Sequence-Independent, Single-Primer amplification next-generation sequencing of hantaan virus cell culture-based isolates

Dong Hyun Song, Won Keun Kim, Se Hun Gu, Daesang Lee, Jeong Ah Kim, Jin Sun No, Seung Ho Lee, Michael R Wiley, Gustavo Palacios, Jin Won Song, Seong Tae Jeong

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Hantaan virus (HTNV), identified in the striped field mouse (Apodemus agrarius), belongs to the genus Hantavirus of the family Bunyaviridae and contains tripartite RNA genomes, small (S), medium (M), and large (L) segments. HTNV is a major causative for hemorrhagic fever with renal syndrome (HFRS) with fatality rates ranging from 1% to 15% in the Republic of Korea (ROK) and China. Defining of HTNV whole-genome sequences and isolation of the infectious particle play a critical role in the characterization and preventive and therapeutic strategies of hantavirus outbreaks. Next-generation sequencing (NGS) provides an advanced tool for massive genomic sequencing of viruses. However, the isolation of viral infectious particles is a huge obstacle to investigate and develop anti-virals for hantaviruses. Here, we report 12 HTNV isolates from lung tissues of the striped field mouse in the highly HFRS-endemic areas. Sequence-independent, single-primer amplification (SISPA) NGS was attempted to recover the genomic sequences of HTNV isolates. The nucleotide sequence of HTNV S, M, and L segments were covered up to 99.4-100%, 97.5-100%, and 95.6-99.8%, respectively, based on the full length of the prototype HTNV 76-118. The whole-genome sequencing of HTNV isolates was accomplished by additional reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification cDNA ends (RACE) PCR. In conclusion, this study will lead to the attempt and usage of SISPA NGS technologies to delineate the whole-genome sequence of hantaviruses, providing a new era of viral genomics for the surveillance, trace, and disease risk management of HFRS incidents.

Original languageEnglish (US)
Pages (from-to)389-394
Number of pages6
JournalAmerican Journal of Tropical Medicine and Hygiene
Volume96
Issue number2
DOIs
StatePublished - Jan 1 2017

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Hantaan virus
Cell Culture Techniques
Hantavirus
Hemorrhagic Fever with Renal Syndrome
Genome
Bunyaviridae
Murinae
Polymerase Chain Reaction
Republic of Korea
Risk Management
Disease Management
Genomics
Taiwan
Virion
Reverse Transcription
Disease Outbreaks
Complementary DNA
RNA
Viruses
Technology

ASJC Scopus subject areas

  • Parasitology
  • Infectious Diseases
  • Virology

Cite this

Sequence-Independent, Single-Primer amplification next-generation sequencing of hantaan virus cell culture-based isolates. / Song, Dong Hyun; Kim, Won Keun; Gu, Se Hun; Lee, Daesang; Kim, Jeong Ah; No, Jin Sun; Lee, Seung Ho; Wiley, Michael R; Palacios, Gustavo; Song, Jin Won; Jeong, Seong Tae.

In: American Journal of Tropical Medicine and Hygiene, Vol. 96, No. 2, 01.01.2017, p. 389-394.

Research output: Contribution to journalArticle

Song, Dong Hyun ; Kim, Won Keun ; Gu, Se Hun ; Lee, Daesang ; Kim, Jeong Ah ; No, Jin Sun ; Lee, Seung Ho ; Wiley, Michael R ; Palacios, Gustavo ; Song, Jin Won ; Jeong, Seong Tae. / Sequence-Independent, Single-Primer amplification next-generation sequencing of hantaan virus cell culture-based isolates. In: American Journal of Tropical Medicine and Hygiene. 2017 ; Vol. 96, No. 2. pp. 389-394.
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AU - No, Jin Sun

AU - Lee, Seung Ho

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