Janet Manson matched a virus genome from an infected person to that of a rodent caught near their home, and that breakthrough moment reveals why her new sequencing tool matters so much in the fight against a deadly threat most people have never heard of.
Hantavirus infections are rare but catastrophic—they kill 30 to 40 percent of infected people, according to the CDC. About 30 Americans are infected each year, with most cases caused by Sin Nombre virus, carried by deer mice. When an outbreak occurs or a single case emerges, public health officials face a critical race against time: they need to know exactly where the person was exposed so they can prevent others from encountering the virus. That's where whole-genome sequencing becomes essential. By mapping the virus's complete genetic blueprint, microbiologists and epidemiologists can trace infections back to their source, understand outbreak patterns, and target interventions with precision.
But sequencing hantavirus genomes has been nearly impossible with existing methods. The viruses have complex genome structures, staggering genetic diversity, and crucially, very low viral concentrations in human samples. These obstacles meant that few complete hantavirus genomes existed in public databases, leaving public health teams working partly blind.
Manson, an APHL-CDC Fellow at the California Department of Public Health, introduced her solution this week at ASM Microbe 2026 in Washington, D.C. Her approach begins with a primer—a small piece of genetic material designed to recognize and bind to the hantavirus genome during RNA-to-DNA conversion. Rather than sequencing the virus in fragments, her team sequences each genome segment as one complete piece. For samples with minimal viral material, they added an amplification step to boost the genetic yield. The result: samples that were previously too weak to analyze could now be successfully sequenced.
In laboratory testing, the method worked on 35 rodent samples already confirmed positive for Sin Nombre virus. But the real validation came in the field. When Manson sequenced the genome from an infected person and compared it to the virus found in a rodent trapped near that person's home, the match confirmed where exposure had occurred. This kind of precision epidemiology transforms abstract outbreak data into actionable intelligence about which neighborhoods, homes, or environments pose the greatest risk.
What makes Manson's innovation particularly significant is its accessibility. The sequencing device—small enough to plug into a laptop—costs around $3,000, making it "comparatively cheap to set up" compared to other genomic technologies. That affordability matters enormously. While some states have high hantavirus infection rates, many lack the resources to establish and maintain whole-genome sequencing infrastructure for rare pathogens. Manson's tool could democratize this capability across state health departments that desperately need it.
The team is already expanding beyond Sin Nombre virus. They recently used the method to sequence a genome similar to Andes virus from a traveler returning from Paraguay, broadening the tool's scope. Manson's larger vision is ambitious: to map hantavirus diversity across the entire United States, track viral evolution markers, and understand what's actually happening with these pathogens at a genetic level.
In a world where 30 Americans face hantavirus exposure each year, and where every hour matters in stopping the next case, this breakthrough represents something rare: a practical, affordable solution that turns microscopic threats into traceable, preventable risks.