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Genome Data from Africa Reveal Millions of New Variants

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H2Africa logo
Credit: Human Heredity and Health in Africa Initiative

The first Homo sapiens emerged in Africa hundreds of thousands of years ago. We are all descended from that common pool of ancestors. Put another way, we are all Africans. While it’s not possible to study the DNA of these vanished original human populations, it is possible to study the genetic material of today’s African peoples to learn more about the human genome and its evolution over time. The degree of genetic diversity in Africa is greater than anywhere else in the world.

Progress continues to be made in this important area of genomic research. The latest step forward is a study just published in the journal Nature that analyzes more than 400 complete human genomes, including 50 distinct groups of people from 13 African countries. This work has uncovered about 3.4 million unique gene variants that had never before been described, greatly expanding our knowledge of human genetic variation and its implications for health and disease.

This work is the latest from the Human Heredity and Health in Africa (H3Africa) Initiative , which I helped establish a decade ago. This partnership between NIH, the Wellcome Trust, and the Alliance for Accelerating Excellence in Science in Africa (AESA) seeks to train a new generation of African scientists in genomic science and other disciplines, while conducting state-of-the-art health research on the African continent. The hope is to help these scientists use their new knowledge to improve human health in Africa and to help fill significant gaps in our knowledge of the diversity within human genomes.

The new study was led by Zané Lombard, the University of the Witwatersrand, South Africa; Neil Hanchard, Baylor College of Medicine, Houston; and Adebowale Adeyemo, NIH’s National Human Genome Research Institute, Bethesda, MD. It also included more than 50 other H3Africa data providers and data analysts from across Africa and around the world.

These researchers sequenced and analyzed the genomes of 426 individuals, almost all from studies and countries within the H3Africa Consortium, the network of NIH and Wellcome Trust-funded research sites in Africa. These individuals were carefully selected to provide broad coverage of the diverse landscape of African genomic variation. They also included many populations that hadn’t been studied at the genetic level before. The team focused its attention on single-letter differences, also known as single nucleotide variants (SNVs), located across the 3 billion DNA letters of the human genome.

All told, the researchers observed more than 31 million confirmed SNVs. Of the 3.4 million newly discovered SNVs, most turned up in the genomes of individuals from previously unstudied African ethnic groups with their own distinct languages. Even among SNVs that had been previously reported, several were found much more often than in other populations. That’s important because medical geneticists often include information about frequency in deciding whether a gene variant is a likely cause of rare disease. So, this more complete picture of normal genetic variation will be valuable for diagnosing such genetic conditions around the globe.

The researchers also found more than 100 regions of the genome where the pattern of genetic variation was suggestive of underlying variants that were evolutionarily favored at some time in the past. Sixty-two of those chromosomal locations weren’t previously known to be under such strong natural selection in human populations. Interestingly, those selected regions were found to contain genes associated with viral immunity, DNA repair, reproduction, and metabolism, or occurred close to variants that have been associated with conditions such as uterine fibroids and chronic kidney disease.

The findings suggest that viral infections, such as outbreaks of Ebola, yellow fever, and Lassa fever, may have played an important role over centuries in driving genetic differences on the African continent. The data also point to the possibility of human adaptation to differences across the African continent in local environments and diets, and these adaptations could be relevant to common diseases and traits we see now.

The researchers used the data to help gain insight into past migrations of human populations. The genetic data revealed complex patterns of ancestral mixing within and between groups. It also uncovered how distinct groups likely moved large distances across Africa in the past, going back hundreds to thousands of years. The findings also offered a more complete picture of the timing and extent of the migration of speakers of Africa’s most common language group (Bantu) as they moved from West Africa to the southern and eastern reaches of the continent—a defining event in the genetic history of Africa.

There’s still much more to learn about the diversity of human genomes, and a need for continued studies, including many more individuals representing more distinct groups in Africa. Indeed, H3Africa now consists of 51 projects all across the continent, focused on population-based genomic studies of many common health conditions, from heart disease to tuberculosis. As the cradle of all humanity, Africa has much to offer genomic research in the years ahead that will undoubtedly have far-reaching implications for people living in all parts of our planet.

Reference:

[1] High-depth African genomes inform human migration and health. Choudhury A et al. 2020 Oct;586(7831):741-748.

Links:

Human Heredity and Health in Africa (H3Africa) (NIH)

H3Africa (University of Cape Town, South Africa)

NIH Support: National Human Genome Research Institute; National Institute of Allergy and Infectious Diseases


Building Resilience During the COVID-19 Pandemic

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Drs. Collins and Everly on a virtual chat

Dating back to our earliest times, humankind has experienced the psychological impact of a wide range of catastrophes, including famines, floods, earthquakes, wildfires, windstorms, wars, and, last but certainly not least, outbreaks of potentially deadly infectious diseases. We are certainly no exception today as people try to figure out how to cope—and help others cope—with the grief, stress, and anxiety caused by biggest health challenge of our time: the coronavirus 2019 (COVID-19) pandemic.

With more than 215,000 Americans having lost their lives and more than 7.8 million infected since COVID-19 first gripped our nation, the pandemic has taken a profound psychological and emotional toll on us all. Still, behavioral and social science researchers have identified some strategies to help us deal with our fears, and even rise to the challenge of supporting others during this unprecedented time.

Recently, I had an opportunity to discuss the science behind mental health responses to disasters with Dr. George Everly Jr., a psychologist and professor at the Johns Hopkins University Bloomberg School of Public Health, Baltimore. A world-renowned expert with more than 40 years experience studying the psychological impacts of disasters, he co-founded the International Critical Incident Stress Foundation, an organization affiliated with the United Nations. Our conversation took place via videoconferencing from our home offices in Maryland. Here’s a condensed transcript of our chat:

Collins: Good morning! At NIH, we are doing everything we can to keep our scientific mission going by supporting groundbreaking research into COVID-19 and a lot of other things. We’re also deeply committed to helping people manage stress and attend to mental health. So, we’ve invited Dr. Everly to share insights that I believe will help us learn some skills to build resilience. Goodness knows, this is a time where we all need resilience, as well as to help others around us. We’re all called upon, I think, to look after our friends and neighbors in the aftermath of a circumstance like the current pandemic.

Everly: It’s a privilege to spend some time with you today and chat about such an important topic. The topic we typically think about in terms of disasters is the physical response. Today, we’ll talk about the psychological impact of the COVID-19 pandemic. This is actually my third pandemic, having consulted in Hong Kong with SARS and Singapore with H1N1. I’ve also done consulting with Ebola.

However, I will tell you that this pandemic, COVID-19, has been the most challenging. I think we can we agree that mental health is an intrinsic value as it relates to us as humans. Anything that threatens mental health, especially in large numbers, threatens the core fabric of society.

According to the United Nations, we may now be looking at an impending international mental health crisis. Some have called this the “hidden” pandemic: people who previously coped well may have challenges and people who had challenges coping before COVID-19 may have increased challenges. Looking at first responders and frontline workers, we have seen heroic efforts on their part, but not without consequences—and mental exhaustion may be one of them

Collins: How is this crisis similar—and how is it different—from most of the disasters that people have dealt with?

Everly: The first thing is expectations. If we expected COVID-19 to be short lived, we have been remarkably, if not catastrophically, disappointed.

So, this connection occurred to me. A number of years ago, I was interested in the psychological impact of the London Blitz, and I went to England to interview people who went through that night upon night upon night of intractable bombing during World War II. I wanted to find out what helped people make it through. It was very clear that their initial belief that the bombing would be short-lived was tragically violated. They then as a community understood that they had to shift into a different mindset, and realize the Blitz wasn’t a sprint—it was marathon. They’d originally sent their children out into the countryside, but later decided to bring them back in the midst of bombing. I will suggest that psychologically, that was the turn of the war. In fact, research later by Anna Freud found that sending the kids away was psychologically more injurious than keeping them in the city. And I think that’s really important. Realizing that we are in for a long haul with COVID-19, in and of itself may be a game changer.

Collins: A very interesting comparison. I hadn’t thought about it that way—an acute disease becoming chronic.

Tell us a little bit more about the undercurrent of malaise in our country even before this COVID-19 pandemic hit—what economists Angus Deaton and Anne Case have recently written about as the “deaths of despair” and the opioid crisis. We are facing a pandemic from coronavirus, but it didn’t land on a completely blank page. It landed in a circumstance where many people were already feeling significant stress, and where depression was increasing risks of overdoses and suicide.

Everly: Fantastic question. You probably remember the work of Hans Selye, an endocrinologist who actually coined the term “stress.” He said, at any given point in time, we have a limited supply of what he called “adaptive energy.” In the best of conditions, this reservoir is quite high and will allow us to meet unusual challenges. However, I would suggest that the background noise of chronic issues that predated COVID-19 did begin to deplete that reservoir of adaptive energy, making us more vulnerable to things that turned out to be far more challenging than we thought. We were starting with one foot in the hole, so to speak.

Collins: All the more reason why our resilience is being called upon. Piled on top of it, many people are facing the serious challenge of trying to telework from home and trying to manage their responsibilities in terms of children or other family members who need care. My heart goes out to those folks as they struggle with this shared set of responsibilities, probably feeling as if there aren’t enough hours in the day and distractions are always getting in the way.

People are also feeling stressed now about the health of their children. What do we know—and what should we be thinking about—in terms of the mental health impact of the COVID-19 pandemic on kids?

Everly: In the spirit of full disclosure, I’m not a child psychologist. But I have studied trauma, crisis, and disaster for quite a while, and, invariably, children are part of that. One of the most powerful things I have seen in my career is that children often become reflections of their parents. Children not only desire, but they need, stability. My message to parents is that your children rely on you. You must be that strength for them. Even when you think you can’t be strong for yourself, reach down deep inside and say, “This isn’t just about you; it’s about others as well.”

I’ve got three young grandchildren, and this is the message I am telling their parents: “This is an important time. This may be one of the defining milestones in your children’s development. It’s an opportunity to show them how to cope.”

Collins: I have grandkids as well and have been watching how they have adapted. In some instances, I can see how they have actually gained in strength, as they’ve learned that this is an opportunity to face up to a challenge and learn how to cope. It does seem to be a mix of providing that foundation of support, but trying not to prevent children completely from having the experience of realizing they can get through some things themselves.

Everly: We can certainly be overprotective. From studying Olympic athletes, we learned that when they were asked what helped them reach the elite tier and win Olympic medals, they answered: challenge, plus adequate support. While well-intended, I think support alone is misdirected.

Collins: That makes sense. I know, during the current crisis, there is an interest in figuring out, in scientifically rigorous ways, what mental health interventions seem to produce good outcomes. Tell me a little bit more about where we stand as far as the opportunities to be doing these sorts of trials of various interventions. It would be a shame to go through this and then say to ourselves, “We missed a great opportunity there to learn more.”

Everly: It’s tough to do a randomized, controlled trial in the middle of a disaster. There are quite literally ethical issues at play. So, we approximate as best we can. For example, in the past, we built our own model of Psychological First Aid and tested it in two randomized controlled trials and three content validation studies, as well as in structural equation modeling studies. Have we tested it in this current environment? Not yet. There may be others doing that—I’m not sure.

If you take a look at the Cochrane Review on resiliency programs, you will perhaps be a little surprised. The review says there’s not a compelling body of evidence that resiliency programs work. However, we believe they work. We know there is this thing called human resilience and we encourage everyone to keep on trying to study it in scientifically rigorous ways.

Collins: I’m glad that you are. We should not miss the opportunity here to learn, because this is probably not our last pandemic—or our last crisis. Any final words?

Everly: So, with the caveat that I’m a diehard optimist …

Collins: That’s okay. I am too!

Everly: … I truly believe that from the greatest adversities, opportunities can emerge. When I spent three years in New York working after the 9/11 terrorist attack, I thought this is the defining moment, not just of my generation, but of others. I got to see it up close and personal, and worked intimately with various agencies. And I did see opportunities. As a result of 9/11, we changed not just the way we go through airports, but the way we look at trauma from a public health standpoint. Perhaps for the first time, we realized that we need to take a far more active preventative and interventional role.

Now, history repeats itself. I believe that this pandemic will change us for the rest of my life—and I don’t think all those changes need be negative. I think there are huge opportunities. I certainly am eager to investigate this at the highest levels of science. Let’s see why things work when they work and why things don’t work. Then, let’s use that information to build programs and test them in randomized, controlled trials.

I think we will come out of this pandemic better than we went into it. I would encourage people to understand that we’re in this together. Way back in the mid-1800s, Darwin told us that the greatest predictor of resilience was collaboration and cohesiveness. This is a time to reach out to each other.

Collins: I totally agree with that. You’re making a really good point: social distancing doesn’t have to mean anything more than physical distancing. We can stay socially close and reach out to each other in different ways.
We’re going to get through this, but get through it in a way that will change us. We will be changed by becoming stronger and more resilient, having learned some lessons about ourselves and about each other. We cannot simply hide our heads under our pillows and wait for this to pass. When you wake up in the morning, say to yourself: “I’m engaged in something that matters. I’m not just a passive victim of this terrible pandemic. I’m trying to do what I can and work toward getting us through.”

Many thanks, Professor Everly, for all your good work and for giving us this time to reflect on this important area of research and how to make the most of it.

Links:

Coronavirus (COVID-19) (NIH)

George S. Everly (Johns Hopkins University Bloomberg School of Public Health/Baltimore)

Video: Coping with the Mental Health Effects of COVID-19, George Everly with Francis Collins (NIH VideoCast)

The Power of Psychological First Aid. Dome. Minkove JF. March/April 2018. (Johns Hopkins Medicine/Baltimore)

Coping with Stress (Centers for Disease Control and Prevention)

Coping With Stress During Infectious Disease Outbreaks (Substance Abuse and Mental Health Services Administration)

Talking with Children: Tips for Caregivers, Parents, and Teachers during Infectious Disease Outbreaks. (SAMHSA)

National Suicide Prevention Lifeline

SAMHSA’s Disaster Distress Helpline, 1-800-985-5990

National Suicide Prevention Hotline, 1-800-273-TALK (8255); TTY number 1-800-799-4TTY (4889)


Genome Data Help to Track COVID-19 Superspreading Event

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Boston skyline
Credit: iStock/Chaay_Tee

When it comes to COVID-19, anyone, even without symptoms, can be a “superspreader” capable of unknowingly infecting a large number of people and causing a community outbreak. That’s why it is so important right now to wear masks when out in public and avoid large gatherings, especially those held indoors, where a superspreader can readily infect others with SARS-CoV-2, the virus responsible for COVID-19.

Driving home this point is a new NIH-funded study on the effects of just one superspreader event in the Boston area: an international biotech conference held in February, before the public health risks of COVID-19 had been fully realized [1]. Almost a hundred people were infected. But it didn’t end there.

In the study, the researchers sequenced close to 800 viral genomes, including cases from across the first wave of the epidemic in the Boston area. Using the fact that the viral genome changes in very subtle ways over time, they found that SARS-CoV-2 was actually introduced independently to the region more than 80 times, primarily from Europe and other parts of the United States. But the data also suggest that a single superspreading event at the biotech conference led to the infection of almost 20,000 people in the area, not to mention additional COVID-19 cases in other states and around the world.

The findings, posted on medRxiv as a pre-print, come from Bronwyn MacInnis and Pardis Sabeti at the Broad Institute of MIT and Harvard in Cambridge, MA, and their many close colleagues at Massachusetts General Hospital, the Massachusetts Department of Public Health, and the Boston Health Care for the Homeless Program. The initial focus of MacInnis, Sabeti, and their Broad colleagues has been on developing genome data and tools for surveillance of viruses and other infectious diseases in and viral outbreaks in West Africa, including Lassa fever and Ebola virus disease.

Closer to home, they’d expected to focus their attention on West Nile virus and tick-borne diseases. But, when the COVID-19 outbreak erupted, they were ready to pivot quickly to assist several Centers for Disease Control and Prevention (CDC) and state labs in the northeastern United States to use genomic tools to investigate local outbreaks.

It’s been clear from the beginning of the pandemic that COVID-19 cases often arise in clusters, linked to gatherings in places such as cruise ships, nursing homes, and homeless shelters. But the Broad Institute team and their colleagues realized, it’s difficult to see how extensively a virus spreads from such places into the wider community based on case counts alone.

Contact tracing certainly helps to track community spread of the virus. This surveillance strategy depends on quick, efficient identification of an infected individual. It follows up with the identification of all who’ve recently been in close contact with that person, allowing the contacts to self-quarantine and break the chain of transmission.

But contact tracing has its limitations. It’s not always possible to identify all the people that an infected person has been in recent contact with. Genome data, however, is particularly useful after the fact for connecting those dots to get a big picture view of viral transmission.

Here’s how it works: as SARS-CoV-2 spreads, the virus sometimes picks up a new mutation. Those tiny spelling changes in the viral genome usually have no effect on how the virus causes disease, but they do serve as distinct genomic fingerprints. Using those fingerprints to guide the way, researchers can trace the path the virus took through a community and beyond, identifying connections among cases that would be untrackable otherwise.

With this in mind, MacInnis and Sabeti’s team set out to help Boston’s public health officials understand just how the epidemic escalated so quickly in the Boston area, and just how much the February conference had contributed to community transmission of the virus. They also investigated other case clusters in the area, including within a skilled nursing facility, homeless shelters, and at Massachusetts General Hospital itself, to understand the spread of COVID-19 in these settings.

Based on contact tracing, officials had already connected approximately 90 cases of COVID-19 to the biotech conference, 28 of which were included in the original 772 viral genomes in this dataset. Based on the distinct genomic fingerprint carried by the 28 genomes, the researchers went on to discover that more than one-third of Boston area cases without any known link to the conference could indeed be traced back to the event.

When the researchers considered this proportion to the number of cases recorded in the region during the study, they extrapolated that the superspreader event led to nearly 20,000 cases in the Boston area. In contrast, the genome data show cases linked to another superspreader event that took place within a skilled nursing facility, while devastating to the residents, had much less of an impact on the surrounding community.

The analysis also uncovered some unexpected connections. The dataset showed that SARS-CoV-2 was brought to clients and staff at the Boston Health Care for the Homeless Program at least seven times. Remarkably, two of those introductions also traced back to the biotech conference. Researchers also found infections in Chelsea, Revere, and Everett, which were some of the hardest hit communities in the Boston area, that were connected to the original superspreading event.

There was some reassuring news about how precautions in hospitals are working. The researchers examined cases that were diagnosed among patients at Massachusetts General Hospital, raising concerns that the virus might have spread from one patient to another within the hospital. But the genome data show that those cases, in fact, weren’t part of the same transmission chain. They may have contracted the virus before they were hospitalized. Or it’s possible that staff may have inadvertently brought the virus into the hospital. But there was no patient-to-patient transmission.

Massachusetts is one of the states in which the COVID-19 pandemic had a particularly severe early impact. As such, these results present broadly applicable lessons for other states and urban areas about how the virus spreads. The findings highlight the value of genomic surveillance, along with standard contact tracing, for better understanding of viral transmission in our communities and improved prevention of future outbreaks.

Reference:

[1] Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. Lemieux J. et al. medRxiv. August 25, 2020.

Links:

Coronavirus (COVID-19) (NIH)

Bronwyn MacInnis (Broad Institute of Harvard and MIT, Cambridge, MA)

Sabeti Lab (Broad Institute of Harvard and MIT)

NIH Support: National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; National Institute of General Medical Sciences


Capturing Viral Shedding in Action

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Credit: Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT

You’ve probably seen some amazing high-resolution images of SARS-CoV-2, the novel coronavirus that causes COVID-19, on television and the web. What you might not know is that many of these images, including the ones shown here, were produced at Rocky Mountain Laboratories (RML), a part of NIH’s National Institute of Allergy and Infectious Diseases (NIAID) that’s located in the small Montana town of Hamilton.

The head of RML’s Electron Microscopy Unit, Elizabeth Fischer, was the researcher who took this portrait of SARS-CoV-2. For more than 25 years, Fischer has snapped stunning images of dangerous viruses and microbes, including some remarkable shots of the deadly Ebola virus. She also took some of the first pictures of the coronavirus that causes Middle East respiratory syndrome (MERS), which arose from camels and continues to circulate at low levels in people.

The NIAID facility uses a variety of microscopy techniques, including state-of-the-art cryo-electron microscopy (cryo-EM). But the eye-catching image you see here was taken with a classic scanning electron microscope (SEM).

SEM enables visualization of particles, including viruses, that are too small to be seen with traditional light microscopy. It does so by focusing electrons, instead of light, into a beam that scans the surface of a sample that’s first been dehydrated, chemically preserved, and then coated with a thin layer of metal. As electrons bounce off the sample’s surface, microscopists such as Fischer are able to capture its precise topology. The result is a gray-scale micrograph like the one you see above on the left. To make the image easier to interpret, Fischer hands the originals off to RML’s Visual Medical Arts Department, which uses colorization to make key features pop like they do in the image on the right.

So, what exactly are you seeing in this image? The orange-brown folds and protrusions are part of the surface of a single cell that’s been infected with SARS-CoV-2. This particular cell comes from a commonly studied primate kidney epithelial cell line. The small, blue spheres emerging from the cell surface are SARS-CoV-2 particles.

This picture is quite literally a snapshot of viral shedding, a process in which viral particles are released from a dying cell. This image gives us a window into how devastatingly effective SARS-CoV-2 appears to be at co-opting a host’s cellular machinery: just one infected cell is capable of releasing thousands of new virus particles that can, in turn, be transmitted to others.

While capturing a fixed sample on the microscope is fairly straightforward for a pro like Fischer, developing a sample like this one involves plenty of behind-the-scenes trial and error by NIAID investigators. As you might imagine, to see the moment that viruses emerge from an infected cell, you have to get the timing just right.

By capturing many shots of the coronavirus using the arsenal of microscopes available at RML and elsewhere, researchers are learning more every day about how SARS-CoV-2 enters a cell, moves inside it, and then emerges to infect other cells. In addition to advancing scientific knowledge, Fischer notes that images like these also hold the remarkable power to make an invisible enemy visible to the world at large.

Making SARS-CoV-2 tangible helps to demystify the challenges that all of us now face as a result of the COVID-19 pandemic. The hope is it will encourage each and every one of us to do our part to fight it, whether that means digging into the research, working on the front lines, or staying at home to prevent transmission and flatten the curve. And, if you could use some additional inspiration, don’t miss the NIAID’s image gallery on Flickr, which includes some of Fischer’s finest work.

Links:

Coronavirus (COVID-19) (NIH)

Rocky Mountain Laboratories (National Institute of Allergy and Infectious Diseases/NIH)

Elizabeth Fischer (National Institute of Allergy and Infectious Diseases/NIH)

NIH Support: National Institute of Allergy and Infectious Diseases


Celebrating 2019 Biomedical Breakthroughs

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Science 2019 Biomedical Breakthroughs and a Breakdown

Happy New Year! As we say goodbye to the Teens, let’s take a look back at 2019 and some of the groundbreaking scientific discoveries that closed out this remarkable decade.

Each December, the reporters and editors at the journal Science select their breakthrough of the year, and the choice for 2019 is nothing less than spectacular: An international network of radio astronomers published the first image of a black hole, the long-theorized cosmic singularity where gravity is so strong that even light cannot escape [1]. This one resides in a galaxy 53 million light-years from Earth! (A light-year equals about 6 trillion miles.)

Though the competition was certainly stiff in 2019, the biomedical sciences were well represented among Science’s “runner-up” breakthroughs. They include three breakthroughs that have received NIH support. Let’s take a look at them:

In a first, drug treats most cases of cystic fibrosis: Last October, two international research teams reported the results from phase 3 clinical trials of the triple drug therapy Trikafta to treat cystic fibrosis (CF). Their data showed Trikafta effectively compensates for the effects of a mutation carried by about 90 percent of people born with CF. Upon reviewing these impressive data, the Food and Drug Administration (FDA) approved Trikafta, developed by Vertex Pharmaceuticals.

The approval of Trikafta was a wonderful day for me personally, having co-led the team that isolated the CF gene 30 years ago. A few years later, I wrote a song called “Dare to Dream” imagining that wonderful day when “the story of CF is history.” Though we’ve still got more work to do, we’re getting a lot closer to making that dream come true. Indeed, with the approval of Trikafta, most people with CF have for the first time ever a real chance at managing this genetic disease as a chronic condition over the course of their lives. That’s a tremendous accomplishment considering that few with CF lived beyond their teens as recently as the 1980s.

Such progress has been made possible by decades of work involving a vast number of researchers, many funded by NIH, as well as by more than two decades of visionary and collaborative efforts between the Cystic Fibrosis Foundation and Aurora Biosciences (now, Vertex) that built upon that fundamental knowledge of the responsible gene and its protein product. Not only did this innovative approach serve to accelerate the development of therapies for CF, it established a model that may inform efforts to develop therapies for other rare genetic diseases.

Hope for Ebola patients, at last: It was just six years ago that news of a major Ebola outbreak in West Africa sounded a global health emergency of the highest order. Ebola virus disease was then recognized as an untreatable, rapidly fatal illness for the majority of those who contracted it. Though international control efforts ultimately contained the spread of the virus in West Africa within about two years, over 28,600 cases had been confirmed leading to more than 11,000 deaths—marking the largest known Ebola outbreak in human history. Most recently, another major outbreak continues to wreak havoc in northeastern Democratic Republic of Congo (DRC), where violent civil unrest is greatly challenging public health control efforts.

As troubling as this news remains, 2019 brought a needed breakthrough for the millions of people living in areas susceptible to Ebola outbreaks. A randomized clinical trial in the DRC evaluated four different drugs for treating acutely infected individuals, including an antibody against the virus called mAb114, and a cocktail of anti-Ebola antibodies referred to as REGN-EB3. The trial’s preliminary data showed that about 70 percent of the patients who received either mAb114 or the REGN-EB3 antibody cocktail survived, compared with about half of those given either of the other two medicines.

So compelling were these preliminary results that the trial, co-sponsored by NIH’s National Institute of Allergy and Infectious Diseases (NIAID) and the DRC’s National Institute for Biomedical Research, was halted last August. The results were also promptly made public to help save lives and stem the latest outbreak. All Ebola patients in the DRC treatment centers now are treated with one or the other of these two options. The trial results were recently published.

The NIH-developed mAb114 antibody and the REGN-EB3 cocktail are the first therapeutics to be shown in a scientifically rigorous study to be effective at treating Ebola. This work also demonstrates that ethically sound clinical research can be conducted under difficult conditions in the midst of a disease outbreak. In fact, the halted study was named Pamoja Tulinde Maisha (PALM), which means “together save lives” in Kiswahili.

To top off the life-saving progress in 2019, the FDA just approved the first vaccine for Ebola. Called Ervebo (earlier rVSV-ZEBOV), this single-dose injectable vaccine is a non-infectious version of an animal virus that has been genetically engineered to carry a segment of a gene from the Zaire species of the Ebola virus—the virus responsible for the current DRC outbreak and the West Africa outbreak. Because the vaccine does not contain the whole Zaire virus, it can’t cause Ebola. Results from a large study in Guinea conducted by the WHO indicated that the vaccine offered substantial protection against Ebola virus disease. Ervebo, produced by Merck, has already been given to over 259,000 individuals as part of the response to the DRC outbreak. The NIH has supported numerous clinical trials of the vaccine, including an ongoing study in West Africa.

Microbes combat malnourishment: Researchers discovered a few years ago that abnormal microbial communities, or microbiomes, in the intestine appear to contribute to childhood malnutrition. An NIH-supported research team followed up on this lead with a study of kids in Bangladesh, and it published last July its groundbreaking finding: that foods formulated to repair the “gut microbiome” helped malnourished kids rebuild their health. The researchers were able to identify a network of 15 bacterial species that consistently interact in the gut microbiomes of Bangladeshi children. In this month-long study, this bacterial network helped the researchers characterize a child’s microbiome and/or its relative state of repair.

But a month isn’t long enough to determine how the new foods would help children grow and recover. The researchers are conducting a similar study that is much longer and larger. Globally, malnutrition affects an estimated 238 million children under the age 5, stunting their normal growth, compromising their health, and limiting their mental development. The hope is that these new foods and others adapted for use around the world soon will help many more kids grow up to be healthy adults.

Measles Resurgent: The staff at Science also listed their less-encouraging 2019 Breakdowns of the Year, and unfortunately the biomedical sciences made the cut with the return of measles in the U.S. Prior to 1963, when the measles vaccine was developed, 3 to 4 million Americans were sickened by measles each year. Each year about 500 children would die from measles, and many more would suffer lifelong complications. As more people were vaccinated, the incidence of measles plummeted. By the year 2000, the disease was even declared eliminated from the U.S.

But, as more parents have chosen not to vaccinate their children, driven by the now debunked claim that vaccines are connected to autism, measles has made a very preventable comeback. Last October, the Centers for Disease Control and Prevention (CDC) reported an estimated 1,250 measles cases in the United States at that point in 2019, surpassing the total number of cases reported annually in each of the past 25 years.

The good news is those numbers can be reduced if more people get the vaccine, which has been shown repeatedly in many large and rigorous studies to be safe and effective. The CDC recommends that children should receive their first dose by 12 to 15 months of age and a second dose between the ages of 4 and 6. Older people who’ve been vaccinated or have had the measles previously should consider being re-vaccinated, especially if they live in places with low vaccination rates or will be traveling to countries where measles are endemic.

Despite this public health breakdown, 2019 closed out a memorable decade of scientific discovery. The Twenties will build on discoveries made during the Teens and bring us even closer to an era of precision medicine to improve the lives of millions of Americans. So, onward to 2020—and happy New Year!

Reference:

[1] 2019 Breakthrough of the Year. Science, December 19, 2019.

NIH Support: These breakthroughs represent the culmination of years of research involving many investigators and the support of multiple NIH institutes.


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