Zoonotic Bird Flu News since 21 Dec 2022 till 3 Jan 2023

Avian Flu Isn't Just For the Birds [Bay Nature, 3 Jan 2023]

by Guanani Gomez-Van Cortright

As the latest strain of avian influenza?Gs/GD HPAI, it’s called?spreads through the U.S., birds are not the only creatures the virus has felled.

As of December 2022, the virus has been detected in a confirmed total of 53 red foxes in eight states. Other mammals have tested positive as well, including scavenger species, such as skunks and racoons, that have likely fed on potentially infected dead birds. So far, 10 species of land mammals have tested positive for the virus in the U.S.

Workers at the Dane County Humane Society in Wisconsin received call after call about red fox kits behaving oddly. The kits were strangely easy to approach, wandering alone, often stumbling or walking in circles. Some struggled to stand, salivated excessively, twitched, and even had seizures, symptoms often soon followed by death. The Humane Society facility admitted some of the sick kits and ruled out rabies and other potential causes before testing revealed that the young foxes were suffering from neurological symptoms triggered by Gs/GD HPAI. Possibly because of the young foxes’ underdeveloped immune systems, the virus proved particularly lethal to them.

In June, the National Oceanic and Atmospheric Administration declared an unusual mortality event for gray seals and harbor seals, which were stranding on the beaches of Maine at three times the normal rate. Four of the eight beached seals tested were positive for Gs/GD HPAI, and over the next five months, over 300 seals were stranded. No birds were found in the stomachs of necropsied seals, but scientists believed the seals were catching the virus from contact with infected birds or their droppings when they came to shore.

Florida residents discovered a young male bottlenose dolphin trapped between a pier and a seawall in March. By the time rescuers got to the scene, the dolphin was dead. Bird flu wasn’t on their short list of possible culprits. But after researchers ruled out common causes and found high levels of inflammation in the dolphin’s brain during the necropsy, one researcher noted cases of avian influenza in wild seabirds in the area. The dolphin’s tissue samples tested positive for Gs/GD HPAI. The following September, Swedish researchers reported finding the virus in a stranded porpoise. These two cases marked the first time an avian influenza has ever been detected in cetaceans.

“We’ve had marine mammals that have been infected,” says Pitesky. “That gives me some pause.”

While it does sicken and kill mammals, Gs/GD HPAI does not seem to spread readily from one mammal to another. But the more spillover infections occur across animal classes, the higher the chances the virus could become capable of spreading between mammals as well.

“The worst-case scenario is, it finds its way to us,” says Richard Webby, an infectious disease and influenza expert at St. Jude Children’s Research Hospital in Memphis, Tennessee. “Those hosts, that’s a step closer to the virus changing from being a bird virus to being a human virus.”

That other pandemic: 2022 was worst year for bird flu this century [The Mendocino Voice, 3 Jan 2023]

By Frank Hartzell

MENDOCINO Co., 1/3/22 ? When one of Renne’s Clark’s ducks died this December, the Albion resident dutifully had it tested through her veterinarian, Village Vet in Mendocino. Then she got unexpected news ? her duck, sent to UC Davis, tested positive for H5N1, or avian flu. She quarantined her flock and observed them with no further deaths. But she took the precaution of warning other poultry keepers on Facebook’s Fort Bragg-Mendocino chicken group.

Clark explained in a recent interview that while she knew there were reasons not to use her name, she is more interested in issuing a call to arms to other poultry lovers.

“We’re taking the necessary steps to deal with it, but wanted to let the community know it’s here on the coast. It’s great that Davis offers free necropsies for dead poultry ? I’ve used it several times over the years,” the Albion resident wrote on Facebook.

At the same time as Clark told this reporter about her case, the California Department of Food and Agriculture announced that the first case of the current strain of avian flu in a domestic flock in Mendocino County was confirmed. Although the timing is right, state agricultural officials could not confirm whether that first case was Clark’s, or even where in the county the confirmation occurred. There is no proof that the two reports are the same.

Such confusion exemplifies the information fog around avian flu, ranging from public disinterest to the spin put on the subject by the commercial poultry industry. This avian flu epidemic was the worst ever among birds and many other species, and it only continues to rage in 2023. Outbreaks in Czechia and South Korea were reported on New Year’s Day, but the flu is not infecting many humans ? yet. It can get any mammal that is likely to touch sick or dead birds- including housecats.

Researchers like virologist Rob Wallace say factory farming of chickens and pigs poses a clear and present danger to humanity, one likely to increase with time. Wallace, credited with predicting the coronavirus pandemic, soon became a pariah in the scientific community where he had flourished for many years. Early research in HIV/AIDS and influenza led him to be a consultant for the United Nations’ Food and Agriculture Organization and the Centers for Disease Control and Prevention. His downfall came when he was tracking bird flu origins in China, asking questions that he says got him shut out from some industry-funded university programs.

Wallace says money, not science, determines where and what research is done, thus directing what courses are considered to save humanity from our unsustainable appetites and practices. Unfortunately, he says, the wrong choices are being made. He and many others, including people inside some of the largest industrial chicken and meat companies, have ideas that might create a less terrifying and more sustainable future. But the available public narrative places the blame for the spread of avian flu on wild birds and backyard flocks, ignoring the fact that both lived in harmony for millennia before the advent of Confined Animal Feeding Operations (CAFOs). The fact that this avian flu pandemic hitting birds is the worst of the century and is worrying for the future, has gone mostly unnoticed due to pandemic news fatigue. Also lacking is credible information about what keeps causing avian flu, apart from books like Dr. Michael Greger’s Bird Flu: A Virus of Our Own Hatching or Wallace’s Big Farms Make Big Flu.

Meanwhile the chicken industry is not seriously considering changing its husbandry practices but instead is utilizing decades of research into gene editing to breed transgenic birds that can resist bird flu.

This flu broader and more deadly
The current outbreak of H5N1 is impacting a much wider array of species than past outbreaks. Even more ominous, it is killing wild birds and domestic ducks that normally survive it.

While H5N1 has infected just one human being so far in the USA ? a prisoner in Colorado assigned to cull chickens ? scientists are worried that a strain of avian flu could someday become a respiratory disease and cause a pandemic along the lines of Covid-19. The California Department of Food and Agriculture says the biggest concern is that people with human flu strains could be exposed to an infected bird, with the two diseases commingling to produce a dangerous new strain that spreads through the air in the way Covid and conventional flu strains are spread.

In 2014 H5N1 mostly disappeared, though it was replaced by H5N6 and H5N8 subtypes from 2014 through 2020. The epidemic of those two varieties wiped out 50 million birds in the Midwest, where factory farms are closer together, especially in Wisconsin and Iowa. California and the West were virtually untouched by those outbreaks.

However, in 2021 H5N1 emerged again in both Western Europe and East Asia. And in the meantime, it had evolved into something more deadly, likely inside Asian factory farms and outdoor markets, a true monster that attacks any mammal or bird that comes in direct contact with the corpses of the wild birds it kills. The virus was brought into factory farms by wild birds, then apparently escaped back out having now evolved to kill its hosts. Historically, avian flus did not kill or even sicken wild birds, and backyard chickens largely survived outbreaks that whirled around the globe.

A wide variety of mammals have been exposed to these dead birds and caught avian flu, which some scientists had thought was not possible. The following, provided to the Voice by the state Department of Food and Agriculture, lists mammal species infected by the current avian flu through December: American black bear, Amur leopard, Bobcat, bottlenose dolphin, Dixie striped skunk and virginia opossum, coyote, fisher, gray seal, harbor seal, raccoon, red fox, all animals believed to have gotten the avian flu directly from wild bird carcasses.

Hon Ip, who runs one of the best sources of information, the Facebook group “Avian Influenza, a.k.a bird flu,” provided US year-end stats for the bizarre worldwide interspecies phenomenon. “There were 98 highly pathogenic avian influenza detections in wild mammals in 2022. These came from 15 states, with Maine and Wisconsin tied at 17 detections each. The 98 detections came from 13 different species of mammals, with red fox making up 54 percent of the total.”

There have been only four human confirmed cases of this outbreak of H1N5 worldwide, two serious with one death and two less serious. To some, this means the disease has less potential human harm than other manifestations of bird flu, including earlier more fatal H151 rounds. To others, it means people have become smarter about handling dead birds. The mortality rate from human avian flu cases from 21st century varieties has been a horrifying 60 percent, according to the World Health Organization.

As of December 22, there have been 192 confirmed detections in wild birds in 37 California counties, including one bird in Mendocino County, since the first confirmed detection on July 13, according to the California Department of Food and Agriculture. People are warned to stay away from the carcasses of birds and leave handling to professionals wearing PPE.

In an interview, Laura Bradley, public information officer for California Department of Food & Agriculture Animal Health Branch, said there had not been any flock-to-flock transmission observed as of Dec. 22, only domestic poultry likely getting the disease from wild birds. Clark had not seen wild ducks with her birds, but Bradley said that is often the case, as the disease can be transmitted from the droppings of waterfowl flying over a backyard flock. A list of wild bird species carrying and often being killed by the disease can be found on the USDA APHIS website: https://www.aphis.usda.gov/animal_health/animal_diseases/avian/images/hpai-wild-birds-map.png

This variant is long-lasting
Another worrisome factor about the current avian flu pandemic is that it has been around for two years, while past manifestations lasted a single flu season. By December the global bird flu outbreak had killed hundreds of millions of chickens and turkeys worldwide. (Bradley pointed out that everything about avian flu is measured by its impact on chickens.)

That Clark’s duck was apparently the first recorded case in Mendocino County and just one case has been confirmed here in a wild bird (unknown area of the county), highlights the fact that California has been largely left out of the global H151 pandemic (at least among chickens).

Bird flu travels by the migratory routes of waterfowl, along the Pacific and Central flyways. The Mississippi Flyway, which includes the Midwestern states where chickens and eggs are largely raised, has seen chicken populations hit harder by the avian flu, as has much of Europe and Asia. But the number of cases in wild birds is similar along the nation’s flyways in 2022.

California’s stronger regulatory structure and greater biosecurity measures by the chicken industry may have helped keep avian flu from killing chickens in the numbers that the Midwest has seen. Avian flu has been found in US commercial and backyard poultry in 44 states and in wild birds in 46 states since early 2022.

This is a huge jump over the last time avian flu created major problems for the poultry industry. The number of chickens, turkeys and other fowl that were killed or died from the bird flu in the USA became the highest ever this December at more than 58 million, surpassing 2015’s total chicken deaths.

This number, relatively low when wild and domestic outbreaks are compared over time, is considered a victory for US reporting and observation practices by government agencies like CDFA, USDA and CDFA, and measures taken by the poultry industry to make factory farms more biosecure. Yet the industry continues to blame backyard flocks and wild birds in its science and media releases. A solution now proposed by industrial interests is mandatory worldwide vaccinations of chickens. This is seen by critics as impractical and possibly obfuscating the real issue; they say a more likely solution is reforming free trade away from pure profit to more sustainable farming practices.

Wallace says in Big Farms, Big Flu that blaming wild birds is a distraction that can no longer be tolerated. Wild birds bring bird flu in “low pathogenic” form to backyard flocks, which can acquire some immunity, as they are often older birds exposed to more diverse conditions.

Industrial flocks, slaughtered after 6-8 weeks for meat chickens to 1-2 years for egg chickens, have very low genetic diversity or variety, which makes it easier for pathogens to get at their immune systems. When the jump is made to the CAFOs, the low pathogenic becomes the deadly “highly pathogenic.” That has been the story in the past, confirmed by research in the Midwest, but this current deadlier virus does not seem to have a low pathogenic component. Bradley said she has only seen cases of highly pathogenic H5N1 in this cycle. Backyard flocks like Clark’s are also both more healthy and better spaced than the industrial model, making their experience with disease different. One duck died, with the rest of Clark’s flock not even showing signs of illness.

In a speech on YouTube, Dr. Michael Greger, author of Bird Flu: a VIrus of Our Own Hatching, said, “The emergence of H5N1 has been widely blamed on free-ranging flocks and wild birds.

This is somehow the fault of people… keeping chickens in the backyard for thousands of years. Birds have been migrating for millions of years. Bird flu has been accompanying them. What suddenly turned bird flu into a killer? Now we put millions of chickens into a chicken factory next door to a pig factory,” he continued. “These chicken factories make billions and billions of these mutations continuously. … The big shift in the ecology of avian influenza has been this intensification of the global poultry sector.”

Greger was praised for his viewpoint by many researchers, including an editorial in Virology journal. Others replay the official line that bird flu comes from mutations in the breeding grounds of migratory waterfowl. Wallace points out that money determines what is studied in labs and universities and what boundaries are pushed. He says most research money goes into vaccines that benefit big Pharma, not into the problem’s source or sustainable solutions.

Lessening the immune response
Chickens in CAFOs are not exposed to the outside and its natural strengthening of the immune system.They have closely matching genetics and they were not bred for the health of the birds. These conditions help evolve much more virulent viruses. Viruses are less virulent in nature because they cannot kill the host or they die themselves.

“In nature, there’s kind of a limit to how virulent these viruses can get,” said Greger. “Or at least there was, until now. Enter intensive poultry production when the next host is just inches away. There may be no limit to how nasty these viruses can get. Evolutionary biologists refer to this as the key to the emergence of hypervirulent so-called predator-type viruses, like HIV.”

Greger continued, “When you have a situation where the healthy cannot escape the disease, where the virus can just knock you flat and still transmit to someone else just because it’s so crowded, then there may be no stopping rapidly mutating viruses from becoming truly ferocious.”

The worst avian flu pandemic and worst overall pandemic in human history was in 1918-20 when a strain of probable avian flu killed 50 million people. Of course, there was no such thing as a CAFO in 1918. The deadly mutations are believed to have come from the packed conditions of troops fighting World War I. The virus spread in barracks and battlefields. This reporter’s great uncle, Floyd Sturm, died from the misnomered “Spanish Flu” in 1918 on his way to war.

“Just like the chickens when this harmless virus found itself in these packed conditions, it mutated and became more deadly,” Greger said. “Millions of soldiers were forced together in these stressful unhygienic conditions with no escaping a sick car. The same trench warfare conditions exist today in every industrial egg operation.”

While it’s not 100 percent sure that Spanish Flu was an avian flu variety that jumped into humans, the consensus among scientists now is that is exactly what happened. Here is a link to a study about the topic in the prestigious science journal Nature. The CDC definitively lists the 1918 pandemic as being an avian originated flu.

Industrial methods create breeding grounds for disease
Omnivores all, chickens, pigs and humans, have some similarities in their respiratory and digestive systems on a molecular level. As these viruses rip through packed chickens, they create something much more virulent, and that virulence could jump to humans. One study, conducted by universities in the USA and China, was suppressed as the information on how avian flu could become a respiratory disease was deemed too dangerous to be released.

These are the kind of alarm bells about the potential of avian flu that Dr. Greger and Wallace warn are being ignored at great potential peril to humanity’s future. Each book offers ways to change meat production and reduce meat consumption. But chicken farming took off in an even bigger way during the pandemic, and CAFO chicken farming is spreading in south Asia with increasing demand for meat. The chicken is also the creature on which genetic engineering is most commonly done. It is unknown the effect transgenic chickens might have on bird flu or other diseases that threaten humans, such as salmonella strains that have become highly virulent and antibiotic-resistant due to CAFO practices. Some in the industry are advocating the creation of new transgenic chicken varieties to resist the bird flu, without changing the conditions that cause it.

? Affected numbers in the United States
1. 2015 HPAI
a. 15 states affected
b. 21 backyard flocks
c. 211 commercial flocks
d. Total birds affected: 50.4 M

2. 2022 HPAI (as of 12/21/22)
a. 47 states affected
b. 404 backyard flocks
c. 303 commercial flocks
d. Total birds affected: 57.82 M

? Affected numbers in California (backyard flock will be denoted as BYF)
1. 2015 HPAI
a. 1 backyard flock
b. 1 commercial flock
c. Total birds affected: 247,201
2. 2022 HPAI (as of 12/21/22)
a. 43 affected counties (domestic, wild, or both)
b. Total birds affected (as of 12/21/22): 719,680
c. Butte County: 2 BYF ? 1,120 birds
d. Calaveras County: 1 BYF ? 20 birds
e. Contra Costa County: 1 BYF ? 60 birds
f. Del Norte County: 1 BYF ? 43,000 birds
g. El Dorado County: 1 BYF ? 150
h. Fresno County: 6 commercial, 1 BYF ? 166,200 birds
i. Mendocino County: 1 BYF ? 20
j. Monterey County: 1 commercial ? 15,100 birds
k. Sacramento County: 1 commercial, 2 BYF: 97,060 birds
l. San Diego County: 1 BYF: 150 birds
m. Stanislaus County: 2 commercial ? 105,900 birds
n. Tuolumne County: 4 commercial ? 290,900 birds

Creating Disease Resistant Chickens: A Viable Solution to Avian Influenza? ? PMC
Almost all flu varieties that infect humans originate in China and other packed parts of Asia, creating mutations that require a new flu vaccine every year. Flu mutates so quickly that it is impossible to be sure that vaccines (or genetically altered chickens) will work against fast-changing strains.

CAFOS were actually stopped cold by a virus shortly after they were invented in Delaware in the 1920s. Large chicken operations suffered total losses of their birds from a virus called Marek’s disease. Researchers believe that Marek’s disease only began to evolve when factory farms were created. A vaccine for Marek’s saved the industry. However, Marek’s disease has been spread to every corner of the world by the chicken industry, especially industrial hatcheries. Now no one can raise chickens without fear of Marek’s disease. Although Marek’s seems to pose no risk to humans, the New York Times did an investigative story into the frightening things that has happened in the evolution of Marek’s that scientists thought impossible for any virus. The Merck veterinary manual says the following about Marek’s disease, wholly created by the chicken CAFOs and now spawning super deadly variants inside chicken factories. “Marek’s Disease is identified in chicken flocks worldwide. Every flock, except for those maintained under strict pathogen-free conditions, is presumed to be infected.”

Large chicken farms have also created massive numbers of new strains of human-sickening bacteria like salmonella, E. coli and Campylobacter. Overuse of antibiotics made these bacteria evolve into strains that are now untreatable by medicine. Although antibiotic use has been greatly curtailed in the USA and Europe, the CAFO industry has been growing exponentially in China, Thailand, Indonesia and Vietnam, where many controls are not in place.

Free trade rules are written by the global meat industry. This reporter, when he raised chickens and eggs for the farmers’ market, found the industry had made it illegal to sell to grocery stores and restaurants unless I chose to drive chickens more than 200 miles to an industrial inspection facility, where they might get their first exposure to industrial pathogens. Chicken raisers in countries like South Africa that signed neo-liberal free trade agreements soon found it impossible to compete with giant industrial concerns. Others, in places like Gambia, can raise chickens in traditional ways and sell to anyone, because their nation did not sign free trade treaties that kill the small farm. Many of these nations have never had large outbreaks of H151. (there was an outbreak in Senegal).

In March 2009, the first case of a novel H1N1 influenza virus infection was reported in the Mexican state of Veracruz. The virus quickly spread through Mexico and the United States, and in June 2009 the World Health Organization officially declared it a pandemic. Within a year, the Centers for Disease Control and Prevention (CDC) estimates, it had killed about 575,000 people worldwide.

Early reports suggested that the source of the outbreak lay in the factory-style pig farms in the area around its epicenter in Veracruz. In-depth research traced the genetic lineage of the virus to a strain that had emerged in a supersized industrial hog farm in Newton Grove, North Carolina, in the late 1990s, where it had circulated and evolved among pigs before crossing to humans.

Industry writes the rules
Materials considered by the creators of the Paris climate accords were written by the meat industry, with claims that industrial meat chickens are better for the climate. The chickens were described as better because they moved less and ate less and thus created less carbon, an outright lie easily disproved by the tremendous consumption of food by the genetically engineered meat chicken, available on any chart used by industry itself. The notion that grass-fed cattle, pigs allowed to forage and pasture, and integrated farms could actually help with climate change was discarded due to meat industry pressures. This reporter obtained the language about agriculture that was considered in the secret meetings held that led to the Paris accords. The following published journal article documents the secrecy and the compromises that led to a Paris agreement that is not enforceable and does not confront issues like factory farming.

The actual Paris accords missed what may have been a key opportunity to take a stance on improving agricultural methods and punted on the entire subject, with agriculture not even appearing in the actual agreement. It did commit to reducing meat-eating overall but initiatives led by industrial agriculture and the Gates foundation have pushed for large scale, industrial monocrops and the destruction of the movement toward local farming. Now, it’s agriculture that is said to be the biggest threat to the Paris agreements. With nothing in the agreements, many nations in Southeast Asia, Africa and South America have greatly increased the size and number of their CAFOS.

Intensive farming worldwide threatens Paris climate accord, report says
What kind of wild birds are being infected?

“Waterfowl species are the natural host of avian influenza viruses, so we tend to see most infections among species of waterfowl,” said Krysta Rogers, senior environmental scientist with the California Department of Fish and Wildlife. “Other species that share habitat with waterfowl may also be susceptible, such as other water birds like American white pelicans, herons, egrets, and cormorants. Also, species that prey or scavenge on sick birds such as bald eagles, hawks, falcons, owls, turkey vultures, and ravens.” Rogers emphasized that all statistics rely on people reporting dead birds, which often doesn’t happen in the wide open spaces of the North Coast area.

“Testing of wild birds is generally biased towards areas with higher human populations. Areas with more people means the bird is more likely to be detected and submitted for testing versus an area with fewer people. As of December 22, the number of confirmed detections in wild birds for Mendocino County is 1, Del Norte County is 0, Humboldt County is 6, Lake County is 0, and Sonoma County is 8,” she said.

Mapping studies indicate this particular strain may have come from both Asia and Europe to the USA.“The strain of highly pathogenic avian influenza H5N1 currently in circulation has not been previously detected in North America. Prior to its detection along the Atlantic Coast in December 2021 (Canada) and January 2022 (U.S.), detections of this strain of highly pathogenic H5N1 had been on the rise across parts of Europe,” she said.

“This current outbreak is unprecedented in terms of the geographic range, diversity of wild birds potentially impacted, and number of wild birds that may die from infection,” she said. “Prior to this outbreak, highly pathogenic avian influenza viruses were considered more of a disease of domestic poultry with occasional spill-over into wild birds which may or may not have caused mortality.”

Operations in Europe have greatly increased biosecurity and worked toward easing the misery and ill health conditions that meat and egg chickens are raised in. This has also happened in California but has been resisted in the farm belt of the USA. During the Trump Administration, measures to regulate the chicken industry were discarded or slowed in favor of making the USA more competitive in the worldwide chicken trade.
What is the solution?
While industry seeks pharmaceutical and bioengineering solutions to specific issues such as transitioning away from antibiotics or bird flu, this does not solve the causal problems with CAFOs. A current bill sponsored by Bay Area Democratic Congressman Ro Khanna and New Jersey Democratic Senator Cory Booker would force existing USA CAFOs to cease operating in that fashion by 2040. But is the problem consumers or CAFOs? As a farmer’s market chicken seller, I got frowns for charging $6 per pound for meat from chickens that lived happy lives outdoors with real nutrition.

During that period, I interviewed a chicken company president who said I could use his name if the article blamed not the industry, but on the consumer demand for $2 per pound chicken. He was right. The enemy, as Pogo said, is us.

The president was part of an industry group trying to interest consumers in better-tasting chicken. The effort largely failed. US chicken companies were sued and prosecuted after Walmart complained they were working together to raise prices. Meanwhile, European chicken producers are downsizing chicken operations but the cost of the chicken they sell must be government-subsidized to be affordable. And free trade brings in super cheap chicken from the world’s largest and worst CAFOs in Vietnam and Indonesia.

Industry leaders say that free trade agreements must be rewritten to force these countries, which are using the USA CAFO model and often working for USA corporations, to create smaller and healthier poultry factories. This crashes headlong into conservative forces that don’t believe in regulation. Even more powerful opposition comes from neoliberal forces, led by Bill Gates and his foundation, that believe bigger is better and work against the continuation of traditional farming practices in favor of genetic engineering, processed fake meat and other fake foods made from genetically modified soybeans. Their plans call for the massive planting of monocrops in the global South, decimating Amazon rainforests and remaining African savannas and jungles.

To some, Gates and his technology will save the world from hunger and global warming in much the way the chemical “green revolution” did with monocrops and sprays in the 1970s. To others, Gates is just creating another type of too big, badly scaled, overly processed and unhealthy food. Critics like Wallace suggest that global agriculture should be forced to pay its real costs including sewage, insect and air pollution. Operations creating weak, sick animals should be regularly tested for the creation of new pathogens and taxed for the cost of those diseases. Authorities already track new strains of the likes of salmonella, and tie them directly to the source, which is usually an industrial hatchery.

In the journal Global Jurist, Federico Regaldo cites CAFOs for pandemics and epidemics they create. Who is Going to Pay for Causing Pandemics?

Throughout human history, animal diseases like smallpox, measles and bubonic plague have been among the worst humans faced. But in the last 50 years, the situation has dramatically worsened.

According to a July 2020 report from the United Nations, three out of four of all “new and emerging human infectious diseases” are zoonotic in origin, and a study in the journal Nature found that agriculture was associated with half of all the zoonotic pathogens that emerged in humans. In Wallace’s view, this increase is “concurrent” with the livestock revolution, the expansion and consolidation of the meat sector that began in the 1970s in the southeastern United States and then spread around the world. Wallace asks how profitable it is to create low-priced food that can kill a billion people. It’s a question we all need to face.

Bird Flu Outbreaks Reach Record 54 in Japan This Season [Nippon.com, 3 Jan 2023]

Tokyo, Jan. 3 (Jiji Press)--The number of outbreaks of highly pathogenic avian influenza in Japan this season has risen to 54, topping the existing record of 52, logged in the 2020-2021 season, it was learned Tuesday.

The total number of birds destroyed due to this season's outbreaks is expected to reach around 7.75 million.

On the day, the prefectural government of Fukuoka in southwestern Japan announced that a bird flu outbreak had occurred at an emu farm in the city of Koga.

Highly pathogenic bird flu was also confirmed at an egg-laying hen farm in the city of Asahi, Chiba Prefecture, east of Tokyo, the same day.

The outbreaks were the 53rd and 54th in the country this season, with about 400 and 9,600 birds to be destroyed at Fukuoka and Chiba, respectively.

7.7 million birds culled in Japan as bird flu continues to spread [INQUIRER.net, 3 Jan 2023]

TOKYO ? Highly pathogenic avian influenza has been raging at poultry farms and facilities across Japan this season, with both the number of outbreaks and that of culled birds increasing at a record pace since late October.

Five prefectures that had never before experienced bird flu outbreaks at poultry farms have confirmed infections for the first time.

The central government has launched an emergency disinfection program nationwide.

However, local governments, which are responsible for culling massive numbers of chickens, have been calling for help, saying that the number of birds is more than they can cope with. Concern is also spreading among poultry farmers.

Limitations of Response
“The current situation [surrounding the culling of domestic poultry] has reached a stage at which local governments can no longer handle it on their own. I would like you to reconsider the approach so far,” Ibaraki Gov. Kazuhiko Oigawa said Dec. 21 at the Agriculture, Forestry and Fisheries Ministry in Kasumigaseki, Tokyo.

Model-trader slay stirs Davao City
Ibaraki is the nation’s largest producer of hens’ eggs. On Nov. 4, an outbreak of bird flu occurred at a poultry farm in Kasumigaura in the prefecture. It took 19 days to kill 1.03 million egg-laying hens, bury and incinerate them, and disinfect the facilities.

Gov. Oigawa asked agricultural minister Tetsuro Nomura for certain requirements to be included in guidelines to be set forth by the central government for large-scale farms, conceived with poultry farms raising over 500,000 birds in mind. Specifically, secure enough workers in advance to cull their birds and prepare lime for disinfection and protective clothing at their own expense.

Nomura told a press conference after the Cabinet meeting on Dec. 27, “We must respond with a sense of urgency because the critical time is approaching.”

‘We can only pray’ The first cases of bird flu at poultry farms and facilities in Japan this season were confirmed in the prefectures of Okayama and Hokkaido on Oct. 28.

On Dec. 30, new outbreaks were detected in Saitama and Hiroshima prefectures, bringing the total number to 51 outbreaks in 22 prefectures as of the day. The outbreaks in Yamagata, Fukushima, Tottori, Nagasaki, and Okinawa were the first ever recorded in those prefectures.

As of the end of 2022, a total of 7.72 million birds had been culled nationwide. The current surge is likely to exceed the previous worst registered between November 2020 and March 2021, when a total of 52 outbreaks occurred in 18 prefectures and 9.87 million birds were culled.

In Aomori Prefecture, 1.39 million egg-laying hens that were being raised at a poultry farm in Misawa were killed over two weeks from Dec. 15, a record number at a single farm.

Ken Sasaki, chairman of the poultry association of Aomori Prefecture and the operator of a poultry farm in Hachinohe said, “We don’t know when or where an outbreak will occur. Ultimately, we can only pray.”

Earlier than usual
Avian influenza is spread by migratory birds that fly southward from their nesting grounds in Siberia, Russia. Wild birds and small animals become infected with the virus, and then bring it into poultry farms and elsewhere.

Outbreak season in Japan is therefore from late fall to spring. In Europe, however, outbreaks continued this summer, though not in large numbers, and there is no “off-season” anymore. In France, as many as 1,487 bird flu outbreaks were recorded at poultry farms in the slightly more than a year from October 2021.

“This season, infected wild birds were found in late September, the earliest time of year on record in Japan. Migratory birds have spread the virus to various regions much earlier than usual,” said Hiroki Takakuwa, a professor of veterinary microbiology at Kyoto Sangyo University.

In late December, the agricultural ministry began emergency disinfection at poultry farms nationwide, including those in prefectures that had not reported infections thus far. The ministry provides poultry farmers with lime for disinfection free of charge, encouraging them to spray it themselves.

Impact on egg prices
According to JA Zen-Noh Tamago (Eggs) based in Tokyo, the wholesale price of hens’ eggs has been hovering above normal since the spring of 2022, apparently affected by the soaring prices of compound feed due to Russia’s invasion of Ukraine.

The average price of medium-size eggs for December was \284 per kilogram in the Tokyo area, the highest monthly average since wholesale prices were first released in 1993. In addition to demand reaching its peak during the Christmas and New Year holiday seasons, “the bird flu has undoubtedly pushed up prices,” an industry official said.

Price increases are expected to level off later this month, when demand is expected to calm down, but the agricultural ministry official said, “We need to carefully watch the trends, based partly on the infection situation.”

‘The equivalent to our Covid pandemic’: bird flu hasn’t gone away and is still spreading [The Guardian, 24 Dec 2022]

By Phoebe Weston

It is more than a year since avian flu began to devastate wild birds in large numbers, and conservationists are fearful of what 2023 will hold. The highly infectious variant of H5N1 has caused Europe’s worst bird flu season and has spread across the globe with little sign of slowing.

In the UK, there were reports of some great skua dying from the H5N1 variant in the summer of 2021 but the mass die-offs started in the autumn and winter. More than a third of Svalbard barnacle geese in the Solway Firth, on the border of England and Scotland, ? 16,500 out of 43,000 ? died last winter.

A year later, there has been no letup, with Greenland barnacle geese on the Scottish island of Islay (the other main site where these geese overwinter) dropping dead in increasingly large numbers. “I’m sitting with a sense of dread that it definitely will get worse as I see more reports coming in from reserves across the UK,” says Claire Smith from RSPB Scotland. “I’m haunted by the numbers of dead great skua that I saw on Shetland in the summer and I’m avoiding going birdwatching on the coast.”

From April to mid-August 2022 avian flu ravaged colonies of seabirds in the UK, peaking in June at the height of the breeding season. These birds had previously been affected by H5N1 at very low levels. Seabirds generally migrate over summer, so numbers dropped again, but already there are outbreaks across the country among wintering waterbirds (which typically gather in large flocks, making them more vulnerable at this time of year). There have been cases in the south-west, the Midlands, East Anglia, Wales and the Isle of Man, each with numbers in the tens or low hundreds of dead water birds, with greylag geese, pink-footed geese, Canada geese and mute swans among the most affected.

Red-listed herring gulls across the north-east are already being impacted, with dead puffins washing up in Norfolk, which is unusual at this time of year when there is no stormy weather. They are yet to be tested, but the presumed cause of death is bird flu.

Cases in other groups of birds have been reported all over the country, and the RSPB called for a temporary ban on the release of game birds this year, to lessen the risk of spreading avian flu, but this was not taken up by government. Positive tests in peregrine falcons, buzzards, wild tawny owls and rooks have been recorded in recent months. Although there are not the same big die-offs, there are a lot of cases over a wide area, with more in urban and semi-urban areas. Positive tests are not an indication of the actual number of birds affected because few carcasses are found, let alone tested.

“We can expect HPAI [highly pathogenic avian influenza] to persist into the next breeding season and beyond, with unpredictable consequences,” a report from the International Seabird Group conference warned in November.

This will be the equivalent to our Covid pandemic, because we’re dealing with major outbreaks, major fatalities …
Prof Kin-Chow Chang, University of Nottingham

It is a case of waiting to see what happens next, says Prof Ian Brown, head of virology at the government’s Animal and Plant Health Agency (APHA). Commercial hens can be shut up, but you cannot control the movement of wild birds.

“That horse has bolted,” he says. “It is unusual that this particular event is dominated by one particular strain over such a big geographical area. I can’t remember any time since 1996 [when H5N1 started], where a single strain has caused so much global spread.”

Bird flu is highly infectious, with scientists saying one bird can infect as many as 100, with the virus present in faeces, mucus, blood and saliva. “You need a very tiny quantity ? a teaspoon of faeces will probably be enough to kill an entire house of chickens or turkeys,” says Brown.

The most common transmission between wild birds and poultry is probably indirectly, through birds in the nearby environment. Unpublished studies have shown that at 4C, the virus can stay in the environment for six weeks, according to Brown. It could be someone walking across a field and treading in infected bird droppings, and then failing to disinfect their boots before going into the poultry house. Or it could be transferred on bedding, or possibly via rodents.

Brown says that more than 99% of cases in poultry in the UK have come from wild birds. Apha knows this by working out the genome of a virus and comparing what it looks like in wild birds with its appearance in poultry. The researchers also look at the affected farm and possible routes of infection into poultry houses.

Prof Kin-Chow Chang, from the veterinary school at the University of Nottingham, agrees commercial populations are getting it either directly or indirectly from wild birds. “The virus is very infectious, it doesn’t need a lot to start an infection,” he says

Little is known about the number of birds with antibodies. Because vaccinations for wild birds are not considered a feasible option, they will need to get some sort of herd immunity. Brown says: “There is a very small proportion of birds that can get infected, can recover from infection and then have immunity which means they won’t get that virus again. And over time that would build, but we don’t understand that at all. We need to do further work. That research is being commissioned and happening across the world.”

The present variant of H5N1 originated in south-east Asia, where it was found in commercial geese. For the past four years, these strains of avian flu have been highly pathogenic, meaning they cause severe disease and death. Scientists at the University of Edinburgh are trying to work out why the current strain is causing longer and larger outbreaks than those that came before, which will also help understand how the disease will evolve and spread in the future.

It could be down to changes in the surface proteins on the virus, meaning they can more easily attach to wild birds, or it may be more stable in the environment, so the virus could live in a pond over summer rather than breaking down in warm temperatures and sunlight as have previous bird flu viruses. It may become less damaging when sufficient numbers of birds have been infected, or the virus could evolve again, making it easier to spill into other species ? including mammals and humans.

In August 2022, Defra said that mitigation strategies “are not very effective in reducing transmission within seabird colonies”. However, there are other ways to reduce the pressures seabirds are under, as they have already been hit by a range of threats including habitat loss, overfishing and the climate crisis. Since 1986, the UK’s population of breeding seabirds has fallen by almost a quarter. Reducing these other pressures would make them more resilient to bird flu, says Smith.

The RSPB says it is generally not picking up dead birds on its reserves because it risks the health of the people doing it, and causes disturbance among living birds which could spread the disease further. Visitors are asked to keep dogs on leads and to clean their shoes thoroughly before and after visiting. However, other wildlife groups, such as those working for the National Trust, have decided to collect carcasses because it could result in the disease spreading further if they are scavenged by others. Conservationists are calling for better monitoring and surveillance of the disease in wild birds, as well as clearer arrangements for carcass collection.

Chang says: “This will be the equivalent to our Covid pandemic, because we’re dealing with major outbreaks, major fatalities, and possibly major disruption to the domestic poultry production market as well.”

Bird flu strikes five more farms [台北時報, 24 Dec 2022]

By Yang Yuan-ting and Jonathan Chin / Staff reporter, with staff writer

VIRAL SPREAD: The latest outbreak has so far affected 39 farms, including 25 chicken farms, 10 duck farms and four goose farms, the Council of Agriculture said

The H5N1 avian influenza virus has been found in five more poultry farms, extending an outbreak that marks the first time the strain has made the leap from waterfowl to farmed landfowl in Taiwan, the Council of Agriculture (COA) said yesterday.

The infection clusters were found in one duck and three free-range chicken farms in Erlin Township (二林), and one goose farm in Pusin Township (埔心), all in Changhua County, COA Deputy Minister Huang Chin-cheng (?金城) said.

The rise in cases shows that avian flu is spreading in Taiwan, although outbreaks have been contained, he said.

Authorities have ruled out the possibility that the latest H5N1 cases were transmitted from a previous cluster in Yilan County, and wild waterfowl remains the most likely vector, Huang said.

The vector for the outbreak in chicken farms was either virus-bearing wild birds that entered the farms through gaps in coop netting or poultry workers who were exposed to the pathogen, he said.

The chicken-raising Erlin and Jhutang (竹塘) townships in Changhua County were flagged as hot zones for increased monitoring and sterilization, he added.

The H5N1 pandemic has impacted the farming of chicken and eggs in the US, Europe and Japan. Last month, Taiwan reported the year’s first cluster of the disease at a duck farm in Yilan County.

The latest outbreak brings the total number of farms affected in Taiwan to 39 ? 25 chicken farms, 10 duck farms and four goose farms.

The outbreaks are not expected to impact the supply of chicken meat during the Lunar New Year, as the virus has not spread to broilers and reserves in cold storage are enough to meet demand, Huang said.

Changhua and Yunlin counties have high concentrations of poultry farms, and the emergence of clusters there is concerning, but other affected regions are safe as there have been no reported cases in the two weeks since the initial outbreak, he said.

Farm operators should streamline work processes to reduce the frequency of round-ups, secure their facilities and ensure compliance with sanitation guidelines, he said.

Additional reporting by CNA

Investigation into the risk to human health of avian influenza (influenza A H5N1) in England: technical briefing 1 [CIDRAP, 21 Dec 2022]

The UK Health Security Agency (UKHSA) is working with the Animal and Plant Health Agency (APHA) and the Department for Environment, Food and Rural Affairs (Defra) to investigate the risk to human health of avian influenza (influenza A H5N1) in England. This briefing is produced to share data useful to other public health investigators and academic partners undertaking related work. It includes early evidence and preliminary analyses which may be subject to change.

Data reported in the technical briefing is as of 13 December 2022 (or as specified in the text) to allow time for analysis.

Levels of human health risk related to the outbreak of avian influenza in England
These risk levels were developed by the Technical Group to help to establish triggers for enhancing assessment and response. The avian influenza outbreak can be considered to fall into one of 6 potential levels of transmission.

Level 0 (Baseline)
Avian influenza circulating in birds within normal bounds of prevalence and with normal epidemiological dynamics.
Level 1
Avian influenza circulating in birds with altered epidemiological dynamics and/or increased prevalence.
Level 2
Level 1 plus detection of spillover into mammals.
Level 3
Evidence of viral genomic changes that provide an advantage for mammalian infection.
Level 4
Sustained transmission in non-human mammalian species or any human detection and mutations in haemagglutinin (HA) which allow transmission. (A single human detection in a person exposed to infected birds, without HA mutations, does not raise the risk level to 4.)
Level 5

Any human-to-human transmission.
The UK risk is currently assessed as at level 3.

Main data points
Since 1 October 2022, the start of the current reporting year for avian influenza, APHAhas notified UKHSA that highly pathogenic avian influenza (HPAI) A(H5N1) has been confirmed in avian species at 130 premises in England. Wild bird testing is undertaken on a geographically representative sample of birds, with 447 influenza A (H5N1) detections at 280 locations in England reported since 1 October 2022. Since the introduction of the poultry housing order on 7 November 2022, numbers of infected premises are decreasing but detections in wild birds continue to suggest high levels of circulating virus in the UK.

From 1 October 2022 to 15 December 2022, health protection systems have recorded 2,085 human exposure episodes (where a person was directly exposed to an infected bird). There is likely to be substantial under ascertainment.

Detailed data on incidents (health protection responses to avian influenza detections) is incomplete. Based on the 29% of incidents for which there is data (1 October 2022 to 13 December 2022), personal protective equipment (PPE) was used in 27.3% of exposures, and antiviral prophylaxis in 15.9% of exposures. Symptoms were reported following 31 (4.3%) exposures, with 24 symptomatic swabs being carried out (77.4% of those eligible). There have been no detections of avian influenza viruses in humans the UK during the current reporting year (from 1 October 2022 to date) and there was one human detection in the UK in the preceding reporting year (1 October 2021 to 30 September 2022).

APHA report that 20 mammals have been retrospectively tested, of which 8 were influenza A (H5N1) positive. Four of these have genome sequences available and all show the presence of a mutation which is associated with potential advantages for mammalian infection. This is very limited data but, together with international data, is suggestive of sporadic mammalian spillover events.

Some clinical and regional public health laboratories undertake influenza subtyping and refer influenza A which is unsubtypable by standard clinical assays to UKHSA for characterisation.

From 1 January 2022 to 8 December 2022, 44 samples were referred to UKHSA as unsubtypable and of these 18 were seasonal H1 or H3 viruses, 11 had no virus detected, 6 had a low viral load precluding further characterisation, and 9 are still being characterised. Assessment of the sensitivity and completeness of this system for the detection of novel influenza viruses is being undertaken.

Part 1. Risk assessment as of 13 December 2022
This assessment is based on reports made from APHA and other partners to UKHSA. Data sharing is being established but UKHSA has not viewed the current data in full.

UK virus population
There is an increase in confirmed cases of influenza A infected birds (high confidence). In 2022, there has been year-round maintenance of influenza infection in indigenous wild birds which represents a change compared to the usual seasonal pattern in which infections die out over the summer. Compared to the previous risk assessment of 11 November 2022, there are a reducing number of infected premises following the introduction of the national housing order for farmed poultry, but still high levels of detections in dead wild birds.

Influenza A H5N1 is the predominant influenza virus subtype detected in wild birds and farmed flocks in the UK (high confidence). There is diversity within the UK population of H5N1 viruses with 11 genotypes detected since October 2021, including some reassortment with low pathogenic avian influenza viruses (LPAIVs). However, 7 of these genotypes have constituted a limited number of detections. The dominant circulating genotypes since October 2021 are AIV09 and AIV07-B2. Since October 2022, AIV09 is the predominant genotype. Another currently detected genotype in poultry is AIV48 which includes genes from gull-associated influenza viruses.

Genomic surveillance is proportionate for poultry outbreaks (a genome is generated for every affected premise). There is a limited genomic surveillance sampling in wild birds. APHA select birds to test and report that testing is distributed in time and space with host species consideration. There is very limited surveillance of mammals. Genomic data lags 7 to 10 days behind date of sample collection for poultry and currently longer for mammals.

Extent of human exposure in the UK
Owing to the disease burden in birds there is an increased interface between humans and infected birds (high confidence). In particular the high number of wild birds and domestic flocks with influenza A infection, especially where personal protective equipment is not worn, increases the likelihood of human exposures to this virus (moderate confidence).

Propensity to cause mammalian and human infection
Available surveillance data reported by APHA do not suggest widespread mammalian adaptation of this virus (low to moderate confidence).

Mutations known to be advantageous in mammalian infections are infrequent in the available genomic data from avian viruses however these data are lagging. APHA report that there is evidence of direct spill over from birds into some ‘scavenger’ wild mammalian species within the UK (and others noted outside the UK). In the UK 8 mammals, out of a total of 20 targeted from samples collected during 2021 to 2022 and retrospectively tested by APHA, were positive for influenza A (H5N1).

The species affected (foxes and otters) are presumed to have direct high-level exposure to infected birds based on feeding behaviour and food preferences. The 4 available influenza genomes from these positive mammals all show the PB2 E627K substitution. This mutation is known to be acquired rapidly after infection of a mammalian host in some influenza viruses and is associated with enhanced polymerase activity.

The rapid and consistent acquisition of the PB2 mutation in mammals may imply this virus has a propensity to cause zoonotic infections and further assessment should be made of the properties of this mutation. There is also recent confirmed transmission of a virus similar to the AIV48 genotype between mink in Spain, but the published genomes available show no evidence of significant HA mutation.

There is incomplete genotype to phenotype understanding and genomic data must be supplemented by in vitro and animal model studies.

There have been 4 instances of influenza A H5N1 2.3.4.4b detection in humans (1 UK, 1 USA, 2 Spain) between December 2021 and December 2022. There is limited asymptomatic testing of human contacts of bird cases in the UK and international surveillance is variable.

Nevertheless, by comparison with other zoonotic infections including influenza viruses, these data suggest that zoonotic infections are infrequent (low confidence).

Ability to cause (a) severe infection and (b) asymptomatic infection in humans There are no detected severe human cases associated with Influenza A H5N1 (clade 2.3.4.4b) in the UK or internationally. There is insufficient information to judge the risk of asymptomatic or mild disease due to limited testing in human contacts of infected birds.

Human-to-human transmission There is no evidence of sustained human to human transmission (moderate to high confidence). Subtyping surveillance in the NHS or through NHS referral to UKHSA is incomplete and could delay detection. There is insufficient information to assess the occurrence of limited human to human transmission such as transmission within households.

The current H5N1 2.3.4.4b viruses in UK birds react well against antisera raised against an available Influenza A(H5) World Health Organization (WHO) candidate vaccine virus (CVV) (A/Astrakhan/3212/2020), developed for pandemic preparedness and coordinated by WHO.

Assessment
The avian influenza outbreak in the UK is assessed as at risk level 3 although there is limited mammalian surveillance data. At present, there are no indicators of increasing risk to human health, however this is a low confidence assessment. The risk assessment is dynamic and requires regular review during this period of unusually high levels of transmission in birds with mammalian spillover. In vitro and animal model data are required. Enhancements to mammalian and human asymptomatic infection surveillance are both in preparation.

Part 2. Epidemiology update

2.1 Current epidemiological situation
There have been unprecedented levels of avian influenza circulating in England over 2021 and 2022. The dominant subtype currently circulating in avian species across England is highly pathogenic avian influenza (HPAI) A(H5N1).

Since 1 October 2022, the start of the current 2022 to 2023 seasonal period, detections of avian influenza have been confirmed in both wild birds and infected premises which can include domestic flocks and poultry farms. APHA undertake diagnostic testing in any flocks where notifiable avian disease cannot be excluded by official veterinarians. The APHA also undertake passive surveillance of wild bird populations from the notification of mortality events by members of the public reported through a Defra helpline. Testing of avian influenza in wild birds is subject to dynamic surveillance policies and thresholds for collection based on resource implications and the current situation regarding infection trends across the UK.

Since the start of the 2022 to 2023 season, the APHA has notified UKHSA that HPAIA(H5N1) has been confirmed in avian species at 130 premises in England. Animal health surveillance has also detected A(H5N1) in 447 wild birds from 280 locations in England. One detection of A(H6N2) avian influenza was confirmed at an infected premises in the North West of England.
Detections of avian influenza at infected premises have continued through the reporting period and have fluctuated during this time (Figure 1). A national housing order for poultry was introduced on 7 November 2022. Wild bird detections have continued to demonstrate that the background risk from avian influenza in wild birds remains very high (Figure 1).

Detections of avian influenza have been concentrated in the East of England and the East Midlands, driven in particular by high numbers of infected premises in these areas (Figures 1 and 2). However, detections in wild birds have been more widespread across the country (Figure 1).
Figure 1. Confirmed detections of avian influenza in poultry and wild birds by setting in England from 1 October 2022 to 13 December 2022. Data provided by APHA

The data used in this graph can be found in the accompanying spreadsheet.

Figure 2. Choropleth map of avian influenza incidents detected in poultry and wild birds across England by upper tier local authority (UTLA), from 1 October 2022 to 13 December 2022

This map contains National Statistics data Crown copyright and database right 2022.
Data source: Animal and Plant Health Agency 2022.

Supplementary data is not available for this figure.

The APHA has undertaken retrospective testing of stored mammalian samples that were found either linked to infected premises or as having unusual clinical behaviours (for example, neurological signs), raising suspicion of infection with avian influenza. This has led to the identification of A(H5N1) infection in 8 out of 20 mammals collected since December 2021. Of these, 4 were from England and were detected in foxes, and 4 detections in Scotland, all of which were in otters.

2.2 Summary of exposed persons
The increase in detections of avian influenza has led to human exposures relating to farmed and wild birds, which are managed by UKHSA health protection teams (HPTs). Workers on farms can usually be easily identified, but the extent of human exposures to infected wild birds is more difficult to determine and there is likely to be substantial under ascertainment.

Public health guidance advises the use of personal protective equipment and antiviral prophylaxis for individuals at risk of exposure to avian influenza. Post-exposure, individuals are offered antiviral prophylaxis with a follow-up or health monitoring period of up to 10 days.

Symptomatic individuals are referred for swabbing to detect possible infection. There is also an option for asymptomatic swabbing for those eligible (individuals who did not wear PPE at the time of exposure but who remain symptom free during the follow-up period) as part of a surveillance pilot. However, the uptake from individuals for this pilot continues to be extremely low.

Details of exposed individuals are recorded on the HPZone case management system at UKHSA. HPZone was interrogated from 1 October 2022 to 15 December 2022. Data was selected for analysis where the infectious agent was ‘avian influenza’.

Over the reporting period, 2,085 exposure episodes were entered into the HPZone system. Exposed individuals were mainly identified as male (71.5%). Females accounted for 19.5% and gender was unknown for 9% of exposure episodes. Distribution of gender was similar across all age ranges (Figure 3). Age was unknown for 33.1% of exposure episodes entered into HPZone.

Figure 3. Age-sex distribution of exposure episodes captured in HPZone from 1 October 2022 to 15 December 2022

The data used in this graph can be found in the accompanying spreadsheet.

Following the epidemiology of avian influenza detections, the distribution of exposed individuals is concentrated in the East of England and the East Midlands (Figure 4).

Figure 4. Exposures reported on HPZone from 1 October 2022 to 15 December 2022

The data used in this graph can be found in the accompanying spreadsheet.

Information is also collected by HPTs using surveillance forms for each situation to document PPE use, antiviral use, symptom status, and any swabbing. These forms are returned to the national epidemiology team and linked to laboratory records held by UKHSA on respiratory testing.

Between 1 October 2022 and 13 December 2022, information was returned for 119 (29%) out of 411 incidents this season and recorded 716 exposure events. Individuals may be recorded in more than one event if they are exposed multiple times (exposure episodes are differentiated by time and location).

Data for other incidents is unavailable at present, however, in regions with high avian influenza activity, HPTs prioritise public health action over data collection and reporting.

The majority of surveillance forms received from HPTs relate to wild bird incidents (90 out of 119 forms returned) comprising 75.6% of data. Wild bird incidents often involve fewer exposed individuals.

Analysis of the available data indicates that PPE use was reported in 268 (37.4%) exposures.

Antiviral prophylaxis was reported for 114 (15.9%) exposures. Symptoms were reported following 31 (4.3%) exposures, with 24 symptomatic swabs being carried out (77.4% of those eligible). Thirteen asymptomatic swabs were performed and reported as part of an enhanced surveillance pilot from consenting individuals.

Data should be interpreted with caution due to the incomplete nature of information collected from exposed individuals. Data receipt is expected to lag to allow for adequate follow-up time of exposed persons to elapse.

There were no human detections of influenza H5 in England during the 2022 to 2023 season.
In December 2021, one human case of A(H5N1) was confirmed in England in an exposed person who remained asymptomatic throughout. However, this detection was in the context of close and prolonged exposure to infected poultry and contaminated material, without PPE. (Oliver and colleagues 2022)

In addition to the human case reported from England, 3 human cases of A(H5N1) of the same clade (A(H5N1) 2.3.4.4.b) were reported internationally by the WHO between December 2021 and December 2022. This includes one case from the USA and 2 cases from Spain. All 3 cases were involved in poultry decontamination and culling activities. The case from USA reported mild fatigue, and the 2 cases from Spain were asymptomatic. No human-to-human transmission has been reported.

UKHSA continues to carry out horizon scanning for epidemiological reports relevant to emerging influenza in humans and animals.

2.3 Capability to detect human cases of H5N1
Weekly national flu and COVID-19 reports are published by UKHSA. These include a detailed breakdown of influenza virus characterisation.

UKHSA receives influenza positive clinical samples referred from NHS and regional public health laboratories (PHLs) for whole genome sequencing, virus isolation and antigenic characterisation, year-round. This provides a picture of circulating influenza viruses in the community and in hospital settings. This system is designed to understand which viruses are causing seasonal influenza and is not calibrated to detect small numbers of novel influenza cases.

UKHSA request that samples detected as influenza A positive in NHS or UKHSA PHLswhich are not assigned a subtype through routine assays are forwarded to the UKHSARespiratory Virus Unit (RVU). The UKHSA RVU performs subtyping by polymerase chain reaction (PCR) and genome sequencing. The sensitivity of this system for detecting emerging viruses is currently under assessment.

Figure 5 shows the results for unsubtypable samples referred in 2022 up to 8 December 2022. As of 8 December 2022, 1.3% of samples (n=44) referred to UKHSAColindale from NHS or UKHSA PHLs in 2022 were influenza A unsubtypable. Of these, 41% (n=18) were characterised as seasonal H1 or H3 viruses, with 25% (n=11) having no virus detected and 14% (n=6) as having detectable but insufficient viral load to achieve a subtyping result.

Characterisation is ongoing for 9 samples.

Figure 5. Influenza A unsubtypable samples referred in 2022 up to 8 December 2022

The data used in this graph can be found in the accompanying spreadsheet.

Part 3. Genomic surveillance
The current genomic analysis is performed by APHA. UKHSA has requested full data access to undertake human health risk assessment in parallel.

APHA has published a pre-print describing the diversity of H5 avian influenza genomes in the UK between 2020 and 2022. The paper describes the genomic diversity sequences between October 2020 and May 2022, as well as the prevalence of some characterised mammalian adaptation mutations. Between October 2020 and October 2021, there were a range of H5Nx infections detected, with all highly pathogenic avian influenza virus (HPAIV) haemagglutinin (HA) sequences belonging to clade 2.3.4.4b. However, when typed by the HA segment, the majority of sequences between October 2021 and May 2022 were H5N1 (195 out of 196 sequences). One avian sequence in this dataset contained the mutation E627K in the polymerase (PB2) protein, which may confer advantages for mammalian infection.

From October 2021 to May 2022, no further avian sequences were found to contain the E627K substitution. In total across the whole period of genomic surveillance of the current influenza A (H5N1) outbreak, APHA report that they have assed 457 influenza genomes from birds for this mutation and detected it only once.

However, APHA have reported that all 4 H5N1 sequences obtained from mammals (foxes and otters) did possess this substitution.

Part 4. Planned rapid laboratory assessments and early data
4.1 Candidate vaccine viruses assessment
The development of influenza candidate vaccine viruses (CVVs), coordinated by WHO, remains an essential component of the overall global strategy for influenza pandemic preparedness.

This assessment was undertaken by the Worldwide Influenza Centre at the Francis Crick Institute as part of the existing UK commitment to supply data to the WHO global influenza programme and is based on haemagglutination inhibition assay data generated by UK and international laboratories in support of the programme.

The virus detected in the UK lies within the H5 clade 2.3.4.4b which is now widespread across Africa, Asia, Europe and North America. However, there is diversity within this clade and viruses from some countries, including in Eastern Europe, West Africa, Cambodia and Vietnam, are less well recognised by antiserum raised against the A/Astrakhan/3212/2020 2.3.4.4b CVV. As a result of this antigenic drift in some geographic areas, a recommendation was made in September to add a second 2.3.4.4b CVV recommendation (A/chicken/Ghana/AVL-76321VIR7050-39/2021-like). Recent antigenic analyses of H5 clade 2.3.4.4b viruses isolated from birds in the UK have all been genetically and antigenically similar to the original A/Astrakhan/3212/2020 CVV.

Although the recommended CVV is a good antigenic match for currently circulating viruses in the UK, partners within this expert technical group will continue to characterise emerging strains, both genetically and antigenically, within poultry and those that might be detected within humans.

4.2 Antivirals assessment
Three influenza specific treatments are approved by the Medicines and Healthcare products Regulatory Agency (MHRA) in the UK. Two neuraminidase inhibitors (NAIs), oseltamivir and zanamivir, are already deployed, and one cap-dependent endonuclease inhibitor (baloxavir marboxil) is not yet marketed in the UK. Evidence suggests that all 3 drugs have activity against influenza A(H5N1).

UKHSA undertakes routine genomic surveillance for antiviral resistance in seasonal influenza viruses, using established databases of mutations associated with reduced drug susceptibility or reduced inhibition by NAIs including among avian influenza viruses, and will extend this to avian viruses routinely once data are made available.

Analysis performed by APHA on 316 full genome A(H5N1) HPAI virus sequences obtained from poultry and wild birds in the UK and Crown Dependencies from October 2021 to October 2022 did not identify any amino acid substitutions in NA associated with NAI reduced inhibition. A single viral sequence with an I38T amino acid substitution was identified. This substitution is known to reduce susceptibility to baloxavir in human seasonal A(H3N2) and A(H1N1)pdm09 viruses.

Phenotypic NAI susceptibility testing requires virus isolation and is performed as an enzyme inhibition assay at the Francis Crick Institute. Phenotypic testing for baloxavir susceptibility is being developed at the Crick Institute.

APHA, UKHSA and the WHO Collaborating Centre at the Francis Crick Institute will collaborate going forwards over avian influenza antiviral susceptibility surveillance.

Part 5. Further planned work
5.1 Preliminary knowledge gaps assessment
UKHSA is currently undertaking a research and evidence gaps analysis relating to the avian influenza outbreak in the UK with internal and external stakeholders. A group of experts were convened to discuss the emerging priority gaps for research, evaluation, and surveillance studies. Further workshops are planned to refine and prioritise these gaps and develop research questions. UKHSA will work with stakeholders, including academic partners and national research funders, to identify active research studies in these areas and develop and implement studies to address remaining gaps.

5.2 Surveillance
Mammalian surveillance
APHA are developing a surveillance pipeline for submission and testing of mammalian samples. Carcasses may be submitted where animals are:
?found dead in areas located near to defined infected premises, or
?are displaying clinical signs that may be considered indicative of potential infection with HPAIV

These surveillance activities are primarily driven through the Diseases of Wildlife Scheme.

Enhancement of asymptomatic surveillance in humans
UKHSA is developing protocols for intensive sampling of individuals working on sentinel infected premises. These can be used to establish human asymptomatic infection parameters at baseline and in response to changes in viral or epidemiological features of the outbreak.

5.3 Improvements to data and analysis
The following areas have been identified for improvements to surveillance, data and analytics:
1. UKHSA should receive full genomic sequencing data in real time from APHA and undertake continuous human health focused genomic risk assessment.

2. Current influenza surveillance systems, which are primarily tailored towards monitoring seasonal influenza, should be assessed for sensitivity and timeliness in detecting emerging influenza viruses.

3. A more detailed assessment is needed of the wild bird sampling framework and consideration should be given to:
?　reporting more detailed metrics including positivity rate, species and numbers of reported but untested birds
?　assessing whether more detailed sampling studies could improve understanding of the viral population and transmission in the UK

Sources and acknowledgments
Data sources
Data relating to animal health surveillance and investigations taking place across England obtained from the APHA. This includes data from wild bird surveillance, notifiable disease reports at infected premises and detections in mammals.
Surveillance forms are completed by UKHSA HPTs for each confirmed setting (includes both poultry and wild bird settings). This includes the follow-up of exposed persons and details of exposure. Data is enhanced with laboratory records for respiratory testing held by UKHSA.
Details of exposed individuals are also collected from HPZone, the UKHSA case management system.
International surveillance data of human cases of avian influenza is reported by the WHO under the International Health Regulations and routinely collated by UKHSA.

Authors of this report
Rachel Abbey, Carolina Arevalo, Ashley Banyard, Wendy Barclay, Ian Brown, Alexander Byrne, Fernando Capelastegui, Lorenzo Cattarino, Meera Chand, David Edwards, Eileen Gallagher, Irene Gonsalvez, Katja Hoschler, Susan Hopkins, Munir Iqbal, Joe James, Angie Lackenby, Nicola Lewis, Thomas Peacock, Richard Puleston, Jess Tarrant, Nick Watkins, Maria Zambon, Anissa Lakhani.

Contributors
? UKHSA Data Science and Geospatial team
? UKHSA Genomics Public Health Analysis
? UKHSA Respiratory Virus Unit
? UKHSA Research and Evaluation
? UKHSA Research Support and Governance Office
? UKHSA Rapid Investigation Team
? Animal and Plant Health Agency
? Imperial College London
? Francis Crick Institute
? The Pirbright Institute

Avian Influenza Technical Group
The Avian Influenza Technical Group includes members with expertise in clinical infectious diseases, clinical research, epidemiology, genomics and virology:
? Meera Chand (Chair), UKHSA
? Wendy Barclay, Imperial College London
? Alexander Byrne, APHA
? Ashley Banyard, APHA
? Ian Brown, APHA
? Neil Ferguson, Imperial College London
? Yper Hall, UKHSA
? Bassam Hallis, UKHSA
? Susan Hopkins, UKHSA
? Katja Hoschler, UKHSA
? Munir Iqbal, The Pirbright Institute
? Joe James, APHA
? Angie Lackenby, UKHSA
? Nicola Lewis, Francis Crick Institute
? Nicholas Loman, UKHSA and University of Birmingham
? Berit Mueller-Pebody, UKHSA
? Derren Ready, UKHSA
? Thomas Peacock, Imperial College London
? Richard Puleston, UKHSA
? Andrew Rambaut, University of Edinburgh
? Nick Watkins, UKHSA
? Maria Zambon, UKHSA
? Esther Robinson, UKHSA

Europe plagued by 'most devastating' bird flu outbreak ever, EU says [FRANCE 24 English, 21 Dec 2022]

Europe has been gripped by its "most devastating" ever outbreak of bird flu in the past year, European health authorities said on Tuesday as experts study the feasibility of vaccinations.

Between October 2021 and September 2022, around 2,500 outbreaks of bird flu were detected on farms in 37 European countries, the European Food Safety Authority, the European Centre for Disease Prevention and Control and the EU said.

In that time "some 50 million birds were slaughtered" on affected farms, the EFSA reported.
The toll did not include preventive culls of chickens, ducks and turkeys that were carried out alongside the outbreaks, the health agency told AFP.

The EFSA said that "for the first time" there had been no marked separation between two epidemic waves, as the virus was not brought under control in the summer.

This autumn, the epidemic was more virulent than last year at the same time, with the number of infected farms 35 percent higher.

Between September 2 and December 10, 2022, around 400 outbreaks were recorded on farms in 18 European countries. The virus has also been detected more than 600 times in wild birds, notably ducks and swans, which the report said may have contributed to the spread of the virus between farms.

Health authorities are studying the possibility of using vaccinations to arrest the spread of the virus.

The European Centre for Disease Prevention and Control said the risk of infection in humans was low, and "low to medium" for people working in contact with birds and poultry.