) for Highly Pathogenic Avian Influenza Quarantine Response” in addition to the existing Central Disaster and Safety Countermeasures Headquarters for Highly Pathogenic Avian Influenza, and will respond with all - out efforts , including daily situation review meetings, on-site inspections of risk areas , and guidance and publicity for livestock industry officials .

* 3 teams : General response team ( intensive management of laying hens ), field inspection team ( inspection of outbreak areas, etc. ), media response team ( public relations, etc. )

Second , starting December 26, we will dispatch section chiefs and others from the Ministry of Agriculture, Food and Rural Affairs to high-risk areas (11 cities and counties) where there is concern about additional outbreaks, including Gyeonggi , South Chungcheong , North Chungcheong , North Jeolla , and Sejong , to conduct special inspections

* Gyeonggi Pyeongtaek and Anseong , Chungnam Cheonan , Chungbuk Eumseong , Jincheon and Cheongju , Sejong , Jeollabuk Buan and Gimje

Third, laying hen farms within the quarantine zone (~10km) of four regions with a high risk of laying hen outbreaks ( Hwaseong , Pyeongtaek , Anseong , and Cheonan ) will be specially inspected and managed for 7 days ( from December 26 to January 1 of the following year ) . 

* Livestock vehicles carrying livestock manure , egg deposits , and vaccinations are prohibited from entering the farm . Vehicles transporting eggs and feed that must enter are subject to special inspection and management through prior registration and conditional entry with the presence of a quarantine officer.

Fourth , to raise awareness of quarantine rules compliance among all poultry farm workers, including foreigners, we will cooperate with local governments and producer groups to strengthen guidance and promotion of quarantine rules for poultry farm workers using quarantine rule videos and promotional posters (in 8 languages * ) , and we will continue to broadcast disaster subtitles to the public in cooperation with the Ministry of the Interior and Safety .

* Korean , English , Thai , Nepali , Cambodian , Indian , Vietnamese , Chinese

4. Requests

Kim Jeong-wook, Director of the Agricultural Innovation Policy Office at the Ministry of Agriculture, Food and Rural Affairs, said , “ This winter, three types of viruses ( H5N1, H5N6, H5N9) were detected in wild birds and poultry farms , and the virus’s infectious power was confirmed to be stronger than in the past. Therefore, all poultry farm workers and local government officials and quarantine agency officials across the country are requested to further strengthen quarantine measures such as controlling the entry and exit of people and vehicles and disinfection and implement them thoroughly . ”

In particular , he emphasized , “ In Gyeonggi and Chungnam , where the recent outbreak of laying hens has been concentrated, we will respond by mobilizing all quarantine personnel and resources, such as controlling the entry and exit of livestock vehicles and disinfecting them, focusing on quarantine areas to prevent the spread to surrounding areas . ”

In addition , he emphasized, “ Recently, there have been many cases where egg transport vehicles were prohibited from entering the farm and the second stage of disinfection was not carried out on the farm. Therefore , it is most important to have the mindset that I protect my own farm and to follow basic quarantine rules such as controlling the entry of people and vehicles and disinfecting them .” He also repeatedly requested, “ Manage dangerous livestock vehicles such as egg transport vehicles from entering the farm and thoroughly carry out the second stage of disinfection on vehicles entering the farm . ”

We rarely see this level of detail published by other governments, which makes it difficult to know how much of an outlier South Korea's current avian flu season might be compared to the rest of the world. 

But even if South Korea is somehow the first beachhead for a new HPAI threat, history has shown that what happens to South Korean poultry rarely stays in South Korean poultry. 

Which suggests we should be taking lessons from what South Korea is currently dealing with, and using them to prepare our own strategies for containment should conditions here follow suit. 

WHO DON: Middle East respiratory syndrome coronavirus - Global update (Dec. 24th)

 

#18,999

Although the number of MERS-CoV cases reported in 2025 is a small fraction of what we were seeing a decade ago, we've seen a slow, but steady increase in numbers since the lows of 2022 (see chart above). 

Meanwhile, new COVID variants continue to emerge, and over the past decade we've seen seen numerous reports of newly discovered coronaviruses circulating in the wild, many of which also appear to have zoonotic potential. 

Just a few, of many, include:

Preprint: A Divergent Betacoronavirus with a Functional Furin Cleavage Site in South American Bats

J. of Infection: Novel Coronaviruses Identified in Livestock

Viruses: Novel Rodent Coronavirus-like Virus Detected Among Beef Cattle with Respiratory Disease in Mexico

Nature: Study on Sentinel Hosts for Surveillance of Future COVID-19-like Outbreaks

Preprint: Human Cell adaptation of the Swine Acute Diarrhea Syndrome Coronavirus Spike Protein

All of which had led to a bit of a resurgence of interest in coronaviruses in general, and MERS-CoV in particular. 

Earlier this month, we looked at The Lancet: The Threat of Another Coronavirus Pandemic, while in October we reviewed Health Sci Rpts (Narrative Review): Pathogenicity and Potential Role of MERS-CoV in the Emergence of “Disease X”. 

Prior to COVID's arrival in late 2019, MERS-CoV was the top contender for sparking a coronavirus pandemic, sporting a high mortality rate (>30%), and spreading easily through hospitals in the Middle East (and South Korea) (see Ziad Memish: Two MERS-CoV Hospital Super Spreading Studies).

Last June we looked at an editorial in Journal of Epidemiology & Global Health on the importance of continued healthcare preparedness and surveillance (see Al-Tawfiq & Memish On Recurrent MERS-CoV Transmission in Saudi Arabia), with an emphasis on identifying asymptomatic carriers.

Three weeks ago France announced the detection of MERS-CoV in 2 travelers returning from the Middle East, reminding us that viruses have no respect for borders. 

While MERS-CoV appears to be less of a threat today than it was a decade ago, it continues to evolve and adapt, making it worth keeping on our radar.  

Additionally, we've seen some reluctance on the part of Middle Eastern nations to report cases, and the evidence suggests that the number of confirmed cases may substantially under represent the true incidence of human infection (something this WHO report mentions as a possibility).  

A few, of many, past reports include:

EID Journal: Sensitivity and Specificity Of MERS-CoV Antibody Testing

Evaluation of a Visual Triage for the Screening of MERS-CoV Patients

EID Journal: Estimation of Severe MERS Cases in the Middle East, 2012–2016

Yesterday the World Health Organization published a year-end update on the global MERS-CoV situation.  Due to its length, I've only posted some excerpts (highlights and emphasis mine). Follow the link to read it in its entirety. 

I'll have a bit more when you return. 

Middle East respiratory syndrome coronavirus - Global update
24 December 2025

Situation at a glance

Since the beginning of 2025 and as of 21 December 2025, a total of 19 cases of Middle East respiratory syndrome coronavirus (MERS- CoV), including four deaths have been reported to WHO globally. Of the 19 cases, 17 were reported by the Kingdom of Saudi Arabia (KSA), and two were reported from France. 

Between 4 June and 21 December 2025, the Ministry of Health (MoH) of KSA reported a total of seven cases of MERS-CoV infection, including two deaths. In addition, at the beginning of December 2025, the National IHR Focal Point (IHR NFP) for France also reported two MERS-CoV travel – associated cases; involving individuals with recent travel to countries in the Arabian Peninsula.

The notification of these latest cases does not change the overall risk assessment, which remains moderate at both the global and regional levels. These cases show that the virus continues to pose a threat in countries where it is circulating in dromedary camels, with regular spillover into the human population. WHO recommends implementation of targeted infection, prevention and control (IPC) measures to prevent the spread of health care-associated infections of MERS-CoV and onward human transmission.

Description of the situation

Since the first report of MERS-CoV in the KSA and Jordan in 2012, a total 2635 laboratory-confirmed cases of MERS-CoV infection, with 964 associated deaths (Case Fatality Ratio (CFR) of 37%), have been reported to WHO from 27 countries, across all six WHO regions (Figure 1). The majority of cases (84%; n=2224), have been reported from the KSA (Figure 2). Since the beginning of 2025 and as of 21 December, a total of 19 cases have been reported to WHO. Overall, 17 cases were reported in the KSA from five regions named: Riyadh (n=10), Taif (n=3), Najran (n=2), Hail (n=1), and Hafr Al-Batin City (n=1) (Figure 3). In addition, two travel associated cases of MERS-CoV infection have been reported in France, with likely exposure occurring during recent travel in the Arabian Peninsula (Figure 3).

This disease outbreak news report focuses on the recent nine cases of MERS-CoV infection reported between 4 June - 21 December 2025: seven cases from the KSA and the two imported cases to France. The details of cases reported earlier in 2025 can be referred to in the previously published disease outbreak news on 13 March 2025 and 12 May 2025.

Between 4 June and 21 December 2025, the MoH of the KSA reported a total of seven cases of MERS CoV infection. The cases were reported from three regions: Najran (2), Riyadh (3), and Taif (2). No epidemiological links were identified between the seven cases. In addition, between 2 and 3 of December 2025, the IHR NFP for France reported two cases of MERS – CoV with recent travel to the Arabian Peninsula during the month of November.

Follow-up has been completed for all contacts and no secondary infections have been identified or reported. From September 2012, France has recorded a total of four laboratory-confirmed cases of MERS-CoV infection, including one death: two cases were reported in 2013, and the latest two cases in December 2025. All cases had been travelers exposed in the Arabian Peninsula and returning back to France.

WHO risk assessment

As of 21 December 2025, a total of 2635 laboratory-confirmed cases of MERS-CoV infection have been reported globally to WHO, with 964 associated deaths. The majority of these cases have occurred in countries on the Arabian Peninsula, including 2224 cases with 868 related deaths (CFR 39%) reported from the KSA.

A notable outbreak outside the Middle East occurred in the Republic of Korea, in May 2015, during which 186 laboratory-confirmed cases (185 in the Republic of Korea and 1 in China) and 38 deaths were reported. However, the index case in that outbreak had a history of travel to the Middle East.

Three limited healthcare-related clusters have recently been reported from the KSA, two in 2024 comprised of three and two cases each, and one in 2025 comprised of 7 cases; the previous cluster before that had been observed in May 2020, also in the KSA. Extensive contact tracing was applied in the 2025 cluster, which lead to detection of four asymptomatic and two mild cases, who fully recovered. Despite these recent clusters, zoonotic spillover remains an important mode of human infection, leading to isolated cases and limited onwards transmission between humans.

Global total cases reflect laboratory-confirmed cases reported to WHO under IHR (2005) or directly by Ministries of Health from Member States. These figures may underestimate the true number of cases if some were not reported to WHO, as they may be missed by current surveillance systems and not be tested for MERS-CoV – either due to similar clinical presentation as other circulating respiratory diseases or because infected individuals remained asymptomatic or had only mild disease. The total number of deaths includes those officially reported to WHO through follow-up with affected Member States.

The notification of these new cases does not change the overall risk assessment. WHO expects that additional cases of MERS-CoV infection will be reported from the Middle East and/or other countries where MERS CoV is circulating in dromedaries, and that cases will continue to be exported to other countries by individuals who were exposed to the virus through contact with dromedaries or their products (for example, consumption of raw camel milk, camel urine, or eating meat that has not been properly cooked), or in a healthcare setting.

Due to the similarity of symptoms with other respiratory diseases that are widely circulating, like influenza or COVID-19, detection and diagnosis of MERS cases may be delayed, especially in unaffected countries, and provide an opportunity for onward human-to-human transmission to go undetected. WHO continues to monitor the epidemiological situation and conducts risk assessments based on the latest available information.

No vaccine or specific treatment is currently available, although several MERS-CoV-specific vaccines and therapeutics are in development. Treatment remains supportive, focusing on managing symptoms based on the severity of the illness.

        (Continue . . . )

Although surveillance and reporting of MERS cases has always been problematic - by trivializing COVID infection and dismantling our global surveillance, testing, and reporting systems (see No News Is . . . Now Commonplace) - we've likely made it far easier for MERS-CoV cases to circulate undetected.  

The obvious risk being; novel viruses that emerge at the end of a long chain of infections in a new species often become more `biologically fit' or better adapted to its host. 

While hopefully there is some biological barrier that prevents MERS-CoV from ever achieving pandemic infamy, we seem intent on wearing this same set of blinders for HPAI, Mpox, and a plethora of other emerging pathogens. 

Recent studies suggest that the frequency, and impact, of pandemics are only expected to increase over the next few decades (see BMJ Global: Historical Trends Demonstrate a Pattern of Increasingly Frequent & Severe Zoonotic Spillover Events  and  PNAS Research: Intensity and Frequency of Extreme Novel Epidemics).

Which suggests this strategy grows risker with each passing day. 

South Korean City (Naju) Orders Extraordinary Emergency Measures Due to HPAI

 
Photo Credit - Naju City

#18,998

South Korea - which has battled outbreaks of HPAI, ASF, and FMD for years - has long been proactive when it comes to dealing with agricultural threats; often quarantining farms, issuing `stop movement' orders for livestock, and setting up elaborate vehicle disinfection stations. 

In mid-2024, South Korea released an updated comprehensive pandemic plan, while last September their CDC conducted A 19-day, Nationwide, Mock-Training Exercise to Prepare for Zoonotic Influenza. 

A little over 2 weeks ago we looked at another scathing report from MAFRA on biosecurity breaches on infected poultry farms, and the issuance of increased heavy fines for non-compliance. 

It is fair to say that South Korea takes these threats seriously. 

But overnight, Naju City (pop. 116K) in South Jeolla Province, raised the ante during an emergency meeting - following their 2nd outbreak of HPAI in 3 days - where they have ordered the cancellation of all outdoor activities for the holidays due to the rising avian flu threat. 

While we saw similar actions taken during the COVID pandemic, and briefly during the 2015 multi-hospital outbreak of MERS-CoV, I can't recall seeing anything of this magnitude ordered by South Korean officials for avian flu in the past. 

That said, I've not seen anything to suggest human cases in the region.  They are, however, calling for local organizations and social groups to cancel or postpone outdoor events, so their concerns obviously go far beyond the farm.

Speculating a bit:

• The western peninsula (where South Jeolla (Jeollanam-do) is located) accounts for 2/3rds of South Korea's poultry production, which may explain their concerns and this unusual response. 
• And it is always possible that the city is using this as an opportunity to test their new pandemic plans (or to show the national authorities how committed they are). 

But any way you slice it, the following (translated) press release (note: highlights & emphasis mine) from Naju City is a remarkably robust response, given what we know now.. 

Naju City is taking all-out measures to prevent the spread of highly pathogenic avian influenza.

Date of registration: December 24, 2025, 3:26 PM
Views : 9 Livestock Division , Registration Department 

Outdoor events during the year-end and New Year's holidays have been canceled... Emergency measures including quarantine and movement restrictions have been strengthened.

Naju City, the largest duck breeding area in the country, is taking the crisis caused by the outbreak of highly pathogenic avian influenza seriously, considering the special circumstances of the region, and is mobilizing all administrative power to prevent the spread, including canceling year-end and New Year's events, restricting movement, and strengthening the operation of disinfection facilities.

Naju City (Mayor Yoon Byeong-tae) announced on the 24th that it has issued an emergency appeal to citizens and livestock farmers, asking them to thoroughly participate in quarantine measures and refrain from movement due to the recent consecutive outbreaks of highly pathogenic avian influenza at two duck farms in Bonghwang-myeon and Donggang-myeon.

In the appeal, the city emphasized, "The current situation is more serious than ever before for the safety of citizens and the protection of the local livestock industry, and a strong response is needed. We ask for the active cooperation of poultry farms as well as nearby residents with quarantine measures."

Naju, which has maintained a livestock infectious disease-free zone for the past two years, has raised its quarantine response level to 'serious' after highly pathogenic avian influenza was confirmed at a duck farm in Donggang-myeon on the 23rd, following a case at a duck farm in Bonghwang-myeon on December 19th.

Accordingly, Naju City held an emergency meeting presided over by Mayor Yoon Byeong-tae on the 24th and canceled all unspecified large-group gatherings during the year-end and New Year's holidays, including the Geumseongsan Sunrise Event on January 1st of next year, to prevent the spread of highly pathogenic avian influenza. In accordance with the Livestock Infectious Disease Prevention Act, the city also recommended that local organizations and social groups cancel or postpone outdoor events.

In addition, the city is making all-out efforts to prevent the spread of the disease, including disinfecting public facilities such as senior citizen centers in towns, townships, and wards, controlling access to poultry farms and restricting vehicle movement, disinfecting livestock vehicles and personnel at key disinfection facilities, refraining from moving between farms and areas adjacent to migratory birds, and prohibiting entry into migratory bird habitats.

On December 20th, immediately after the antigen was detected, the city held an emergency situation response meeting chaired by the mayor and immediately decided on response measures such as controlling the outbreak farm, temporarily halting movement, conducting thorough inspections and intensive disinfection of poultry within the quarantine zone, and strengthening the operation of key disinfection facilities.

Mayor Yoon Byung-tae visited the Dongsu-dong key disinfection facility on the 23rd to inspect the quarantine response status and the operation of the facility, and closely checked whether on-site quarantine measures were being implemented.

The city is currently continuing thorough surveillance and intensive disinfection within a 10km radius of the outbreak farm and is continuing preemptive quarantine measures such as strengthening the disinfection of livestock vehicles to block horizontal transmission.

Mayor Yoon Byung-tae of Naju said, “Compared to chickens, ducks tend to show symptoms later and milder, so careful surveillance and thorough disinfection on farms are of utmost importance. Please thoroughly check basic quarantine rules once again, such as changing boots when entering and exiting livestock sheds and checking the expiration date of disinfectants.”

In particular, “This year, the arrival period of migratory birds has been earlier than usual, the number of birds has increased significantly, and we believe that the infectivity of the highly pathogenic avian influenza virus has increased by more than 10 times and the risk of outbreak has increased by up to 20 times,” he said. “Since the initial response to highly pathogenic avian influenza determines the success or failure of quarantine, there should not be any gaps in quarantine centered on disinfection facilities,” he emphasized, “We will do our best to protect the safety of citizens and livestock farms by mobilizing all administrative power to prevent further outbreaks.”

Naju City plans to make all-out efforts to prevent the spread of highly pathogenic avian influenza through thorough quarantine management centered on the field and continuous inspections.

(Photo caption)
1. Naju Mayor Yoon Byeong-tae (second from the right) visited the Dongsu-dong disinfection facility and inspected the quarantine response status and operational status.
2. Naju City is operating a disinfection facility to prevent the spread of highly pathogenic avian influenza (AI).
3. Naju City is operating a central disinfection facility to prevent the spread of highly pathogenic avian influenza (AI).
(Photo provided by Naju City)

While this response is likely due to an abundance of caution, given its unusual nature, it is worth keeping our eye on the region in the days ahead. 

Stay tuned.