(Editor’s Note – The following is an updated repost of a story on the USAF School of Aerospace Medicine Epidemiology Reference Laboratory at Wright Patterson Air Force Base in Dayton, Ohio, which was originally published on March 27, 2018. It contains new information on the lab’s mission during the COVID-19 pandemic.)
For the latest Air Force information and guidance on COVID-19 go to https://www.af.mil/News/Coronavirus-Disease-2019/
Update – COVID-19 and the USAFSAM Epi Lab
The United States Air Force School of Aerospace Medicine’s epidemiology laboratory is the Air Force’s sole clinical reference laboratory, and as such, is testing and processing samples of COVID-19 sent from military treatment facilities around the world.
The lab was authorized by the Defense Health Agency to test samples from Department of Defense beneficiaries for COVID-19 in early March, and received its test kit from the Centers of Disease Control and Prevention shortly after.
“The USAFSAM Epi Lab is currently working long hours, testing and processing samples of COVID-19 that are coming in from MTFs globally,” said Col. Theresa Goodman, USAFSAM commander. “If you ask anyone on this team how they’re doing, they’ll tell you they’re fine–that they’re just doing their jobs. But I couldn’t be more proud of them right now — their selfless and tireless dedication to this mission. COVID-19 testing is our primary mission right now and the members of the Epi Lab are my front line to this fight.”
USAFSAM’s epidemiology laboratory, nested in the Air Force Research Laboratory’s 711th Human Performance Wing, has a long history of testing and identifying various infectious respiratory diseases, including those that occur on a regular basis like influenza, and the ones similar to COVID-19 that become a public health issue, spreading globally. Because of this, the team works closely with the CDC and other agencies.
“We have been in operation for approximately 30 years, and therefore involved with many other infectious disease outbreaks, for example SARS,” said Col. Dana Dane, USAFSAM Public Health Department chair.
This laboratory is only authorized to test samples coming in from DoD beneficiaries, but those outside this demographic have the support of their state public health departments for testing purposes. USAFSAM is working closely with public health professionals across the DoD, as well as with the CDC as the situation evolves. Per CDC guidelines, reference laboratories are no longer required to submit samples to the CDC for further testing and final confirmation. If the tests do show as positive, the USAFSAM Epi Lab marks the sample “confirmed positive.”
USAFSAM’s laboratory is not participating in vaccine development. It also is not the type of laboratory where people go to get blood drawn, nasal swabs, etc., like a CompuNet or clinic at a doctor’s office or in a hospital. USAFSAM’s clinical reference lab is set up to receive these samples from military treatment facilities. They run the tests on those samples and log the data.
“We’re all sensitive to those around the world who are grieving losses due to this awful virus as well as to others who are just downright scared. Our hearts go out to you,” said Goodman. “But just know that our epidemiology laboratory here in USAFSAM is waiting at the door 24/7 for any and all samples that come in from our DoD family.
Goodman also stated that the team is lockstep with public health personnel around the world as well as with our partners at the CDC.
“We truly are all in this together,” she said. “Fighting this virus will take all of us doing our part–from those staying at home washing their hands a little more often and checking on neighbors to USAFSAM’s public health team testing samples and getting the data where it needs to go.”
The Disease Detectives (Original post – March 27, 2018 )
After slowly using a blade to cut through thick tape, a technician in a protective gown and glasses opens the flaps of a cardboard box revealing a polystyrene container. As her gloved hands cautiously remove the lid, a wisp of vapor rolls slowly over the edge of the box, clinging to its surface as it descends onto the tabletop.
The technician gingerly reaches through the fog and removes a plastic bag filled with clear vials from the container. This process is repeated over a hundred times each morning as carts filled with boxes of clinical patient specimens arrive at the U.S. Air Force School of Aerospace Medicine’s Epidemiology Laboratory Service at the 711th Human Performance Wing at Wright Patterson Air Force Base, Ohio.
Created in 1990, the Epi Lab, as it is referred to at USAFSAM, focuses on clinical diagnostic, public health testing and force health screening, performing 5,000 to 8,000 tests six days a week (or about 2.1 million tests a year) for clinics and hospitals treating active duty service members, reservists and National Guard members and their dependents and beneficiaries.
The data collected from these tests not only enables the analysis of disease within the joint force, but is shared with civilian public health agencies contributing to the tracking of diseases, such as influenza and sexually transmitted diseases (STDs), as well as supporting disease prevention efforts, such as the formulation of vaccines.
While the lab receives most of its medical samples from Air Force bases around the world, it also tests specimens sent by Navy and Army hospitals and clinics, totaling more than 200 military medical facilities around the globe.
The Epi Lab’s workload is a result of its efficiency and economics, according to Elizabeth Macias, Ph.D., a clinical microbiologist, and director of the Epi Lab.
“A lot of the testing is very specialized, and in some cases can be very expensive. Many of our Air Force clinics and laboratories are small and don’t have the personnel to do that kind of thing or the funding to get all the specialized instruments that we have,” Macias said. “Our personnel are comprised of military, government civilians and contractor civilians, so we have the expertise and the personnel to handle the workload.”
Nearly 30 people work throughout the morning, removing samples packed in dry ice from their boxes, ensuring the patient information on the specimen tubes and paperwork match the orders on the computer system and then re-labeling them for the lab’s computer system before sending the samples to the appropriate testing departments.
“The laboratory consists of three branches; Customer Support, Immunodiagnostics and Microbiology. Immunodiagnostics and Microbiology perform testing, such as immune status and screening for STDs, like Human Immunodeficiency Virus (HIV), gonorrhea, syphilis and hepatitis and some other serology assays,” said Tech. Sgt. Maryann Caso, noncommissioned officer in charge of the immunodiagnostic section of the Epi Lab.
Just over a year ago, the Epi Lab adopted fourth-generation HIV testing, which enables the lab to detect an HIV infection two weeks sooner after a patient is exposed. This newer technology allows patients to receive treatment and counseling sooner.
There is a constant flow of samples requiring STD screening and immune status testing, as these are gathered as part of the in-processing screening for each new service member. The tests help screen for potentially infectious diseases as well as establish a baseline of antibody types and levels for each new recruit to precisely target which vaccines they need.
“For example, all the new recruits are tested for measles, mumps, and rubella. So if they have antibodies to those diseases then they’re not vaccinated again. This saves the Department of Defense because they don’t waste manpower and money to vaccinate somebody that is already protected against those diseases,” Macias said.
The lab has become more efficient and safer for laboratory technicians after the installation of an automated testing system last year.
“The samples come in now and are put on an automated line. It will actually uncap the sample, spin it down, aliquot it (divide the sample into smaller portions for multiple tests) and sort it to whatever section and analyzer it needs for a particular test,” Caso said.
“Before, our techs had to manually uncap the tubes, aliquot the samples and sort them. When you have thousands of samples that you have to uncap and then recap by hand, you get repetitive-motion injuries to the wrist – such as carpal tunnel. The whole idea is to have automated processes and to eliminate or mitigate pre-analytical errors, such as specimen contamination.”
Once tested, the results are automatically returned to the submitting hospital or clinic via computer, unless the system notifies a technician to intervene and manually certify the test result.
“Specimens are collected at hospitals and clinics around the world and sent to us,” Macias said. “We receive the boxes within 24 hours and most of the results are completed within 24 hours… So, generally, we get those results back to the submitting clinic within 48 hours from when they are shipped to us, so the docs can then treat their patients appropriately and with a good turnaround time.”
In addition to the immunology testing that is performed in the lab, the Microbiology branch performs testing on bacterial cultures, examines fecal samples for parasites that cause intestinal disease, and performs influenza testing.
The Air Force began an influenza surveillance program in 1976 to collect data about disease and its spread in response to an outbreak of what was called “Bootcamp Flu.” In the close quarters of basic training, the virus spread through many barracks, according to Donald Minnich, technical supervisor for the Virology and manual testing section at the Epi Lab.
To combat illness, recruits needed to be regularly monitored, giving birth to Operation Gargle, in which recruits gargled with a solution and spit it back into a specimen cup which was then tested for influenza and other respiratory pathogens.
The Air Force program is now part of the Defense Health Agency’s Global, Laboratory-Based Respiratory Pathogen program which grows, sequences and collects data on influenza, parainfluenza, adenovirus and the Respiratory Syncytial Virus, or RSV.
The flu surveillance program at the Epi Lab has approximately 95 submitting laboratories scattered across the continental United States and the globe, from deployed areas to Europe, Japan and Guam.
In a typical flu season, the surveillance program receives between 5,000 and 6,000 specimens. This year, the Epi Lab has received 5,000 specimens in just the first few months of the flu season, according to Minnich.
“We’re on track to probably double what we saw last year. We’re receiving about 200 new specimens a day for culture and molecular subtyping,” he said.
Testing in the microbiology section is still performed hands-on by technicians. Once a sample has been cultured, it is tested to determine whether it’s an influenza or another respiratory pathogen, and, if influenza, whether it is type A or B.
Then the molecular section of the lab determines the subtype of the influenza based on the hemagglutinin and the neuraminidase genes of the virus, the H or the N in the flu typing which gives each strain its name, such as H3N2 or H1N1.
Once typing is completed, the entire genome of the eight-segmented RNA virus must be sequenced to search for changes to those genes, referred to as a point mutation or “drift”.
“Mostly what we see is drift; small point mutations,” Minnich said. “If a drift is just one or two deletions in a gene, the vaccine may still be effective because your antibodies may still attach to virus, but, they won’t attach as well. It (the vaccine) will be effective but not as effective as it would have been against the original vaccine strain.”
It is when there is an exchange of RNA from another species that carries influenza, such as a bird or pig that a more radical change in the virus strain can occur.
“When one of those genes changes abruptly, we call that a ‘shift’. That would be an entirely new strain of influenza that we are not protected against by a vaccine. Drifts happen pretty regularly, but shifts don’t happen very often. The last one happened in 2009 with H1N1,” Minnich said. “The virus has eight separate genes, but if you take one of those away and you put a new one in, it’s a complete different virus. Antigenically, your body’s immune system does not recognize it as the flu.”
According to Minnich, the formula for each influenza vaccine is finalized by the Centers for Disease Control and Prevention (CDC) in February of each year, based on influenza type and subtype data collected up to that time, because it takes until August for a vaccine to be manufactured in quantities necessary to inoculate the public.
Influenza virus mutates so quickly and often the type spreading in August could be quite different from the one used to formulate that season’s vaccine the previous February. That is what happened this flu season as the H3 virus drifted after the vaccine for the upcoming year was formulated and production well under way. Luckily, the vaccine still offers some protection because the drift was not overwhelming.
“Once that decision’s made and things are rolling, it’s kind of too late to change after that. Fortunately, the strain of influenza we have this year matches up very closely to the vaccine strain,” Minnich said.
Of the data the CDC gathers to formulate each season’s influenza vaccine, 25 percent comes from gene sequencing performed at USAFSAM.
“The CDC evaluates data from all over the world, but they particularly like our laboratory because we receive specimens from areas that they don’t have access to, like some of our deployed sites, for example, and some of our bases,” Macias said.
The Epi Lab is also part of a network of labs that receives samples of reemerging or unknown pathogens for testing.
The CDC can determine the nature of a pathogen more quickly by sending samples to multiple laboratories at once. In this way, results between labs can be quickly compared for confirmation of the nature and type of the pathogen.
Unknown pathogens and more highly infectious airborne pathogens, such as tuberculosis, are examined in the Epi Labs’ Biosafety Level Three laboratory, the only such clinical facility in the Air Force. There, negative air pressure keeps potentially dangerous pathogens from escaping and work is performed by technicians in a biological safety cabinet where the air is circulated through a series of filters before being exhausted outside.
According to Macias, the capabilities and efficiency of the Epi Lab not only supports force readiness, but establishes the Public Health Department of USAFSAM as a key partner with civilian public health agencies, contributing to the overall health of the general population.