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.

        (SNIP)

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.

       (Continue . . . )

 

New Zealand Reports 1st Detection of H5N1 in a `Sea Bird'

 

#19,248

We've a bare-bones report today from New Zealand's Ministry for Primary Industries on that country's first detection of H5N1, which come less than a month after Australia's first report. 

While the bird species isn't specified (`ocean going sea bird'), and no collection dates are provided, this suggests the eastward spread of H5N1 across more than 3,300 miles of oceania in a matter of a few weeks. 

The official statement follows:

SITUATION UPDATE: 15 July 2026

A single ocean-going sea bird has tested positive for H5 bird flu in New Zealand.

The bird was found on Petone Beach in Wellington and reported to our exotic pest and disease hotline. Subsequent testing confirmed H5 bird flu (H5N1 avian influenza clade 2.3.4.4b).

This is the first detection of H5 bird flu in New Zealand. It hasn't been found in any other birds and there are no detections in poultry.

The risk to human health remains low.

New Zealand is well prepared to respond and will react quickly to protect poultry production, and to reduce impacts on wildlife and communities.

While this was fully expected after the arrival of the virus to mainland Australia (see New Zealand: DOC to vaccinate ‘at risk’ birds against bird flu), it is disappointing how quickly the last H5-free dominos on earth are falling. 

H5N1 marches on. 

 

Australia: 8th Confirmed Bird Flu Detection in WA - Nationally Confirmed (N=14)

 

#19,247

Overnight Western Australia has confirmed an 8th H5N1 detection in a bird (petrel), found at Lancelin Beach (70 km North of Perth), and are awaiting confirmation from CSIRO on an additional a dead giant petrel, found on WA South Coast.

This brings the nation's total to 14 confirmed. 

This from the WA government website, after which I'll have more on some of the challenges of collecting, transporting, and testing wildlife samples in Australia.

New bird flu cases at Lancelin and Denmark
Media release

 
Western Australia has recorded a new positive detection of H5 bird flu in a migratory seabird at Lancelin bringing the State’s total to eight confirmed cases.

Last updated: 15 July 2026

Western Australia has recorded a new positive detection of H5 bird flu in a migratory seabird at Lancelin bringing the State's total to eight confirmed cases.

Testing at the CSIRO's Australian Centre for Disease Preparedness this week confirmed the 'presumed positive' detection in a dead giant petrel, found at Lancelin Beach, north of Perth.

While testing was unable to fully determine the specific H5 bird flu strain, likely due to the sample quality from a decomposed carcass, it will be treated as a positive case.

On the WA South Coast, a dead giant petrel found at Parry Beach in Denmark has also tested positive for the H5 strain.

In this case, additional testing by CSIRO to confirm the H5 bird flu strain has not been finalised and may also not be possible due to carcass degradation. It is likely to be treated as a presumed positive detection.

Both cases were reported by members of the public to the Emergency Animal Disease (EAD) Hotline for further investigation.

There have been more than 1700 wildlife-related reports from WA to the hotline since the first confirmed case on 19 June. Of these reports, 283 have been assessed for further investigation or testing based on the likelihood of disease risk.

To date, a total of 117 negative test results have been recorded across the State.

The risk to human health remains low, but people are reminded to avoid handling 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.

The logistics of following up each prioritized hotline report of dead birds are both extensive and time consuming:

• Physically collecting and preserving carcasses (assuming they haven't been degraded by exposure or predation), often from remote regions. 

• Preliminary tests are run by local/state agricultural institutes to quickly confirm the presence the H5 subtype 

• Followed by packaging and sending biological samples to the only national testing laboratory (CSIRO Australian Centre for Disease Preparedness (ACDP) in Geelong, Victoria)

• Upon arrival, confirmation (and full sequencing) can take several days, assuming the sample had not degraded too badly. 

All of which helps to explains why it can take a week or longer to get confirmation on a suspected case.

While I've only seen aggregate totals posted by WA, it is apparent that the number of daily reports to their hotline far exceeds their ability to collect and test samples.  

 Graphic generated by Gemini

Over the past 12 days the number of tested samples has risen from 63 to 125 (avg 5/day), while the number of hotline reports has grown by 900 (avg 75/day).  Even if we limit it to prioritized reports, that number has averaged 13.75/day. 

Although testing has increased over the past 12 days, the number of new reports of sick or dead birds far outpaces those gains. 

 Graphic generated by Gemini

None of this is a criticism of Australia's response, only an acknowledgment of the enormity of the problem facing them. No surveillance and testing program can hope to capture more than a fraction of the HPAI activity in birds or animals in the wild. 

What testing can do is give us an idea as to the spread, intensity, and host range of HPAI H5 across the continent. And sequencing can alert us to any reassortments or significant changes to the virus over time.

While the absolute number of confirmed detections remains small (n=14) - and we've seen no reports of outbreaks in poultry or mammalian wildlife - the trends are nevertheless concerning.  

Respiratory Illness Low In The U.S., But Taiwan & Hong Kong Report Increased COVID Activity

 
Credit CDC

#19,246

Reassuringly, in their latest update (July 10th), the CDC is reporting very low respiratory illness in the United States right now.

What to know

• As of July 10, 2026, the amount of acute respiratory illness causing people to seek health care is very low. 

• RSV activity is very low in most areas of the country. Emergency department visits and hospitalizations for RSV are low but remain highest among infants and children younger than 4 years old. 

• COVID-19 activity is low and stable nationally but is beginning to increase from low in a few areas of the country. 

• Seasonal influenza activity is low. 

• Parainfluenza (PIV), a respiratory virus that can cause illnesses such as croup, is elevated nationally. Rhinovirus/enterovirus (RV/EV), which often cause cold-like respiratory illness, are also elevated nationally but is going down. Whooping cough (pertussis) is still circulating.

But, as mentioned above, some states are showing signs of increasing COVID activity, as depicted in the following CDC map.

While we've yet to see a summer surge in COVID this year in the United States, the virus continues to circulate - and evolve - around the globe, and some places are reporting increased activity. 

The most recent update from Hong Kong indicates COVID cases are rising:

Meanwhile, Taiwan's CDC issued the following (translated) statement today (July  14th).

As the COVID-19 pandemic continues to escalate, the public is urged to get vaccinated; those at risk of severe illness should seek medical attention immediately if they experience suspected symptoms.

 

 Release Date: 2026-07-14

The Centers for Disease Control (CDC) stated today (July 14th) that the domestic COVID-19 epidemic continues to escalate. To protect their own health and the health of others, the CDC urges the public to take self-prevention measures and get vaccinated against COVID-19 this season. It is recommended to wear masks when entering and exiting medical care facilities and in crowded places where proper social distancing cannot be maintained or ventilation is poor. If fever or respiratory symptoms occur, it is recommended to stay home and avoid unnecessary outings. Individuals with severe risk factors should seek medical attention as soon as possible if they experience suspected symptoms. A doctor can assess and conduct a rapid test, or they can use a commercially available home rapid test. A doctor can also assess and prescribe antiviral drugs for those with severe risk factors who test positive for COVID-19, reducing the risk of serious complications or death after infection.

The CDC stated that the domestic COVID-19 epidemic continues to rise. In the 27th week (July 5th-July 11th), there were 2,811 outpatient and emergency room visits for COVID-19, an increase of 34.4% compared to the previous week. Last week (July 7th-July 13th), there were 17 new local cases of severe COVID-19 complications, with no new local deaths. Since October 2025, a total of 136 local cases of severe COVID-19 complications have been reported, with 18 deaths. The majority of severe cases were among those aged 65 and above (72.1%) and those with a history of chronic diseases (83.8%). 94.9% of these cases were not vaccinated this season.

Globally, the COVID-19 positivity rate has recently increased, showing an upward trend in all regions except the Eastern Mediterranean region. Neighboring countries/regions such as China, Hong Kong, Japan, South Korea, and Singapore are also experiencing rising cases. Currently, the predominant circulating strain globally is NB.1.8.1, followed by JN.1 and XFG.

The Centers for Disease Control (CDC) indicates that as of July 12, 2026, approximately 1.732 million COVID-19 vaccinations have been administered this season. The vaccination rates among those aged 65 and above are 20.97% for the first dose and 0.51% for the second dose. International research has found that receiving the current season's COVID-19 vaccine provides additional protection on top of existing immunity.

Vaccination with the current season's COVID-19 vaccine can reduce the risk of visiting the emergency room or emergency outpatient clinic due to COVID-19 by approximately 48%–50%, and reduce the risk of hospitalization by approximately 53%–55%. This demonstrates that COVID-19 vaccination effectively reduces the severity of the disease and the medical burden caused by COVID-19, and has a significant protective effect in preventing severe illness and hospitalization.

The Taiwan Centers for Disease Control (CDC) urges that, as the majority of severe local COVID-19 cases in Taiwan are still among the elderly aged 65 and above and those with a history of chronic diseases, and most of them have not yet received the current season's COVID-19 vaccine, the CDC urges high-risk individuals, such as those aged 65 and above, who have not yet been vaccinated or have received their first dose at least 6 months ago, to get vaccinated as soon as possible to enhance their immune protection and reduce the risk of severe illness and hospitalization.

(Continue . . .)

 

Whether we get a significant summer surge in COVID remains to be seen, but the recent extended lull is no guarantee that futures outbreaks will not occur.  The CDC adds:

Season Outlook

CDC has observed a trend of declining COVID-19 hospitalizations nationally over time. However, it remains possible that there could be larger increases this summer, particularly if a variant that the immune system no longer recognizes becomes more common .

Scenario modeling indicates that regions which did not experience a substantial level of COVID-19 activity during the most recent winter months (South and West) are expected to experience increases in COVID-19 activity in the summer months. Read more: 2026 COVID-19 Summer Outlook | CFA: Qualitative Assessments | CDC

Which is why I've recently (May) gotten a COVID booster shot to hopefully boost my protection through the summer.