How scientists used immunohistochemistry to detect SARS-CoV-2 related viruses in local bat populations and what this means for pandemic prevention
The COVID-19 pandemic irrevocably changed our world, bringing with it a single, pressing question: where did SARS-CoV-2, the virus responsible for the disease, come from?
While the search led global scientists to wildlife markets and caves in distant continents, a team of researchers right here in the United States began looking closer to home. In the arid landscapes of New Mexico, a silent, flying population was going about its business: bats. Could these often-misunderstood creatures be carrying relatives of the virus that shook the globe?
To find the answer, scientists turned to a powerful, classic technique used in a new way, peering into preserved bat tissues to uncover clues about a modern threat.
Identifying SARS-CoV-2 related viruses in wildlife populations
Using immunohistochemistry on preserved tissue samples
Understanding spillover events to protect public health
For decades, scientists have known that bats are exceptional hosts for coronaviruses. They are what epidemiologists call a "reservoir host"—a species that can carry and spread a pathogen without getting sick from it themselves. Bats have unique immune systems that allow them to coexist with viruses that would be deadly to other mammals.
A species that harbors pathogens long-term without showing symptoms, serving as a natural source of infection for other species.
The transmission of a pathogen from its reservoir host to a new species, potentially causing disease in the new host.
The theory is that a SARS-CoV-2-like virus circulates harmlessly in a bat population. Through a process called "spillover," the virus can jump into a new, intermediate species (or directly to humans) where it then adapts and can cause disease. Finding these viral relatives in bats is like finding pieces of a puzzle; it helps us understand the virus's evolution and identify potential hotspots for future spillover events.
You can't just ask a bat if it has a virus. Traditional methods like PCR are great for detecting viral genetic material, but they don't tell you where the virus is or what it's doing inside the animal's body. This is where Immunohistochemistry (IHC) becomes a super-sleuth.
We're looking for the SARS-CoV-2 nucleocapsid protein—a key part of the virus's internal structure. It's our "suspect."
Scientists use a primary antibody that is specially designed to recognize and latch onto this specific protein. This antibody is highly specific; it will ignore everything else.
A secondary antibody, linked to a colorful enzyme (like a dye), is then added. This one binds to the primary antibody.
When a chemical substrate is applied, the enzyme triggers a color change (usually a brown or red stain). Wherever we see this stain under a microscope, we know the SARS-CoV-2 protein was present.
In short, IHC doesn't just tell us the virus was in the bat; it shows us the virus was in a specific organ or cell type, providing a snapshot of the infection.
A team from the University of New Mexico and federal wildlife agencies embarked on a surveillance mission. Their goal was to screen local bat populations for SARS-CoV-2 using IHC on archived tissue samples.
Bats from different species across New Mexico were humanely collected, often as part of unrelated wildlife studies or after natural deaths.
Key organs—like the lung, intestine, and kidney—were carefully preserved in formalin and embedded in paraffin blocks (FFPE process).
The wax blocks were sliced into incredibly thin sections (a few micrometers thick) and mounted on glass slides.
A multi-step process involving deparaffinization, antigen retrieval, antibody incubation, and color development.
A veterinary pathologist examined the stained slides under a microscope, looking for distinctive brown staining indicating a positive result.
| Research Reagent | Function in the Experiment |
|---|---|
| Formalin (10% Neutral Buffered) | A fixative solution that preserves the tissue architecture by cross-linking proteins, preventing decay and maintaining cellular structure for long-term storage. |
| Paraffin Wax | An embedding medium that infiltrates the dehydrated tissue, allowing it to be sliced into extremely thin, consistent sections for microscopic analysis. |
| Anti-SARS-CoV-2 Nucleocapsid Antibody | The "primary antibody." This is the highly specific molecular key that seeks out and binds only to the nucleocapsid protein of the virus, marking its location. |
| Enzyme-Linked Secondary Antibody | The "signal amplifier." This antibody binds to the primary antibody and carries an enzyme that, when activated, produces a visible color change, highlighting the target. |
| DAB (3,3'-Diaminobenzidine) Chromogen | The "color developer." This chemical substrate reacts with the enzyme on the secondary antibody to produce a stable, brown precipitate at the site of the target protein. |
| Hematoxylin Counterstain | A blue dye that stains the cell nuclei. This provides contrast, making the overall tissue structure visible and allowing researchers to pinpoint the location of the brown viral stain within specific cells. |
The results were striking. While most bats were negative, the IHC analysis revealed the presence of the SARS-CoV-2 nucleocapsid protein in the tissues of one specific species: the Big Brown Bat (Eptesicus fuscus).
| Bat ID | Species | Location Found | IHC Result | Tissue Distribution of Virus |
|---|---|---|---|---|
| NM-Bat-047 | Eptesicus fuscus | Eddy County | Positive | Focal staining in lung alveoli |
| NM-Bat-118 | Eptesicus fuscus | Otero County | Positive | Widespread staining in intestinal epithelium |
| NM-Bat-156 | Eptesicus fuscus | Lincoln County | Positive | Multifocal staining in lung and intestine |
Crucially, the viral protein was found primarily in the lungs and the intestinal lining. This pattern is highly significant because:
The discovery of a SARS-CoV-2-related virus in New Mexico's bats is a major scientific finding, but it is not a reason for public alarm. These bats have likely been living with their own suite of coronaviruses for millennia.
This research proves that proactive wildlife surveillance is crucial. By monitoring viruses in animal populations, we can better understand the threat landscape and potentially predict or prevent future pandemics.
The virus found is a relative of SARS-CoV-2, not the pandemic strain itself. The risk of direct spillover from these bats to humans is considered low, especially with no direct contact.
Bats are essential to our ecosystem as pollinators and insect controllers. This research underscores the importance of studying them with respect and protecting their habitats, not persecuting them.
The silent sentinels of the New Mexico night have given us a valuable clue. By listening to them through powerful tools like immunohistochemistry, we are building the knowledge needed to safeguard global health for the future.