Jin Sun No

Korea Disease Control and Prevention Agency

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Seung‐Ho Lee

Woosuk University

Won‐Keun Kim

Hallym University Medical Center

Terry A. Klein

59th Medical Wing

Kyungmin Park

Korea University

Se Hun Gu

Agency for Defense Development

Il‐Hwan Kim

Korea Disease Control and Prevention Agency

Seungchan Cho

Korea Institute of Materials Science

Jin‐Won Song

Korea University

Seong Tae Jeong

Agency for Defense Development

Dae-Sang Lee

Uijeongbu St. Mary's Hospital

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Korea Disease Control and Prevention Agency

Korea University

Korea Center for Disease Control and Prevention

Seoul National University

Yonsei University

Hallym University

Korea National Institute of Health

Kyungpook National University

New Generation University College

Government of the Republic of Korea

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Molecular Epidemiology and Genetic Diversity of Orthohantaviruses in Small Mammals in Western Poland

American Journal of Tropical Medicine and Hygiene (2020)

Seung‐Ho Lee Jin Sun No Won‐Keun Kim Ewa Gajda Agnieszka Perec‐Matysiak

Orthohantaviruses are negative-sense, single-stranded RNA viruses harbored by multiple small mammals. Dobrava-Belgrade virus (DOBV) and Puumala virus (PUUV) cause hemorrhagic fever with renal syndrome (HFRS) in Europe. In Poland, serological surveys have demonstrated antibodies against DOBV and PUUV in patients with HFRS. Molecular evidence of DOBV and PUUV has been found in Apodemus flavicollis and Myodes glareolus, respectively, in southeastern Poland, and Seewis virus (SWSV) has been reported in Sorex araneus in central Poland. However, data on the geographic distribution and phylogeny of orthohantaviruses are unavailable for other regions in Poland. To ascertain the prevalence and genetic diversity of orthohantaviruses in western and northern Poland, lung tissues from 106 small mammals were analyzed for the presence of orthohantavirus RNA. DOBV and SWSV were detected in two of 42 (4.8%) Apodemus agrarius and in three of 10 (30%) S. araneus, respectively. Phylogenetic analyses of partial L- and S-segment sequences of DOBV indicated a shared genetic lineage with the Kurkino genotype from Slovakia, Russia, and Hungary, whereas the partial M segment of DOBV clustered with the Kurkino genotype from Germany. Phylogenetic relationships of the SWSV L and S segments showed a geographic lineage with SWSV strains from central Poland, Czech Republic, and Germany. In conclusion, the study provides insights into the molecular prevalence, phylogenetic diversity, and evolutionary relationship of DOBV in A. agrarius and SWSV in S. araneus. This report increases awareness among physicians for HFRS outbreaks in western Poland.

Apodemus agrarius

Sorex

Araneus

Lineage (genetic)

Puumala virus

Molecular Epidemiology

10.4269/ajtmh.19-0802

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Citations (8)

Discovery and Genetic Characterization of Novel Paramyxoviruses Related to the Genus Henipavirus in Crocidura Species in the Republic of Korea

Viruses (2021)

Seung‐Ho Lee Kijin Kim Jongwoo Kim Jin Sun No Kyungmin Park

Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a critical threat to human public health. Currently, 78 species, 17 genera, and 4 subfamilies of paramyxoviruses are harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Henipaviruses are critical zoonotic pathogens that cause severe acute respiratory distress and neurological diseases in humans. Using reverse transcription-polymerase chain reaction, 115 Crocidura species individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was observed in 26 (22.6%) shrews collected at five trapping sites, Republic of Korea. Herein, we report two genetically distinct novel paramyxoviruses (genus: Henipavirus): Gamak virus (GAKV) and Daeryong virus (DARV) isolated from C. lasiura and C. shantungensis, respectively. Two GAKVs and one DARV were nearly completely sequenced using next-generation sequencing. GAKV and DARV contain six genes (3′-N-P-M-F-G-L-5′) with genome sizes of 18,460 nucleotides and 19,471 nucleotides, respectively. The phylogenetic inference demonstrated that GAKV and DARV form independent genetic lineages of Henipavirus in Crocidura species. GAKV-infected human lung epithelial cells elicited the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. In conclusion, this study contributes further understandings of the molecular prevalence, genetic characteristics and diversity, and zoonotic potential of novel paramyxoviruses in shrews.

Zoonosis

10.3390/v13102020

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Citations (52)

Neutralization Testing–based Immunogenicity Analysis of Recent Prevalent Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Sublineages

Annals of Laboratory Medicine (2023)

E. Lee Hyeokjin Lee Sang Won O Jee Eun Rhee Jeong‐Min Kim

Eun Ju Lee, M.S., Hyeokjin Lee, M.S., Sang Won O, M.S., Jee Eun Rhee, Ph.D., Jeong-Min Kim, Ph.D., Dong Ju Kim, M.S., Il-Hwan Kim, Ph.D., Jin Sun No, Ph.D., Ae Kyung Park, Ph.D., Jeong-Ah Kim, Ph.D., Chae Young Lee, B.S., Young-Ki Choi, Ph.D., and Eun-Jin Kim, Ph.D.. Ann Lab Med -0001;0:. https://doi.org/10.3343/alm.2023.0256

10.3343/alm.2023.0256

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Emergence of the D614A mutation in the spike protein of SARS-CoV-2: Imported cases to the South Korea

medRxiv (Cold Spring Harbor Laboratory) (2020)

Ae Kyung Park Jin Sun No E Hyun Shin Yoon‐Seok Chung Il‐Hwan Kim

Abstract We identified imported cases of a novel D614A mutation in the spike glycoprotein of SARS-CoV-2 in the South Korea. SARS-CoV-2 harboring the novel mutation was isolated from returning travelers from Uzbekistan. These results emphasized the possibility that new mutations have emerged in that area.

spike protein

10.1101/2020.09.04.20184721

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Citations (2)

Genomic epidemiology of SARS-CoV-2 variants in South Korea between January 2020 and February 2023

Virology (2023)

Il‐Hwan Kim Jin Sun No Jeong-Ah Kim Ae Kyung Park Hyeokjin Lee

The Korea Disease Control and Prevention Agency (KDCA) has been conducting national genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). To monitor and characterize circulating SARS-CoV-2 variants in South Korea, 102,873 oropharyngeal/nasopharyngeal swab samples collected from patients with confirmed COVID-19 were sequenced, assigned lineages, and phylogenetically analyzed. Each wave followed a pattern of variants emerging first abroad and then spreading domestically. In 2020, B.41 lineage led the first wave, and B.1.497 dominated the second and third waves. In 2021, the fourth wave was driven by Delta (AY.69 and AY.122.5). In 2022, the fifth to seventh waves were dominated by Omicron sub-lineages BA.1/BA.1.1 and BA.2/BA.2.3, BA.5/BA.5.2, and BN.1, sequentially. The KDCA detected and monitored increasing variants in advance prior to large-scale epidemics, but the repeated emergence of new variants could threaten public health again. Therefore, it is important to continue to monitor and characterize emerging and circulating variants through national genomic surveillance.

Lineage (genetic)

Molecular Epidemiology

10.1016/j.virol.2023.109869

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Citations (7)

Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus

Clinical Infectious Diseases (2019)

Won‐Keun Kim Jin Sun No Dae-Sang Lee Jaehun Jung Hayne Park

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.

Hantaan virus

10.1093/cid/ciz234

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Citations (25)

Urinary genome detection and tracking of Hantaan virus from hemorrhagic fever with renal syndrome patients using multiplex PCR-based next-generation sequencing

PLoS neglected tropical diseases (2021)

Seungchan Cho Won‐Keun Kim Jin Sun No Seung‐Ho Lee Jaehun Jung

Background Hantavirus infection occurs through the inhalation of aerosolized excreta, including urine, feces, and saliva of infected rodents. The presence of Hantaan virus (HTNV) RNA or infectious particles in urine specimens of patient with hemorrhagic fever with renal syndrome (HFRS) remains to be investigated. Methodology/Principal findings We collected four urine and serum specimens of Republic of Korea Army (ROKA) patients with HFRS. We performed multiplex PCR-based next-generation sequencing (NGS) to obtain the genome sequences of clinical HTNV in urine specimens containing ultra-low amounts of viral genomes. The epidemiological and phylogenetic analyses of HTNV demonstrated geographically homogenous clustering with those in Apodemus agrarius captured in highly endemic areas, indicating that phylogeographic tracing of HTNV genomes reveals the potential infection sites of patients with HFRS. Genetic exchange analyses showed a genetic configuration compatible with HTNV L segment exchange in nature. Conclusion/Significance Our results suggest that whole or partial genome sequences of HTNV from the urine enabled to track the putative infection sites of patients with HFRS by phylogeographically linking to the zoonotic HTNV from the reservoir host captured at endemic regions. This report raises awareness among physicians for the presence of HTNV in the urine of patients with HFRS.

Hantaan virus

Apodemus agrarius

10.1371/journal.pntd.0009707

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Citations (12)

Clinical and Immunological Predictors of Hemorrhagic Fever with Renal Syndrome Outcome during the Early Phase

Viruses (2022)

Geum‐Young Lee Won‐Keun Kim Jin Sun No Yongjin Yi Hayne Cho Park

The ability to accurately predict the early progression of hemorrhagic fever with renal syndrome (HFRS) is crucial for reducing morbidity and mortality rates in severely affected patients. However, the utility of biomarkers for predicting clinical outcomes remains elusive in HFRS. The aims of the current study were to analyze the serum levels of immune function-related proteins and identify novel biomarkers that may help ascertain clinical outcomes of HFRS. Enzyme-linked immunosorbent assay, Luminex, and bioanalyzer assays were used to quantitatively detect 15 biomarkers in 49 serum samples of 26 patients with HFRS. High hemoglobin (HGB) and low urine output (UO) levels were identified as potential biomarkers associated with the acute HFRS. The serum soluble urokinase plasminogen activator receptor (suPAR) and C-X-C motif chemokine ligand 10 (CXCL10) values increased in the early phase of diseases. Elevated suPAR, interleukin-10 (IL-10), CXCL10, and decreased transforming growth factor-beta 3 (TGF-β3) were representative predictors of the disease severity. Upregulation of the HGB showed a significant correlation with high levels of suPAR and CXCL10. Reduced UO positively correlated with increased suPAR, CXCL10, and TGF-β2, and decreased vascular endothelial growth factor and TGF-β3. The changing HGB and UO criteria, high suPAR, IL-10, CXCL10, and low TGF-β3 of HFRS raise significant awareness for physicians regarding prospective biomarkers for monitoring early warning signs of HFRS. This study provides critical insights into the clinical and immunological biomarkers for disease severity and progression in patients with HFRS to identify early predictions of fatal outcomes.

SuPAR

10.3390/v14030595

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Complete Genome Sequence of Monkeypox Virus Strain MPXV-ROK-P1-2022 Isolated from the First Monkeypox Patient in the Republic of Korea

Microbiology Resource Announcements (2022)

Chi‐Hwan Choi Jin Sun No Jin‐Won Kim Minji Lee Hwachul Shin

We report the complete genome sequence of the monkeypox virus strain MPXV-ROK-P1-2022, isolated from the first patient diagnosed with monkeypox in the Republic of Korea in June 2022. The virus was fully sequenced on the Illumina MiSeq instrument, and the phylogenetic tree showed that the strain belongs to lineage B.1.1.

Monkeypox

Lineage (genetic)

Strain (injury)

Sequence (biology)

Orthopoxvirus

10.1128/mra.00853-22

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Epidemiological Surveillance and Genomic Characterization of Soochong Virus From Apodemus Species Using Multiplex PCR‐Based Next‐Generation Sequencing, Republic of Korea

Journal of Medical Virology (2024)

Kyungmin Park Jin Sun No Sara Puspareni Prayitno Y. W. Seo Seung‐Ho Lee

ABSTRACT Orthohantavirus hantanense causes hemorrhagic fever with renal syndrome in Eurasia, posing a substantial public health threat. Although the Hantaan virus is the primary etiological agent in the Republic of Korea (ROK), evidence suggests the potential zoonotic transmission of the Amur virus (AMRV), closely related to the Soochong virus (SOOV), to humans in China and Russia. This study examined 31 Apodemus spp. captured from six regions in Gangwon Province, ROK, between 2015 and 2018. Of these, 5/31 (16.1%) tested positive for anti‐SOOV immunoglobulin G and SOOV RNA, with 3/6 (50%) in Hongcheon‐gun and 2/5 (40%) in Pyeongchang‐gun. Utilizing a multiplex polymerase chain reaction‐based next‐generation sequencing approach, we achieved complete genomic sequencing of SOOV from rodent lung tissues, with coverage rates of 90.3%−98.2% for the S segment, 92.3%−98.1% for the M segment, and 88.1%−93.0% for the L segment. Five novel whole‐genome sequences of SOOV were obtained from rodents in Hongcheon‐gun and Pyeongchang‐gun, representing the first documented SOOV in Pyeongchang‐gun. The evolutionary rate analysis of SOOV tripartite genomes demonstrated lower divergence in the S segment. Phylogenetic analysis revealed a well‐supported divergence of the SOOV and AMRV lineages across the ROK, China, and Russia, with incongruences suggesting differential segment evolution. Co‐divergence analysis indicated the inter‐species transmission of SOOV Aa18‐104 from Apodemus agrarius in Pyeongchang‐gun. The high zoonotic potential of all SOOV strains underscores the need for extensive monitoring and surveillance. This report provides crucial insights for the development of effective control strategies against hantaviral outbreaks in the ROK.

Apodemus agrarius

10.1002/jmv.70077

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Citations (1)