Hantavirus infections are rare but dangerous, and 30 to 40 percent of infected people die. When cases occur, public health officials need rapid and detailed information about the virus to identify the strain and its origin to prevent others from being exposed to the disease. Whole-genome sequencing is an essential part of this research, but the genomes of these viruses are difficult to sequence using existing approaches.
A new method to sequence the entire genome of hantaviruses improves today’s strategies for identifying outbreaks. Dr. Janet Manson, the microbiologist who led the development of the method, introduced it this week at ASM Microbe 2026 in Washington, DC. Mr. Munson is an APHL-CDC Fellow at the California Department of Public Health.
According to the Centers for Disease Control and Prevention, about 30 people in the United States become infected with hantavirus each year, and most cases in the United States are caused by the Sin Nombre virus, which is transmitted by deer mice. Whole genome sequencing will help microbiologists and epidemiologists better understand the complexity of hantaviruses. Having the sequences also helps researchers track infections. “When there is an outbreak or an infected person, we need to know where that person got infected so that we can prevent others from getting infected,” Manson explained.
However, sequencing these hantaviruses can be challenging due to their complex genome structure, high genetic diversity, and the often low concentrations of virus found in human specimens. As a result of this challenge, very few whole genome sequences have been published.
To overcome these obstacles, Manson and his colleagues first designed primers (small blobs of genetic material that bind to viruses) that could recognize and bind to the genome as the virus’s RNA was converted to DNA. They then developed a method to sequence each segment of the genome as one long piece. For samples with low virus concentrations, the researchers added a second step to increase genome yield. This approach makes it possible to successfully sequence samples that contain too little viral material to be analyzed.
In clinical testing, their sequencing approach has already generated whole-genome sequence data from 35 rodent samples that have tested positive for Sin Nombre virus. And it has already proven useful in the field, Manson said, in a recent case by matching the genome sequence of an infected person with that of a rodent caught near that person’s home. This type of information helps scientists see where people are exposed to hantaviruses and is used to better target public health interventions and education to where they are most needed.
Munson said he hopes the tool will be useful beyond the California Department of Public Health. Other states have higher rates of human infection, but many lack the resources to accomplish and maintain full genome sequencing of rarer viruses. The new method is “relatively cheap to set up” compared to other common technologies, she said. This sequencing device connects to your laptop and costs only about $3,000.
The researchers are now extending this method to apply to hantaviruses other than Sin Nombre. And they’ve made progress, recently using it to sequence the genome of a virus similar to the Andes virus taken from a person who traveled to Paraguay last year.
“We want to better understand the diversity of hantaviruses across the United States. We want to be able to look at markers of virus evolution to understand what’s going on,” Manson said.
sauce:
American Society for Microbiology
