Are we at the edge of another pandemic? H5N1

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More evidence of Bird Flu evolving in California.

Bird Flu (H5N1) Explained: California Farms Quarantined After Detecting Virus Strain In Dairy Herds

Three dairies in central California detected the bird flu virus among its herds and have been quarantined, according to the California Department of Food and Agriculture.

I came across another encrypted story. So I guess I will unwrap it and see if it has anything interesting to say.

As bird flu virus mutates and jumps to humans, the potential grows for another pandemic

A flu virus is identified by the two most important proteins on its surface called hemagglutinin and neuraminidase. The first has 18 varieties and the second has 11. They are designated respectively by H and N followed by a number for the variant.

As these viruses slightly mutate or “drift," they require annual updates of vaccines, but we still retain some passive immunity from previous exposures. Sometimes an entirely new flu virus enters the population for which we have little existing immunity. This is called a “shift” and has been responsible for all previous flu pandemics.

In 1996, a new bird flu called H5N1 was identified. It has killed millions of wild and domestic birds. Varieties have mutated as it has jumped from birds to cattle and finally to people. Person-to-person transmission is still rare, but if the virus further mutates to make this easy, there is the potential for a devastating pandemic.

The H1N1 flu pandemic of 1918 killed more than 50 million people over three years, or less than 3% of those infected. By comparison, of those infected with H5N1, more than half of them died.

H5N1 has a standard incubation period of about one to five days, but it could take as long as two weeks after exposure before symptoms appear. If, like COVID (caused by a different kind of virus called a corona virus), there was easy transmissibility during an asymptomatic period, a “community spread” might occur. This is where there is no clearly identifiable contact source for an individual’s infection. Without aggressive public health measures, the situation could quickly get out of hand.

H5N1 avian influenza virus found in multiple bird species in Antarctica

A team of virologists with the U.K.'s Animal and Plant Health Agency, working with colleagues from the British Antarctic Survey, the KEMH Pathology and Food, Water & Environmental Laboratory, and the Department of Agriculture, both in the Falkland Islands, has found that the global spread of the H5N1 avian influenza virus has made its way to multiple bird species in Antarctica.

In their paper published in Nature Communications, the group describes how they tested multiple birds for the virus in the region over the years 2022–23 and what they learned by doing so.

The H5N1 avian influenza virus, as its name suggests, infects mainly birds, though it has been found to infect a few mammals, including humans. It was first observed in 1959 and then again in 1997. Early outbreaks were stopped by mass killing of animals in the infected areas.

More recently, infections have become widespread, infecting birds, both wild and domestic, across the globe. Billions of birds have been killed, thus far, and there is no indication that the pandemic is slowing. In this new effort, the researchers have found that the virus has even made its way to birds living in Antarctica—one place on the planet that is generally safe from such outbreaks.

The researchers traveled to several sub-Antarctic and Antarctic sites and tested birds that were living there, finding infected birds in all the places they visited. They also noted that the virus was infecting multiple species, ranging from Antarctic terns, to South Georgia shags, to brown skuas. They also found the virus had infected several marine mammals, such as the southern elephant seal.

In conducting a genetic analysis of the viruses they found, the research team was able to determine that the virus had spread to the sub-Antarctic (likely via migratory birds) from South America, and from there to Antarctica.

Cambodia's recent H5N1 case involved novel reassortant

The World Health Organization (WHO) yesterday shared more details from Cambodia about its latest fatal H5N1 avian flu case, including that it involves the older 2.3.2.1c clade but noting that the virus that infected the girl is a novel reassortant that include internal genes from the newer 2.3.4.4b clade.

Investigators found that poultry died in the girl's Prey Vent province village and that her family was given some of them to eat and that the girl was exposed to the chicken while preparing food. Her symptoms began on August 11, and, when her condition worsened, she was hospitalized about a week later in Phnom Penh and treated with oseltamivir (Tamiflu). She died on August 20.

Sequencing of the patient's virus sample at the Pasteur Institute in Cambodia found that the hemagglutinin gene from the 2.3.2.1c clade that has been circulating in Cambodia and Southeast Asia since 2013. The internal genes, however, belonged to the newer 2.3.4.4b, which is circulating globally. "This novel reassortant influenza A(H5N1) virus has been detected in human cases reported in Cambodia since late 2023," the WHO said.

The country has reported an uptick in human H5N1 infections since 2023, reporting 6 cases last year and 10 this year, of which 2 were fatal.

Note this girl was treated with Oseltamivir (Tamiflu) which is the last line of defense. But if this treatment is not given early enough, the body will within about a day reach the point of no return and death is the result.

Forgotten epidemic: with over 280 million birds dead how is the avian flu outbreak evolving?

With at least 280 million birds dead since October 2021, the highly infectious H5N1 strain of avian flu has devastated poultry and caused the biggest sudden drop of the world’s wild bird population in decades. The millions of wild birds killed includes tens of thousands of endangered and endemic species – and tens of thousands of mammals have died too.

Today, new data, published in Nature Communications, documents the disease’s spread to the southernmost tip of the planet – the Antarctic region – where it has inflicted significant die-offs in elephant seals and fur seals. This outbreak has affected every continent except Oceania, and yet there has been little coverage of the impact on global biodiversity and farming systems – or of potential risks to human health.

“I’m not sure the public is aware of the significance of the avian influenza,” said lead author Prof Ashley Banyard, a virologist at the UK’s Animal and Plant Health Agency (APHA) lab in Weybridge, Surrey. “It’s not been front-page news.”

Dr Connor Bamford, an assistant professor in virology from Queen’s University Belfast, said there could be further surprises. “One major open space for the virus remains the human population.”

I came across an interesting study. Someone is looking at the connection between H5N1 Bird Flu and Rats.

Pathogens: Susceptibility of Synanthropic Rodents to H5N1 Subtype HPAI Viruses

While they haven't gotten the attention they deserve, rodents - which are often abundant around poultry and dairy farms - likely contribute to the spread of HPAI viruses (see 2016's The role of rodents in avian influenza outbreaks in poultry farms: a review).

Since early June we've seen nearly 100 rodents (house mouse, deer mice) added to the list, and they now comprise nearly 25% of all of the confirmed mammals on the list. We've also seen the recent addition of domestic cats (n=53), prairie voles (n=1), and desert cottontails (n=1) to that list.

And just last week, in Emer. Microbe & Inf.: HPAI Virus H5N1 clade 2.3.4.4b in Wild Rats in Egypt during 2023, we a surprisingly high percentage of wild rats testing positive for H5 antibodies in Egypt.

All of which brings us to a new study, published today in Pathogens, where researchers challenged several rodent species (house mice, brown rat, black rat) with two (older 2010, 2007) HPAI H5N1 viruses, and found they are both susceptible to the virus and could potentially play a role it its evolution and spread.

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In my humble opinion, this is an extremely important study. Rats are the mechanism by which H5N1 will spread to humans. They exist in very large numbers within all our cities. They are buried invisible living within and under our homes by the billions. They are the spreaders of the future H5N1 plague. They create an unseen epidemic in rats and insects such as mosquitoes pass this plague onto the human race.

Alarming development as Missouri patient becomes first American to catch H5N1 bird flu with no exposure to animals

After being hospitalized on August 22, the unnamed Missouri patient was tested for a battery of illnesses, and the Missouri Department of Health and Senior Services (MDHSS) reported that he had the H5N1 virus.

He told officials that he had not been exposed to animals, which means they are unsure where he got the virus from.

The patient had several 'underlying medical conditions' but recovered in the hospital and was discharged and sent home.

In general we are not testing people for H5N1 Bird Flu in the U.S. Very limited testing is being done and only to a small select few. So we are essentially operating in the BLIND.

Government agencies are struggling to monitor and respond to highly pathogenic avian influenza, which is echoing the early months of the COVID pandemic.

It’s been about five months since the Texas Department of State Health Services announced that a worker on a dairy farm had tested positive for the highly pathogenic avian influenza A (H5N1) virus after being exposed to apparently infected cattle. Since then, the U.S. public health response has been slow and disjointed, bringing back memories of how the federal government responded during the early phase of the COVID-19 pandemic.

Despite having a pandemic playbook in early 2020, the U.S. appeared flat-footed in its response to COVID-19, including inadequate testing and unavailable personal protective equipment. And throughout the pandemic, mixed messaging on masks and later vaccines set back public health efforts.

As H5N1 circulates, it seems that lessons from COVID-19 remain unlearned. It appears that missteps are being made regarding testing, surveillance, transparency, and failure of communication and coordination throughout the health care system, the same kinds of things that hurt the response to COVID-19.

Bird Flu Map Update as US Cases Rise to 14

‘It’s just a matter of when’: Australia war-gaming deadly bird flu outbreak

The spring migration of birds from Antarctica to Australia could soon bring a deadly virus that wipes out entire species of native birds and marine mammals, which is why the Commonwealth is war-gaming its biosecurity response to potential wildlife carnage.

Scientists say it is inevitable the virus will come to Australia – the only continent free of the particularly virulent h5N1 strain of bird flu that has killed millions of birds around the world and tens of thousands of at-risk mammals.

Biosecurity agencies, environmental authorities and industry groups will leap into action at news of a simulated virus outbreak, enacting plans to slow the spread of the virus and shield at risk animals like black swans and sea lions.

Dubbed Exercise Volare, the fictitious scenario starts with an outbreak among the multitudes of birds in the Coorong wetlands near the mouth of the Murray River in South Australia, which then spreads to the sea lions on Kangaroo Island.

Australia’s black swans are particularly susceptible to the virus and studies show they could be made extinct in an outbreak. Officials have also warned it could wipe out the 12,000 Australian sea lions left on the planet.

When the virus hit South America, it claimed 30,000 sea lions and 18,000 southern elephant seal pups, while half of Peru’s pelicans were dead within a few months of its arrival.

“We are very concerned about the impact this disease could have on our native wildlife, vulnerable threatened species and broader environment and on our agricultural systems, including on production and trade,” says Agriculture Minister Julie Collins.

University of Melbourne senior research fellow at the Centre for Pathogen Genomics Michelle Wille told this masthead in July that the virus had made it to every continent including Antarctica, and it will inevitably arrive here.

This is a unique idea, turn the threat of H5N1 into a video war game.
Here is another article that describes the Australian Approach.

Far south coast of NSW preparing for potential bird flu outbreak in wildlife

The NSW Government is taking action to prepare for a potential wildlife emergency if a dangerous strain of avian influenza reaches Australian shores this spring.

H5N1 is a highly contagious strain which is affecting bird species and some mammals overseas. It has seen mass deaths of wild birds and marine mammals as well as animals that prey or scavenge on birds.

Australia is the only continent that has not yet detected cases of H5N1 avian influenza. But migratory birds pose a risk of introducing it from the north and from Antarctica.

The NSW Government recognises the risk to wildlife, ecosystems, food security, the economy and potentially human health.

Several locations on the far south coast of NSW have been identified as high priority sites for risk assessment and response planning. Work is underway at Barunguba – Montague Island Nature Reserve, which is home to bird and seal colonies.

The island is considered a potential risk from an H5N1 incursion due to the large number of migratory birds arriving to breed over the coming months. Response strategies will also consider the risk to little penguins and fur seals.

If this strain of bird flu arrives in Australia, communities can assist with early detection by reporting what they see. Symptoms of avian influenza usually appear in several or all birds in a flock and include:

-- lack of coordination, arched head, paralysis, seizures, tremors

-- conjunctivitis, nasal secretions, laboured breathing

-- unusual sudden death.

I might add that these symptoms also apply to humans.

I consider West Nile Virus to be like a twin disease to H5N1. So tracking WNV in the U.S. is worth doing. The following link provides the latest information on WNV in the U.S.

As of 3 September 2024 there has been 377 cases of West Nile Disease in the U.S. This outbreak is detected in 38 of our states. The outbreak produced 255 cases of West Nile virus neuroinvasive disease.

West Nile Virus

Europe has also reported cases. Since the beginning of 2024, and as of 5 September 2024, 15 countries in Europe reported human cases of West Nile virus infection: Albania, Austria, Bulgaria, Croatia, France, Germany, Greece, Hungary, Italy, Kosovo*, North Macedonia, Romania, Serbia, Spain and Türkiye. Slovenia reported human cases of West Nile Virus infection through EpiPulse in Mura and Drava statistical regions.

Surveilance of West Nile virus infections in humans, weekly report - Week 36, 2024

WOAH reports new cases of H5N1 HPAI in Denmark, Nigeria

The World Organisation for Animal Health (WOAH) has reported new cases of highly pathogenic avian influenza (HPAI) in poultry in Denmark and Nigeria.

The presence of HPAI was confirmed at a poultry holding in Vester Ulslev, Denmark. According to the WOAH report, on September 8, 2024, a clinical suspicion was reported to the Danish Veterinary and Food Administration. The affected poultry holding consists of approximately 3,500 ducks and 2,800 hens. On the premises, 200 of the susceptible 6,300 birds had died.

WOAH reported a new outbreak of HPAI in Ugbeyiyi, Nigeria. In late August, it was reported that an entire flock of 1,590 poultry birds had died. Samples from the flock were tested and found consistent with H5N1 HPAI. According to WOAH, a total of 2,410,875 birds in Nigeria have been lost as a result of H5N1 HPAI.

I came across an interesting article about wastewater tracking of H5N1. It contained some useful information.

Circulating H5N1 Bird Flu Spotted by Wastewater Monitoring During Summer

H5N1 influenza surfaced in wastewater samples across all 10 Texas cities monitored by the TexWEB team at the Texas Epidemic Public Health Institute in Houston.

From March 4 through July 15, the group detected H5N1 in 10 of 10 cities, at 22 of 23 sites, and in 100 of 399 samples, Anthony Maresso, PhD, of Baylor College of Medicine in Houston, and colleagues reported in a correspondence piece in the New England Journal of Medicine.

They said the detections have not correlated with influenza-related hospitalizations, nor has the group picked up mutations that would signal adaptation to humans, notably the E627K mutation in the virus' polymerase basic protein 2 (PB2) gene.

Instead, the data suggest multiple animal sources, as all of their sequences "best match H5N1 genomes from birds and mammals" and are from the 2.3.4.4b clade, the investigators wrote.

The article then goes on to report results from another study.

Another team from Verily Life Sciences, Emory University, and Stanford University reported earlier this year that it detected influenza A at 59 wastewater treatment plants in the U.S. this spring. Those researchers then searched for -- and found -- the H5 gene using PCR at three wastewater treatment plants with a positive flu A signal.

That team has since identified the H5 gene at 25 sites across nine states, according to the correspondence.

Three more California dairy herds infected with H5N1 bird flu

California officials have identified three new outbreaks of H5N1 bird flu in Central Valley dairy herds, bringing the total number of infected farms to six.

Nationwide, 201 herds have been affected across 14 states. Another infected herd was identified in Michigan earlier this week.

The article then goes on to discussing the possible transfer of H5N1 through drinking milk in California.

The risk of H5N1 remains low for the general population, and the state's milk supply and dairy foods are safe and "not impacted by these events," the statement said. Health officials say pasteurization inactivates the virus so there is no cause for concern for consumers of pasteurized milk or dairy products.

But some people do not drink pasteurized milk.

Steve Lyle, a spokesman for the state's agriculture department, said none of the affected farms are raw milk farms.

There are at least four raw milk dairies in California. Three are located in the Central Valley, the fourth in Grenada, north of Mt. Shasta.

Mark McAfee, the owner of Raw Milk Farms — which operates farms in Fresno and Hanford — said he tests his milk regularly and so far, his herds are negative for the virus.

WAR ON MOSQUITOES

The primary transmission agent for H5N1 in my humble opinion is transmitted to humans by mosquitoes and other insects. An infected human/animal/bird is bitten by a mosquito who carries the infection to another human and thereby spreads the infection. Therefore it makes sense that one way to limit the spread of the disease is by reducing and controlling the mosquito population. How is this done?

Most mosquitoes prefer to feed on animals other than humans and are rarely encountered. However, mosquitoes that do feed on humans can not only cause local skin irritation, but sometimes transmit disease. Scientists have found that only three or four species of mosquitoes are the main disease transmitters to humans or other animals. There are at least four viruses carried by mosquitoes: West Nile (WNV), St. Louis encephalitis (SLE), LaCrosse encephalitis (LAC), and Eastern equine encephalitis (EEE).

I am making the judgement call that H5N1 and from a historical perspective H1N1 (or the cause of the Spanish Flu) should also be added to this list.

From 1918 to 1919, the Spanish flu infected an estimated 500 million people globally. This amounted to about 33% of the world's population at the time. In addition, the Spanish flu killed about 50 million people. About 675,000 of the deaths were in the U.S.

There are basically two ways to prevent problems from mosquito bites. The first is to control or reduce mosquito populations as much as possible. If you reduce the number of mosquitoes, you reduce the chance of being bitten. Obviously, if you don't get bitten, then you can't get infected with a mosquito-borne disease. This can be done by physical means such as source reduction and trapping, or by chemical and biological means such as larviciding and adulticiding. The second prevention tool is to avoid being bitten by any remaining adult mosquitoes.

The best mosquito control program is an integrated one including point source reduction of breeding areas, routine larviciding (killing the baby mosquitoes) in those breeding areas that cannot be eliminated, and adulticiding (killing adult mosquitoes).

Mosquitoes have four life stages – eggs, larvae, pupae, adults. Since three of the stages (eggs, larvae, pupae) are found in water, eliminating water sources that can breed mosquitoes eliminates the chances of mosquitoes biting, and thus disease transmission. Source reduction includes the following:

-- Pick up and haul away all trash piles, broken down washing machines, junk cars, bottles and cans, and related items from around houses.
-- Avoid having open water areas or containers around the house such as puddles, open water tanks, damaged water pipes, tires, etc. that might breed mosquitoes.
-- Fill tree holes with mortar.
-- Drill holes in the bottom of tire swings.
-- Empty or change water in pet dishes, bird baths, horse troughs, etc. at least once a week.
-- Keep roof gutters clean.
-- Avoid accumulation of decaying material and garbage in and around the home.
-- Cover water tanks.
-- Support natural enemies of insects like birds, frogs, lizards, and fish.
-- Fix any low spots in the yard that hold water for long-term control.

Larviciding

Larviciding is one of the most commonly employed methods of mosquito control used today and is considered the best course of action after source reduction. When mosquitoes are in their immature stages, they are concentrated in a relatively small or fixed area (like a captive audience). The kill occurs before mosquitoes get out flying around, capable of causing biting nuisances and transmitting diseases to people, pets, and domestic animals. However, every place containing standing water need not be larvicided. It is best to larvicide only areas where standing water cannot be eliminated and in which larvae are actually found.

There are all kinds of larvicides, but some of the safest to people and the environment are methoprene products and a bacteria called "Bti". Bti (Bacillus thuringiensis israelensis) is a strain of bacteria that was isolated from a dead mosquito larvae found in Israel in 1977. Bti has since been developed into wettable powder, liquid, granular, capsule, and briquette formulations that are commercially available to mosquito control personnel. It is also available to homeowners at local garden stores as dunks (donut-looking objects) and bits (granules).

Mosquito dunks

The dunks (Mosquito Dunks®) are sustained-release products that float on water and release a long-term larvicide at the water's surface which must be eaten by the mosquito larvae. Under typical environmental conditions it will work for 30 days or longer. See the package directions to determine the appropriate number of dunks to use for amount of water you are treating. These dunks can be used in water sources such as bird baths, flower pots, tree holes, rain barrels and roof gutters, unused swimming pools, old automobile tires, and water gardens. The bits, sold as Mosquito Bits™, provide a fast kill (within 24 hours) versus the dunks that generally take longer to kill since they have a lower dose of Bti. However, the bits do not provide long-term control. Another option is to use the bits for a quick kill and then use a dunk for sustained control. The dunks and bits can be found in a combination pack called Mosquito Bits™ and Mosquito Dunks®. This pack contains 8 oz. of Mosquito Bits™ and two Mosquito Dunks®.

Methoprene

Methoprene is an insect growth regulator and is sold at pet stores or garden stores for larviciding as Zodiac® Preventative Mosquito Control. Zodiac® can be used in bird baths, old tires, flower pots, ornamental fountains, urns, rain barrels, roof gutters, abandoned swimming pools, tree holes, water gardens, pool covers, and other water holding receptacles. These granules also offer long-lasting control for up to 21 days. When used as directed, this product will not adversely affect humans, animals, fish, or vegetation.

It is very important when using pesticides of any kind that you read and follow all label directions. The label is the law. Following directions will ensure that you and the environment around you are protected and safe while using the product.

Advantages to both Bti and methoprene are that they can provide long-lasting, environmentally friendly, cost-effective mosquito control even in areas that flood intermittently. One disadvantage is that larvae must eat these products for them to work. So if the larvae are at a stage where they are about to emerge as adults, then the products will not be ingested (older larvae and pupae don't eat).

Fish and mosquitoes

Fish can also help get rid of larval mosquitoes. Mosquito fish (Gambusia affinis) have been called "the perfect fish" because they can live in just about any type of water, are extremely tolerant to pollution and changes in salinity, and will eat available vegetation (you don't have to feed them). The females are live bearers having 50-100 babies at a time. These babies begin feeding on mosquito larvae the day they are born. The female can have babies every 6 weeks and they can live 2-3 years.

Source: Mosquito Prevention: What the Homeowner Can Do

The source of this information is from Mississippi but other regions of the U.S. and the world, have the ability to reduce and control the population of mosquitoes in their region.

In the U.S. birds will soon be flying south for the winter. Will this lead to another explosion of H5N1?

The U.S. is entering a riskier season for spread of H5N1 bird flu. Here’s why experts are worried.

Fall and winter months present more opportunities for H5N1 to spread and change since both cows and other flu viruses will be on the move.

Will a seasonal change (birds flying south for the winter) spawn another surge of infections.

The article then goes on to discus an outbreak that is occurring in California.

... three dairy herds in California’s Central Valley tested positive for H5N1 last month. As of September 12, the total number of infected herds in California had jumped to eight, Deeble said Thursday.

California is home to about 1.7 million dairy cows, about one-sixth of the national total, making it the nation’s largest dairy producing state.

How and when the virus made its way to California is still under investigation. But genetic testing at the USDA’s National Veterinary Services Laboratories shows that the virus that infecting the California herds is very closely related to the viruses that have infected more than 200 herds from 13 other states, Deeble said.

The first infections of cows with the H5N1 virus were confirmed in herds in Texas and Kansas in late March. Evolutionary biologists think cows became infected months earlier, perhaps around the first of the year, when the virus probably spread from migrating birds who were carrying it. (Now these migrating birds are soon flying south for the winter).

This article then goes on to make a very important point.

Stopping the next pandemic

Adam Kucharski, a professor of infectious disease epidemiology at the London School of Tropical Hygiene, says viruses that cause pandemics emerge in stages: They infect animals and establish a reservoir in stage one; these animals infections cause isolated spillover infections into humans in stage two; spillovers cause localized clusters of human infections in stage three; widespread transmission among people is stage four.

Kucharski argues that the most feasible and impactful stage for pandemic prevention is at stage two, when there are spillovers that cause localized clusters of infections. He says that the recent clusters of infections of farmworkers culling poultry in Colorado suggest that the H5N1 outbreak in the US is in that second stage, when prevention efforts can be less costly and more impactful.

“So really, it’s those situations where you’re starting to see evidence of ability to infect humans but not ability to sustain transmission very easily where there’s a prime potential for intervention,” Kucharski said.

But the US is not doing enough to take advantage of the H5N1s currently limited spread, he said.

Kucharski points to an outbreak of H7N9 in 2013 as a prime example of a situation where this worked. People were starting to catch this flu from live poultry markets in China, which shut down those markets and effectively stopped transmission of the virus.

“We haven’t had an H7N9 pandemic. We haven’t actually had many cases at all subsequently,” Kucharski said.

The U.S. is running a risk letting H5N1 infections continue to spread in cattle without more widespread testing, and the world is watching.

“I think at the moment, the response doesn’t seem to be at the level it needs to be for this kind of threat,” Kucharski said.

“I think we saw, even in the early stages of COVID, that a lot of countries – lot of Europe, lot the US – basically wasn’t looking hard enough for COVID and then got caught out very badly when they realized that there was a lot more transmission than the raw data suggested,” Kucharski said.

“And so I think, particularly in this situation, getting a good grasp of what’s going on is kind of key, and I think we haven’t been getting that anywhere near the scale we need to.”