Genomic Epidemiology and Active Surveillance to Investigate Outbreaks of Hantaviruses

Won Keun Kim, Seungchan Cho, Seung Ho Lee, Jin Sun No, Geum Young Lee, Kyungmin Park, Daesang Lee, Seong Tae Jeong, Jin Won Song

Research output: Contribution to journalReview articlepeer-review

13 Citations (Scopus)


Emerging and re-emerging RNA viruses pose significant public health, economic, and societal burdens. Hantaviruses (genus Orthohantavirus, family Hantaviridae, order Bunyavirales) are enveloped, negative-sense, single-stranded, tripartite RNA viruses that are emerging zoonotic pathogens harbored by small mammals such as rodents, bats, moles, and shrews. Orthohantavirus infections cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome in humans (HCPS). Active targeted surveillance has elucidated high-resolution phylogeographic relationships between patient- and rodent-derived orthohantavirus genome sequences and identified the infection source by temporally and spatially tracking viral genomes. Active surveillance of patients with HFRS entails 1) recovering whole-genome sequences of Hantaan virus (HTNV) using amplicon (multiplex PCR-based) next-generation sequencing, 2) tracing the putative infection site of a patient by administering an epidemiological questionnaire, and 3) collecting HTNV-positive rodents using targeted rodent trapping. Moreover, viral genome tracking has been recently performed to rapidly and precisely characterize an outbreak from the emerging virus. Here, we reviewed genomic epidemiological and active surveillance data for determining the emergence of zoonotic RNA viruses based on viral genomic sequences obtained from patients and natural reservoirs. This review highlights the recent studies on tracking viral genomes for identifying and characterizing emerging viral outbreaks worldwide. We believe that active surveillance is an effective method for identifying rodent-borne orthohantavirus infection sites, and this report provides insights into disease mitigation and preparedness for managing emerging viral outbreaks.

Original languageEnglish
Article number532388
JournalFrontiers in Cellular and Infection Microbiology
Publication statusPublished - 2021 Jan 8

Bibliographical note

Funding Information:
This work was supported by the Agency for Defense Development (UE202026GD) and the Research Program to Solve Social Issues of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (NRF-2017M3A9E4061992).

Publisher Copyright:
© Copyright © 2021 Kim, Cho, Lee, No, Lee, Park, Lee, Jeong and Song.


  • RNA viruses
  • epidemiological survey
  • next-generation sequencing
  • preventive strategies
  • rodent trapping
  • tracking hantaviral genomes

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Microbiology (medical)
  • Infectious Diseases


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