Front. Vet. Sci: Biosecurity deficiencies in HPAI-affected poultry farms in Korea, 2020/2021–2024/2025 seasons

Biosecurity Violations - Photo Credit MAFRA

#19,254

South Korean farmers, and their agricultural department (MAFRA), have been dealing with outbreaks of HPAI H5 for more than 2 decades, and yet they continue to report major biosecurity lapses leading to large culls.  

In January of 2025, in South Korea: MAFRA Orders Fines For Biosecurity Breaches On Poultry Farms, we looked at a scathing report that found of the 15 infected poultry farms investigated since October 2024, the vast majority have failed to comply with established biosecurity protocols, and that strong punitive action would be taken.

Ten months ago,South Korea's CDC Announced A 19-day, Nationwide, Mock-Training Exercise to Prepare for Zoonotic Influenza, and South Korea's Ministry of Environment issued a new statement on mandatory steps to increase the safety of personnel dealing directly with avian influenza, and to ensure a more coordinated and efficient quarantine response.

And yet, in December of last year (see South Korea: MAFRA Identifies Biosecurity Breaches On HPAI Infected Poultry Farms), we saw the same patterns emerge; including failures to disinfect vehicles, and allowing people to enter farms and barns without protective clothing.

From the report's summary:

Choi Jeong-rok, Director of the Quarantine Policy Bureau of the Ministry of Agriculture, Food and Rural Affairs, said , “ As a result of the epidemiological investigation into poultry farms where highly pathogenic avian influenza occurred this winter , it was confirmed that most farms were not properly following basic quarantine rules.

Therefore , each local government should strictly punish those who violate related regulations and provide repeated education and inspections so that farms can manage quarantine on their farms with a sense of alertness . ”

Late in December MAFRA reported Increased Infectivity & Pathogenicity of This Year's Avian Flu Strains, and warned again on the importance of increasing biosecurity, and on January 5th announced  Special Quarantine Measures Implemented for one Month to Prevent the Spread of HPAI.

In March, in an Investigation Into Biosecurity Lapses on HPAI Affected Poultry Farms, MAFRA reported that of 50 of that year's 53 infected poultry farms, 70% had at least one serious violation.

• 70%: No disinfection or protective clothing for people entering farms
• 68%: Vehicles entering/exiting farms not disinfected
• 66%: Poor overall sanitation management
• 62%: Workers not using farm-specific clothing/footwear
• 48%: Inadequate barriers to prevent entry of wild animals

Given the constant warnings, and threats to reduce culling compensation by 50% and heavy fines for non-compliance, achieving and maintaining biosecurity on a working farm is obviously easier said than done. 

Amid reports of greatly increased infectivity of South Korean bird flu strains we also saw a sharp increase in HPAI activity around the globe over the 2025-2026 avian flu season. 

This is obviously not just a South Korean problem, although they have been far more transparent about the challenges of containing avian flu than most other countries.  

All of which brings us to an analysis of biosecurity lapses on South Korean poultry (duck & chicken) farms between 2020/21 and 2024/2025.  While this does not include data from last year's outbreaks, it closely aligns with what we saw reported last winter by MAFRA.

Due to its length and technical nature, I've just posted the abstract and a brief excerpt.  Those involved with raising poultry, or biosecurity on farms, will want to do a deeper dive. 

I'll have a bit more after the break.

Front. Vet. Sci., 16 July 2026
Sec. Veterinary Infectious Diseases
Volume 13 - 2026 | https://doi.org/10.3389/fvets.2026.1863522
Biosecurity deficiencies in HPAI-affected poultry farms in Korea, 2020/2021–2024/2025 seasons
Hachung Yoon * , Kyoungsook Kim , Keesung Hong
Veterinary Epidemiology Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
 
Abstract

Introduction:

Highly pathogenic avian influenza (HPAI) remains a persistent threat to poultry production systems despite reinforced biosecurity measures. This study aimed to characterize biosecurity deficiencies in HPAI-affected farms in Korea and to identify structured patterns of deficiencies.

Methods:

Outbreak investigation reports from 311 HPAI-affected farms (2020/2021–2024/2025 seasons) were analyzed, yielding 3,172 biosecurity deficiency records classified into 16 categories across three operational domains. Frequency analysis, k-means clustering, and association rule analysis were applied to identify deficiency patterns and co-occurrence structures.

Results:

Wildlife control was the most frequent deficiency (85.9%), followed by operational management (65.9%) and deficiencies related to anteroom biosecurity measures in barns (56.3%). Four distinct farm-level deficiency profiles were identified, with significant differences in cluster membership between chicken and duck farms. Association rule analysis revealed consistent co-occurring deficiency pairs, particularly involving farm-entry measures such as visitor and vehicle disinfection.

Discussion:

These findings indicate that biosecurity deficiencies are not isolated but form structured and interconnected patterns. A system-level approach incorporating targeted, pattern-based biosecurity interventions and risk-based surveillance prioritization may improve the sustainability and effectiveness of HPAI prevention and control in poultry production systems.

        (SNIP)

Together, these findings indicate that biosecurity deficiencies in HPAI-affected farms are structured, sector-specific, and tend to cluster into interpretable farm-level patterns. Recurrent co-occurring deficiency pairs suggest that weaknesses accumulate in consistent combinations, particularly around farm-entry measures. This supports a shift from single-item compliance checks toward integrated, system-level approaches to biosecurity. From a practical perspective, the identified deficiency profiles may support risk-based prioritization of biosecurity interventions according to farm characteristics and dominant vulnerability patterns.

Farms with entrance-focused profiles may benefit from strengthened visitor control and disinfection measures, whereas barn- or management-dominant farms may require improvements in worker practices, equipment handling, and operational oversight. Training and technology-assisted monitoring, including CCTV, may further enhance compliance, particularly for behaviorally demanding procedures (27, 36, 38). Collectively, these findings may help inform more targeted surveillance strategies and adaptive biosecurity policies in poultry production systems.

This study is limited to farms with confirmed HPAI outbreaks, and the identified patterns do not establish direct causality. However, these deficiencies represent conditions that may contribute to disease introduction and spread, and their consistent implementation remains essential for effective HPAI prevention.

        (Continue . . . )

 

We are two, maybe three months away from arrival of the next wave of avian flu in the Northern Hemisphere. Migratory birds that are currently breeding in their high-latitude roosting spots - where they can easily swap viruses - will once again head south in the fall. 

While these HPAI viruses could be similar to what we saw last year - they might include new, potentially game-changing, genotypes - which could either increase or decrease their threat.

Now is the time for poultry producers - from commercial operations to back-yard hobby farms - to review their biosecurity procedures, and to make necessary adjustments before the fall. 

The APPA estimates `Eleven (11) million U.S. households own backyard chickens (a 28% increase from 2023)', yet a recent survey (see MMWR: Knowledge, Attitudes, and Practices Regarding Avian Influenza Among Owners of Backyard Flocks) found significant gaps in their knowledge of dealing with HPAI.

Over the past 18 months we've seen at least 3 U.S. backyard flock owners infected with HPAI H5, resulting in 2 deaths. This is an all-too familiar pattern, which we've seen repeated dozens of times in many other countries.

If battle-tested South Korean farmers are having this much trouble maintaining adequate biosecurity, then it is probably worth reviewing our own practices before the next wave of the virus heads our way. 

Infection: Severe pneumonia and acute respiratory distress syndrome caused by avian influenza A (H10N3) in a young female: a case report

 

#19,253

Although reporting has been sporadic, since 2021 China has reported at least 7 human infection with LPAI H10N3. The most recent case (Dec 2025) was announced by Hong Kong last February in an cryptic 1-line notice (see below) in their weekly avian flu report. 

In late April the WHO published a brief report where we learned this patient - who worked with poultry - was hospitalized with severe pneumonia, severe acute respiratory distress syndrome (ARDS) and sepsis for roughly 2 weeks before a diagnosis of avian H10 infection was confirmed. 

WHO WPRO reported a 6th case last summer, but as with earlier announcements, details were limited. We continue to see cautionary reports, however, from Chinese researchers on the human health threat from this emerging subtype.

• In July of 2024, in Frontiers: Phylogenetic and Mutational Analysis of H10N3 Avian Influenza A virus in China: Potential Threats to Human Health, we looked at a report that described 4 mutations of concern in the 2023 case (HA Q226L, PB2 D701N, PA S409N, and M2 S31N), along with the patient's treatment and course of illness.

• In December of 2024 Vet. Microbiology: The novel H10N3 Avian Influenza Virus Acquired Airborne Transmission Among Chickens: An Increasing Threat to Public Health reported the virus has become better adapted to poultry, is highly pathogenic in mice, can be transmitted via respiratory droplets between guinea pigs, and can also be transmitted via the airborne route by chickens.

• And last summer,  Vet. Research: E627V Mutation in PB2 Protein Promotes the Mammalian Adaptation of Novel H10N3 Avian Influenza Virus reported that that PB2-626V is becoming increasingly common in AIV poultry isolates - including H10N3 - and that it significantly enhances mammalian adaptation while maintaining fitness in avian hosts.

While no deaths have been reported, in nearly every case the patient is described as having symptoms of severe ARDS or pneumonia, often with other complications. 

Today we have a detailed case report on the 4th known case - a 23 year-old female who was infected in December of 2024 - and who ended up being hospitalized for > 3 months.

I've posted the abstract and some excerpts from the report, but you'll want to follow the link to read it in its entirety.

Severe pneumonia and acute respiratory distress syndrome caused by avian influenza A (H10N3) in a young female: a case report

Published: 17 July 2026

Mei Zhao, Qiyun Shi, Lin Zhao, Meng Wang, Jingwen Li, Zhiyi Wan, Tun Ouyang & Yang Yu  

Download PDF  

Abstract

Background

Human infection with avian influenza A (H10N3) is a rare but severe emerging zoonotic disease. To date, only a limited number of cases have been reported, which restricts a comprehensive understanding of its clinical features and public health risks. We report the fourth documented case of human H10N3 infection, which is the first to be identified in a female patient. Additionally, we compared the clinical and genomic characteristics of all four cases.

Case presentation

A 23-year-old female with no prior comorbidities developed severe pneumonia and acute respiratory distress syndrome due to infection with avian influenza A (H10N3) virus. The patient, working in a fresh market with recent training at a slaughterhouse, presented a one-week history of high fever, cough, and dyspnea. Despite initial broad-spectrum antibiotics, her condition rapidly worsened, requiring mechanical ventilation and veno-venous extracorporeal membrane oxygenation (V-V ECMO). Metagenomic next-generation sequencing of bronchoalveolar lavage fluid, confirmed by the Centers for Disease Control and Prevention, identified avian influenza A (H10N3).

Following approximately three months of intensive treatment, the patient recovered and was discharged. Phylogenetic analyses showed that her virus strain was closest to the third human H10N3 case (Kunming, China, 2024). In addition, this strain had a human-adapted substitution (P221) but lacked the G228S substitution in the haemagglutinin protein, suggesting that the latter is not essential for human infection.

Conclusions

This case highlights the potential for severe human infection by the H10N3 virus. It is imperative that surveillance is enhanced in both human and animal populations.

       (SNIP)

A comparative analysis of the four reported human H10N3 infections to date (Table 1) reveals a consistent pattern of severe disease [7,8,9]. All four patients were hospitalized 4–7 days after onset of common respiratory symptoms. The disease generally progresses rapidly, with transfer to the RICU due to ARDS typically occurring 8–10 days after symptom onset (Table 1). Notably, 75% (3/4) of patients required mechanical ventilation or ECMO (Table 1).

 

These data suggest that H10N3 viruses may induce serious, life-threatening disease in humans.

In addition, this patient received prolonged inpatient treatment for approximately 3 months before discharge, significantly longer than the three previously reported H10N3 cases. The extended hospitalization was primarily attributable to numbness and motor dysfunction of the right lower extremity that developed after successful V-V ECMO weaning.

The patient received inpatient rehabilitation for more than two additional months to achieve full functional recovery before discharge. Similar neurological complications were not documented in the three previously reported human H10N3 cases, which explains the marked difference in the length of hospitalization between this case and prior cases.

        (SNIP)

In conclusion, we have presented a case of severe pneumonia and ARDS due to avian influenza virus (H10N3) infection in a 23-year-old female. This case highlights the severe pathogenic potential of the H10N3 subtype in humans. This report emphasizes the need for continued surveillance of avian influenza viruses in both animal and human populations.

        (Continue . . . ) 

While the authors call for `continued surveillance', H10N3 (along with H9N2 and a number of other LPAI viruses), are not considered to be a `reportable' disease in poultry by WOAH. 

Human cases are reportable to WHO, but - as we've seen - case reports are often vague or sometimes delayed for months.  And we've no idea how many cases are missed.

The FAO acknowledges and presents a broad overview of avian flu viruses with zoonotic potential, but no global agency does dedicated tracking of  H10N3, H9N2, and similar LPAI viruses in poultry. 

Instead we rely on a informal patchwork of sporadic national surveillance, independent research projects, and reports of occasional spillovers into humans (see WHO DON: Avian Influenza A(H9N2) - Italy (Ex Senegal)) to try to monitor these subtypes. 

While out attitudes towards these LPAI threats may change over time, hopefully that's not a lesson we'll have to learn the hard way.

H5N1: NZ Reports 2nd Detection (local bird) & Australian Detections Increase to 17

 
Credit Wikipedia

#19,252

Two days after announcing their first detection (in an unspecified ocean-going sea bird), New Zealand reports finding H5N1 in a local bird (a swamp harrier hawk) found in the sparsely populated Wairarapa region on the north island (see map above).

SITUATION UPDATE: 17 July 2026

Second detection of H5 bird flu confirmed

Response and surveillance work continues to step up in close coordination with industry partners and others after a single kāhu, swamp harrier hawk, found in the Wairarapa, was confirmed to have H5 bird flu (H5N1 avian influenza clade 2.3.4.4b).

• This is the second bird in New Zealand confirmed to have H5 bird flu, following a single detection in a brown skua seabird found on Petone Beach in Wellington on 15 July. In addition to New Zealand’s continuous bird flu surveillance and testing programme, additional work will include:extra checking of birds at selected sites in the Wairarapa over coming days
• alongside industry, MPI will offer one-on-one support and advice to poultry and egg operations in Wellington and the Wairarapa

• establishing a technical advisory group of expert scientists to supplement advice from MPI’s internationally recognised experts.

The Department of Conservation will continue its vaccination programme for 300 core breeding birds from 5 of our most endangered birds – kākāpō, takahē, tūturuatu/shore plover, kakī/black stilt, and kākāriki karaka/orange-fronted parakeet.

There continues to be no detections in poultry.

Chicken and eggs remain safe to eat and bird flu is a very low risk to human health.

Be alert and use good habits to limit the impact of bird flu

Keep your distance. Stay away from sick or dead wildlife. Keep pets away too.

Keep clean. Wash your hands and clean your gear after being outdoors.

You'll find a more extensive press release on New Zealand's Beehive press release website (excerpts below).

17 July 2026
Bird flu work steps up - second case confirmed

Hon Tama Potaka   Hon Andrew Hoggard

 Work on the ground will step up after confirmation today a single Kāhu, swamp harrier hawk, which was found in the Wairarapa, is the second bird in New Zealand confirmed to have H5 bird flu, says Biosecurity Minister Andrew Hoggard and Conservation Minister Tama Potaka.

“While it’s disappointing to find a native bird with H5 bird flu, it’s not unexpected following the confirmation earlier this week of our first case in a single brown skua seabird found at Petone Beach,” says Mr Hoggard. “There has been no detection in poultry.”

“The find shows our continuous bird flu surveillance and testing programme is working well, and as a result, we will step up our actions in response to bird flu in close co-ordination with our industry partners and others.”

Mr Hoggard said that work would include:

• Extra checking of birds at selected sites in the Wairarapa over coming days.
• Alongside industry, MPI will offer one-on-one support and advice to poultry and egg operations in Wellington and the Wairarapa.
• Establishing a technical advisory group of expert scientists to supplement advice from MPI’s internationally recognised experts.
• The Department of Conservation continues its vaccination programme for 300 core breeding birds from five of our most endangered birds - kākāpō, takahē, tūturuatu/shore plover, kakī/black stilt and kākāriki karaka/orange-fronted parakeet.

“This hawk can go out to the coast - especially in winter to hunt. Hawks can get bird flu by hunting, eating, or scavenging infected birds,” says Mr Hoggard.

“It’s important we continue to work closely with the egg and poultry industry as we have over the past several years preparing for bird flu’s arrival. On-site biosecurity plans and measures are very important for chicken and egg producers, and we will up our work alongside sector groups to provide support and advice.

“While it’s an individual decision for businesses, we support free range farmers taking precautionary action to protect their birds by temporarily housing them while we continue to gather more information about the spread of H5 bird flu.

“We will have to learn to live with bird flu as it cannot be eradicated, and overseas experience shows strong biosecurity measures on-farm help.”

       (Continue . . . )

Meanwhile, the number (of reported bird deaths & confirmed cases) in Australia continues to rise, with Western Australia reporting 2 more confirmed cases overnight.

Wild petrel positive for bird flu at Seabird

Media release

 
Two additional cases of H5 bird flu have been confirmed in Western Australia, taking the State's total number of detections to ten.

Last updated: 17 July 2026

Two additional cases of H5 bird flu have been confirmed in Western Australia, taking the State's total number of detections to ten.

Testing at CSIRO’s Australian Centre for Disease Preparedness today confirmed the ‘presumed positive’ detection in a petrel found at Seabird in the Shire of Gingin, and in a previously reported suspect petrel found at Parry Beach in Denmark.

In both cases, testing was unable to sequence the virus to definitively determine the H5 bird flu strain. This is not unexpected, particularly in wildlife samples from decomposed carcasses.

The Department of Primary Industries and Regional Development is taking a precautionary approach and treating these as positive detections based on the species involved, the circumstances of the detection and available evidence.

At this time, there is no evidence of any large-scale deaths in wildlife, nor any evidence of infection in poultry or in our agricultural production system.

There have been more than 1800 wildlife-related reports from WA to the hotline since the first confirmed case on 19 June. Each report is assessed for further investigation or testing based on the likelihood of disease risk.

To date, a total of 130 negative test results has been recorded across the State.

The risk to human health remains low, but people are reminded to avoid handing the animals, record their observations by photo or video and report to the EAD hotline on 1800 675 888.

More information is available on the Australian Government's Bird flu (Avian influenza) website.

While both governments continue to stress that there have been no outbreaks in poultry - or large-scale deaths in wildlife - sadly, H5N1's history suggests both scenarios are highly likely.

Stay tuned. 

Australia: NSW Confirms 2nd Detection of H5N1 (National ttl=15)

 

#19,251

New South Wales has reported its 2nd confirmed H5N1 detection, bringing the nation's total to 15 (WA has at least one suspected case with results pending).  

As we discussed yesterday, the backlog of reported bird death reports is growing, and so confirmed cases likely significantly under represent the true incidence across the country. 

This brief update from Australia's Department of Agriculture. 

H5 bird flu testing updates

16 July 2026

Attributable to the Australian Chief Veterinary Officer, Dr Beth Cookson:

Testing at CSIRO’s Australian Centre for Disease Preparedness has confirmed a further positive detection of H5 high pathogenicity avian influenza (bird flu) in a petrel, found at Hawks Nest, New South Wales.

There have now been 15 confirmed or presumed positive detections of H5 bird flu in Australia.  

All of these have been individual wild seabirds found in coastal locations. All but one have been wild migratory seabirds.

There remains no evidence of any mass mortality events and there are no detections in poultry or in our agricultural production system.

The risk to human health remains low.

EID Journal: Detection of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Genotype D1.2 Virus in Swine after Experimental Inoculation

 

#19,250

Although reports have been sporadic, over the past 2 decades we've seen growing field and laboratory evidence that H5N1 can infect pigs, albeit often asymptomatically. A few past reports include:

WHO H5N1 detected in pigs in China (2004)

EID Journal: Asymptomatic H5N1 In Pigs (2010)

An Unusual Report Of H5N1 in Pigs (Indonesia 2016)

Sci. Rpts.: Evidence Of H5N1 Exposure In Domestic Pigs - Nigeria (2018)

In May of 2023, in Netherlands: Zoonoses Experts Council (DB-Z) Risk Assessment & Warning of Swine As `Mixing Vessels' For Avian Flu, we looked at growing concerns in Europe that avian H5N1 could increase its pandemic threat by spreading (and evolving) in farmed swine.

• A few days later Italy confirmed an H5N1 spillover event at a `mixed species' farm (poultry & swine), and the subsequent seroconversion of the majority of the pigs tested on that farm (see Study: Seroconversion of a Swine Herd in a Free-Range Rural Multi-Species Farm against HPAI H5N1 2.3.4.4b Clade Virus).

• In late 2024, we saw two pigs infected with a new, recently emerged genotype (D1.2) in Oregon (see USDA Confirms 2nd Pig on Oregon Farm Tested Positive for H5N1).

• And last fall, in Transboundary & Emerg Inf: Serological Evidence of HPAI (H5N1) in Invasive Wild Pigs in Western Canada, we looked at a study which found (limited) serological evidence of HPAI H5 infection in wild pigs in western Canada.

But the reality is, testing for avian flu viruses in pigs is both voluntary and rare. 

Surveillance is generally passive, and since avian flu in pigs is usually mild, and self-limiting - and there could be significant downsides to reporting it (quarantines, economic losses, stigma, etc.) -  there is little incentive to delve deeper. 

According to the USDA, as of Sept.1, 2025 there were 74.5 million hogs and pigs on U.S. farms, and according to their last published Influenza A Virus in Swine Surveillance report (Q4), in they tested 977 samples in 2025.

The USDA further notes:

Due to the voluntary nature of this surveillance, the information in this report cannot be used to determine regional and/or national incidence, prevalence, or other epidemiological measures, but it may help identify IAV-S trends.

All of which suggests that were HPAI H5 to spillover into commercial swine - in the U.S. or elsewhere in the world - we'd be hard pressed to detect it.

All of which brings us to an EID research article, published yesterday, which finds (unlike previous studies on other H5 strains) that genotype D1.2 appears well suited to mildly or asymptomatically infect, and replicate systemically, in pigs. 

Due to its length, and technical nature, I've only posted the link, abstract, and some extended highlights.  But many will want to read it in its entirety.

I'll have a brief postscript after the break.

Research

Detection of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Genotype D1.2 Virus in Swine after Experimental Inoculation

Hannah Seger, Amy L. Baker, Alexandra C. Buckley, Tavis K. Anderson, Alexey Markin, Alessandra Campos, Bruno Caetano Trindade, Marissa Vincent, Giovana Ciacci Zanella, Mia Torchetti, Kristina Lantz, and Bailey Arruda

Abstract

Highly pathogenic avian influenza H5NX clade 2.3.4.4b viruses continue to circulate globally. Reintroduction of Eurasian lineage viruses into North America and reassortment with endemic low pathogenicity strains have resulted in new genotypes, including D1.2. To assess pathogenicity and cellular tropism, we intranasally inoculated genotype D1.2 virus into pigs.

We isolated virus from nasal secretions from most inoculated animals for multiple days. At 5 days postinoculation, PCR and immunohistochemistry detected virus in musculoskeletal, respiratory, digestive, lymphatic, and nervous systems and isolates from meat juice.

At 35 days postinoculation, we detected viral antigen and low levels of RNA in the brain of an animal with lesions consistent with a viral etiology and found viral antigen in the ethmoid of 2 animals.

Consistent detection in nasal swab specimens, combined with subclinical respiratory infection, systemic distribution, and protracted detection of clade 2.3.4.4b virus in swine, suggest identifying infection in commercial swine without overt respiratory signs could be difficult.

(SNIP)

On October 29, 2024, HPAI H5N1 clade 2.3.4.4b genotype D1.2 was confirmed in 1 sow housed in a backyard animal holding in Oregon, USA (15). We sought to assess the pathogenicity and cellular tropism of an HPAI H5N1 strain that was collected from that Oregon farm site in other swine by experimental infection via an intranasal route. The animal study (Appendix 1 Figure 1) was conducted in compliance with the Institutional Animal Care and Use Committee of the US Department of Agriculture Agricultural Research Service National Animal Disease Center under the Biosafety Level 3 guidelines.

        (SNIP)

Subclinical Respiratory and Mild Enteric Signs Observed

We compiled results for the clinical scoring system (Appendix 1 Table 1) into clinical scores (Appendix 1 Table 2). We did not observe respiratory clinical signs or fever in any animal throughout the study (Appendix 1 Tables 2, 3). We observed moderate diarrhea in 1 inoculated animal, starting at 3 DPI through necropsy at 5 DPI. We noted lethargy and diarrhea in the 3 remaining inoculated animals at 7 DPI, resolving at 14 DPI, and anorexia at 7 and 8 DPI. We did not note enteric signs in control animals.

        (SNIP)

We documented evidence of replication in multiple tissues and detection and viral isolation in nasal secretions of all intranasally (2 mL) inoculated pigs across multiple days. Other studies in swine have reported inconsistent detection in nasal swab specimens, limited detection outside the respiratory tract, and variable transmission (20,34; H. Feldmann et al., unpub. data, External Link).).

The consistent detection in nasal secretions, broader viral distribution within tissues, and protracted detection of low viral levels in 2 of 3 animals necropsied at 35 DPI documented in this work compared with the other studies might reflect study design, host, strain, or a combination of those. The more consistent detection in nasal secretions, turbinate and ethmoid compared with the trachea and lung within this study could suggest other viral mechanisms of host and tissue tropism beyond α-2,3 and α-2,6 sialic acid distribution that have not yet been characterized in swine (35).

(SNIP)

In conclusion, the intercontinental circulation of HPAI H5Nx viruses of the Gs/Gd lineage is a historic occurrence that has resulted in the infection of many avian and mammalian species with variable clinical manifestations, ranging from subclinical infections to mass mortality events. Host responses to HPAI infection, expression of clinical disease, and associated pathology vary depending on numerous interactions including the host, route of infection, dose, day postinfection, and virus strain (1). In this study, we observed no apparent respiratory or systemic signs and minimal neutralizing antibody response, despite consistent detection in nasal swab specimens and systemic distribution including skeletal muscle in inoculated animals.

Our data raise concerns over our ability to identify infection in commercial swine that do not exhibit overt respiratory signs while also exhibiting minimal neutralizing antibody response in affected animals. The apparent increased fitness of clade 2.3.4.4b H5Nx viruses and their reassortants in swine raises concerns over public health risks and highlights the need to clarify mammalian adaption and reassortment potential and supports the need for continued surveillance. 

Dr. Seger is an anatomical pathology resident at Iowa State University Veterinary Diagnostic Laboratory. Her research efforts focus on infectious disease pathology of food animal diseases of human importance. 

Although this research is limited to HPAI H5N1 genotype D1.2, we continue to follow a great many other novel flu viruses - equally poorly tracked - spillover and/or spread in swine. 

 The CDC's IRAT (Influenza Risk Assessment Tool) lists 3 North American swine viruses as having at least some pandemic potential (2 added in 2019).

H1N2 variant [A/California/62/2018] Jul 2019  5.8 5.7 Moderate
H3N2 variant [A/Ohio/13/2017]         Jul 2019  6.6 5.8 Moderate
H3N2 variant [A/Indiana/08/2011]     Dec 2012 6.0 4.5 Moderate

There is even greater diversity among swine flu viruses around the globe, with China's EA H1N1 `G4' virus often cited as the world's biggest pandemic threat. We've also followed repeated spillovers in Brazil, and last year the Eurasian 1C Swine Influenza A Virus was labeled a `high pandemic risk'.

But our reluctance to aggressively test livestock (pigs, cattle, sheep, goats, mink, etc.) for novel viruses means that we are likely only seeing the tip of the viral iceberg. 

Which could end up being a mistake of titanic proportions.   

CDC HAN: Domestically Acquired Cyclosporiasis Cases in Multiple U.S. States, 2026

#19,249

Yesterday the CDC released a HAN Advisory on a multi-state outbreak of cyclosporiasis that we've been following for the past two weeks (see here and here). 

Due to its length, I've only posted the summary and the advice to the public. Clinicians, public health workers, and other interested parties should follow the link to read it in its entirety.

For now the source of the infection remains unknown, but is likely linked to lettuce, berries, or other produce.

Domestically Acquired Cyclosporiasis Cases in Multiple U.S. States, 2026
July 14, 2026

At a glance
Distributed via the CDC Health Alert Network
July 14, 2026
CDCHAN-00531

Summary

The Centers for Disease Control and Prevention (CDC) is notifying clinicians, public health practitioners, and laboratorians of cases of domestically acquired cyclosporiasis in multiple U.S. states. Since May 1, 2026, CDC has received reports of 1,645 confirmed domestic cases of cyclosporiasis and is aware of more than 5,100 cases that require further analysis to confirm the illness as domestically acquired cyclosporiasis. This is substantially higher than the 249 cases reported nationally by this same time last year. 

Of the 1,645 case-patients with available information, 141 (9%) were hospitalized, and none have died. CDC, the U.S. Food and Drug Administration (FDA), and state and local health departments are working together to investigate multistate outbreaks of Cyclospora infections and to identify the sources of illness. Because cyclosporiasis is often underdiagnosed and underreported, the true number of illnesses is likely higher than what has been reported to CDC. This Health Advisory provides background information about cyclosporiasis, current U.S. surveillance data, and recommendations for clinicians, laboratorians, and public health departments to support recognition, diagnosis, and reporting.

Background

Cyclosporiasis is a gastrointestinal illness caused by the microscopic parasite Cyclospora. People can become infected by consuming food or water contaminated with the parasite. This illness is not usually spread directly from person to person. Case counts typically rise during spring and summer months, and CDC considers May 1-August 31 the annual cyclosporiasis season. Previous outbreaks have been linked to consuming contaminated fresh produce.

Symptoms of cyclosporiasis typically begin about 1 week after exposure. Onset of symptoms can occur 2-14 days after being exposed. The most common symptoms include watery diarrhea, which can be frequent, along with loss of appetite, weight loss, bloating, nausea, and fatigue. Less common symptoms include low-grade fever and vomiting. Without treatment, symptoms can follow a remitting-relapsing course that can last from a few days to a month or longer. Illness can be severe, but is not usually life-threatening. Complications can include malabsorption, cholecystitis, and reactive arthritis. Laboratory detection of Cyclospora in stool can be challenging even in symptomatic patients, and standard ova and parasite exams might not detect it reliably. Clinicians should specifically request diagnostic testing for Cyclospora when it is clinically suspected.

Since May 1, 1,645 lab-confirmed cases were reported to CDC in people who acquired cyclosporiasis in the United States. Cases were reported by 34 states. Case-patients developed illness after eating food in the United States and did not report any travel during the previous 14 days. Case-patients ranged in age from 2-95 years, with a median age of 44 years, and 56% were female. Of 1,645 case-patients with information available, 141 (9%) were hospitalized. No deaths have been reported. This is substantially higher than the 249 cases reported nationally from May 1–July 16, 2025.

CDC is working closely with FDA and state health authorities to investigate multiple clusters of cyclosporiasis. CDC has posted an investigation notice about an outbreak with more than 400 cases in at least four U.S. states that appear to be epidemiologically linked, suggesting that there could be a common source of these infections.

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Recommendations for the Public

• Visit a clinician if you have prolonged or watery diarrhea, especially if it lasts more than a few days.

• Reduce your risk by thoroughly washing fresh produce under clean running water before eating and by following safe food handling practices. Be aware that chemically disinfecting or sanitizing produce might not fully eliminate Cyclospora. It is important to thoroughly wash produce even if it is labeled as pre-washed.

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