HIV and Swollen Lymph Nodes
Bloodborne Pathogens
If you can reasonably anticipate facing contact with blood and/or other potentially infectious materials as part of your job duties, you should receive additional training from your instructor or supervisor including an opportunity for interactive questions and answers.
Bloodborne PathogensBloodborne pathogens are microorganisms such as viruses or bacteria that are carried in blood and can cause disease in people. There are many different bloodborne pathogens including Hepatitis C, malaria, or syphilis, but Hepatitis B (HBV) and the Human Immunodeficiency Virus (HIV) are the two diseases specifically addressed by the OSHA Bloodborne Pathogen Standard.
While this module will focus primarily on the human pathogens HBV and HIV, it is important to know which bloodborne pathogens (from humans or animals) you may be exposed to at work, especially in laboratories. For example, personnel working with animals might have the potential for exposure to rabies, tularemia, or Q fever and it would therefore be important to know specific information about those diseases.
Hepatitis B (HBV)In the United States, approximately 300,000 people are infected with HBV annually. Of these cases, a small percentage are fatal.
"Hepatitis" means "inflammation of the liver," and, as its name implies, Hepatitis B is a virus that infects the liver. While there are several different types of Hepatitis (A, B, C, D, & E), Hepatitis B is easily transmitted primarily through "blood to blood" contact. Hepatitis B initially causes inflammation of the liver, but about 10% of those infected become chronic carriers and may develop conditions such as cirrhosis (failure) and liver cancer leading to death.
Of note is Hepatitis C which is on the rise in the United States. It too is transmitted by blood and body fluids but is harder to transmit. On the other hand once people become infected around 40% develop liver disease.
The Hepatitis B virus is very durable, and it can survive in dried blood for up to seven days. For this reason, this virus is the primary concern for employees such as housekeepers, custodians, laundry personnel and other employees who may come in contact with blood or potentially infectious materials in a non first-aid or medical care situation.
Symptoms: There are very few signs and symptoms to Hepatitis B. Most people who become infected develop no signs or symptoms until later in life when the signs of liver failure become apparent. Therefore, most carriers do not know they are infected and infective.
Human Immunodeficiency Virus (HIV)AIDS, or acquired immune deficiency syndrome, is caused by a virus called the human immunodeficiency virus, or HIV.
Once a person has been infected with HIV, it may be many years before AIDS actually develops. HIV attacks the body's immune system, weakening it so that it cannot fight other deadly diseases. AIDS is the final stages of the disease when the immune system fails and other diseases become overwhelming. While treatment for it is improving, there is no known cure.
Estimates on the number of people infected with HIV vary, but some estimates suggest that an average of 35,000 people are infected every year. By the year 2002, it is possible that 2%-9% of the American population will be infected, or 5 to 15 million people. Many people who are infected with HIV may be completely unaware of it.
The HIV virus is very fragile and will not survive very long outside of the human body. It is primarily of concern to employees providing first aid or medical care in situations involving fresh blood or other potentially infectious materials. Because it is such a devastating disease, all precautions must be taken to avoid exposure.
Symptoms: Symptoms of HIV infection are mild and usually not noticed. They may, at most, be a simple low-grade fever or "cold". Symptoms of AIDS infection can vary, but often include weakness, fever, sore throat, nausea, headaches, diarrhea, a white coating on the tongue, weight loss, swollen lymph glands and eventually death.
If you believe you have been exposed to HBV or HIV, especially if you have experienced any of the signs or symptoms of these diseases, you should consult your physician or doctor as soon as possible.
Modes of TransmissionBloodborne pathogens such as HBV and HIV can be transmitted through contact with infected human blood and other potentially infectious body fluids such as:
It is important to know the ways exposure and transmission are most likely to occur in your particular situation, be it providing first aid to a student in the classroom, handling blood samples in the laboratory, or cleaning up blood from a hallway.
HBV and HIV are most commonly transmitted through:
Accidental puncture from contaminated needles and other sharps can result in transmission of bloodborne pathogens.
In most work or laboratory situations, transmission is most likely to occur because of accidental puncture from contaminated needles, broken glass, or other sharps; contact between broken or damaged skin and infected body fluids; or contact between mucous membranes and infected body fluids. For example, if someone infected with HBV cut their finger on a piece of glass, and then you cut yourself on the now infected piece of glass, it is possible that you could contract the disease. Anytime there is blood-to-blood contact with infected blood or body fluids, there is a slight potential for transmission.
Unbroken skin forms an impervious barrier against bloodborne pathogens. However, infected blood can enter your system through:
Bloodborne pathogens may also be transmitted through the mucous membranes of the
For example, a splash of contaminated blood to your eye, nose, or mouth could result in transmission.
Prevention: Work Practices & Engineering ControlsAvoiding exposure is the best protection. To do this personal protection devices and practices listed below are to be used or followed.
However, because no system is perfect, anyone who works with human blood or blood products or is at risk of exposure during their job (i.E. Custodial services or housekeeping in a medical facility) will be offered free vaccinations for Hepatitis B. This vaccination consists of three shots given at 0, 1, and 6 months apart with no boosters in the future.
"Universal Precautions" is the name used to describe a prevention strategy in which all blood and potentially infectious materials are treated as if they are, in fact, infectious, regardless of the perceived status of the source individual. In other words, whether or not you think the blood/body fluid is infected with bloodborne pathogens, you treat it as if it is. This approach is used in all situations where exposure to blood or potentially infectious materials is possible. This also means that certain engineering and work practice controls shall always be utilized in situations where exposure may occur.
Emergency ProceduresIn an emergency situation involving blood or potentially infectious materials, you should always use Universal Precautions and try to minimize your exposure by wearing gloves, splash goggles, pocket mouth-to-mouth resuscitation masks, and other barrier devices.
If you are exposed, however, you should:
Bloodborne Pathogens Control Plan
Prevention: Personal Protective EquipmentProbably the first thing to do in any situation where you may be exposed to bloodborne pathogens is to ensure you are wearing the appropriate personal protective equipment (PPE). For example, you may have noticed that emergency medical personnel, doctors, nurses, dentists, dental assistants, and other health care professionals always wear latex or protective gloves. This is a simple precaution they take in order to prevent blood or potentially infectious body fluids from coming in contact with their skin. To protect yourself, it is essential to have a barrier between you and the potentially infectious material.
Rules to follow:
If you work in an area with routine exposure to blood or potentially infectious materials, the necessary PPE should be readily accessible. Contaminated gloves, clothing, PPE, or other materials should be placed in appropriately labeled bags or containers until it is disposed of, decontaminated, or laundered. It is important to find out where these bags or containers are located in your area before beginning your work.
Normal clothing that becomes contaminated with blood should be removed as soon as possible because fluids can seep through the cloth to come into contact with skin. Contaminated laundry should be handled as little as possible, and it should be placed in an appropriately labeled bag or container until it is decontaminated, disposed of, or laundered.
Remember to use universal precautions and treat all blood or potentially infectious body fluids as if they are contaminated. Avoid contact whenever possible, and whenever it's not, wear personal protective equipment. If you find yourself in a situation where you have to come in contact with blood or other body fluids and you don't have any standard personal protective equipment handy, you can improvise. Use a towel, plastic bag, or some other barrier to help avoid direct contact.
Prevention: Hygiene PracticesHandwashing is one of the most important (and easiest) practices used to prevent transmission of bloodborne pathogens. Hands or other exposed skin should be thoroughly washed as soon as possible following an exposure incident. Use soft, antibacterial soap, if possible. Avoid harsh, abrasive soaps, as these may open fragile scabs or other sores.
Hands should also be washed immediately (or as soon as feasible) after removal of gloves or other personal protective equipment.
Because handwashing is so important, you should familiarize yourself with the location of the handwashing facilities nearest to you. Laboratory sinks, public restrooms, janitor closets, and so forth may be used for handwashing if they are normally supplied with soap. If you are working in an area without access to such facilities, you may use an antiseptic cleanser in conjunction with clean cloth/paper towels or antiseptic towelettes. If these alternative methods are used, hands should be washed with soap and running water as soon as feasible.
If you are working in an area where there is reasonable likelihood of exposure, you should never:
No food or drink should be kept in refrigerators, freezers, shelves, cabinets, or on counter tops where blood or potentially infectious materials are present.
You should also try to minimize the amount of splashing, spraying, splattering, and generation of droplets when performing any procedures involving blood or potentially infectious materials, and you should NEVER pipette or suction these materials by mouth.
Prevention: Decontamination & SterilizationAll surfaces, tools, equipment and other objects that come in contact with blood or potentially infectious materials must be decontaminated and sterilized as soon as possible. Equipment and tools must be cleaned and decontaminated before servicing or being put back to use.
Decontamination should be accomplished by using
If you are cleaning up a spill of blood, you can carefully cover the spill with paper towels or rags, then gently pour your 10% solution of bleach over the towels or rags, and leave it for at least 10 minutes. This will help ensure that the bloodborne pathogens are killed before you actually begin cleaning or wiping the material up. By covering the spill with paper towels or rags, you decrease the chances of causing a splash when you pour the bleach on it.
If you are decontaminating equipment or other objects (be it scalpels, microscope slides, broken glass, saw blades, tweezers, mechanical equipment upon which someone has been cut, first aid boxes, or whatever) you should leave your disinfectant in place for at least 10 minutes before continuing the cleaning process.
Of course, any materials you use to clean up a spill of blood or potentially infectious materials must be decontaminated immediately, as well. This would include mops, sponges, re-usable gloves, buckets, pails, etc.
By using Universal Precautions and following these simple engineering and work practice controls, you can protect yourself and prevent transmission of bloodborne pathogens.
Prevention: Signs, Labels & Color CodingWarning labels need to be affixed to containers of regulated waste, refrigerators and freezers containing blood or other potentially infectious material; and other containers used to store, transport, or ship blood or other potentially infectious materials.
These labels are fluorescent orange, red, or orange-red. Bags used to dispose of regulated waste must be red or orange red, and they, too, must have the biohazard symbol readily visible upon them. Regulated waste should be double-bagged to guard against the possibility of leakage if the first bag is punctured.
Regulated waste refers to:
All regulated waste must be disposed in properly labeled containers or red biohazard bags. These must be disposed at an approved facility. Most departments or facilities that generate regulated waste will have some sort of contract with an outside disposal company that will come pick up their waste and take it to an approved incineration/disposal facility.
Non-regulated waste (ie. Does not fit the definition of regulated waste provided above) that is not generated by a medical facility such as the Student Health Center, Wellness Center, or human health-related research laboratory may be disposed in regular plastic trash bags if it has been decontaminated or autoclaved prior to disposal.
All bags containing such materials must be labeled, signed, and dated, verifying that the materials inside have been decontaminated according to acceptable procedures and pose no health threat.
Custodians and housekeepers will not remove bags containing any form of blood (human or animal), vials containing blood, bloody towels, rags, biohazardous waste, etc. From laboratories unless the bag has one of these labels on it. They have been given very strict instructions not to handle any non-regulated waste unless it has been properly marked and labeled (including signature).
Custodians will not handle regulated waste.
The Uncharted World Of Emerging Pathogens
This article was originally featured on Undark.
It all started when Christopher Mason's 3-year-old daughter licked a subway pole.
Like any parent, he was horrified, but also keenly curious: What types of microbes might be clinging to a metal pipe gripped by countless commuters every day?
Mason, a geneticist at Weill Cornell Medicine, soon became obsessed with that question. His toddler's gross interlude inspired him to embark on a journey to unveil the world of bacteria, fungi, and viruses co-mingling with more than 8 million people in New York City's urban jungle.
In 2013, he launched a project that began dispatching a small army of students shouldering backpacks crammed with latex gloves, vials, and sterile Q-tips. They sampled turnstiles, benches, and kiosks at every open metro stop in the city. It was an expedition into a largely unexplored terrain, like Mars or a deep-sea canyon, brimming with lifeforms both familiar and unknown.
The swabbers were sampling what's called environmental DNA, or eDNA, representing the assortment of cells that all humans, animals, and microorganisms naturally shed as they go about their everyday lives, leaving genetic fingerprints. The scientists gradually quantified and mapped the unseen biological diversity—the microbiome—of the entire city. In 2015, they reported that they'd found more than 1,600 different types of microbes, nearly half of which were previously known to science. Most were harmless, associated with human skin and gastrointestinal tracts. About 12 percent were known pathogens, including fragments of genomes similar to Bubonic plague and anthrax, though there was no evidence that these small bits could make anyone sick. They hadn't found any new deadly viruses lurking in New York's underground—yet.
Four years later, in late 2019, Mason and his colleagues started hearing about a mysterious pneumonia-like disease circulating in China. "We weren't immediately worried," he said, "but by January it was clear that it had jumped across the ocean and was spreading." Suddenly the subway swabbers became front-line workers monitoring Covid-19's presence, not only in transit systems, but also in hospitals, and wastewater. "We had a new medical focus," Mason said, "with protocols and tools that could be deployed anywhere."
Today Covid-19 has killed nearly 80,000 New Yorkers, almost 1.2 million Americans, and nearly 7 million people worldwide. The pandemic catalyzed a push for new technologies that allow scientists to quickly characterize organisms leaving a genetic trace in the environment. Similar to how city-leveling hurricanes have fueled innovations in weather surveillance and building engineering, the pandemic has helped propel the science of pathogen hunting.
The field of eDNA research has mushroomed in the last 15 years as sequencing, computing technology, and metagenomics—the study of DNA from multiple organisms—has advanced. Now, scientists around the world can sample from a cup of dirt, a vial of water, or even a puff of air, and survey the eDNA present for thousands of microbial species. And while the field at-large has faced concerns about privacy and technical limitations, many scientists see an opportunity to further early detection of emerging pathogens. Wastewater surveillance is the most advanced method for monitoring population-level virus spikes, but other realms are catching up. As a result, health officials are becoming better prepared to detect an outbreak—and quickly take steps to contain it.
Experts say the technology may soon become so advanced that an environmental sample, such as air filtered from a high-risk area—a wet market, a hospital, a conference hotel—could be automatically sequenced in a portable device that will report if a threatening pathogen is present. Researchers are using genomic databases to aid rapid identification of pathogens and other microbes. Scientists are getting close to "being able to monitor these high-risk interfaces in real time," said Erik Karlsson, a virologist at Institut Pasteur du Cambodge, a nonprofit research institution in Cambodia.
"We like to say, we're trying to get left of sneeze."
The ultimate goal in virus hunting is an early warning system: to find a pathogen that could spark a disease outbreak before it has the chance to do so. The key, say scientists, is monitoring high-risk areas where animals and people intermingle. Those places are usually on the boundaries between areas where humans live and tropical forests, where people hunt and capture animals for food, pets, and ingredients in medicine, or in markets where animals are slaughtered for consumption.
"We like to say, we're trying to get left of sneeze," said Karlsson, who monitors for avian influenza and other pathogens in Cambodia's live bird markets. That means they're trying to identify potentially threatening pathogens before they spill over into humans, or before they jump into a different animal type and causes an outbreak. "We want to be able to get ahead of that," he said.
Studies show more than 70 percent of the infectious diseases that have emerged in the 21st century—including Ebola, HIV, and mpox (formerly monkeypox)—leapt to humans from wildlife. What's more, there has been a significant increase in zoonotic disease hopping from wildlife to humans over the past 80 years. These events are commonly known as "spillovers."
Research shows there is one main phenomenon, often in a remote faraway place, that precedes a spillover: a forest clearing.
As forests are felled for timber, farming, and human development, people living and working in the adjacent areas hunt and scavenge for animals to be used for food, or sold—at times illegally—as pets or made into medicinal products. Those who handle the animals can become exposed to new pathogens. Whether or not one of those pathogens makes the leap to a person and triggers an outbreak depends on a variety of factors, including how the virus evolves and human immunity.
Forested areas in Africa and Southeast Asia, where vast tracts of previously pristine wilderness are being logged, are among the leading hotspots for emerging animal-borne, or zoonotic, disease. In Africa, there has been a 63 percent rise in the number of zoonotic outbreaks in the last decade, according to the World Health Organization. Those outbreaks include Ebola, viral hemorrhagic fevers, dengue, anthrax, plague, and mpox.
Ebola is one of the most famous and feared among the group. First discovered in 1976, the virus kills by storming the immune system, causing it to go into hyperdrive, damaging blood vessel walls so severely the arteries, veins, and capillaries start to leak blood, causing medical shock and organ failure.
The most widespread Ebola outbreak began in December 2013, when a virus living in a bat somehow spilled over to a 18-month-old boy named Emile Ouamouno in southern Guinea. Ouamouno—"patient zero"—was suffering from a fever, passing stool blackened with blood, and vomiting. He died within days, and was quickly followed by his mother, young sister, and grandmother.
Soon the disease appeared in nearby Guéckédou, a city of nearly 350,000, alerting world health officials to an Ebola outbreak. Ultimately the outbreak spread to Sierra Leone, Liberia, Nigeria, and six other countries, including the United States, with three cases in Dallas, Texas. By the time the epidemic ended in 2016, it had killed more than 11,300 people and infected 28,600.
Eeva Kuisma is a veterinary scientist working for the Wildlife Conservation Society, a global nonprofit conservation group. In the Republic of Congo, she is working to expand a project that could become the first long-term surveillance program for Ebola and other diseases based on forest environmental DNA sampling. The research builds on an ongoing public education and disease surveillance program in which researchers visit rural communities to provide information about the dangers of Ebola virus and other animal-borne diseases, and how to minimize the risk of exposure. Hunters and foragers are encouraged to report sightings of animal carcasses in the forest to a hotline. So far, the program has engaged 5,800 hunters in more than 290 villages.
As part of the new study Kuisma is launching, survey teams will spend 12 months every five years walking systematic transects across more than 8 million acres of forest. Along their path, they'll swab eDNA samples from animal carcasses and feces.
Representing a wide range of animals, from gorillas and chimpanzees to river hogs and antelopes, the samples are being tested for Ebola and other pathogens. Kuisma and her colleagues are using the latest advancements in DNA analysis to compare the genetic material against a database of DNA sequences, revealing the identity of many microorganisms present, from bacteria to pathogens and viruses.
Kuisma said long-term data from the project could become valuable for monitoring the appearance of Ebola or any other pathogens against the backdrop of big landscape changes. One example is a proposed $1.7 billion road project connecting Congo, Chad, and the Central African Republic, "areas which have been really pristine rainforest up until now," she said.
It's early days for the research, but ongoing environmental sampling for Ebola virus might one day short circuit a spillover and save lives. "If we have indications, for example from the feces or from carcasses, that there is an active epidemic in the animal population," Kuisma said, "we can inform people, to warn them that this is happening and to educate them to not go and eat carcasses, not to pick them up, not to touch them."
Over the last century, Southeast Asia has been another major hotspot for emerging zoonotic diseases, but recently, the risk of a spillover has picked up. Population growth, deforestation, climate change, and the expansion of poultry and pig farming have all led to the emergence of a long list of diseases, including Middle East Respiratory Syndrome, Zika virus, and Highly Pathogenic Avian Influenza, or HPAI.
Karlsson, the virologist in Cambodia, helps oversee researchers in Phnom Penh collecting environmental samples in areas where people and animals intermingle. Whereas previously, researchers would have to hand collect feces, blood, urine, and other biological samples, recent developments in rapid genetic sequencing have made it easier for them to do their work more quickly and safely. "Environmental samples are really, really good for speed," Karlsson said. "We don't have to capture animals. We don't have to get the same kinds of permits. You don't have to have people that are trained to handle potentially dangerous animals like bats and things like that. You can go out in the environment, get these samples very quickly."
Recently, a new tool for hunting viruses has become more widely available: air sampling. Karlsson's team is using air filters designed for construction workers to wear on the job, or to purify the air in hotel lobbies to sample public markets where vendors slaughter, clean, and defeather chickens—high risk areas for an avian influenza outbreak.
In a study published in March 2023, the researchers recruited vendors scattered throughout a market to wear personal air samplers 30 minutes a day for a week while going about their business during periods when the circulation of avian influenza in poultry is predictably high in February and low in May. In February, they found viral RNA in 100 percent of air samples. They could also see the virus decreasing as they got farther from the chicken slaughter area, confirming that slaughter areas are potentially the "most high-risk area of the market," Karlsson said, and illustrating the need for interventions such as improved ventilation.
Karlsson's team is now using hand-held air-filtering devices no bigger than a credit card reader to sample for viruses in places that are both challenging and sometimes dangerous for researchers to go swabbing, such as bat caves. Bats are reservoirs for a wide variety of viruses that infect people—including Covid-19. They're pairing the small samplers with toy drones and remote-control cars that can easily access a cave while the scientists wait outside.
Karlsson often thinks about other types of technology that could be deployed for passive, remote sampling — and one day a comprehensive machine that could not only collect a sample, but also process it on the spot. "Can we hook it up to a Roombaa, or something like that, constantly cleaning the floors and then sucking in the sample," he said. "You see there's a lot of options."
Peter Thielen is a molecular biologist at Johns Hopkins Applied Physics Laboratory, where he leads viral genomic surveillance projects, including in collaboration with Karlsson. He said Karlsson has been uniquely positioned in a high-risk area for disease spillover to pilot some of the latest technologies to improve response time to outbreaks. "This ability to take the lab to the sample is exactly what's needed," he said.
While some scientists are working to detect pathogens floating in the air, the Covid-19 pandemic really opened the floodgates to the concept of hunting for viruses in wastewater. Since people shed genetic material from the virus in their feces and urine, wastewater surveillance became one of the best way to track disease spikes, including which city apartment building and what university dormitory contained people with Covid-19—even before they became symptomatic.
It wasn't a novel concept. Wastewater surveillance dates all the way back to the mid-1800s, when John Snow, a British physician, was investigating a mysterious cholera outbreak in London. Citizens called it the "blue death," because the dehydration caused by intense diarrhea and vomiting led to sunken eyes, shriveled skin and a bluish-gray pallor that made patients look like living corpses. Many believed a "miasma," an evil cloud of poisonous air, was to blame.
"We don't have to capture animals. We don't have to get the same kinds of permits. You don't have to have people that are trained to handle potentially dangerous animals like bats."
Snow, however, had a hunch that cholera was waterborne. He painstakingly mapped the cases and finally traced their origin to a contaminated water pump on Broad Street in London's West End. When he convinced the local council to remove the pump's handle, the outbreak ceased. Today Snow is celebrated as the father of modern-day epidemiology.
During the last century, wastewater has become an important tool for monitoring community health, particularly for tracking drug use trends in cities and finding—and quickly eliminating—polio outbreaks. Still, wastewater was on the margins of widespread use in the U.S. A decade ago, when a scientist with the Environmental Protection Agency proposed a nationwide system to monitor community health. He couldn't get anyone to back the idea then.
In September 2020, the Centers for Disease Control and Prevention finally launched the country's first National Wastewater Surveillance System, which collects and tests samples as wastewater flows into treatment plants, and reports those results to the CDC to help guide local response. By then, though, more than 200,000 Americans had died from Covid-19. If the surveillance system had been up and running when the virus first came ashore in the U.S., it might have been detected much sooner, said Mason, the geneticist at Weill Cornell Medicine. "We would have known immediately within a day or two where the virus was appearing."
Wastewater continues to provide important intel about where the virus is circulating and the public's risk of exposure, particularly as clinical testing has been replaced by readily available home test kits. It's also helping health officials track the arrival and spread of new Covid-19 variants as they're emerging.
"We're out of the pandemic officially, but we still have circulating viruses, so what's interesting is we can see them in the wastewater," Mason said. If the abundance of the virus spikes, as it did recently in early September 2023—nearing the same levels as in late 2020—health officials can warn the public to take precautions to minimize exposure, such as mask wearing, hand washing, and social distancing. "It's good that most people have either been vaccinated or already infected, or both," Mason added.
Resources spent on developing the infrastructure for pathogen surveillance in wastewater has put the country in a better position to identify and respond to other health threats, including antibiotic resistance, foodborne diseases, mpox, and respiratory syncytial virus (RSV), experts say, but the program is still young, and there are some ethical and privacy concerns too.
It's a lot cheaper and more time-efficient to test sewage than to swab hundreds of people, or do blood testing, but wastewater is largely unregulated for privacy. What kinds of rights people have over what they flush and what's done with it is extremely murky. The National Academies of Sciences recently published a report detailing the ways in which the national wastewater surveillance system needs to implement sufficient oversight to protect privacy rights while further developing to monitor more communities, track multiple pathogens at the same time, and pivot to deal with emerging threats when a pathogen spikes.
"I like to joke, and say every time that a toilet flushes and if nobody takes a sample, somewhere an epidemiologist is crying," Mason said, laughing. "The amount of information that's present in every bit of wastewater is extraordinary. I think we're just beginning to tap it."
Mason's work mapping New York City's microbiome prompted researchers around the globe to contact him to discuss plans to swab their cities too. As interest grew, Mason and Evan Afshin, a medical student at New York Medical College, founded a global organization comprised of scientists from more than a hundred cities, known as Metagenomics and Metadesign of Subways and Urban Biomes, or MetaSUB consortium, rubbing Q-tips on surfaces in their countries' transit systems, sewage canals, hospitals, and other public places.
Similar to how naturalists have assembled volumes representing all the birds in North America, or all the fish in the Pacific, Mason and his colleagues have created an atlas of microorganisms found in urban mass transit systems around the globe. The scientists are now using sequencing technology and AI-powered software to develop a worldwide reference library of microbes and an open-sourced platform that allows users to enter a pathogen DNA sequence and see where else it has appeared in the world. "We want to make it so anybody anywhere can upload their sequence, and compare it to anything else that's ever been sequenced," Mason said.
In late October, GeoSeeq Foundation, a nonprofit data platform associated with a health-tech company Mason co-founded, announced it was teaming up with the Pasteur Network, an organization with an international network of scientists. The collaboration's aim is to closely examine rising infectious disease driven by climate change, including mosquito-borne illnesses like malaria and dengue. An Oct. 31 press release said the partnership could "usher in a new era of global pathogen surveillance and response." It combines the Pasteur Network's reach—32 institutes spread across 25 countries on 5 continents—with GeoSeeq's AI platform pulling from a wide variety of data streams, including climate, genomics, and public health.
"This connects all the labs around the world to be able to see if any new virus is emerging," Mason said in an email. "We can keep people safe once we know where the risks are, and we also can discover entirely new kinds of creatures in the world!" By identifying all types of microbes, researchers might also discover new antibiotics, and they're gaining the ability to track and map antibiotic resistance. Whether such an early warning system will catch a future pandemic pathogen remains to be seen.
Still, many pathogen trackers say the big dream is to one day have a worldwide disease surveillance system on par with current weather forecasting. Information about such factors as air pressure, temperature, and wind currents feed into weather maps that help forecasters identify developing storm patterns and aid response plans. The same can be done with microbial data feeding a global disease surveillance system, a costly endeavor, but worth it, Mason said, because "money spent on pathogen surveillance is much cheaper than a shutdown of the entire economy."
Scientists have learned a lot of lessons during the Covid-19 pandemic, he said. Now they just need to apply them.
How The Additives In Your Vaccines Rev Up Your Immune System
French veterinarian Gaston Ramon was researching diphtheria vaccines in the 1920s when he noticed something unusual. Adding breadcrumbs, tapioca, and other seemingly random ingredients made the vaccines work better.
Ramon used the word adjuvants to describe these additives, based on the Latin word adjuver, which means "to help." Today, there are more than half a dozen of them in use for various vaccines, and scientists continue to refine their understanding of how these helpers work to take the reins of the immune system and optimize inflammation. The research, experts say, might be the key to a new generation of vaccines that fight off more diseases for longer periods of time.
Vaccines already work by stimulating the inflammatory processes necessary to fight off infections, says Bali Pulendran, an immunologist at Stanford University in Palo Alto, California. Adjuvants take the process a step further, helping our bodies produce enough of the right type of inflammation but not too much of it. "You need just that Goldilocks zone—not too hot, not too cold, but just the right kind of inflammation of the right level and in the right place," Pulendran says. "That's where adjuvants can do their magic."
Controlled burnThe basic idea of a vaccine is to mimic the disease you want to protect against so that the immune system will respond in a specific way, says Larry Corey, an expert in virology, immunology, and vaccine development at the Fred Hutchinson Cancer Center in Seattle. Many vaccines do this with a killed version of a germ, a weakened version of a germ, or a toxic product of the germ that is packaged into a shot. Once injected, usually in the arm, the shot starts to trigger the immune system as soon as the offending agent, known as an antigen, enters the body. For an antigen that is new to the body, it takes two weeks to mobilize a measurable response.
The immediate reaction to a foreign antigen is called the innate immune response, and it involves specialized cells, such as dendritic cells and monocytes, which emit cytokines, prostaglandins, and other proteins that induce inflammation, Corey says. Symptoms of that immediate inflammation can include pain and swelling that may make your arm red and sore. In some cases, people also feel sick for a day or two.
In the meantime, immune cells carry the vaccine antigen to nearby lymph nodes, setting off a more lasting, "adaptive" immune response, during which yet more specialized cells, such as T cells and B cells, produce antibodies and develop a memory for the antigen. After they have been programmed, memory cells retreat to the bone marrow and lymph nodes, where they lay in wait until a similar invader appears again. The adaptive response is what leads to protection that can last for months to decades, Corey says.
Both the innate and adaptive immune responses rely on inflammatory processes, and vaccines are designed to try and induce just the right amount of it. "Vaccination is a form of inflammation," says Corey. "You're trying to elicit an immune response against the foreign antigen in a controlled way so you don't get sick."
Help neededSome vaccines do a good job of inducing immunity simply by showing the immune system part of the pathogen being targeted; the meningococcal vaccine targeting meningitis is one example. But some diseases are particularly hard to develop vaccines for. HIV, for example, employs multiple strategies to avoid recognition by immune cells and downplay their response. Influenza and SARS-CoV-2 evolve variants that can evade immune recognition. The malaria parasite has a complicated life history with still poorly understood impacts on the immune system.
To develop vaccines for these and other elusive pathogens, scientists are tapping into the intricacies of the immune system—many of them still not completely understood. For the ever-evolving SARS-CoV-2 and influenza viruses, for example, some researchers are working on universal vaccines that would recognize the parts of antigens that remain stable even as other parts mutate to produce new strains.
Adjuvants are a major part of the effort to harness inflammation with vaccines, based on work dating back to Ramon's era. The Frenchman's discovery began with what was a routine procedure at the time. For decades, scientists had been injecting a toxin made by the diphtheria bacteria into horses to elicit an immune reaction. They would then extract the horse's blood, which was now filled with antibodies, and use the serum to treat people who were sick with diphtheria.
Ramon noticed that when horses developed infections around the site of the vaccine injection, they produced a more powerful anti-diphtheria serum. Soon he was adding breadcrumbs and other items to shots to try and spur the same inflammatory reaction and aid immunity.
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COVID-19 can ruin your sleep in many different ways—here's whyAround the same time that Ramon was doing his research, British immunologist Alexander Glenny, also working with shots of diphtheria toxin, found that he could accentuate their effects in rabbits by adding aluminum salts. Aluminum was the first adjuvant used in licensed vaccines in the U.S. And the only one used in these vaccines for the next 70 years. It is still the most commonly used, Pulendran says, contained in billions of doses of vaccines given today.
Adjuvant biology got its next boost in the mid-1990s with the discovery of receptors on innate immune cells that, Pulendran says, ar
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