All research at a Fort Detrick laboratory that handles high-level disease-causing material, such as Ebola, is on hold indefinitely after the Centers for Disease Control and Prevention found the organization failed to meet biosafety standards.

No infectious pathogens, or disease-causing material, have been found outside authorized areas at the U.S. Army Medical Research Institute of Infectious Diseases.

The CDC inspected the military research institute in June and inspectors found several areas of concern in standard operating procedures, which are in place to protect workers in biosafety level 3 and 4 laboratories, spokeswoman Caree Vander Linden confirmed in an email Friday.

The CDC sent a cease and desist order in July.

After USAMRIID received the order from the CDC, its registration with the Federal Select Agent Program, which oversees disease-causing material use and possession, was suspended. That suspension effectively halted all biological select agents and toxin research at USAMRIID, Vander Linden said in her email.

The Federal Select Agent Program does not comment on whether a program such as USAMRIID is registered and cannot comment on action taken to enforce regulations, Kathryn Harben, a spokeswoman for the CDC, wrote in an email.

“As situations warrant, [Federal Select Agent Program] will take whatever appropriate action is necessary to resolve any departures from regulatory compliance in order to help ensure the safety and security of work with select agents and toxins,” Harben said in the email.

The suspension was due to multiple causes, including failure to follow local procedures and a lack of periodic recertification training for workers in the biocontainment laboratories, according to Vander Linden. The wastewater decontamination system also failed to meet standards set by the Federal Select Agent Program, Vander Linden said in a follow-up email.

“To maximize the safety of our employees, there are multiple layers of protective equipment and validated processes,” she said. Vander Linden could not say when the laboratory would be able to continue research.

“USAMRIID will return to fully operational status upon meeting benchmark requirements for biosafety,” she said in an email. “We will resume operations when the Army and the CDC are satisfied that USAMRIID can safely and consistently meet all standards.”

USAMRIID has been working on modified biosafety level 3 procedures and a new decontamination system since flooding in May 2018. This “increased the operational complexity of bio-containment laboratory research activities within the Institute,” she said.

At the time of the cease and desist order, USAMRIID scientists were working with agents known to cause tularemia, also called deer fly or rabbit fever, the plague and Venezuelan equine encephalitis, all of which were worked on in a biosafety level 3 laboratory. Researchers were also working with the Ebola virus in a biosafety level 4 lab, Vander Linden said.

Of the pathogens, Ebola, bacteria Yersinia pestis (plague), and bacterium Francisella tularensis (tularemia) are on the list of the Health and Human Services select agents and toxins. The three are considered Tier 1 agents, which pose a severe public health and safety threat.

Venezuelan equine encephalitis also falls under the Federal Select Agent Program, according to the Code of Federal Regulations.

The military research institute is looking at each of its contracts to see what will be affected by the shutdown. USARMIID work outside the lab is not expected to be affected, including on Ebola, Vander Linden said.

“We are coordinating closely with the CDC to ensure that critical, ongoing studies within bio-containment laboratories are completed under appropriate oversight and that research animals will continue to be cared for in accordance with all regulations,” she said in an email. “Although much of USAMRIID’s research is currently on hold, the Institute will continue its critical clinical diagnostic mission and will still be able to provide medical and subject matter expertise as needed to support the response to an infectious disease threat or other contingency.”

According to the Code of Federal Regulations, which also lists required training, records and biosafety plans, Federal Select Agents Program registration can be suspended to protect public health and safety. It is not clear if this is why the USAMRIID registration was suspended.

The code also gives the Department of Health and Human Services, under which the CDC falls, the right to inspect any site and records, without prior notifications. Vander Linden said in the email that the CDC inspected USAMRIID several times over the past year, both unannounced and on a regularly scheduled basis.

USAMRIID will work to meet requirements set by the Army and the CDC and have its suspension lifted, Vander Linden said.

“While the Institute’s research mission is critical, the safety of the workforce and community is paramount,” she said. “USAMRIID is taking the opportunity to correct deficiencies, build upon strengths, and create a stronger and safer foundation for the future.”

Australia had an unusually early and fairly severe flu season this year. Since that may foretell a serious outbreak on its way in the United States, public health experts now are urging Americans to get their flu shots as soon as possible.

“It’s too early to tell for sure, because sometimes Australia is predictive and sometimes it’s not,” said Dr. Daniel B. Jernigan, director of the influenza division of the Centers for Disease Control and Prevention. “But the best move is to get the vaccine right now.”

The number of cases of flu in this country is still quite low, according to the weekly C.D.C. FluView released Friday. But as the weather cools, it is expected to ramp up.

In 2017, Australia suffered its worst outbreak in the 20 years since modern surveillance techniques were adopted. The 2017-2018 flu season in the United States, which followed six months later as winter came to the Northern Hemisphere, was one of the worst in modern American memory, with an estimated 79,000 dead.

This year’s Australian outbreak began in April, two months earlier than usual, and persisted into October.

Alarming early reports said the number of deaths might surpass those in 2017, but that did not quite happen. (The country did have more positive flu tests than ever before, but that was in part because far more tests were performed.)

Nonetheless, there were more flu-related deaths than usual, while hospitalization rates and nursing home outbreaks “were at moderate to high levels,” said Ian Barr, deputy director of World Health Organization Collaborating Center for Reference and Research on Influenza in Melbourne.

Direct comparisons of mortality rates are difficult, because Australia counts only deaths in which a hospital declares influenza the cause; there were 662 this year, and 745 in 2017.

Not only is the United States population 13 times bigger, but the C.D.C. — aware that flu triggers even more deaths from pneumonia, sepsis, heart attack and other illnesses — looks at the increased death rates from many illnesses in bad flu years, and calculates how many were probably due to influenza.

At the peak of the 2017-2018 season, the C.D.C. estimated that more than 56,000 Americans would die. Officials later calculated that 79,000 had — which, the agency noted, is more people than usually fill a Super Bowl stadium.

In 2017, Australia’s deadly season set off alarm bells in Britain, where tabloids featured headlines about the “killer Aussie flu.”

But no such dire warnings were issued to Americans, in part because of turmoil at the C.D.C. and its parent agency, the Department of Health and Human Services.

The Trump administration’s first H.H.S. secretary, Dr. Tom Price, resigned in September 2017 after it was revealed that he had spent $400,000 chartering private jets at taxpayer expense. (One day earlier, Dr. Price had set an example by getting a flu shot on camera, but the room was filled with political reporters shouting questions, and he fled with his suit jacket in hand.)

The administration’s first C.D.C. director, Dr. Brenda Fitzgerald, was also under fire because of investments in biotech, health informatics and tobacco; she resigned in early 2018.

Last month, Dr. Price’s successor, Alex M. Azar II, also got a flu shot on camera at a news conference that National Foundation for Infectious Diseases holds every year to urge Americans to get vaccinated.

Mr. Azar — who stayed through the question and answer session — made it clear that the Trump administration is firmly behind vaccination.

(In his first years in office, Mr. Trump was vague about the topic; in a 2015 radio interview, he boasted that he had never had a flu shot, saying, “I don’t like the idea of injecting bad stuff into your body.” In April, however, as a measles outbreak struck New York and other states, he said American children “have to get their shots” — an about-face that earned him praise from public health experts.)

Mr. Azar said vaccination “is an important public health issue for the entire Trump administration” and noted that Mr. Trump had just signed an executive order directing his department to pursue modernization of flu vaccine production.

Most flu vaccines are still grown in fertilized eggs and that process, he said, consumes 900,000 eggs a day and takes more than six months.

On Monday, the National Institute of Allergy and Infectious Diseases announced that it was forming a consortium of research centers to pursue better methods.

Australia’s current flu season was dominated by the H3N2 strain, as was the 2017 season in both countries. H3N2, which emerged for the first time in the 1968 “Hong Kong flu” pandemic, tends to cause more hospitalization and deaths than other strains.

H3N2 may also dominate in the United States this year, Dr. Jernigan said, but it is too early to be sure. In some years, he said, different strains appear in various Southern Hemisphere countries, including New Zealand, Chile and South Africa.

At the same news conference, Dr. William Schaffner, the foundation’s medical director, lamented that only 45 percent of adults and 63 percent of children get flu shots each year.

Half of all adults who do not get vaccinated, he said, do so because they believe the vaccines don’t work.

The overall efficacy of the 2017 vaccine was only 40 percent, according to the C.D.C., and only 25 percent against the H3N2 strain.

“We know it isn’t perfect,” Dr. Schaffner said, “but we need to emphasize the importance of partial protection.”

“If you get the shot and you still get the flu,” he added, “you are less likely to get pneumonia, less likely to be hospitalized and less likely to die.”

Dr. William B. Borden, a preventive cardiologist at George Washington University, said at the same conference that patients with cardiovascular disease were six times as likely to have a heart attack in the week after a flu diagnosis than they normally were — even if their heart problems were under control with cholesterol and blood-pressure medicines.

Asthma and diabetes patients were three times more likely to die of flu complications than other patients, he added.

At the news conference, Dr. Patricia N. Whitley-Williams, the foundation’s president-elect, described standing in an intensive care unit last winter with the mother of a 9-month-old child with severe flu who was sedated and on a ventilator for seven days.

“This mother did not believe in vaccinating, because she felt that the flu vaccine was not effective and she was concerned about vaccine safety,” Dr. Whitley-Williams said. “She looked at me and said, ‘You mean I could have prevented this?’”

As illnesses and deaths linked to vaping continue to rise, health experts on Friday updated their advice to doctors on how best to recognize symptoms and treat patients, and warned that the start of the flu season would make it harder to arrive at the right diagnosis.

“I can’t stress enough the seriousness of these lung injuries associated with e-cigarettes or vaping products,” [Dr. Anne Schuchat (born 1960)], principal deputy director of the federal Centers for Disease Control and Prevention, said at a news briefing. “We are not seeing a meaningful drop-off in new cases, and unfortunately many more people have been hospitalized with lung injury each week.”

A new concern has come to light. She said a handful of patients, fewer than five, were hospitalized for vaping illness, recovered and went home, and then wound up back in the hospital again, from five to 55 days later. The reason is not yet known, she said. One possibility is that the patients may have started vaping again.

Dr. Schuchat said those cases highlight the importance of follow-up for patients who have been treated for vaping-related illnesses. The C.D.C. says they should see doctors no later than a week or two after leaving the hospital, and some may need referrals for counseling for marijuana use disorder, a form of dependence.

Of the 1,299 cases reported to the C.D.C. since mid-August, 70 percent of the patients are male, and 80 percent are under 35 years old. The majority, 76 percent, have vaped THC, the psychoactive ingredient in marijuana, and many have also used nicotine. Twenty-nine deaths have been reported. Only Alaska has no reported cases.

The cause of the illnesses is not known, and the C.D.C. says no vaping products can be considered safe. Dr. Schuchat said there might turn out to be more than one cause, and it might take months to find the answer.

Health officials have given the illness a formal name, “e-cigarette, or vaping, product use associated lung injury,” or Evali.

The start of the flu season may make it harder to diagnose cases, because some symptoms of lung damage from vaping — cough, shortness of breath, fever — can mimic those of influenza. The C.D.C. recommends testing patients with those symptoms for flu and other respiratory infections, but it is possible for patients to have both a lung injury from vaping and the flu or some other viral or bacterial ailment affecting their lungs.

Many patients with vaping illness also have stomach pain, nausea, vomiting and diarrhea, and it is important to ask people with those symptoms about vaping.

Doctors should “strongly consider” admitting patients to the hospital if they have become ill after vaping and are short of breath, have underlying illnesses that could affect their lungs or their blood oxygen level is less than 95 percent, the C.D.C. said. That level, called oxygen saturation, can be measured with a device clipped to the fingertip, the agency said in its Morbidity and Mortality Weekly Report, published on Friday.

The report also said that some patients who initially had mild symptoms then deteriorated rapidly within 48 hours. And many patients who ended up in the hospital had previously been sent home after seeking help at emergency rooms or clinics.

Because the vaping illnesses often involve severe inflammation in the lungs, many patients have been treated with corticosteroid drugs. But the report said it was not known whether the drugs really helped or whether the patients might have recovered on their own. And corticosteroids can increase the risk of infection.

The report says that “in some circumstances,” it might be best to avoid corticosteroids in patients who are being tested for illnesses like fungal pneumonia, which could worsen with the drugs. But the report also says that in patients who are severely ill, it may be necessary to give them corticosteroids along with other drugs to fight infection.

Patients who have had high doses of corticosteroids may need to see a specialist in endocrinology to help minimize or manage the side effects.

Patients older than 50 who become ill after vaping tend to be sicker than younger ones: more likely to need ventilators and to stay longer in the hospital. These older patients may need special consideration, the report said, adding that a quick diagnosis, treatment with steroids and consultation with specialists in pulmonary and critical care “might be lifesaving in this patient population.”

Dr. Ned Sharpless, acting commissioner of the Food and Drug Administration, said his agency had received more than 700 samples of vaping products for testing. So far, the cause of the outbreak has not been identified. The tests have found varying levels of THC and nicotine in different products, and some of the THC products also contain vitamin E acetate, which some sellers use to dilute the THC.

In a move that worries many public health experts, the federal government is quietly shutting down a surveillance program for dangerous animal viruses that someday may infect humans.

The United Nations Environment Program estimates that a new animal disease that can also infect humans is discovered every four months. Ending the program, experts fear, will leave the world more vulnerable to lethal pathogens like Ebola and MERS that emerge from unexpected places, such as bat-filled trees, gorilla carcasses and camel barns.

The program, known as Predict and run by the United States Agency for International Development, was inspired by the 2005 H5N1 bird flu scare. Launched 10 years ago, the project has cost about $207 million.

The initiative has collected over 140,000 biological samples from animals and found over 1,000 new viruses, including a new strain of Ebola. Predict also trained about 5,000 people in 30 African and Asian countries, and has built or strengthened 60 medical research laboratories, mostly in poor countries.

[Dr. Dennis Thomas Carroll (born 1948)], the former director of USAID’s emerging threats division who helped design Predict, oversaw it for a decade and retired when it was shut down. The surveillance project is closing because of “the ascension of risk-averse bureaucrats,” he said.

Because USAID’s chief mission is economic aid, he added, some federal officials felt uncomfortable funding cutting-edge science like tracking exotic pathogens.

Congress, along with the administrations of George W. Bush and Barack Obama, were “enormously supportive,” said Dr. Carroll, who is now a fellow at Texas A&M’s Bush School of Government and Public Service.

“But things got complicated in the last two years, and by January, Predict was essentially collapsed into hibernation.”

The end of the program “is definitely a loss,” said [Dr. Peter Daszak (born 1965)], president of the EcoHealth Alliance, a nonprofit global health organization that received funding from the program. “Predict was an approach to heading off pandemics, instead of sitting there waiting for them to emerge and then mobilizing. That’s expensive."

“The United States spent $5 billion fighting Ebola in West Africa,” he added. “This costs far less.”

The goal of Predict was to speed up and organize the previously haphazard hunt for zoonotic diseases — those that may jump from animals to humans. In recent years, scientists have discovered many lethal viruses lurking in wild and domestic animals.

It has long been known, of course, that AIDS originated in chimpanzees and probably was first contracted by bushmeat hunters. Ebola circulates in bats and apes, while SARS was found in captive civet cats in China.

In South Asia, Nipah virus reaches humans through pigs or date palm sap infected by bats carrying the virus. In Saudi Arabia, MERS also is carried by bats; they infect camels, which then infect humans. The virus can jump from human to human, especially in hospitals.

Novel influenza viruses originate in migratory ducks and geese. The viruses spread first to domestic poultry flocks, then to pigs and humans. Mutations picked up along that viral highway can render the viruses far more dangerous.

These discoveries led to new ways of preventing spillovers of infections into human populations: closing markets where wildlife is butchered for food,; putting bamboo skirts on sap-collection jars to keep bats out; or penning pigs and camels in places where they cannot eat fruit that bats have gnawed.

Predict teams have investigated mysterious disease outbreaks in many countries, including a die-off of 3,000 wild birds in a Mongolian lake. One team proved that endangered otters in a Cambodian zoo were killed by their feed — raw chickens infected with bird flu.

A Predict laboratory helped identify bat-borne viruses that a boys’ soccer team might have been exposed to while trapped for weeks in a cave in Thailand.

Allowing Predict to end “is really unfortunate, and the opposite of what we’d like to see happening,” said Dr. Gro Harlem Brundtland, the former prime minister of Norway and former World Health Organization director-general.

She was co-chair of a panel that in September issued a report detailing the world’s failure to prepare for pandemics. “Americans need to understand how much their health security depends on that of other countries, often countries that have no capacity to do this themselves,” Dr. Brundtland said.

Even though USAID is “incredibly proud and happy over the work Predict has done,” the program is closing because it reached the end of a 10-year funding cycle, said Irene Koek, acting assistant administrator of the agency’s global health bureau.

“We typically do programs in five-year cycles, and it had two,” she said. Some similar research will be part of future budget requests, “but it’s still in the design-and-procurement cycle, so exactly what will continue is a bit of a black box.”

In mid-October, the agency said it would spend $85 million over the next five years helping universities in Africa and Asia teach the “one-health” approach that Predict used. (“One health” describes the nexus between animal, human and environmental medicine).

But it will not involve the daring fieldwork that Predict specialized in.

Among the institutions that worked on Predict projects are those staffed by wildlife veterinarians and disease-trackers like the University of California, Davis’s One Health Institute; the EcoHealth Alliance; the Wildlife Conservation Society, which runs the Bronx Zoo; the Smithsonian Institution, which manages the National Zoo in Washington; and Columbia University’s Center for Infection and Immunity.

Some Predict projects will be taken over by other government agencies, such as the Pentagon’s [Defense Threat Reduction Agency] or the National Institutes of Health. But those agencies have different missions, such as basic research or troop protection. They do not share USAID’s goal of training poor countries to do the work themselves.

As an agency that gives money to countries, USAID often has a friendlier, more cooperative relationship with governments in poor nations than, for example, Pentagon-led efforts might.

“I’ve always been impressed with the way they were able to work with ministries of health,” said Dr. James M. Hughes, a former chief of infectious diseases at the Centers for Disease Control and Prevention who was on Predict’s advisory board. “They have a high level of trust, and they help countries comply with the International Health Regulations.”

(Those regulations, in force since 2007, require countries to report all major disease outbreaks to the World Health Organization and allow the W.H.O. to declare health emergencies.)

USAID still supports some health-related programs like the President’s Malaria Initiative and the President’s Emergency Plan for AIDS Relief. But Dr. Carroll described those as “cookbook portfolios.”

How to fight those diseases is well-known, he explained, so the agency just comes up with a budget for drugs, diagnostic kits, insecticides, mosquito nets, condoms or other long-established interventions.

Predict more often placed medical detectives in the field, training local doctors, veterinarians, wildlife rangers and others to collect samples from wild and domestic animals.

It can be highly specialized work. Getting blood samples from pigs or wild rodents is fairly routine, but catching birds, bats or monkeys alive is not. Gorillas are harder. (Scientists usually content themselves with just collecting gorilla feces.)

Predict also experimented with novel ways to catch and release animals unharmed, to transport samples without refrigeration and to use DNA testing that can scan for whole viral families instead of just known viruses, said Dr. Christine Kreuder Johnson, associate director of the One Health Institute at the University of California, Davis.

Predict sponsored epidemiological modeling to predict where outbreaks are likely to erupt. It also sought ways to curb practices, such as hunting for bushmeat or breeding racing camels, that encourage eruptions.

After that West African Ebola outbreak, Predict researchers determined exactly which bat species carried the Ebola Zaire strain that caused it. Another team in Sierra Leone discovered a new strain of the virus, now known as Ebola Bombali.

The Zaire strain was found in a bat that roosts in caves and mines, said Dr. Jonathan Epstein, an EcoHealth Alliance veterinarian, while the Bombali type was in a species that roosts in houses.

Distinctions like that are important for telling people — especially people who eat bats — which species are dangerous.

“We generated an illustrated book on how to keep bats out of houses by putting screens on windows or mesh below the roof thatch,” he said. “That’s the kind of thing Predict paid for.”

Predict served as a proof of concept for a much more ambitious idea that Dr. Carroll proposed several years ago: the Global Virome Project, which envisioned trying to compile a genetic atlas of all the viruses circulating in all animals. By some estimates, there are more than 800,000 such viruses waiting to be discovered.

Many scientists questioned the wisdom of spending as much as would be needed to do that — over $3 billion. But those experts also argued that Predict, which is focused on viruses dangerous to humans, was very much worth the relatively modest amounts of money it cost.

“Predict needed to go on for 20 years, not 10,” Dr. Epstein said. “We were getting to the point of having a trained work force that could gather animal samples and labs that could test for unknown viruses, not just known ones.”

“Once it stops, it’s going to be hard to maintain that level of proficiency.”

For decades, scientists and doctors have treated common bacterial and viral infections with fairly blunt therapies. If you developed a sinus infection or a stomach bug, you would likely be given a broad-spectrum antibiotic that would clear out many different types of bacteria. Antiviral drugs help treat viral illnesses in much the same way, by hindering the pathogen’s ability to reproduce and spread in the body.

But microorganisms are quick to evolve, and many have developed defenses against the methods devised to kill them. An increasing number of bacteria are now resistant to one or more antibiotics. Each year roughly 700,000 people around the world die from such infections, and by 2050 the number could rise to 10 million, according to United Nations estimates. Viruses, too, quickly evolve new ways of disguising themselves from drugs, often by hiding inside host cells. Less than 100 antiviral drugs have successfully made it all the way to the clinic since the first was approved in 1963.

Desperate to find new medicines against pathogenic microorganisms, scientists are turning to Crispr, the gene-editing tool. Crispr has typically been considered for macroscopic tasks: altering mosquitoes so they can’t spread malaria, editing tomatoes so they are more flavorful and curing certain genetic diseases in humans. Now researchers are harnessing Crispr to turn a bacterium’s machinery against itself, or against viruses that infect human cells.

“Crispr is the next step in antimicrobial therapy,” said David Edgell, a biologist at the Western University in London, Ontario, and the lead author of a study published earlier this month in Nature Communications.

Crispr is a specialized region of DNA that creates what amount to genetic scissors — enzymes that allow the cell (or a scientist) to precisely edit other DNA or its sister molecule, RNA. (Crispr is shorthand for “clustered regularly interspaced short palindromic repeats.”) Crispr was originally discovered in bacteria, where it helps keep track of past injury. When a virus attacks, the bacterium stores small chunks of the viral genome within its own DNA. This helps the bacterium recognize viral infections when they occur again. Then, using Crispr-associated enzymes, it can disarm the virus and prevent the infection from spreading.

In their recent study, Dr. Edgell and his colleagues successfully used a Crispr-associated enzyme called Cas9 to eliminate a species of Salmonella. By programming the Cas9 to view the bacterium itself as the enemy, Dr. Edgell and his colleagues were able to force Salmonella to make lethal cuts to its own genome.

The team began with a conjugated plasmid — a small packet of genetic material that can replicate itself and be passed from one bacterium to the next. To the plasmid the scientists added the encoded instructions for Crispr enzymes that would target Salmonella DNA. The plasmid was then tucked inside E. coli bacteria. Dr. Edgell reasoned that most types of E. coli are typically part of a healthy gut microbiome, and would already be present if a person ingested pathogenic Salmonella by, say, eating a contaminated salad. The E. coli could then transfer the engineered plasmid to the Salmonella, where the Crispr system would activate, destroying the bad bacteria.

That is exactly what the researchers observed in a petri dish. The Crispr system wiped out nearly all Salmonella bacteria, while leaving E. coli intact.

“This represents a significant advance in being able to target bacteria in a highly specific way,” said Mitch McVey, a biologist at Tufts University who was not involved in the study.

Crispr-based antibiotic pills aren’t yet anywhere near pharmacy shelves. But developing such treatments could allow scientists to harness the power of the human body’s own resident microbes in preventing disease.

“Scientists are starting to figure out that microbiota can also be extremely beneficial for our health,” said Luciano Marraffini, a microbiologist at Rockefeller University and the Howard Hughes Medical Institute.

Conventional antibiotics do not distinguish between good and bad bacteria, eradicating everything indiscriminately and occasionally creating problems for people with weakened immune systems.

“A major benefit of Crispr is that we can program it to kill only specific pathogenic bacteria and leave alone the rest of our healthy microbes,” Dr. Marraffini said.

A few companies have started to pursue Crispr-based antibiotics that can be delivered through viruses that have been engineered so that they cannot reproduce or cause infections themselves, as well as other methods. Dr. Marraffini is a co-founder of one such start-up, Eligo Bioscience.

The specificity of Crispr is equally enticing to researchers looking to target pathogenic viruses. Instead of having Crispr kill viruses that infect bacteria, as it does in nature, scientists are programming it to chop up viruses that infect humans. In a study, also published this month in Molecular Cell, scientists at the Broad Institute of M.I.T. and Harvard demonstrated that another Crispr enzyme, Cas13, could be programmed to detect and kill three different single-stranded RNA viruses that infect human cells: influenza A virus, lymphocytic choriomeningitis virus and vesicular stomatitis virus.

Using this Crispr system, researchers saw up to a 40-fold reduction in viral RNA within 24 hours. The enzymes damaged the viral genomes significantly enough that few viruses could infect new cells. In the case of the flu virus, Cas13 reduced its infectiousness by more than 300-fold.

“This is a great proof-of-concept,” said Rodolphe Barrangou, a microbiologist at North Carolina State University, who also co-founded a company for Crispr-based antimicrobial products and was not involved in the study. If researchers can design Crispr technology against three fairly mild human viruses, such as influenza, lymphocytic choriomeningitis virus and vesicular stomatitis virus, they can likely modify it to treat more deadly viral infections as well.

Compared to current antiviral drugs, Crispr has the advantage of being easy to tweak as needed. “If a virus evolves and mutates, we can simply change the Crispr system to match whatever the virus is doing,” said Cameron Myhrvold, a postdoctoral researcher at Broad.

Now researchers face the challenge of demonstrating that Crispr antibacterial and antiviral drugs are effective in living animals and in humans, not just in the lab, and that they will be cheaper than conventional therapies, Dr. Barrangou said.

“We’re not ready for clinical prime time yet,” he said. “But we’re getting there.”

Health officials are warning doctors to more closely monitor patients with severe lung damage caused by vaping, because some have relapsed or died shortly after being sent home from the hospital.

The recommendations are part of four new reports about the nationwide outbreak of severe illnesses from vaping, which has hospitalized 2,506 people and killed 54 as of Dec. 17. The reports were published on Friday, two by the Centers for Disease Control and Prevention, and two by The New England Journal of Medicine.

In the new reports, researchers pinpointed the beginning of the outbreak to early June, and said that evidence was mounting to connect the illness to vitamin E acetate — an additive to the illicit THC-based products that most patients have vaped.

The C.D.C. is confident that vitamin E acetate was “strongly linked” to an explosive increase in cases last summer, Dr. Anne Schuchat, principal deputy director of the agency, said at a news briefing on Friday.

But she and other health officials warned that even if THC suppliers stopped adding vitamin E acetate, that would not necessarily make illicit THC safe, because providers could switch to other dangerous substances. Sellers use additives to extend the THC and increase their profits.

The C.D.C. is still recommending that people avoid vaping nicotine, because it may also contain unknown additives that may not be safe.

Separately, the Food and Drug Administration announced on Friday that 44 websites had been seized by the agency and the Drug Enforcement Administration for marketing illicit THC vaping cartridges. By seizing the sites, the agencies basically shut them down.

The F.D.A., which has been investigating the supply chain involved in the outbreak, said it did not have evidence directly connecting the lung illnesses to the sites, but had obtained information about some of them from patients and their families.

Although most of the lung injuries this year have been attributed to vaping products containing THC, the high-inducing ingredient in marijuana, the new research also suggests that nicotine vaping may be causing health problems in young people. One of the studies found that starting in 2017, long before the outbreak of severe illness, there was a gradual increase in emergency room visits for lung trouble by people using e-cigarettes, especially patients 10 to 19 years old.

The scientists said that the growing use of e-cigarettes by teenagers may have caused the increase in those visits to the emergency room. But Dr. Shuchat emphasized that the evidence was not clear and needed more study.

In the outbreak of severe lung damage, cases peaked in September. But new ones are still being reported every week — nearly 100 occurred from Dec. 10 to Dec. 17 — and more deaths are being investigated.

One of the new reports found that among 2,409 cases reported to the C.D.C. by early December, 31 patients had to be rehospitalized and seven others died after being sent home. Their median time to winding up back in the hospital was four days, and the median time to death after hospital discharge was three days.

Those rehospitalized were more likely than others to have a history of chronic conditions like heart disease, respiratory problems and diabetes. The ones who died after being sent home were more likely to be age 50 or older.

Vaping-related emergency room visits peaked in early September and mostly involved younger people, especially young men and boys.

Because of those cases, the C.D.C. is urging that patients who are sent home see a doctor within two days, which is sooner than previously recommended. The advice is especially important for people with underlying chronic illnesses, the agency said. It is also providing new guidelines for doctors.

It is not clear whether any of the patients who relapsed or died had started vaping again when they got home, Dr. Schuchat said, but she said that it was important for addiction counseling to start before patients leave the hospital.

She added: “I think it’s likely that there are a variety of factors here, and the medical conditions were particularly important.”

Another study addressed the lingering question of whether the outbreak, first widely recognized in August, was really a new illness, or actually something that had been going on for a long time without being detected.

The illness appears to be new: Cases spiked in early June, the researchers found, based on analyzing emergency-room visits reported to a database called the National Syndromic Surveillance Program, which was created to detect bioterrorism after the attacks on Sept. 11, 2001. They examined the reasons for visits, looking for mention of e-cigarettes, along with lung symptoms like shortness of breath and chest pain.

Why the surge occurred in June is not known, though researchers suspect it was because of increased use of vitamin E acetate, and other potentially toxic additives, by suppliers of illicit THC vaping products. Minnesota authorities who seized illicit THC vapes found that in 2018, 10 of 10 products contained no vitamin E, whereas 20 of 20 seized in September 2019 did contain it.

“I believe the practice of diluting THC vaping products with vitamin E really took off this past year,” Dr. Schuchat said, adding that the idea of using the vitamin additive had been promoted on YouTube and other social media platforms.

But how to explain the gradual increase in emergency room visits by young patients 10 to 19 years old starting in January 2017, well ahead of the outbreak? Though some cases could be linked to whatever later caused the severe illnesses, the researchers said the problems could also have been the result of the increasing use of nicotine e-cigarettes. Among high school students, the proportion who said they had vaped nicotine in the previous 30 days rose to 27.5 percent in 2019, from 11.7 percent in 2017.

A few years earlier, in 2015, the e-cigarette maker Juul had introduced nicotine salts, which make inhaled nicotine feel gentler on the throat and are more potent because they allow people to inhale higher concentrations of nicotine without discomfort. The ease of vaping with Juul’s wildly popular, sleek devices, and the addictiveness of high levels of nicotine could have led some people to vape more and more, exposing them to higher amounts of potential toxins like flavorings and to overdoses of nicotine, which can make people feel quite sick.

A study published in 2017 found increased rates of chronic cough and other respiratory problems in teenagers who vaped nicotine, including those who had never smoked cigarettes.

Research published last week on adults found that while e-cigarette users were better off than smokers, they were more likely than nonsmokers to develop respiratory disease. The risk was greatest among those who both vaped and smoked, which was common.

One of the new articles, published on Friday in The New England Journal of Medicine, strengthens the case against vitamin E acetate, reporting that it was found in lung fluid from 48 of 51 people with the vaping illness — 94 percent. Earlier research had made the same finding, but in a smaller number of patients.

The 51 patients came from 16 states, indicating that vitamin E acetate was in widespread use, and not from “just a single, local supplier of tainted products,” Dr. Schuchat said.

The new study compared the patients with 99 healthy people who had previously given samples of lung fluid as part of other research on smoking that involved nonsmokers, smokers and vapers. None of the healthy people had the vitamin E additive in their lungs.

Researchers don’t know how vitamin E acetate could harm the lungs, but they suggested two possible ways. It could disrupt a substance called surfactant, which helps keep open tiny air sacs deep in the lungs and is essential for normal breathing. A second theory is that the heat of vaping could break down the vitamin E acetate into ketene, a dangerous molecule that might produce the kind of chemical burns found in the lungs of some patients.

Both ideas need more study and testing in animals, the researchers said.

The vitamin E acetate was first found in a THC-vaping product from a sick patient that was analyzed in August by scientists at the New York State Department of Health’s Wadsworth Center.

Since then, the center has found the substance in more than 100 THC samples, about 69 percent of all the THC vaping cartridges it has tested, David C. Spink, director of the organic and analytical chemistry lab, said in an interview.

Most of the samples are 40 percent to 50 percent vitamin E acetate, Dr. Spink said.

The lab has also tested six products marketed over the internet to dilute THC for vaping.

“They came in brown bottles, with nice, professional looking labels on them, but they didn’t have a list of ingredients,” Dr. Spink said. Three of the six were pure vitamin E acetate.

The United States may be headed into a bad flu season, according to figures recently released by the Centers for Disease Control and Prevention.

As of the last week of December, “widespread” flu activity was reported by health departments in 46 states. More ominously, a second measure — the percentage of patients with flu symptoms visiting medical clinics — shot up almost to the peak reached at the height of the 2017-18 flu season, which was the most severe in a decade.

About 61,000 Americans died of flu that season, the C.D.C. said. (The original estimate of 79,000 was revised downward last year; the agency said the number changed as more death certificate information became available.)

This year’s flu vaccine may not be particularly effective against the strain of the virus now widespread in the United States, experts said. But even so, it’s worth getting the shot: people who are vaccinated fare better if struck by the flu than those who are not.

It is still too early to know how severe this season will be, said Lynnette Brammer, leader of the agency’s domestic influenza surveillance team.

Although many people are coming down with flu, the two chief indicators of severity — hospitalizations and deaths — are not yet elevated, she noted.

Deaths from pneumonia and flu are actually lower than normal at this time. But reports of hospitalization and death normally lag other indicators by at least two weeks.

The current season did begin unusually early. By late November, the flu had hit hard in the Deep South, from Texas to Georgia. The virus then broke out in California and the Rocky Mountain states, but was not widespread in the Northeast until recently.

That pattern echoes what happened in Australia, where winter runs from June through August. Flu came unusually early to the Southern Hemisphere in 2019. In seasons when Australia has a bad flu season, the Northern Hemisphere sometimes does, too.

In another important way, however, the United States is not following Australia’s lead. The A(H3N2) strain of influenza was dominant there last year, while most American cases this season have been caused by a very different strain, called B Victoria. (B strains are named for the cities where they were first isolated.)

B strain flus do not normally arrive until late in the season. But when they do, “they often impact children more than adults and older adults,” Ms. Brammer said.

[What parents need to know about this flu season ... see https://parenting.nytimes.com/childrens-health/flu-season-children ]

The C.D.C. tracks the deaths of children individually, rather than making estimates, as is done for adults. Those over 65 are usually the group hardest hit by flu. Thus far this season, 27 children have died of flu — in 2017-18, 187 died — but pediatric deaths don’t normally start peaking until mid-January.

On the rise now is the A(H1N1)pdm09 strain, which is a descendant of the pandemic “swine flu” that first appeared in 2009 and then morphed into a seasonal flu.

H1N1 strains are usually the first to appear. They usually cause fewer hospitalizations and deaths per capita than B strains or A(H3N2).

Thus far, based on limited testing data, this season’s flu shot does not look like a good match for the B Victoria flu and may not be very effective, the C.D.C. said. But the shot does still appear to be well matched for the A(H1N1)pdm09 strain.

C.D.C. flu data relies on reports from doctors’ offices, clinics and hospital emergency rooms about how many patients come in with flu symptoms.

An even faster measurement of flu’s spread comes from Kinsa Health, which collects daily readings of fevers from up to two million users around the country who own its thermometers. The devices connect to smartphones and instantly upload readings to the company’s app.

Kinsa readings indicate that flulike activity peaked on Dec. 24 at a level just below the 2017-18 level — confirming what the C.D.C. found — and has since dropped by almost a third, said Nita Nehru, a company spokeswoman.

But even this week’s lower figure “is much higher than is typical of this time of year,” she added. It may bounce up again soon, now that students have returned to school from holiday vacations.

The company assumes that fevers lasting three or more days indicate flu rather than a common cold, said Inder Singh, the company’s founder.

The C.D.C. has not endorsed Kinsa’s methods, but the data does show flu patterns at least a week or two ahead of reports from medical clinics.

Thus far, almost none of the hundreds of samples tested by the C.D.C. have been resistant to Tamiflu or any other common antiflu drug. Those medications do not cure the flu; they only reduce the severity of an infection, and only if they are taken early.

WASHINGTON — Life expectancy increased for the first time in four years in 2018, the federal government said Thursday, raising hopes that a benchmark of the nation’s health may finally be stabilizing after a rare and troubling decline that was driven by a surge in drug overdoses.

Life expectancy is the most basic measure of the health of a society, and declines in developed countries are extremely unusual. But the United States experienced one from 2015 to 2017 as the opioid epidemic took its toll, worrying demographers who had not seen an outright decline since 1993, during the AIDS epidemic. An uptick in what have become known as “deaths of despair” — younger people dying from overdoses, suicide and alcoholism — has drawn considerable attention from politicians and policymakers.

The 2018 data, released in a report on Thursday, confirmed the first decline in drug deaths in 28 years, an important improvement after decades of rises.

[...]

The increase in life expectancy might have been greater if not for rising mortality due to influenza and pneumonia — the death rate grew by 4.2 percent — as well as suicide and nutritional deficiencies. But while there has been increased concern about suicide as a public health crisis, the growth in reported cases — to 48,344 in 2018 from 47,173 in 2017 — was relatively small. The suicide rate grew by 1.4 percent overall, with a larger rise for men than women.

[...]