Hantavirus infections are rare—roughly 30 people are infected in the United States each year—but they are deadly, killing 30 to 40 percent of those infected. Most U.S. cases are caused by Sin Nombre virus, carried by the deer mouse. When cases occur, public health officials need rapid, detailed genomic information to identify the strain, trace its origin, and prevent further exposure. A new method for whole-genome sequencing of hantaviruses, introduced at ASM Microbe 2026, offers a more effective and lower-cost approach to that challenge.
The method was developed by Janet Manson from the California Department of Public Health. Sequencing hantavirus genomes has historically been difficult due to the virus’s complex genome structure, high genetic diversity, and the low viral concentrations typically found in human specimens—factors that have left few whole genome sequences publicly available.
To overcome these obstacles, Manson and her colleagues designed a primer capable of recognizing and attaching to the hantavirus genome during conversion of viral RNA into DNA, then developed a method to sequence each genome segment in one long piece. For samples with low viral concentration, a second step was added to increase genome yield, making it possible to successfully sequence samples that would otherwise contain too little viral material to analyze.
In lab testing, the approach generated whole genome sequencing data from 35 rodent samples that had previously tested positive for Sin Nombre virus. It has also proven useful in real-world public health work. In one recent case, Manson was able to match the genome sequence from an infected person to that of a rodent caught near the person's home—the kind of information that helps confirm where exposures occur and directs public health interventions to where they are most needed.
"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.
Beyond its scientific utility, the method is designed to be accessible. The sequencing device can be plugged into a laptop and costs approximately $3,000—comparatively cheap to set up relative to other common technologies. Manson hopes the tool will be adopted by other states, many of which lack resources to maintain whole genome sequencing capacity for rarer viruses.
The team is now expanding the method to other hantaviruses beyond Sin Nombre, recently sequencing the genome of a virus similar to Andes virus from a person who had traveled to Paraguay. "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.
The method was developed by Janet Manson from the California Department of Public Health. Sequencing hantavirus genomes has historically been difficult due to the virus’s complex genome structure, high genetic diversity, and the low viral concentrations typically found in human specimens—factors that have left few whole genome sequences publicly available.
To overcome these obstacles, Manson and her colleagues designed a primer capable of recognizing and attaching to the hantavirus genome during conversion of viral RNA into DNA, then developed a method to sequence each genome segment in one long piece. For samples with low viral concentration, a second step was added to increase genome yield, making it possible to successfully sequence samples that would otherwise contain too little viral material to analyze.
In lab testing, the approach generated whole genome sequencing data from 35 rodent samples that had previously tested positive for Sin Nombre virus. It has also proven useful in real-world public health work. In one recent case, Manson was able to match the genome sequence from an infected person to that of a rodent caught near the person's home—the kind of information that helps confirm where exposures occur and directs public health interventions to where they are most needed.
"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.
Beyond its scientific utility, the method is designed to be accessible. The sequencing device can be plugged into a laptop and costs approximately $3,000—comparatively cheap to set up relative to other common technologies. Manson hopes the tool will be adopted by other states, many of which lack resources to maintain whole genome sequencing capacity for rarer viruses.
The team is now expanding the method to other hantaviruses beyond Sin Nombre, recently sequencing the genome of a virus similar to Andes virus from a person who had traveled to Paraguay. "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.