A guide to vaccinology: from basic principles to new developments

flu epidemic 2019 :: Article Creator

In US, Experts Are Increasingly Worried About A Bird Flu Epidemic Spreading To Humans

A year ago, a strain of avian flu was discovered in dairy cattle in the United States, but authorities have failed to take strong measures to contain it. These mistakes and omissions are now taking their toll. Virus experts say conditions are right for a dangerous jump to humans.

Cramped barns provide ideal conditions for the rapid spread of bird flu viruses.

Andres Kudacki / AP

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Five years after the emergence of COVID-19, it appears that its lessons have not been fully learned. It is possible that we are watching a «made in USA» pandemic unfold in real time. Strains of the H5N1 bird flu virus have been spreading widely in the United States for the past three years, resulting in the deaths of more than 153 million farm-raised birds. In February 2024, the virus unexpectedly appeared in dairy cows. Since that time, a total of 973 farms nationwide have reported infections (as of Feb. 25, 2025). The latest bad news came in January, when, for the first time, a person died from an H5N1 infection in the United States.

Public health experts, veterinarians, and virologists are increasingly concerned. In another five years, prominent Frankfurt virologist Sandra Ciesek recently predicted, people will no longer be talking about COVID-19, but rather about bird flu.

Previous influenza pandemics have killed millions of people. For example, the Spanish flu that circulated between 1918 and 1920 claimed up to 50 million lives. That's why experts are genuinely worried – and are not just looking for a new reason to sound an alarm.

Like Russian roulette

At present, the conditions are again right in the United States for a virus that normally affects animals to mutate into a virus that can easily infect humans, what scientists call a zoonosis. Influenza viruses are notoriously unstable, changing their genes quickly and easily. Such changes can be small, within an individual gene. However, flu viruses are also known for their ability to exchange entire segments of their genetic material with each other if two viruses infect the same animal or person at the same time.

Such changes give the viruses the chance to adapt to new hosts. And especially if viruses jump back and forth between different animal species such as birds and mammals, multiplying millions of times with each infection, then chances increase that a mutation will occur that allows the virus to efficiently infect human cells. It's a kind of Russian roulette.

In 1918, viruses were the winners. Scientists have found evidence that the pandemic started with an avian influenza virus that first circulated widely in waterfowl. It then jumped to pigs and horses. Numerous genetic changes led to the emergence of a strain that could efficiently infect humans, and could easily be passed on from person to person. The data suggest, ironically, that this mutation emerged first in the United States. Soldiers then brought the deadly cargo to Europe at the end of World War I.

From a public health perspective, the top priority is to give viruses with the potential to jump from animals to humans as few opportunities to mutate as possible. In other words, to allow little reproduction and no circulation in mammals. But today, the exact opposite is happening in the United States. In recent months, U.S. Farmers and authorities at all levels have done exactly what China was accused of doing in 2020: reacting too late, providing too little information and launching half-baked attempts at containment. This has created a situation conducive to the emergence of a pandemic virus.

Parallels to Wuhan in 2019

«The dynamics, the extent and also the infections of so many mammals make the outbreak in the United States unique,» says Martin Beer, veterinarian specialist for microbiology and virology, in an interview. Beer is head of the Institute for Diagnostic Virology at the Friedrich Loeffler Institute, on the island of Riems in northeast Germany.

The start of the epidemic in cows is very reminiscent of the situation in Wuhan in November 2019. There, it took weeks to identify the pathogen that was causing a new type of pneumonia. Despite this experience, farmers and authorities in the United States took their time tracking down the cause of an initially unexplained disease.

In February 2024, a few cows on a farm in Texas were barely producing any milk, and the milk they did produce was thick and yellowish. The animals became apathetic and developed a fever. It took more than five weeks to identify H5N1 influenza as the cause, in large part because cows were previously considered to be resistant to bird flu viruses. It wasn't until cats on the farm died with suspicious symptoms that researchers thought to test for bird flu.

It is still unclear exactly how and when H5N1 first infected dairy cows. Genetic analyses have shown that it probably jumped from wild birds to dairy cows only once before December 2024. One theory is that milking machines might have been accidentally contaminated with bird droppings containing the virus. To enter a cell, viruses attach themselves to receptors – proteins on the cell surface that act like docking stations, allowing a virus to bind. Udder cells have receptors that are similar to those in bird cells, so it might have been relatively easy for H5N1 viruses to enter there and continue to multiply happily in the udder.

Early in February 2025, a new report caused a stir. The U.S. Department of Agriculture (USDA) announced that a slightly different strain of H5N1 had again spread from wild birds to dairy farms. This variant has evidently been circulating in wild birds and farm-raised poultry for months. It's an extremely unlucky development.

The udders of dairy cows offer an ideal environment for the rapid multiplication of bird flu viruses. In the United States, H5N1 influenza has been detected on more than 960 dairy farms.

Matthew Ludak / WAPO / Getty

Lax controls allowed spread

However, the spread of H5N1 in cattle has mostly occurred from cow to cow and farm to farm. This is due to the lax and uncoordinated handling of sick dairy cows by both farmers and the authorities. This was exacerbated by a second mistake: Instead of immediately sealing off affected regions, animals were transported to distant farms as part of the standard practice of raising young milking cows at one location before selling them to dairies. The virus went along, spreading to distant states.

A third rule for suppressing an emerging virus has also been consistently disregarded in the United States. None of the affected farms have been subject to a thorough epidemiological investigation. Which animals were affected, and in what order? Were there infections that did not show any symptoms? How long were the cows contagious? Have nonlactating animals also been infected?

All these questions could have been clarified with a reasonable expenditure of effort and resources. Tests for H5N1 were readily available last spring. «To date, there has been no such study – or else the data has not been published,» says Beer. As a result, it remains difficult to say exactly what happens at a dairy once the viruses arrive. «Precise epidemiological investigations are extremely important,» he says, especially now that scientists know that H5N1 has jumped from birds into dairy cows a second time. «They have to include a search for how the jump happened,» he adds.

At the beginning of the epidemic in cows, milk was not tested, although all the infected dairy cows suffered from mastitis, an inflammation of the udder. Such testing was carried out sporadically beginning only in early summer. It wasn't until December 2024 that the USDA launched a nationwide milk testing program. There is one glimmer of good news: According to laboratory tests, pasteurized milk is not dangerous. However, farmyard cats and mice have died, evidently as a result of exposure to contaminated raw milk.

All these errors have made targeted containment measures difficult or even impossible. «I'm really not a fan of the way the avian flu epidemic is being handled in the United States,» says University of Minnesota epidemiologist Michael Osterholm in an interview, sighing deeply. «The pandemic clock is ticking.»

A recent report by the Center for Strategic and International Studies think tank argues that these failures have in large part been attributable to authorities' fears of the dairy and agriculture-sector lobbies. The dairy industry is a billion-dollar business in the United States, the report notes. Authorities did not want to upset farmers, dairies and the sector's many other stakeholders by temporarily reducing their incomes or imposing restrictions, the authors write. In addition, they note, there has been disagreement from the very beginning about who was responsible.

The virus has been the primary beneficiary of this inaction. It took advantage of the opportunities provided to spread ever further. It also began a dangerous pingpong game between species. Over the summer, an H5N1 strain from dairy cows mysteriously found its way onto two poultry farms in Colorado. It also infected wild birds. In December 2024, house cats in several U.S. States died after eating food contaminated with H5N1. It's likely that poultry meat from infected animals had been processed to make the cat food, which was not cooked.

Genetic changes in the H5N1 virus

Humans, too, have become part of this pingpong game. As of Feb. 25, 70 people in the United States had been infected with H5N1 since the beginning of 2024. Within this group, 41 were infected by strains circulating among dairy cows and 24 with strains from poultry. The origin of the other infections is not known. Small-scale screening operations conducted on a few farms and among veterinarians suggest that the actual number of H5N1 infections in humans greatly exceeds the number of official reports.

These infections likely could have been prevented if farm employees had worn protective goggles and suits when milking cows, cleaning stables or disposing of dead chickens. However, according to reports from the United States, such safety gear has generally not been made available to farmworkers. So far, with the exception of one case, those infected have suffered only from mild respiratory illnesses and eye inflammation.

As expected, the viruses have changed genetically in recent months, making them better adapted to mammals. Studies have shown that the viruses infecting cows have mutated in such a way that they now multiply more rapidly in mammalian cells. In December, a research group from the National Institute of Allergy and Infectious Diseases in the U.S. Discovered that just one more change in the H5N1 strains infecting cows would be enough for the virus to bond with receptors on human cells.

In December, scientists found that viral strains from two people who had been infected via wild birds had mutated in a way that made them better adapted to human cells. One of the people died. It is not clear whether the strain behind the deadly infection was more aggressive, or whether the patient's health had been weakened by preexisting illnesses. Still, concern is growing – especially because the new strain recently discovered in dairy cows is the same one that caused the death.

In some regions of the United States, markets with live poultry have been banned due to the ongoing bird flu epidemic.

Lokman Vural Elibol/Anadolu/ Getty

No transmission between humans yet

One bright spot remains: So far in the U.S. There has been no documented transmission of the virus from person to person. Only if a virus manages to efficiently spread between people can it trigger a dangerous pandemic.

«We simply don't know whether the H5N1 viruses that are rampant in the United States can develop these fatal characteristics,» says Beer, the virus expert. But perhaps our luck will hold. So far, H5N1 viruses have been relatively slow to adapt to humans.

Pediatric Flu Deaths Jump To 68, With 11 Children Dying In The Last Reported Week Alone Amid Media Blackout

A patient is given a flu vaccine on October 28, 2022, in Lynwood, California. [AP Photo/Mark J. Terrill]

The latest influenza data from the US Centers for Disease Control and Prevention (CDC), for the week ending February 8, shows an increase in flu-associated mortality which has already claimed 13,000 lives this season. Particularly troubling are 11 flu deaths in children in the week between February 2-8 alone, bringing the total pediatric flu deaths this season to 68.

All indicators point to the likelihood that the ongoing 2024-2025 flu season will surpass recent years' figures for both pediatric and adult flu deaths in the United States.

This past week the CDC indicated that it was updating the classification of the season to "high severity" for all age-groups for the first time since the 2017-18 season. Every state is reporting significant increases in influenza hospitalizations. Dr. John Swartzberg, clinical professor emeritus at the UC Berkeley School of Public Health told the California based Mercury News, "This may become the worst influenza season we've had so far in the 21st century," with infection reporting data showing that patients are presenting evenly with both H3N2, subtypes of influenza A and H1N1.

For the first time since the start of the COVID-19 pandemic began, influenza is causing more deaths in California than the coronavirus, according to the state's Department of Public Health with a total of 751 confirmed flu deaths in the state. Eleven of those are of children, with San Diego County alone reporting four deaths. The ages of the children were 14, 15, 16, and 17 years old and officials confirmed that none of them had received their influenza vaccine.

Michigan, Wisconsin, North Carolina, and Virginia are each reporting two children have died in each state. In Virginia one child between the ages of 5 and 12, and the other was between 13 and 17.

One child in Kentucky was reported having died, no further information was given but officials confirmed that the child had not received a flu vaccine this season.

Five children have died so far in Texas, according to the latest data from the Texas Department of State Health Services. Only two media outlets have reported the five deaths.

These figures represent only what is being reported in the media and comprise less than half of the total pediatric deaths, pointing to a government and media blackout of critical public health information. Florida's Weekly Flu Review for the week ending February 8, 2025, makes reference to pediatric flu deaths this season, but the agency does not specific give a specific number.

Schools have also been shut down in a number of states as large percentages of students, staff, and teachers have been out sick. These include schools in Texas, where at least three districts closed schools, as well as in Ohio, Tennessee, Alabama, Georgia, Virginia, Oklahoma, Iowa and Missouri.

The greatest contributing factor to the high levels of sickness is the decline in the percentage of children receiving the annual flu vaccine since the start of the COVID-19 pandemic.

Flu vaccination rates were highest for the 2019- 2020 flu season that ran October 2019 through May 2020 when 63.7 percent of children received at least one dose of the vaccine. According to WebMD and figures from the CDC, as of December 2024, only 37 percent of children had received flu shots, down from 44 percent at the same time the previous year.

This means that more than 40 percent fewer children are receiving the influenza vaccine than were five years ago. This staggering figure suggests that since the start of the COVID-19 pandemic, the anti-vaccination campaigns led by the far right and anti-science hacks such as Health and Human Services secretary Robert F. Kennedy, Jr. Have had a significant and detrimental effect on the wider population.

According to the CDC, there have so far been at least 29 million people infected with influenza, resulting in 370,000 hospitalizations and 16,000 deaths. The best way to prevent severe illness and death is vaccination. The CDC estimates that in 2023, influenza vaccination prevented approximately 6 million illnesses, 65,000 hospitalizations, and 3,700 deaths.

A 2022 study published by the Infectious Disease Society of America and cited by the CDC showed that "flu vaccination reduced children's risk of severe life-threatening influenza by 75%." Furthermore, in a significant and recent study published in JAMA this past December, by a team led by Dr. Kelsey M. Sumner, showed that in a review of nearly 16,000 children in the US from 2015 to 2020, the children who received at least one influenza vaccine dose were associated with a 50 percent reduction in severe influenza-related outcomes in pediatric patients.

Just one day before the latest flu figures were released, Kennedy was confirmed as US president Donald Trump's health secretary, representing an escalated attack on public health and science. Kennedy, notorious for spreading anti-vaccine disinformation, played a central role in stoking up vaccine hesitancy in the Samoan population months before a 2019 measles outbreak claimed the lives of 83 children.

Among the critical public health agencies that Kennedy will oversee under HHS are the National Institutes of Health (NIH) and the CDC, the very agencies currently reporting on weekly infection rates for the flu and a wide number of other viruses and diseases.

On Friday when the latest flu deaths were published, Kennedy announced the firing of 5,200 HHS employees or six percent of its workforce including 1,300 CDC workers and 1165 at the NIH. A number of the CDC's webpages have suspended, including their weekly publication, Morbidity and Mortality Weekly Report (MMWR).

Kennedy has pledged to "give infectious disease a break for about eight years," essentially promising that he and the Trump administration will ensure that all reporting and monitoring of viral and infectious diseases are halted and censored, denying the public the right to know about viral spread. Under such dictatorial measures vaccinations and access to vaccines will further plummet as one component of a broader attack on public health.

Despite the alarming rise in flu deaths, there is no national campaign to raise vaccination rates for children or the broader population, nor will there be until the working class enters onto the scene and begins waging a broader political fight to wrestle control of these critical questions out of the hands of the financial oligarchy.

Scientific achievements have advanced to a high degree from the initial recorded influenza cases in the 16th century to the 1918 influenza pandemic that infected more than 500 million across the globe and killed over 50 million. Air quality researchers now understand that influenza is an airborne virus, spread primarily by breathing infected particles in shared unventilated air in indoor or crowded spaces.

Dr. Donald Milton, professor of environmental health, and his research team at the University of Maryland School of Public Health's watershed study from 2012-2013, found that participants infected with the flu contaminated the air around them just by breathing. The conclusions from the study prove that the most commonly suggested measures such as handwashing, surface cleaning, and covering coughs and sneezes, were insufficient at preventing the spread of influenza.

These facts, so critical to a scientific understanding of the rapid spread of the SARS-2 virus which causes COVID-19, were widely and purposefully ignored in place of the "large-droplet" theory and six-foot distancing measures that were employed to get money flowing for Wall Street and corporations in the push to reopen schools and businesses in 2021.

The World Socialist Web Site made the critical observation that the disappearance of influenza in the 2020-21 season—when limited mitigation measures were widely implemented—proved that the eradication of SARS-CoV-2 and more is possible and that contrary to claims by the capitalist supporters of mass infection, that there is no disease or virus that humanity must "live with."

The logical conclusions based on the highest understanding of viral transmission points directly to a broader fight for ventilation and clean air. Hand in hand with critical tools such as vaccinations, the deaths the population is told it must accept, are largely preventable.

Adding to the situation is the growing threat of an H5N1 "bird flu" pandemic, including the more dangerous D.1 variant which has infected humans, a measles outbreak in Texas, an ongoing tuberculosis outbreak in Kansas, the continued spread of COVID-19, RSV, and the guarantee of future pandemics with the continued subordination of public health to profit interests.

The question at hand is which social force will get to decide, the ruling oligarchy which is hostile to science and public health, or the working class which can carry out the socialist reorganization of society to ensure the highest scientific achievements are employed to raise public health, life expectancy and living standards to new heights which are incompatible with capitalism.

Join the fight to end the COVID-19 pandemic

Someone from the Socialist Equality Party or the WSWS in your region will contact you promptly.

Worst Flu Season In Years Swamps California: 'Particularly Long And Difficult'

The worst flu season in years is swamping California, prompting a renewed surge in hospitalizations as officials warn the disease could continue circulating at high levels for weeks to come.

By one measure, this season has already been more potent than any seen since the onset of the COVID-19 pandemic in early 2020, according to data from the California Department of Public Health. The rate at which flu tests returned positive results at the state's clinical sentinel labs surged to 27.8% for the week ending Feb. 1, the most recent for which complete data are available.

That's higher than the peak of the "tripledemic" winter of 2022-23, when California's hospitals were stressed by simultaneous high circulation of flu, COVID and respiratory syncytial virus, or RSV.

"We're still on the way up," Dr. Peter Chin-Hong, an infectious-disease expert at UC San Francisco, said of flu. Since the pandemic began, he said, "this is the first time that we're mainly talking about flu rather than COVID."

The rate at which flu tests are coming back positive in California's clinical sentinel labs has reached a level not seen in the last five years.

(California Department of Public Health)

There have been at least 10 pediatric flu deaths this season in California, according to data from the Department of Public Health. That includes three teenagers in San Diego County.

"These recent flu deaths among our youth are tragic and concerning as we head into what historically is the peak of flu season," Dr. Ankita Kadakia, the county's interim public health officer, said in a statement.

None of the teens had received a flu vaccine, which Kadakia said remains "the best protection against getting seriously sick." Nationally, the U.S. Centers for Disease Control and Prevention estimates there have been at least 11,000 deaths from flu this season, including 47 children, and at least 250,000 hospitalizations.

"I think in COVID, we got used to the idea that kids are, quote-unquote, fine," Chin-Hong said. Flu, however, "can be very severe in kids. Pediatricians are telling me that they're seeing tons of flu in kids right now."

Complicating matters has been an unusually low vaccination rate against flu for children this winter — the lowest since at least the 2019-20 season. Nationally, 44.5% of children age 17 and younger were vaccinated against flu as of late January, down from 49.1% at the same time last year and 51.7% from the year before.

A chart with many dots and several lines.

The vaccination rate against flu for children age 17 and younger is at its lowest level since at least the 2019-20 respiratory virus season.

(Centers for Disease Control and Prevention)

The trend is similar in California: 47.7% of California's children have been vaccinated against flu as of late January, also the lowest since at least the 2019-20 flu season. Last year at this time, 53.7% of children were vaccinated against flu.

The CDC recommends everyone 6 months or older get a flu shot — ideally by the end of October to boost protection against the disease during high-circulation winter months.

But given how potent this flu season has already proved to be, officials say those who have yet to be vaccinated should consider doing so.

"This has been a particularly long and difficult flu season compared to recent years. And it's not over yet," Kadakia said.

The two types of flu generally circulating now are H1N1 — related to the swine flu strain that caused a flu pandemic in 2009 and 2010 — and H3N2, which "is notorious for just causing more serious illness in general," Chin-Hong said. Of about 3,500 influenza type A viruses genetically analyzed nationally over a recent week among public health labs, 54% were H1N1 and 46% were H3N2.

There were no bird flu viruses identified in humans that week. Health officials say the current risk to the public from bird flu remains low, as no person-to-person spread has been detected. Nationwide, 68 human cases have been confirmed, including 38 in California. The vast majority of those cases are associated with exposure to infected poultry or cattle.

A man in a white coat looks at something on a table.

Pharmacist Deep Patel prepares a flu and COVID-19 vaccine for Brandon Guerrero, right, at a CVS in Huntington Park on Aug. 28, 2024.

(Christina House / Los Angeles Times)

Overall, flu activity "is high and increasing," California health officials said in their latest respiratory virus weekly report, but they are not seeing similarly concerning spread of either COVID or RSV at the moment.

COVID activity is low statewide, and RSV activity is low and decreasing. The most recent test positive rate for COVID was 2.4%, and for RSV, 5%.

Some experts caution that the test positivity rate isn't necessarily the best metric to compare flu seasons with one another, as testing practices and healthcare usage vary from season to season.

A chart of the United States with different shades of blue.

Flu levels in California's wastewater are considered "very high."

(Centers for Disease Control and Prevention)

Levels of flu detected through surveillance in California's wastewater are "very high," as is the case in most other states, data show. In California, RSV levels are considered "high," while COVID levels are considered low.

California's rate of hospital admissions from flu is also on the rise, possibly indicating a second peak of the winter. According to the latest state report, the hospitalization rate had climbed to 10.1 new admissions per 100,000 people, the highest mark of the season.

The overall rate of hospital admissions for the flu may be reaching a second peak in California.

(California Department of Public Health)

"Influenza predictions suggest that emergency department visits will remain high and may increase in most states," the CDC said.

At UC San Francisco, staffers got an alert that the hospital is full, "and I haven't seen that for a while," Chin-Hong said. "A lot of people have flu in the hospital, so that could be part of it."

The situation is much the same in Los Angeles County, where this winter's flu season appears to be the most durable and potent of the post-COVID-emergency era.

The test positivity rate for flu has been above 20% for seven straight weeks in L.A. County and rose to 28.83% for the most recent week available.

The rate at which flu tests have come back positive in L.A. County has exceeded 20% for seven straight weeks. The 2020-21 flu season is not shown because flu levels were so minimal during the first full season of the COVID-19 pandemic.

(L.A. County Department of Public Health)

The last time there was such a sustained surge in positive flu tests was during the 2019-20 season, where there were 10 straight weeks the test positivity rate for flu was above 20%.

Nationwide, emergency room visits are very high for flu and moderate for RSV, according to the CDC. But they're low for COVID-19.

The rate at which flu tests are coming back positive nationally is 31.6% and has been increasing. The RSV test positive rate is 6.6% and decreasing. The COVID test positivity rate is also decreasing and was at 4.9%, as of the last report issued Friday.

A map shows that respiratory illness levels are "very high" in the eastern United States while moderate in California.

(Centers for Disease Control and Prevention)

"COVID predictions for the next two weeks suggest that emergency department visits will remain at a lower level compared to prior winter seasons," the CDC said.

Should that trend hold, this would be the first winter of the COVID era in which California does not see a pronounced surge of the disease.

"The late surge of COVID seen last summer and early fall likely decreased the portion of the population susceptible to COVID-19 this winter," the L.A. County Department of Public Health said in a statement.

Also possibly helping matters, Chin-Hong said, was that a new blockbuster COVID subvariant has not emerged in recent months.

The overall level of respiratory illnesses — including flu, COVID and RSV — is worst in the eastern U.S. Levels of respiratory illness are considered moderate in California and much of the West.

Vaccines for COVID and RSV are also available, and health officials recommend residents, particularly those at high risk of developing severe symptoms, consider getting those shots as well. RSV immunizations were first approved for use in the U.S. In 2023.

All those 6 months and older are recommended to get the COVID vaccination that was updated in the fall. An RSV vaccine is recommended for all adults age 75 and up, and those ages 60 to 74 who are at increased risk. To prevent severe RSV in infants, officials recommend either maternal vaccination or immunizing the infant with a monoclonal antibody.

"With respiratory infections circulating in our community this time of year, it is more important than ever for people to get a flu vaccine, as well as an updated COVID-19 vaccine and the RSV vaccine if you are eligible," Dr. Rais Vohra, Fresno County's interim health officer, said in a statement.

A report published in the CDC's Morbidity and Mortality Weekly Report in October noted that flu vaccination rates have declined in other countries, including in South America, where they were below pre-pandemic norms.

"This finding is consistent with postpandemic declines in vaccination coverage across the Americas associated with vaccine misinformation, hesitancy and disruptions in routine immunization services," the report said.

Some health experts have expressed alarm about the rise in skepticism surrounding vaccine safety — including from Robert F. Kennedy Jr., President Trump's nominee to run the U.S. Department of Health and Human Services. Health experts say the nation's recommended vaccines are safe.

"I just wonder if it's part of a general, you know, with RFK Jr. All that stuff, just more questions about vaccines," Chin-Hong said. The reduction in flu vaccination rates among children, he added, "that is kind of striking to me."

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