Maybe the saying is true: you don’t know what you had until it is gone. For the families in this episode, the absence of public health laboratories turned their worlds upside down and negatively impacted both the present and future. These families represent us all and highlight the vulnerabilities that would exist if there were no public health laboratories working continuously to keep our communities and populations safe.
Interviewer: Samir Patel, PhD, FCCM, (D)ABMM, clinical microbiologist, Public Health Ontario; Toronto, Canada
Expert: Vanessa Allen, MD, MPH, medical microbiologist, chief of microbiology, Public Health Ontario; Toronto, Canada
Narrator: Erin Bowles, B.S., MT(ASCP), Wisconsin Clinical Laboratory Network coordinator and co-biosafety officer, Communicable Disease Division, Wisconsin State Laboratory of Hygiene, School of Medicine and Public Health, University of Wisconsin-Madison
100 years ago, an influenza (flu) pandemic swept the globe, infecting an estimated one-third of the world’s population and killing at least 50 million people. The pandemic’s death toll was greater than the total number of military and civilian deaths from World War I, which was happening simultaneously. At the time, scientists had not yet discovered flu viruses, but we know today that the 1918 pandemic was caused by an influenza A (H1N1) virus. The pandemic is commonly believed to have occurred in three waves. Unusual flu-like activity was first identified in U.S. military personnel during the spring of 1918. Flu spread rapidly in military barracks where men shared close quarters. The second wave occurred during the fall of 1918 and was the most severe. A third wave of illness occurred during the winter and spring of 1919.
Here are 5 things you should know about the 1918 pandemic and why it matters 100 years later.
1. The 1918 Flu Virus Spread Quickly
500 million people were estimated to have been infected by the 1918 H1N1 flu virus. At least 50 million people were killed around the world including an estimated 675,000 Americans. In fact, the 1918 pandemic actually caused the average life expectancy in the United States to drop by about 12 years for both men and women.
In 1918, many people got very sick, very quickly. In March of that year, outbreaks of flu-like illness were first detected in the United States. More than 100 soldiers at Camp Funston in Fort Riley Kansas became ill with flu. Within a week, the number of flu cases quintupled. There were reports of some people dying within 24 hours or less. 1918 flu illness often progressed to organ failure and pneumonia, with pneumonia the cause of death for most of those who died. Young adults were hit hard. The average age of those who died during the pandemic was 28 years old.
2. No Prevention and No Treatment for the 1918 Pandemic Virus
In 1918, as scientists had not yet discovered flu viruses, there were no laboratory tests to detect, or characterize these viruses. There were no vaccines to help prevent flu infection, no antiviral drugs to treat flu illness, and no antibiotics to treat secondary bacterial infections that can be associated with flu infections. Available tools to control the spread of flu were largely limited to non-pharmaceutical interventions (NPI’s) such as isolation, quarantine, good personal hygiene, use of disinfectants, and limits on public gatherings, which were used in many cities. The science behind these was very young, and applied inconsistently. City residents were advised to avoid crowds, and instructed to pay particular attention to personal hygiene. In some cities, dance halls were closed. Some streetcar conductors were ordered to keep the windows of their cars open in all but rainy weather. Some municipalities moved court cases outside. Many physicians and nurses were instructed to wear gauze masks when with flu patients.
3. Illness Overburdened the Health Care System
An estimated 195,000 Americans died during October alone. In the fall of 1918, the United States experienced a severe shortage of professional nurses during the flu pandemic because large numbers of them were deployed to military camps in the United States and abroad. This shortage was made worse by the failure to use trained African American nurses. The Chicago chapter of the American Red Cross issued an urgent call for volunteers to help nurse the ill. Philadelphia was hit hard by the pandemic with more than 500 corpses awaiting burial, some for more than a week. Many parts of the U.S. had been drained of physicians and nurses due to calls for military service, so there was a shortage of medical personnel to meet the civilian demand for health care during the 1918 flu pandemic. In Massachusetts, for example, Governor McCall asked every able-bodied person across the state with medical training to offer their aid in fighting the outbreak.
As the numbers of sick rose, the Red Cross put out desperate calls for trained nurses as well as untrained volunteers to help at emergency centers. In October of 1918, Congress approved a $1 million budget for the U. S. Public Health Service to recruit 1,000 medical doctors and more than 700 registered nurses.
At one point in Chicago, physicians were reporting a staggering number of new cases, reaching as high as 1,200 people each day. This in turn intensified the shortage of doctors and nurses. Additionally, hospitals in some areas were so overloaded with flu patients that schools, private homes and other buildings had to be converted into makeshift hospitals, some of which were staffed by medical students.
4. Major Advancements in Flu Prevention and Treatment since 1918
The science of influenza has come a long way in 100 years! Developments since the 1918 pandemic include vaccines to help prevent flu, antiviral drugs to treat flu illness, antibiotics to treat secondary bacterial infections such as pneumonia, and a global influenza surveillance system with 114 World Health Organization member states that constantly monitors flu activity. There also is a much better understanding of non-pharmaceutical interventions–such as social distancing, respiratory and cough etiquette and hand hygiene–and how these measures help slow the spread of flu.
There is still much work to do to improve U.S. and global readiness for the next flu pandemic. More effective vaccines and antiviral drugs are needed in addition to better surveillance of influenza viruses in birds and pigs. CDC also is working to minimize the impact of future flu pandemics by supporting research that can enhance the use of community mitigation measures (i.e., temporarily closing schools, modifying, postponing, or canceling large public events, and creating physical distance between people in settings where they commonly come in contact with one another). These non-pharmaceutical interventions continue to be an integral component of efforts to control the spread of flu, and in the absence of flu vaccine, would be the first line of defense in a pandemic.
5. Risk of a Flu Pandemic is Ever-Present, but CDC is on the Frontlines Preparing to Protect Americans
Four pandemics have occurred in the past century: 1918, 1957, 1968, and 2009. The 1918 pandemic was the worst of them. But the threat of a future flu pandemic remains. A pandemic flu virus could emerge anywhere and spread globally.
CDC works tirelessly to protect Americans and the global community from the threat of a future flu pandemic. CDC works with domestic and global public health and animal health partners to monitor human and animal influenza viruses. This helps CDC know what viruses are spreading, where they are spreading, and what kind of illnesses they are causing. CDC also develops and distributes tests and materials to support influenza testing at state, local, territorial, and international laboratories so they can detect and characterize influenza viruses. In addition, CDC assists global and domestic experts in selecting candidate viruses to include in each year’s seasonal flu vaccine and guides prioritization of pandemic vaccine development. CDC routinely develops vaccine viruses used by manufacturers to make flu vaccines. CDC also supports state and local governments in preparing for the next flu pandemic, including planning and leading pandemic exercises across all levels of government. An effective response will diminish the potential for a repeat of the widespread devastation of the 1918 pandemic.
Visit CDC’s 1918 commemoration website for more information on the 1918 pandemic and CDC’s pandemic flu preparedness work.
Public health laboratories do a great deal of work that impacts the daily lives of everyone in America. Do you know exactly how much they’re doing? The first episode produced by members of the Emerging Leader Program cohort 10 looks at some of the work performed by public health lab scientists.
You can listen to our show via the player embedded below or on iTunes, Stitcher or wherever you get your podcasts. Please be sure to subscribe to Lab Culture so you never miss an episode.
(*indicates ELP cohort 10 member)
Water Quality Testing
Interviewer: *Amanda Hughes, program manager of ambient air quality monitoring, State Hygienic Lab at the University of Iowa
Michael Schueller, assistant director of operations, State Hygienic Lab at the University of Iowa
Nancy Hall, program manager, Environmental Microbiology, State Hygienic Lab at the University of Iowa
Expert: *Denny Russell, bioterrorism coordinator, Washington State Public Health Laboratory
Foodborne Outbreak Linked to Flour
Interviewer: *Rebecca Lindsey, Whole Genome Sequence Project lead, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC)
Heather A. Carleton, bioinformatics team lead, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC)
Samuel J. Crowe, National Outbreak Reporting System team lead, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC)
In 1918, no one even knew for sure that influenza was a viral disease; but then, the field of public health laboratory practice was still in its infancy. One hundred years later, public health is in a much better place, but critical preparedness gaps still persist. As our feature article shows, public health laboratories are working to keep their communities safe, through often difficult funding circumstances.
Seasonal flu activity has been intense this season. As of February 16, 2018 most of the United States continues to experience intense and widespread flu activity, with record-breaking levels of influenza-like-illness and hospitalization rates recorded. While H3N2 viruses are still most common, there is an increasing number of influenza B viruses being detected. It’s not uncommon for second waves of B virus activity to occur during a flu season. It’s likely that flu activity will continue for several more weeks.
Here are some important things to know right now to protect yourself and your loved ones from flu:
1. What are the symptoms of flu?
Flu viruses can cause mild to severe illness, and at times can lead to death. The flu is different from a cold. The flu usually comes on suddenly. People who have the flu often feel some or all of these symptoms:
Fever* or feeling feverish/chills
Runny or stuffy nose
Muscle or body aches
Some people may have vomiting and diarrhea, though this is more common in children than adults
* It’s important to note that not everyone with flu will have a fever.
2. What do I do if I get sick?
Most people with the flu have mild illness and do not need medical care or antiviral drugs. If you get flu symptoms, in most cases you should stay home and avoid contact with other people, except to get medical care.
CDC recommends that antiviral drugs be used early to treat people who are very sick with the flu (for example, people who are in the hospital) and people who are sick with the flu and are at high risk of serious flu complications, either because of their age or because they have a high risk medical condition.
3. Is it too late to get a flu shot?
No! As long as flu viruses are still circulating, it is not too late to get a flu shot. Flu vaccination is the best way to prevent flu illness and serious flu complications, including those that can result in hospitalization. Unfortunately, flu vaccines don’t work as well against H3N2 viruses, which means that some people who got vaccinated will still get sick; however, there are some data to suggest that flu vaccination may make illness milder. Flu vaccines usually work better against H1N1 viruses, which is another good reason to get vaccinated, since H1N1 is circulating too.
4. Why should I get a flu shot?
In addition to protecting yourself, getting vaccinated also protects people around you, including people who are more vulnerable to serious flu illness, like babies and young children, older people, pregnant women and people with certain chronic health conditions.
5. Does the flu shot work?
Vaccine effectiveness data for this season are not available yet, but we know that flu vaccines do not work as well against H3N2 viruses, which are predominant so far this season.
6. What else can I do to protect myself from flu?
Definitely try to avoid close contact with sick people. If you do get sick, limit contact with others as much as possible to keep from infecting them. Stay home for at least 24 hours after your fever is gone without the use of fever-reducing drugs (unless you need medical care or other necessities).
Other tips for stopping the spread of germs:
Make sure you cover your nose and mouth with a tissue when you cough or sneeze. Throw the tissue in the trash after you use it.
Wash your hands often with soap and water.
Avoid touching your eyes, nose, and mouth. Germs spread this way!
Clean and disinfect surfaces and objects that may be contaminated with germs like the flu.
NCBI now offers a flu sequence submission wizard that makes submissions easier and will provide you with accession numbers sooner. To get started, sign in to NCBI, go to the Submission Portal and choose the link for “Ribosomal RNA (rRNA), … Continue reading →
NCBI’s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive … Continue reading →
One of the best parts of my job is the opportunity to learn from a wide range of experiences. We have an obligation to not only respond to emergencies today, but to prepare for tomorrow by learning from the past. Our work extends to households affected by disease, communities ravaged by disasters, and U.S. territories battling new and changing threats. In fact, all over the world – we try to get ahead of, and manage, complex responses that touch many lives through ever changing circumstances. In an ideal world the health in every community would be at a level that would make recovery and reliance easier. The reality is that emergencies happen in all kinds of environments and populations.
The Public Health Preparedness and Response National Snapshot is our annual report that gives us an opportunity to showcase the work that we and our state partners do. The report reminds us that no matter how big the emergency, we need to work together to respond to the best of our ability—with the cards we are dealt.
1) Four Responses at Once: An Unprecedented Challenge
CDC experts continue to provide 24/7 monitoring, staffing, resources, and coordination in response to natural disasters, terrorist attacks, and infectious disease threats. In early 2016, CDC managed four public health emergencies at the same time through our Emergency Operations Center :
CDC scientists and responders were activated in CDC’s Emergency Operations Center, where they combed through research, developed and distributed diagnostic tests, and provided on-the-ground mosquito control and education to protect people at higher risk for the virus, including pregnant women and infants.
CDC’s Strategic National Stockpile is ready to send critical medical supplies quickly to where they are needed most to save lives. The stockpile is the nation’s largest supply of life-saving pharmaceuticals and medical supplies that can be used in a public health emergency if local supplies run out.
Last year, we helped conduct 18 full-scale exercises and provided training for 2,232 federal and state, local, tribal, and territorial emergency responders to ensure that systems for delivering medicines are functioning well before they are needed in an actual emergency. We continue to work with our federal, state, local, and commercial partners to make sure every step of the medical supply chain – from manufacture to delivery – is coordinated.
CDC connects with state and local partners to provide support and guidance, helping every community get ready to handle emergencies like floods, hurricanes, wildfires, or disease outbreaks.
This year, we created a new process to evaluate how well state and local jurisdictions can plan and execute a large-scale response requiring the rapid distribution of critical medicines and supplies. Through this program, we conducted assessments of 487 state and local public health departments. The information from these assessments will be used to help improve the ability to get emergency supplies quickly to those who need them most.
To protect lifesaving research, CDC experts in biosafety and biosecurity conducted approximately 200 laboratory inspections and thousands of assessments of those who handle dangerous select agents and toxins like anthrax, plague, and ricin to keep these materials safe, secure, and out of the hands of those who might misuse them.
CDC’s Laboratory Response Network (LRN)l also develops and deploys tests to combat our country’s most pressing infectious and non-infectious health issues, from Ebola to Zika virus to opioid overdose. The network connects over 150 labs to respond quickly to high priority public health emergencies.
CDC supports efforts all across the country to help those who may not be able to help themselves when a crisis strikes. Some populations, like children, older adults, and others with functional and access needs may need extra help during and after an emergency.
From planning for the 69 million children who may be in school when disaster strikes to the millions of Americans who need to make sure prescriptions are filled, medical equipment is working, and help arrives even if power is out and roads are blocked, it’s up to us to protect our most vulnerable in emergencies.
Learn about an innovative program to help people with disabilities stay safe in emergencies
7) Emergency Leaders: The Future of Incident Response
When every minute counts, we need people who have the knowledge to step in and take immediate action. Learning and using a common framework like the CDC Incident Management System helps responders “speak the same language” during an event and work more seamlessly together.
CDC experts train leaders from around the world—25 countries in 2016—through an innovative, four-month fellowship based at our Atlanta headquarters. Lessons learned from this course were put to work immediately to head off an outbreak of H5N1 influenza in Cameroon.
8) The Power of Preparedness: National Preparedness Month
Throughout September, CDC and more than 3,000 organizations—national, regional, and local governments, as well as private and public organizations— supported emergency preparedness efforts and encouraged Americans to take action.
The theme for National Preparedness Month 2016 was “The Power of Preparedness.” During our 2016 campaign , we recognized the successes of countries and cities who have seen the direct benefits of being prepared, looked at innovative programs to help children and people with disabilities get ready for emergencies, and provided tips for home and family on making emergency kits.
As part of the Global Health Security Agenda, teams of international experts travel to countries to report on how well public health systems are working to prevent, detect, and respond to outbreaks. In May, a team made a five-day visit to the U.S. to look at how well we’re doing.
In the final report, the assessment team concluded that, “the U.S. has extensive and effective systems to reduce the risks and impacts of major public health emergencies, and actively participates in the global health security system.” They recognized the high level of scientific expertise within CDC and other federal agencies, and the excellent reporting mechanisms managed by the federal government.
Flu (influenza) is a serious disease caused by influenza viruses. Flu viruses change constantly. They are among the fastest mutating viruses known. These changes can impact how well the flu vaccine works, or can also result in the emergence of new influenza viruses against which people have no preexisting immunity, triggering a pandemic. Year round, scientists from CDC, World Health Organization (WHO), and other partners monitor the influenza viruses that are infecting people. These scientists study the viruses in the laboratory to see how they are changing.
CDC is using next-generation gene sequencing tools to analyze flu viruses as part of CDC’s Advanced Molecular Detection (AMD) initiative. The technology allows CDC to study more influenza viruses faster and in more detail than ever before. AMD technology uses genomic sequencing, high-performance computing, and epidemiology to study pathogens and improve disease detection. CDC is using this Next Generation-Sequencing (NGS) technology to monitor genetic changes in influenza viruses in order to better understand and improve the effectiveness of influenza vaccines.
To share more information about this revolutionary NGS technology and its impactful work, CDC expert John Barnes, PhD, Team Lead of the Influenza Genomics Team within the Virology, Surveillance, and Diagnosis Branch within CDC’s Influenza Division took part in a Reddit Ask Me Anything digital Q & A, to answer the public’s question on AMD technology and how these tools are helping to improve influenza virus monitoring and the development of better-performing influenza vaccines. This post includes some highlights from that discussion.
Question 1: What exactly does the AMD technology platform do that is different from the current approaches used to guide vaccine development? And what are the most common reasons that we “guess wrong” in terms of which viral strains will be responsible for the next season’s flu?
Dr. Barnes: One example of how AMD technology is used in vaccine development is to address mutations that may occur in vaccine viruses during growth in eggs used in the production of vaccine viruses. These mutations can change the vaccine virus so much that the immune response to vaccination may not protect as well against circulating viruses. This means that vaccinated people may still get sick. CDC is using AMD technology to try to solve this problem. Scientists are looking at the genetic sequences of 10 generations of H3N2 flu viruses as they grow and evolve in eggs. CDC will test all of the viruses to find out what genetic changes cause a good immune response and good growth in eggs. Once the “good” genetic changes are identified, CDC will then synthesize H3N2 viruses with those properties that can be used to make vaccine that offers better protection against H3N2 flu infection. One of the main reasons that the virus is challenging, is due to its’ RNA polymerase. The polymerase of influenza is very mistake prone and causes the virus to mutate rapidly. For example, in some years certain influenza viruses may not appear and spread until later in the influenza season, making it difficult to prepare a candidate vaccine virus in time for vaccine production. This can make vaccine virus selection very challenging. We are currently using AMD techniques to sequence all clinical specimens that come into the CDC to improve our ability to find and track mutations that may be of concern.
Question 2: Why are chicken embryos typically the go-to for flu vaccine cultivation?
Dr. Barnes: Thanks for this question – it’s one we get a lot! Flu vaccines have been made using an egg-based manufacturing process for more than 70 years. In the past, when making a vaccine for production manufacturers utilized eggs as a safe host to make the vaccine and to provide high yield. As birds are the natural reservoir host for flu, influenza typically grows well in eggs and maintains a safe distance between species you’re using to make the vaccine and the target. Mammalian cell lines were subjected to extensive safety testing to establish a cell line that is human pathogens free, while maintaining sufficient vaccine yield. You can learn more about how AMD technology is improving the development of flu vaccines made using egg-based technology, here.
Question 3: What about the flu virus causes it to mutate so quickly from year to year requiring a new vaccine every season? For example with chickenpox there is one virus and one vaccine, why then with the flu are there countless strains and a new vaccine every year?
Dr. Barnes: As you know, influenza is a virus and can only replicate in living cells. Influenza viruses survive by infecting host cells, multiplying, and then exiting host cells. The enzyme influenza uses to copy itself is very error prone which causes the virus to rapidly mutate. Each host has its own defense mechanisms and these defenses are collectively referred to as environmental pressures. It’s difficult to predict how a virus will mutate when attempting to get around a host’s immune defenses, but the changes can happen rapidly, as you said.
Because flu viruses are constantly changing, the formulation of the flu vaccine is reviewed each year and sometimes updated to keep up with changing flu viruses. More information about how influenza viruses can change is available here.
Question 4: Do you have any insight on the universal vaccine that was developed?
Dr. Barnes: Great question! Yes, I can provide some insight. A longer-term goal for seasonal flu vaccines is the development of a single vaccine, or universal vaccine, that provides safe, effective, and long-lasting immunity against a broad spectrum of different flu viruses (both seasonal and novel). Right now, CDC is a part of an inter-agency partnership coordinated by the Biomedical Advanced Research and Development Authority (or BARDA) that supports the advanced development of new and better flu vaccines. These efforts have already yielded important successes (i.e. a high dose flu vaccine specifically for people 65 years and older that creates a stronger antibody response), but a part of this effort is the eventual development of a universal vaccine. A number of government agencies and private companies have already begun work to advance this type of vaccine development, but, as you can imagine, this task poses an enormous scientific and programmatic challenge.
Question 5: How would you convince someone who is staunchly against flu vaccines that they’re a good thing?
Dr. Barnes: Help address misconceptions about the flu. Remind people that a flu shot cannot cause flu illness. They should understand that anyone can get the flu, and each year, thousands of people in the United States die from flu, and many more are hospitalized. It’s important to stress that the flu vaccine can keep people from getting flu, make flu illness less severe if they do get it, AND keep them from spreading flu to their family and other people that could be at high risk of severe flu complications.
Interested in learning more? Check out Dr. Barnes’ full Reddit AMA here.
John Barnes, Ph.D., is Team Lead of the Influenza Genomics Team (IGT) at the Virology, Surveillance, and Diagnosis Branch of the CDC’s Influenza Division. He earned his Ph.D. degree in Biochemistry and Molecular Biology from University of Georgia in Athens, Georgia. Dr. Barnes began his career at CDC in the Influenza Division in 2007 after working at a postdoctoral fellow at the Emory University Department of Human Genomics. His current work includes managing a staff of nine to serve the sequencing and genetic analysis needs of the Influenza Division. Current numbers of viruses sequenced by the IGT make CDC’s Influenza Division the largest contributor of influenza sequence data among the WHO Influenza Collaborating Centers.
Fever, body aches, cough… you suspect the flu. You drag yourself out of bed to visit your healthcare provider where they use a swab to take a small sample from your throat or nose for a point-of-care diagnostic test. It’s positive; you’ve got the flu. After stopping at the pharmacy to pick up the antiviral medication that was prescribed, you head home to hunker down under the covers and queue up Netflix.
Unfortunately for the sample your healthcare provider collected, there is no time to rest. The point-of-care diagnostic test was just the beginning; that test gives your healthcare provider the information they need to provide treatment. But the public health system needs more information on how your case fits into the national – and, in many ways, the global – flu picture. At the end of the week, your healthcare provider’s laboratory staff sends all relevant samples to the public health laboratory. This is where your sample’s journey in the public health system begins.
Samples like yours inform the WHO, WHAT, WHEN and WHERE of influenza activity:
WHO is being most affected? Young children or the elderly? Are positive patients hospitalized or outpatient? Were they vaccinated or not?
WHAT type/subtype of flu is making people sick and how prevalent is that type/subtype? Furthermore, what is the specific strain and does it match well with the current vaccine?
WHEN did the season start, when does it peak and when will it end?
WHERE are people getting sick? What is happening in each state and/or region?
This is a look at the journey your sample will take and how it will help the public health system respond to this flu season and prepare for the next. Get ready, little sample! It’s a long ride…
Your sample arrives at the public health laboratory’s centralized check-in where the package is opened, paperwork is reviewed and a laboratory identity is created (your personal identity no longer accompanies the sample). Because public health labs receive hundreds of samples every day for not only respiratory illnesses such as flu, but also diarrheal illnesses, sexually transmitted infections, newborn genetic screening and many others, this process is critical to ensure each sample is accurately documented and delivered to the appropriate laboratory for testing. In fact, during the course of one flu season, a state public health laboratory can receive approximately 4,000 samples for influenza testing alone!
Once that process is completed, your sample is delivered to the virology lab for testing.
Your sample has been kept cold and properly stored to maintain the integrity of the virus, which is important for the laboratory testing. This lab uses a molecular method called PCR to rapidly amplify and detect a region of viral RNA. In fact, the PCR test performed at public health labs is specially designed to not only confirm and subtype flu, but also to detect new and emerging flu viruses. This is an important function of public health labs as our nation’s first line of detection for novel flu viruses.
Results received and reporting begins
The test results for your sample indicate you are sick with influenza B. Because your case is typical for flu season, state epidemiologists do not initiate further investigation. However, the data from your sample does get included in their weekly summary report informing physicians and the public of influenza activity in your state. Furthermore, this information is recorded electronically in the laboratory information management system (LIMS) and a lab report is faxed back to your healthcare provider’s office. (This information typically would not impact your treatment.) Data is also transmitted to the Centers for Disease Control and Prevention (CDC) for national flu surveillance using the Public Health Laboratory Interoperability Project (PHLIP). Standardized PHLIP messaging simplifies the secured electronic transfer between public health laboratories. Once at CDC the data contributes to FluView, their weekly flu surveillance report.
Further characterization of specimen
Your sample was selected to be included in your state public health lab’s biweekly shipment to their designated national Reference Center – one of three National Influenza Surveillance Reference Centers, state public health laboratories that act as an extension of CDC’s Influenza Division – where it will be isolated and further characterized.
Every two weeks during flu season, all state and some local public health laboratories participate in national surveillance by sending up to eight influenza specimens to one of three National Influenza Surveillance Reference Centers. These eight specimens consist of up to two samples of the four seasonal strains of flu: influenza A(H3N2), influenza A(H1N1)pdm09, influenza B/Yamagata lineage and influenza B/Victoria lineage positive specimens. When combined with all of the other public health lab submissions, this relatively small number of samples allows CDC to watch closely for drift. (Drift happens when small genetic changes accumulate over time as a virus replicates and result in viruses that are antigenically different. When this happens, the body’s immune system may not recognize those viruses and may have trouble fighting them off). And with all of that information, CDC can be 95% confident that, should a drift variant emerge at 3% prevalence or higher across the country, at least one of those drift variants will be detected over a month surveillance period. Knowing about drift sooner would hopefully lead to a quicker response than before this submission guidance was in place. At the reference centers and CDC, these specimens undergo further antigenic and genetic characterization which generates data that helps select strains to be used in the development of future seasonal vaccines.
Finally your sample gets to rest
After a whirlwind of tests, your sample finally gets to rest in a chilly -80°C freezer. Public health laboratories keep samples like yours should additional testing be needed and to aid in the development and validation of new laboratory tests or methods.
Your little sample contributes in a big way
While the sample sits frozen, the data remains actively in play. Public health officials will look at the data from your sample along with thousands of other data points to determine what influenza strains are circulating in the United States, detect novel viruses and monitor whether the virus begins to drift away from the strains in the vaccine. On an even bigger scale, vaccine strain selection is a global process so your sample may ultimately inform vaccine strain selection for the entire world.
Next time you are sick and your healthcare provider takes a little sample from your nose, remember that you are not only getting the diagnosis necessary for your own treatment but you’re contributing to national and global influenza response.