Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus

Won Keun Kim, Jin Sun No, Daesang Lee, Jaehun Jung, Hayne Park, Yongjin Yi, Jeong Ah Kim, Seung Ho Lee, Yujin Kim, Sunhye Park, Seungchan Cho, Geum Young Lee, Dong Hyun Song, Se Hun Gu, Kkothanahreum Park, Heung Chul Kim, Michael R. Wiley, Patrick S.G. Chain, Seong Tae Jeong, Terry A. KleinGustavo Palacios, Jin Won Song

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

BACKGROUND: Endemic outbreaks of hantaviruses pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) causes hemorrhagic fever with renal syndrome (HFRS) in humans. Using comparative genomic analyses of partial and nearly complete sequences of HTNV from humans and rodents, we were able to localize, with limitations, the putative infection locations for HFRS patients. Partial sequences might not reflect precise phylogenetic positions over the whole-genome sequences; finer granularity of rodent sampling reflects more precisely the circulation of strains. METHODS: Five HFRS specimens were collected. Epidemiological surveys were conducted with the patients during hospitalization. We conducted active surveillance at suspected HFRS outbreak areas. We performed multiplex polymerase chain reaction-based next-generation sequencing to obtain the genomic sequence of HTNV from patients and rodents. The phylogeny of human- and rodent-derived HTNV was generated using the maximum likelihood method. For phylogeographic analyses, the tracing of HTNV genomes from HFRS patients was defined on the bases of epidemiological interviews, phylogenetic patterns of the viruses, and geographic locations of HTNV-positive rodents. RESULTS: The phylogeographic analyses demonstrated genetic clusters of HTNV strains from clinical specimens, with HTNV circulating in rodents at suspected sites of patient infections. CONCLUSIONS: This study demonstrates a major shift in molecular epidemiological surveillance of HTNV. Active targeted surveillance was performed at sites of suspected infections, allowing the high-resolution phylogeographic analysis to reveal the site of emergence of HTNV. We posit that this novel approach will make it possible to identify infectious sources, perform disease risk assessment, and implement preparedness against vector-borne viruses.

Original languageEnglish
Pages (from-to)464-473
Number of pages10
JournalClinical infectious diseases : an official publication of the Infectious Diseases Society of America
Volume70
Issue number3
DOIs
Publication statusPublished - 2020 Jan 16

Fingerprint

Hantavirus
Hemorrhagic Fever with Renal Syndrome
Rodentia
Disease Outbreaks
Infection
Genome
Viruses
Geographic Locations
Multiplex Polymerase Chain Reaction
Phylogeny
Hospitalization
Public Health
Interviews

Keywords

  • active targeted surveillance
  • epidemiology
  • hantavirus
  • hemorrhagic fever with renal syndrome
  • next-generation sequencing

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

Cite this

Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus. / Kim, Won Keun; No, Jin Sun; Lee, Daesang; Jung, Jaehun; Park, Hayne; Yi, Yongjin; Kim, Jeong Ah; Lee, Seung Ho; Kim, Yujin; Park, Sunhye; Cho, Seungchan; Lee, Geum Young; Song, Dong Hyun; Gu, Se Hun; Park, Kkothanahreum; Kim, Heung Chul; Wiley, Michael R.; Chain, Patrick S.G.; Jeong, Seong Tae; Klein, Terry A.; Palacios, Gustavo; Song, Jin Won.

In: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, Vol. 70, No. 3, 16.01.2020, p. 464-473.

Research output: Contribution to journalArticle

Kim, WK, No, JS, Lee, D, Jung, J, Park, H, Yi, Y, Kim, JA, Lee, SH, Kim, Y, Park, S, Cho, S, Lee, GY, Song, DH, Gu, SH, Park, K, Kim, HC, Wiley, MR, Chain, PSG, Jeong, ST, Klein, TA, Palacios, G & Song, JW 2020, 'Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus', Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, vol. 70, no. 3, pp. 464-473. https://doi.org/10.1093/cid/ciz234
Kim, Won Keun ; No, Jin Sun ; Lee, Daesang ; Jung, Jaehun ; Park, Hayne ; Yi, Yongjin ; Kim, Jeong Ah ; Lee, Seung Ho ; Kim, Yujin ; Park, Sunhye ; Cho, Seungchan ; Lee, Geum Young ; Song, Dong Hyun ; Gu, Se Hun ; Park, Kkothanahreum ; Kim, Heung Chul ; Wiley, Michael R. ; Chain, Patrick S.G. ; Jeong, Seong Tae ; Klein, Terry A. ; Palacios, Gustavo ; Song, Jin Won. / Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus. In: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2020 ; Vol. 70, No. 3. pp. 464-473.
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abstract = "BACKGROUND: Endemic outbreaks of hantaviruses pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) causes hemorrhagic fever with renal syndrome (HFRS) in humans. Using comparative genomic analyses of partial and nearly complete sequences of HTNV from humans and rodents, we were able to localize, with limitations, the putative infection locations for HFRS patients. Partial sequences might not reflect precise phylogenetic positions over the whole-genome sequences; finer granularity of rodent sampling reflects more precisely the circulation of strains. METHODS: Five HFRS specimens were collected. Epidemiological surveys were conducted with the patients during hospitalization. We conducted active surveillance at suspected HFRS outbreak areas. We performed multiplex polymerase chain reaction-based next-generation sequencing to obtain the genomic sequence of HTNV from patients and rodents. The phylogeny of human- and rodent-derived HTNV was generated using the maximum likelihood method. For phylogeographic analyses, the tracing of HTNV genomes from HFRS patients was defined on the bases of epidemiological interviews, phylogenetic patterns of the viruses, and geographic locations of HTNV-positive rodents. RESULTS: The phylogeographic analyses demonstrated genetic clusters of HTNV strains from clinical specimens, with HTNV circulating in rodents at suspected sites of patient infections. CONCLUSIONS: This study demonstrates a major shift in molecular epidemiological surveillance of HTNV. Active targeted surveillance was performed at sites of suspected infections, allowing the high-resolution phylogeographic analysis to reveal the site of emergence of HTNV. We posit that this novel approach will make it possible to identify infectious sources, perform disease risk assessment, and implement preparedness against vector-borne viruses.",
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AU - No, Jin Sun

AU - Lee, Daesang

AU - Jung, Jaehun

AU - Park, Hayne

AU - Yi, Yongjin

AU - Kim, Jeong Ah

AU - Lee, Seung Ho

AU - Kim, Yujin

AU - Park, Sunhye

AU - Cho, Seungchan

AU - Lee, Geum Young

AU - Song, Dong Hyun

AU - Gu, Se Hun

AU - Park, Kkothanahreum

AU - Kim, Heung Chul

AU - Wiley, Michael R.

AU - Chain, Patrick S.G.

AU - Jeong, Seong Tae

AU - Klein, Terry A.

AU - Palacios, Gustavo

AU - Song, Jin Won

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N2 - BACKGROUND: Endemic outbreaks of hantaviruses pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) causes hemorrhagic fever with renal syndrome (HFRS) in humans. Using comparative genomic analyses of partial and nearly complete sequences of HTNV from humans and rodents, we were able to localize, with limitations, the putative infection locations for HFRS patients. Partial sequences might not reflect precise phylogenetic positions over the whole-genome sequences; finer granularity of rodent sampling reflects more precisely the circulation of strains. METHODS: Five HFRS specimens were collected. Epidemiological surveys were conducted with the patients during hospitalization. We conducted active surveillance at suspected HFRS outbreak areas. We performed multiplex polymerase chain reaction-based next-generation sequencing to obtain the genomic sequence of HTNV from patients and rodents. The phylogeny of human- and rodent-derived HTNV was generated using the maximum likelihood method. For phylogeographic analyses, the tracing of HTNV genomes from HFRS patients was defined on the bases of epidemiological interviews, phylogenetic patterns of the viruses, and geographic locations of HTNV-positive rodents. RESULTS: The phylogeographic analyses demonstrated genetic clusters of HTNV strains from clinical specimens, with HTNV circulating in rodents at suspected sites of patient infections. CONCLUSIONS: This study demonstrates a major shift in molecular epidemiological surveillance of HTNV. Active targeted surveillance was performed at sites of suspected infections, allowing the high-resolution phylogeographic analysis to reveal the site of emergence of HTNV. We posit that this novel approach will make it possible to identify infectious sources, perform disease risk assessment, and implement preparedness against vector-borne viruses.

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