Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing

Won Keun Kim, Jeong Ah Kim, Dong Hyun Song, Daesang Lee, Yong Chul Kim, Sook Young Lee, Seung Ho Lee, Jin Sun No, Ji Hye Kim, Jeong Hoon Kho, Se Hun Gu, Seong Tae Jeong, Michael Wiley, Heung Chul Kim, Terry A. Klein, Gustavo Palacios, Jin Won Song

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)


Emerging and re-emerging infectious diseases caused by RNA viruses pose a critical public health threat. Next generation sequencing (NGS) is a powerful technology to define genomic sequences of the viruses. Of particular interest is the use of whole genome sequencing (WGS) to perform phylogeographic analysis, that allows the detection and tracking of the emergence of viral infections. Hantaviruses, Bunyaviridae, cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) in humans. We propose to use WGS for the phylogeographic analysis of human hantavirus infections. A novel multiplex PCR-based NGS was developed to gather whole genome sequences of Hantaan virus (HTNV) from HFRS patients and rodent hosts in endemic areas. The obtained genomes were described for the spatial and temporal links between cases and their sources. Phylogenetic analyses demonstrated geographic clustering of HTNV strains from clinical specimens with the HTNV strains circulating in rodents, suggesting the most likely site and time of infection. Recombination analysis demonstrated a genome organization compatible with recombination of the HTNV S segment. The multiplex PCR-based NGS is useful and robust to acquire viral genomic sequences and may provide important ways to define the phylogeographical association and molecular evolution of hantaviruses.

Original languageEnglish
Article number26017
JournalScientific reports
Issue number1
Publication statusPublished - 2016 May 25

Bibliographical note

Funding Information:
This work was funded by a grant from the Agency for Defense Development (ROK; UE134020ID) and the Defense Threat Reduction Agency (DTRA). Partial funding was provided by the Armed Forces Health Surveillance Branch-Global Emerging Infections Surveillance and Response System (AFHSC-GEIS), Silver Spring.

ASJC Scopus subject areas

  • General


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