Prepared for the worst

LJI scientists explore the immune system from every angle. Their research is key to stopping the next pandemic.

The naturalist E.O. Wilson once wrote, “Fascination creates preparedness, and preparedness, survival.”

And is there anything more fascinating than a pathogen? They mutate into endless forms. They twist and collapse and morph their very beings as they infect their hosts.

Scientists at La Jolla Institute for Immunology (LJI) have the tools to dissect the many ways pathogens try to slip into our bodies and discover how the equally wonderous human immune system fights back. Every day, these researchers learn more about how we can combat the next pandemic.

Illustration of three bacteria illustrated in shades of blue with descriptions: 

Bordetella pertussis - Resembles a bean with hair-like appendages. Description:  This bacterium causes whooping cough. Vaccines exist—but immunocompromised people are still at risk. Cases in the United States are rising as vaccination rates fall.

Mycobacterium tuberculosis. This is a rod-shaped bacterium. Causes tuberculosis. A vaccine exists—but around 10 million people around the world are still infected by this bacterium every year.

Streptococcus pneumoniae. This bacterium resembles segmented strings. Causes pneumonia and
pneumococcal meningitis. There are vaccines—but cases are still rising in the United States.

An eye on emerging threats

Pathogens don’t come out of nowhere. LJI scientists have shown that better understanding past outbreaks can help us fight future threats.

Illustration of two paramyxoviruses with descriptions. These viruses are illustrated in shades of pink and orange. They resemble spheres with protruding surface proteins that look like small florets.

Nipah virus - Carried by bats. Known for its high mortality rate. Has caused deadly outbreaks in southeastern Africa and Southeast Asia. There are no approved vaccines or treatments.

Measles virus - A growing cause of childhood death worldwide. Vaccination rates are dropping. Pregnant people and immunocompromised people cannot receive the vaccine.

Since 2019, we’ve discovered so much about how the immune system responds to coronaviruses. But there are many more deadly pathogens out there—and new threats can “spill over” from wildlife populations at any time.

Illustration of Lassa virus with description. The virus is illustrated with shades of blue and red. It resembles a sphere with protruding surface receptors. Inside the sphere is a string-like proteins and genetic materia.  

Description: Lassa virus is spread by a type of rat in West Africa. High mortality rate, especially in pregnant and immunocompromised people. Vaccines are in development and at the clinical-testing stage.

LJI scientists work closely with international partners to monitor these emerging diseases. By combining experimental studies with computational work, researchers have uncovered how specific immune cells handle these diseases.

These insights are crucial for developing vaccines that teach the body how to ward off severe infection.

Learning from past pandemics

LJI scientists are investigating how the immune system fights different members of the same family of pathogens. Spotting these “family resemblances” is key to developing better vaccines and new drug treatments.

Illustration of human immunodeficiency virus with description. The virus is illustrated in shades of blue and grey. It is a sphere with protruding surface proteins. There are additional proteins inside the virus that resemble fuzzy threads and blobs.

Description: Human immunodeficiency virus (HIV) - Causes AIDS. No vaccine or cure
exists—but scientists have developed protective therapies (such as PReP) and life-saving treatments.

There are many cases in which efforts to stop one pathogen can help us fight its close relatives. For example, when mpox began spreading across North America back in 2022, scientists at LJI worked quickly to investigate vaccine strategies. They found that a vaccine originally designed to stop smallpox would likely also teach our T cells to combat the closely related mpox.

Illustration of two orthopoxviruses with description. These viruses are illustrated with shades of blue and pink. They resemble rectangles with rounded edges. 

Descriptions: Mpox virus
Causes outbreaks worldwide.
Low-level transmission is ongoing
in the United States. There are
effective vaccines, and there are
experimental treatments.

Variola virus - Causes smallpox. Eradicated. Success story: Smallpox was a global killer for thousands of years. Fortunately, smallpox vaccines were some of the first vaccines ever developed. Many countries launched massive smallpox vaccination campaigns in the 1800s and early 1900s. In 1980, smallpox was declared eradicated across the globe.
Illustration of two viruses with descriptions. The viruses are illustrated in shades of pink and light blue.

Ebola virus resembles a twisted filament or worm. The surface of the virus is covered in protruding receptors. Description: Ebola virus is spread by infected wild animals. Known for its high mortality rate. Two licensed vaccines exist.

Influenza virus resembles a sphere. It is studded with protruding surface receptors that resemble florets or rounded rods. Description: Influenza is the seventh leading cause of death in the United States. There are four types of influenza virus and many rapidly evolving strains, including H5N1—better known as “bird flu.” Seasonal vaccines can provide some immunity. But many people—especially infants and older adults—are still vulnerable
to life-threatening infection.
Illustration of SARS-CoV-2 with description. The virus is illustrated in shades of pink and yellow. Large "Spike" proteins stick out of its surface, and genetic material is packed into the center of the circle.

This virus causes COVID-19. It is
known for evolving rapidly into
new “variants of concern”—such
as the Omicron variant. Vaccines
and therapies are effective for
many people.

Our mission: Fight entire families of pathogens

LJI scientists are investigating how the immune system fights different members of the same family of pathogens. Spotting these “family resemblances” is key to developing better vaccines and new drug treatments.

Illustration of three herpesviruses with descriptions. These viruses are illustratied in shades of orange. They are round viruses with protruding surface proteins.

Cytomegalovirus - Many people unknowingly carry this virus. Rarely causes severe symptoms unless contracted when a person is pregnant. Infections during pregnancy can lead to debilitating birth defects in newborns. No vaccine exists.

Epstein-Barr virus - Causes mononucleosis, aka “mono.” Associated with several other diseases— including Burkitt lymphoma and stomach cancer. No vaccine exists.

Varicella-zoster virus - Causes chicken pox. Can hide in the nervous system for decades and emerge to cause shingles. Vaccines exist.

The COVID-19 pandemic highlighted the importance of this research. Since 2020, LJI researchers have found that human immune cells can target vulnerable spots that many coronaviruses have in common. This discovery led LJI scientists to pursue “pan-coronavirus” vaccines to protect people from SARS-CoV-2 variants and future coronaviruses with pandemic potential.

A large infographic with illustrations of dengue virus, Zika virus, Powassan virus, and Chikungunya virus. These viruses are illustrated in shades of green and yellow. The viruses resemble golf balls with textured surfaces. A detailed illustration of dengue virus also shows the genetic material inside the virus. 

Three of the viruses are flaviviruses. Here are those descriptions:

Dengue virus - Spread by
mosquitoes. There are four types of dengue virus—and we have no effective vaccines for any of them.

Zika virus- Spread by mosquitoes. Can cause flu-like symptoms in adults and microcephaly in newborns who were infected in the womb. Vaccines are in development.

Powassan virus Spread by ticks. Causes severe disease. A rising number of cases have been reported in the Northeast and Great Lakes regions of the United States. No vaccines exist

We also see that Chikungunya is a related virus but not a flavivirus. Instead, it is related because it is also an arbovirus. This section reads: Arboviruses: Hiding in nature Scientists call any virus spread by arthropods (such as mosquitos and ticks) an “arbovirus.” These viruses use arthropods as vectors to jump between animals and humans. Arboviruses are especially important to monitor because they can evolve in wildlife populations for years before spilling over to infect humans.

There is also a specific description for Chikungunya.

Chikungunya - Spread by mosquitoes. Can cause fever and chronic joint pain. One vaccine exists— but there is no treatment
for the disease.

Today, LJI researchers are pioneering efforts to train immune cells to fight dengue virus, Zika virus, and Japanese encephalitis virus with a single “pan-flavivirus” vaccine.

They have also found clues to developing a “pan-ebolavirus” vaccine to fight Ebola virus, Bundibugyo ebolavirus, and other deadly relatives.

LJI scientists are building a strong foundation for stopping future pandemics. If, one day, a new threat emerges—one we’ve never seen before—LJI is prepared to help save lives around the world.

An illustration of a hypothetical virus termed "Virus X." It is illustrated in shades of red, green and blue. It has a mix of surface proteins and a question mark in the center. Description: Virus X - The pathogen we haven't met yet. The next pandemic threat may come from a newly emerged or evolved pathogen —one we've never faced. This uncertainty is why researchers need a solid understanding of how the immune system targets many different kinds of pathogens. With
scientists on the ready, we can
respond to unknown pathogens
faster than ever before.

About the artist

This issue’s cover art and infographic illustrations were completed by San Diego artist Patricia Pauchnick. Pauchnick specializes in paintings, drawings, textiles, and ceramics that explore Southwestern history, land use, and urban/suburban development, as well as societal and natural borders. See more at patriciapauchnick.com.

The watercolor painting at the top of this article depicts Ebola virus (red and pink filaments) attacking a host cell (in blue).