New Hantavirus Rapid Test Paves Way for Early Outbreak Control

These zoonotic pathogens have been the focus of extensive research, particularly for controlling outbreaks and devising intervention strategies. In South Korea's Gyeonggi Province, a notable number of HFRS cases have been reported, highlighting the need for diligent epidemiological surveillance and a deeper understanding of orthohantaviruses' genomic diversity. Now, new research has unveiled the potential of cost-efficient Flongle sequencing for rapid hantavirus genome-based diagnostics and phylogeographical surveillance.

A research team from Korea University College of Medicine (Seoul, South Korea) undertook a study in the Gyeonggi Province to investigate the prevalence, viral loads, and genetic variations of Hantaan orthohantavirus (HTNV). They utilized Flongle sequencing, an innovative and budget-friendly approach, for detecting HTNV genomes, emphasizing the use of the Oxford MinION nanopore sequencer in the field of next-generation sequencing technologies. The team's methodology included capturing rodents and shrews from various areas using live traps, followed by mitochondrial DNA analysis, indirect immunofluorescence antibody tests, and other molecular methods for species identification and virus detection.

During the 2017-2018 surveillance in Gyeonggi Province, a substantial presence of Apodemus agrarius, a common rodent species, was noted. Among these, 12.4% were found to be seropositive for HTNV, indicating the virus's prevalence in the region. The use of Flongle sequencing was key in acquiring full-length genomic sequences from positive samples, achieving high coverage rates and accuracy on par with Illumina sequencing. The study's phylogeographical analysis revealed distinct evolutionary divergence among HTNV's tripartite genomes, with genetic clustering and evolutionary pattern incongruences highlighting the virus's segment-specific evolution.

While the study offers critical insights, the researchers acknowledge limitations like the need for enhanced sensitivity testing of Flongle-based diagnostics and the requirement for broader genomic and epidemiological data in certain endemic areas. This research represents a major advancement in the understanding of orthohantaviruses and sets the stage for more focused strategies to combat HFRS outbreaks. The findings underscore the importance of genomics in disease surveillance and hold promise for improved responses to emerging infectious diseases.

“We developed a rapid and sensitive on-site diagnostic using a nanopore-based Flongle chip with a reasonable cost of around $100. This approach enables virtually whole-genome sequencing of HTNV within 3 hours,” said Prof. Jin-Won Song from Korea University College of Medicine who led the research. "We believe our findings provide important insights into on-site diagnostics, genome-based surveillance, and the evolutionary dynamics of orthohantaviruses to mitigate hantaviral outbreaks in HFRS-endemic areas in the ROK. Our study pioneers the integration of cost-efficient Flongle sequencing into hantavirus diagnostics, offering a rapid and accurate tool for on-site detection. This innovation has the potential to transform how we approach and manage hantavirus outbreaks."

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Korea University College of Medicine