Washington, D.C. — Infections by hantaviruses are rare but dangerous, killing 30-40% of infected people. When cases occur, public health officials need rapid, detailed information about the virus to identify the strain and its origin, so they can stop others from being exposed to the disease. Whole genome sequencing is an integral part of this work, though the genomes of these viruses are difficult to sequence using existing approaches.
A new method for whole-genome sequencing of hantaviruses improves on today’s strategies for identifying outbreaks. Microbiologist Janet Manson, Ph.D., who led the development of the method, introduced it this week in Washington, D.C. at ASM Microbe 2026. Manson is an APHL-CDC Fellow at the California Department of Public Health.
About 30 people are infected by hantaviruses in the United States every year, according to the Centers for Disease Control and Prevention, and most U.S. cases are caused by Sin Nombre virus, which is carried by the deer mouse. Whole genome sequencing can help microbiologists and epidemiologists better understand the complexities of hantaviruses. Having the sequence in hand can also help researchers trace infections. “When there’s an outbreak or even a case, we need to know where that person was exposed so we can stop other people from being exposed,” Manson explained.
Sequencing these hantaviruses can be difficult, however, because of their complex genome structure, high genetic diversity and the often low viral concentrations found in human specimens. As a result of this challenge, few whole genome sequences are publicly available.
To overcome these obstacles, Manson and her colleagues first designed a primer—a small chunk of genetic material that binds to the virus— that could recognize and attach to the genome during the conversion of viral RNA into DNA. Then, they developed a method for sequencing each genome segment in 1 long piece. For samples with low viral concentration, the researchers added a second step to increase the genome yield. This approach makes it possible to successfully sequence samples that would otherwise have too little viral material to analyze.
In lab tests, their sequencing approach generated whole genome sequencing data from 35 rodent samples that had already tested positive for the Sin Nombre virus. And it’s already proven useful in the field: In a recent case, Manson said, she was able to match the genome sequence from an infected person to that of a rodent caught near the person’s home. This type of information helps scientists confirm where people are exposed to hantaviruses and is used to help better target public health interventions and education to the places that need it the most.
Manson said she hopes the tool will be useful beyond the California Department of Public Health. While other states have higher incidence rates of human infection, many lack the resources to bring on and maintain whole genome sequencing for rarer viruses. The new method, she said, “is comparatively cheap to set up” compared to other common technologies. The sequencing device, which can be plugged into a laptop, only costs about $3,000.
The researchers are now expanding the method to apply it to hantaviruses beyond Sin Nombre. And they’ve made headway, recently using it to sequence the genome of a virus similar to Andes virus from a person who had traveled to Paraguay last year.
“We really want to better understand the diversity of hantaviruses across the U.S., and we want to be able to look at markers of viral evolution, just to understand what’s happening,” Manson said.
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