H5N1

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

Via Nature Communications: Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region. The abstract:

Until recent events, the Antarctic was the only major geographical region in which high pathogenicity avian influenza virus (HPAIV) had never previously been detected. Here we report on the detection of clade 2.3.4.4b H5N1 HPAIV in the Antarctic and sub-Antarctic regions of South Georgia and the Falkland Islands, respectively. 

We initially detected H5N1 HPAIV in samples collected from brown skuas at Bird Island, South Georgia on 8th October 2023. Since this detection, mortalities were observed in several avian and mammalian species at multiple sites across South Georgia. Subsequent testing confirmed H5N1 HPAIV across several sampling locations in multiple avian species and two seal species. Simultaneously, we also confirmed H5N1 HPAIV in southern fulmar and black-browed albatross in the Falkland Islands. 

Genetic assessment of the virus indicates spread from South America, likely through movement of migratory birds. Critically, genetic assessment of sequences from mammalian species demonstrates no increased risk to human populations above that observed in other instances of mammalian infections globally. 

Here we describe the detection, species impact and genetic composition of the virus and propose both introductory routes and potential long-term impact on avian and mammalian species across the Antarctic region. We also speculate on the threat to specific populations following recent reports in the area.

Stop H5N1 influenza in US cattle now

An editorial in Science; Stop H5N1 influenza in US cattle now.

The relentless march of a highly pathogenic avian influenza virus (HPAIV) strain, known as H5N1, to become an unprecedented panzootic continues unchecked. The leap of H5N1 clade 2.3.4.4b from Eurasia and Africa to North America in 2021 and its further spread to South America and the Antarctic have exposed new avian and mammalian populations to the virus and led to outbreaks on an unrivaled scale. 

The virus has infected wild birds across vast geographic regions and caused wildlife deaths in some of the world’s most biodiverse ecosystems. Hundreds of millions of poultry have died or been culled, affecting global food security in some of the world’s poorest regions. Numerous mammalian species, including sea lions and fur animals, have been infected. Outbreaks in dairy cows in the United States have been occurring for months, seemingly unchecked in most affected states. Why is there not a greater sense of urgency to control these infections? 

Although the H5 2.3.4.4b virus seems poorly optimized for infection or spread in humans, with fewer than 20 cases since 2016, influenza leaves no room for complacency. The sheer number of infected wild birds and poultry has caused spillover infections to occur in wild carnivores, marine mammals, and farmed animals, providing additional pathways for exposure and perhaps infection in humans. The H5 virus has evolved continuously since 1996 but has never infected so many bird species nor been able to transmit to, and replicate in, cows. 

The more than 140 dairy farms in 12 US states with the virus and the detection of viral RNA in milk products in grocery stores speak for themselves. Infection in cattle creates new possibilities for direct contact between the virus and humans, and also risks the virus evolving the ability to spread in cattle, a new livestock reservoir of around 1.5 billion animals worldwide. 

Until now, human infections with H5 viruses were mainly associated with the keeping of infected poultry. But over the past 3 months, the United States has identified human H5 cases in farmworkers associated with one of the world’s most industrialized dairy production systems. Even difficult viral adaptations can occur if there are enough opportunities for contact and replication in new host species. Adaptation of the virus to cattle must be prevented. The outbreak in cattle in the United States must therefore be brought under control quickly. 

Key measures that should be initiated or intensified immediately include surveillance of all US dairy farms by testing, for example, bulk milk for influenza virus RNA, implementation of strict quarantine for infected cattle, and restriction of within-state transport to stop the circulation of the virus in cows. Only a couple of states are attempting this currently. 

Biosecurity and hygiene measures on US dairy facilities must be enhanced to avoid virus spread and spillover infections. This should include simple and practical steps such as keeping work clothing on the farm, thoroughly decontaminating stock vehicles and equipment, ensuring restricted access and movement of personnel among premises, and providing appropriate personal protective equipment. 

Human influenza surveillance should be bolstered during the summer and before the usual human seasonal influenza wave begins in the fall. The timely development of vaccine candidates for both livestock and humans should be undertaken along with associated policies on their distribution. This is the ultimate insurance against a worst-case scenario in which viral variants emerge that spread more easily in mammals. 

Globally, surveillance of mammalian cases should be intensified and real-time genomic information on the virus should be made publicly available, especially in at-risk populations (such as pig and fur animal farms). There must be increased global awareness of data collection and data sharing on zoonotic influenza. Analyses for incursion risk and pandemic preparedness based on both genetic and phenotypic data (including identifying mammalian adaptive changes, antiviral therapeutic resistance, and diagnostic robustness) in all regions need to be substantially improved, and the detection of human infection clusters needs to be further optimized. 

National and international coordination in the spirit of a modern “One Health” approach is essential, and the quadripartite comprising the Food and Agricultural Organization of the United Nations, United Nations Environment Programme, World Health Organization, and World Organisation for Animal Health should step up to take a leading role.

Cambodia: Two Takeo boys confirmed infected by H5N1 bird flu

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Thanks to Peter O'Meagher for alerting me to this Khmer Times report: Two Takeo boys confirmed infected by H5N1 bird flu. Takeo is a province south of the capital, Phnom Penh. The 3-year-old case was reported yesterday, but not the 5-year-old. Excerpt:

The Takeo Health Department said two boys, ages three and five, have been confirmed to be infected with the H5N1 bird flu, while 29 others are still waiting for test results from the National Institute of Public Health (NIPH) and the Pasteur Institute (PI) of Cambodia.  

H5N1 is a subtype of influenza that predominantly infects birds. However, the H5N1 virus can also infect mammals that have been exposed to infected birds in some cases. In these cases, symptoms are frequently severe or fatal.  

Takeo Health Director Nhea Sithan said yesterday that two children have been diagnosed with the H5N1 bird flu virus, while 29 people were waiting on results of blood tests from the NIPH and PI. He said that the Takeo Provincial Health Department has asked experts to cooperate with the relevant ministries to identify everyone who ate chickens that are suspected of having been infected with the H5N1 bird flu virus.  

“We have dealt with the situation in a timely manner and we’ve sent 29 people who may have been exposed to H5N1 to analyse their blood to see whether they have contracted bird flu or not,” he said.  

The director of the Takeo Provincial Production and Veterinary Office, Thai Ly, said yesterday that more than 600 chickens that were thought to be at high risk of being infected with the H5N1 virus were destroyed after the Takeo Provincial Department of Agriculture, Forestry, and Fisheries identified a case of bird flu in Por village.  

He added that according to past studies of the bird flu virus, this level of infection is unlikely to spread to other villages. However, he urged people not to eat sick or already-dead birds to avoid H5N1 infection.  

“We are calling on people to be vigilant against infection by bird flu by not eating and cooking the chickens and ducks that are sick or die from unknown causes due to the danger caused by H5N1,” he said.

H5N1: International failures and uncomfortable truths

An editorial in The Lancet: H5N1: international failures and uncomfortable truths.

If you ask an infectious diseases specialist whether we should start worrying about influenza A H5N1, they will probably tell you that we should always be worrying about it. An influenza pandemic has long topped the list of global threats to health, and avian influenza poses a particularly serious concern. 

H5N1 has infected over 800 people since its identification in 1996, with a mortality rate exceeding 50%. Since 2020, it has become endemic in bird populations, triggering an unparalleled animal pandemic, affecting at least 26 mammal species. There is nothing new in influenza strains evolving, shifting their epidemiological habits, and causing infections in people, although human-to-human transmission of H5N1 is rare. 

Nonetheless, although developments over the past 3 months may or may not signal the start of a global pandemic, they are at the very least a pressing and unwelcome reminder of the caprices of zoonotic influenza and our continued collective complacency about it. 

An unprecedented outbreak of highly pathogenic avian influenza A(H5N1), the first documented infection in dairy cows, was reported on March 25, 2024 in Texas, Kansas, and New Mexico, raising the potential of cow-to-human transmission. Three confirmed human cases in the USA, all farm workers, have been reported so far, with the third person presenting with respiratory symptoms. 

Genetic analysis shows that the virus lacks changes that would make it better adapted to transmit between people and the risk to human health remains low, but it did detect adaptation to mammalian hosts. 

Despite calls for increased surveillance, the US response has been slow, with many cases likely going undetected. There has been resistance from the farming industry around testing and prevention, driven by a lack of awareness or understanding around changing practice and fear of trade restrictions and product loss. The US Department of Agriculture (USDA) and the US Centers for Disease Control and Prevention are incentivising dairy producers to supply personal protective equipment and offer laundering services for employees, but the USDA has been accused of being slow in sharing crucial virus sequence data, complicating our understanding of the outbreak. 

In Canada, early warning systems have been implemented to screen for H5N1 in milk. The UK says it has intensified its response to the US outbreak, but according to a report last month, it is not yet testing cows for the virus.

Action to curb this outbreak is needed urgently, including improving testing, surveillance, and reporting of infected animals and food products; vaccinating animal populations; transparent information sharing; developing and stockpiling human vaccine; and promoting protective measures among farm workers. All countries should build capacities to test, detect, and report infections, cases, and deaths above expected levels and share this information. Countries in need of external assistance to bolster their capacity should receive support.

 

The need for a robust and coordinated response to highly pathogenic avian influenza A(H5N1), as described in a Comment by Kojima and colleagues, serves to highlight the scale of the failure of countries to secure an international agreement on the pandemic accord. The 77th World Health Assembly, which closed on June 1, was meant to see a finalised draft of an international instrument on pandemic prevention, preparedness, and response. As The Lancet has noted, negotiations have been mired in disagreement and draft provisions have been unjust and inequitable (although changes to the International Health Regulations have been agreed). The process is not over yet—discussions continue with the hope of securing an agreement by May, 2025. Until then, the continued absence of a meaningful and effective accord undermines the ability to respond appropriately to international health threats, such as H5N1. Despite COVID-19, most countries are not prepared for a new pandemic.

 

Beyond the proximal drivers of outbreaks and potential interventions though, there is a need to confront an uncomfortable truth that the US H5N1 outbreak once again raises. Spillover of zoonoses into human populations stems ultimately from our ways of life and how they shape the human–animal interface. Our diets, our intensive farming practices, our livelihoods, our behaviours, and our cultures. Our exploitation of the natural world and our destruction of the environment. These issues are tractable through interdisciplinary education, intersectoral collaboration, adequate funding, and integrated policies. The concept of One Health, although often acknowledged, is rarely prioritised and operationalised. The result is a missed opportunity to not just respond to pandemic threats, but to prevent them altogether.

 

WHO: Avian Influenza A (H5N1) - Australia

A WHO DON: Avian Influenza A (H5N1) - Australia. Excerpt:

Situation at a glance  

On 22 May 2024, the World Health Organization (WHO) was notified of a laboratory-confirmed case of human infection with avian influenza A(H5N1) virus (clade 2.3.2.1a) by the International Health Regulations (IHR) National Focal Point (NFP) of Australia. This is the first confirmed human infection caused by avian influenza A(H5N1) virus detected and reported by Australia.  

Although the source of exposure to the virus in this case is currently unknown, the exposure likely occurred in India, where the case had travelled, and where this clade of A(H5N1) viruses has been detected in birds in the past. According to the IHR (2005), a human infection caused by a novel influenza A virus subtype is an event that has the potential for high public health impact and must be notified to the WHO. Based on available information, WHO assesses the current risk to the general population posed by this virus as low.  

Description of the situation  

On 17 May 2024, the WHO Collaborating Centre (WHO CC) for Reference and Research on Influenza in Australia notified the NFP of Australia of a suspected case of human A(H5N1) avian influenza (HPAI) in Melbourne, Victoria. The state Victorian Department of Health confirmed this case on 18 May 2024. Under Article 44, the NFP of Australia advised the NFP of India of the confirmed case on 21 May 2024. Under Article 8, the IHR NFP of Australia notified WHO of the case on 22 May 2024.  

The case is a 2.5-year-old female child with no underlying conditions.  She had a history of travel to Kolkata, India from 12 to 29 February 2024. She returned to Australia on 1 March 2024. Upon returning to Australia, the child presented at a hospital in Victoria on 2 March 2024, where she received medical care and was admitted on the same day. 

On 4 March, the patient was transferred to the intensive care unit at a referral hospital in Melbourne, Victoria, due to worsening symptoms, for a period of one week. The patient was discharged from hospital after a 2.5-week admission. The case is now reported to be clinically well.  

The Victorian Department of Health reported on 23 May 2024 that the family advised that the child started to feel unwell on 25 February 2024, with loss of appetite, irritability and fever, and was taken to a doctor on the evening of 28 February 2024 in India. She was febrile, coughing and vomiting and was given paracetamol. It was not reported to an Australian airport biosecurity officer that the child was unwell when she arrived in Australia on 1 March 2024.  

Additional information provided by the family indicates that the case did not travel outside of Kolkata, India, and did not have any known exposure to sick persons or animals while in India. It is understood that no close family contacts of the case in Australia or India developed symptoms, as of 22 May 2024.  

A nasopharyngeal swab and endotracheal aspirate taken on 6 and 7 March respectively tested positive for influenza A at the referral hospital. The samples were sent to the WHO CC for further characterisation on 3 April as part of a batch, as there was insufficient knowledge from the referring practitioners at the hospital to connect the case to the H5N1 virus.  

Virus genetic sequence obtained from the samples confirmed the subtype A(H5N1) and indicated that the haemagglutinin (HA) gene belonged to clade 2.3.2.1a, which circulates in South-East Asia and has been detected in previous human infections and in poultry.

Cows infected with bird flu have died in five US states

Via Reuters: Exclusive: Cows infected with bird flu have died in five US states. I sincerely hope that sick cows sent to slaughter do not then enter the food chain. Excerpt:

June 6 (Reuters) - Dairy cows infected with avian flu in five U.S. states have died or been slaughtered by farmers because they did not recover, state officials and academics told Reuters.  

Reports of the deaths suggest the bird flu outbreak in cows could take a greater economic toll in the farm belt than initially thought. Farmers have long culled poultry infected by the virus, but cows cost much more to raise than chickens or turkeys. 

A U.S. Department of Agriculture spokesperson said the agency knew of a few deaths but that the vast majority of cows recover well. Reuters was not able to determine the total number of cows with bird flu that died or were killed in South Dakota, Michigan, Texas, Ohio and Colorado.  

Avian flu has infected dairy cows in more than 80 herds across 10 states since late March, according to the USDA.  

Some of the animals died of secondary infections contracted after bird flu weakened their immune systems, said state veterinarians, agriculture officials, and academics assisting in state responses to bird flu. Other cows were killed by farmers because they failed to recover from the virus.  

Cattle infected with bird flu suffer reduced milk production, digestive issues, fever, and diminished appetite, according to farmers and veterinarians.  

In South Dakota, a 1,700-cow dairy sent a dozen of the animals to slaughter after they did not recover from the virus, and killed another dozen that contracted secondary infections, said Russ Daly, a professor with South Dakota State University and veterinarian for the state extension office who spoke with the farm. 

"You get sick cows from one disease, then that creates a domino effect for other things, like routine pneumonia and digestive issues," Daly said.  

A farm in Michigan killed about 10% of its 200 infected cows after they too failed to recover from the virus, said Phil Durst, an educator with Michigan State University Extension who spoke with that farm.

WHO: Human infection caused by avian Influenza A(H5N2)- Mexico

A Disease Outbreak News report from WHO: Human infection caused by avian Influenza A(H5N2)- Mexico. Excerpt:

Situation at a glance

On 23 May 2024, the Mexico International Health Regulations (IHR) National Focal Point (NFP) reported to PAHO/WHO a confirmed fatal case of human infection with avian influenza A(H5N2) virus detected in a resident of the State of Mexico who was hospitalized in Mexico City.  

This is the first laboratory-confirmed human case of infection with an influenza A(H5N2) virus reported globally and the first avian H5 virus infection in a person reported in Mexico. Although the source of exposure to the virus in this case is currently unknown, A(H5N2) viruses have been reported in poultry in Mexico. According to the IHR (2005), a human infection caused by a novel influenza A virus subtype is an event that has the potential for high public health impact and must be notified to the WHO. 

Based on available information, WHO assesses the current risk to the general population posed by this virus as low.   

Description of the situation  

On 23 May 2024, the Mexico IHR NFP reported to PAHO/WHO a confirmed case of human infection with avian influenza A(H5N2) virus detected in a 59-year-old resident of the State of Mexico who was hospitalized in Mexico City and had no history of exposure to poultry or other animals. The case had multiple underlying medical conditions. The case’s relatives reported that the case had already been bedridden for three weeks, for other reasons, prior to the onset of acute symptoms.  

On 17 April, the case developed fever, shortness of breath, diarrhoea, nausea and general malaise. On 24 April, the case sought medical attention, was hospitalized at the National Institute of Respiratory Diseases “Ismael Cosio Villegas” (INER per its acronym in Spanish) and died the same day due to complications of his condition.  

Results from Real-Time Polymerase Chain Reaction (RT-PCR) of a respiratory sample collected and tested at INER on 24 April indicated a non-subtypeable influenza A virus. On 8 May, the sample was sent for sequencing to the Laboratory of Molecular Biology of Emerging Diseases Center for Research in Infectious Diseases (CIENI per its acronym in Spanish) of INER, which indicated that the sample was positive for influenza A(H5N2).  

On 20 May, the sample was received at the Institute of Epidemiological Diagnosis and Reference (InDRE per its acronym in Spanish) of the Mexico National Influenza Centre, for analysis by RT-PCR, obtaining a positive result for influenza A. On 22 May, sequencing of the sample confirmed the influenza subtype was A(H5N2).  

No further cases were reported during the epidemiological investigation. Of the 17 contacts identified and monitored at the hospital where the case died, one reported a runny nose between 28 and 29 April. Samples taken from these hospital contacts between 27 and 29 May tested negative for influenza and SARS-CoV 2.  

Twelve additional contacts (seven symptomatic and five asymptomatic) were identified near the case's residence. Samples of pharyngeal exudate, nasopharyngeal swabs and serum were obtained from these individuals. On 28 May, the InDRE reported that all twelve samples from contacts near the patient's residence tested negative for SARS-CoV-2, influenza A and influenza B, as determined by RT-PCR. The results of the serological samples are pending.  

In March 2024, a high pathogenicity avian influenza A(H5N2) outbreak was detected in a backyard poultry farm in the state of Michoacán, which borders the State of Mexico where the case was residing  

Additionally, in March 2024, an outbreak of low pathogenicity avian influenza (LPAI) A(H5N2) was identified in poultry in Texcoco, State of Mexico, and a second outbreak of LPAI A(H5N2) in April in the municipality of Temascalapa in the same state. Thus far, it has not been possible to establish if this human case is related to the recent poultry outbreaks (1).  

A study describing the continuous circulation of low pathogenicity avian influenza H5N2 viruses in Mexico and spread to several other countries was published in 2022 (2).

MMWR: Outbreak of Highly Pathogenic Avian Influenza A(H5N1) Viruses in US Dairy Cattle and Detection of Two Human Cases — United States, 2024

Via MMWR: Outbreak of Highly Pathogenic Avian Influenza A(H5N1) Viruses in U.S. Dairy Cattle and Detection of Two Human Cases — United States, 2024. The summary:

What is already known about this topic? 

Influenza A(H5) virus infection was detected in two U.S. farm workers during a multistate outbreak of A(H5N1) viruses in dairy cows; these are the first known instances of presumed cow-to-human transmission of avian influenza A viruses.  

What is added by this report?  

Approximately 350 exposed farm workers are being monitored; one of the two cases was identified via daily, active monitoring. Surveillance has identified no unusual influenza activity trends in the United States. A(H5) candidate vaccine viruses are available, and laboratory analyses indicate that A(H5N1) viruses circulating in cows and other animals are susceptible to FDA-approved antivirals.  

What are the implications for public health practice?  

Current risk to the U.S. public from A(H5N1) viruses is low; however, persons exposed to infected animals or contaminated materials, including raw cow’s milk, are at higher risk and should take precautions and self-monitor for illness. A One Health (human, animal, and environmental) approach is critical to preparing for circumstances that could increase risk to human health.

MMWR: Outbreak of Highly Pathogenic Avian Influenza A(H5N1) Viruses in U.S. Dairy Cattle and Detection of Two Human Cases — United States, 2024

Via MMWR: Outbreak of Highly Pathogenic Avian Influenza A(H5N1) Viruses in U.S. Dairy Cattle and Detection of Two Human Cases — United States, 2024. The summary and abstract:

Summary

What is already known about this topic?  

Influenza A(H5) virus infection was detected in two U.S. farm workers during a multistate outbreak of A(H5N1) viruses in dairy cows; these are the first known instances of presumed cow-to-human transmission of avian influenza A viruses.  

What is added by this report?  

Approximately 350 exposed farm workers are being monitored; one of the two cases was identified via daily, active monitoring. Surveillance has identified no unusual influenza activity trends in the United States. A(H5) candidate vaccine viruses are available, and laboratory analyses indicate that A(H5N1) viruses circulating in cows and other animals are susceptible to FDA-approved antivirals.  

What are the implications for public health practice?  

Current risk to the U.S. public from A(H5N1) viruses is low; however, persons exposed to infected animals or contaminated materials, including raw cow’s milk, are at higher risk and should take precautions and self-monitor for illness. A One Health (human, animal, and environmental) approach is critical to preparing for circumstances that could increase risk to human health.

Abstract  

On April 1, 2024, the Texas Department of State Health Services reported that a dairy farm worker had tested positive for highly pathogenic avian influenza A(H5N1) virus after exposure to presumably infected dairy cattle; CDC confirmed these laboratory findings. A(H5N1) viruses were found in high concentrations in unpasteurized (raw) milk from infected cows.  

CDC is collaborating with the U.S. Department of Agriculture, the Food and Drug Administration, the Administration for Strategic Preparedness and Response, the Health Resources and Services Administration, the National Institute of Allergy and Infectious Diseases, and state and local public health and animal health officials using a coordinated One Health approach to identify and prepare for developments that could increase the risk to human health.  

Activities include monitoring of exposed persons, conducting syndromic and laboratory surveillance, planning epidemiologic investigations, and evaluating medical countermeasures. As of May 22, 2024, approximately 350 farm workers with exposure to dairy cattle or infected raw cow’s milk had been monitored.  

These monitoring efforts identified a second human A(H5) case with conjunctivitis in Michigan, which was reported on May 22, 2024. CDC considers the current risk to the U.S. public from A(H5N1) viruses to be low; however, persons with exposure to infected animals or contaminated materials, including raw cow’s milk, are at higher risk for A(H5N1) virus infection and should take recommended precautions, including using recommended personal protective equipment, self-monitoring for illness symptoms, and, if they are symptomatic, seeking prompt medical evaluation for influenza testing and antiviral treatment if indicated.  

Pasteurization inactivates A(H5N1) viruses, and the commercial milk supply is safe for consumption; however, all persons should avoid consuming raw milk or products produced from raw milk.  

Importantly, the risk to the public might change based on whether A(H5N1) viruses acquire genetic changes that increase their transmissibility to and among humans, which could increase the risk of an influenza pandemic.

Human case of H5N1 avian influenza (bird flu) detected in returned traveller to Victoria

Thanks to FluTrackers for posting this report from the Victoria health department: Human case of avian influenza (bird flu) detected in returned traveller to Victoria. This case seems unrelated to the avian flu reported yesterday in poultry farms in Victoria. The key points:

• A human case of avian influenza A(H5N1) infection, also known as “bird flu”, has been reported in Victoria.  

• There is a current global outbreak of avian influenza in birds and animals. Avian influenza does not usually infect people, but in rare cases human infection can occur.  

• The recently reported case in Victoria was in a child who returned to Australia from overseas in March 2024. The child experienced a severe infection but is no longer unwell and has made a full recovery.  

• There is no evidence of transmission in Victoria and the chance of additional human cases is very low as avian influenza does not easily spread between people.