1.Amplicon-Based MinION Sequencing Complements Severe Fever With Thrombocytopenia Syndrome (SFTS) Diagnosis via Real-Time RT-PCR in Patients With Suspected SFTS
Sara P. PRAYITNO ; Yeong Geon CHO ; Eun Sil KIM ; Kyungmin PARK ; Seonghyeon LEE ; Augustine NATASHA ; Jieun PARK ; Jin-Won SONG ; Yang Soo KIM ; Seung Soon LEE ; Won-Keun KIM
Journal of Korean Medical Science 2025;40(19):e69-
Background:
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a lethal threat.Increasing Severe fever with thrombocytopenia syndrome (SFTS) risk in Asia and the United States stems from the spread of natural host, Haemaphysalis longicornis. Rapid and accurate SFTSV molecular diagnosis is crucial for treatment decisions, reducing fatality risk.
Methods:
Blood samples from 17 suspected SFTS patients at Chuncheon Sacred Heart Hospital (September-December 2022) were collected. SFTSV was diagnosed using two reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays from Gangwon Institute of Health and Environment (RT-qPCR/GIHE) and Asan Medical Center (RT-qPCR/AMC). To address RT-qPCR disparities, amplicon-based MinION sequencing traced SFTSV genomic sequences in clinical samples.
Results:
In two samples (N39 and N50), SFTSV was detected in both RT-qPCR/GIHE and RTqPCR/AMC. Among 11 samples, RT-qPCR/AMC exclusively detected SFTSV. In four samples, both assays yielded negative results. Amplicon-based MinION sequencing enabled nearly whole-genome sequencing of SFTSV in samples N39 and N50. Among 11 discordant samples, five contained significant SFTSV reads, aligning with the RT-qPCR/AMC findings. However, another six samples showed insufficient viral reads in accordance with the negativity observed in RT-qPCR/GIHE. The phylogenetic pattern of SFTSV demonstrated N39 formed a genetic lineage with genotype A in all segments. SFTSV N50 grouped with the B-1 sub-genotype for L segment and B-2 sub-genotype for the M and S segments, indicating genetic reassortment.
Conclusion
The study demonstrates the robust sensitivity of amplicon-based MinION sequencing for the direct detection of SFTSV in clinical samples containing ultralow copies of viral genomes. Next-generation sequencing holds potential in resolving SFTSV diagnosis discrepancies, enhancing understanding of diagnostic capacity, and risk assessment for emerging SFTSV.
2.Amplicon-Based MinION Sequencing Complements Severe Fever With Thrombocytopenia Syndrome (SFTS) Diagnosis via Real-Time RT-PCR in Patients With Suspected SFTS
Sara P. PRAYITNO ; Yeong Geon CHO ; Eun Sil KIM ; Kyungmin PARK ; Seonghyeon LEE ; Augustine NATASHA ; Jieun PARK ; Jin-Won SONG ; Yang Soo KIM ; Seung Soon LEE ; Won-Keun KIM
Journal of Korean Medical Science 2025;40(19):e69-
Background:
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a lethal threat.Increasing Severe fever with thrombocytopenia syndrome (SFTS) risk in Asia and the United States stems from the spread of natural host, Haemaphysalis longicornis. Rapid and accurate SFTSV molecular diagnosis is crucial for treatment decisions, reducing fatality risk.
Methods:
Blood samples from 17 suspected SFTS patients at Chuncheon Sacred Heart Hospital (September-December 2022) were collected. SFTSV was diagnosed using two reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays from Gangwon Institute of Health and Environment (RT-qPCR/GIHE) and Asan Medical Center (RT-qPCR/AMC). To address RT-qPCR disparities, amplicon-based MinION sequencing traced SFTSV genomic sequences in clinical samples.
Results:
In two samples (N39 and N50), SFTSV was detected in both RT-qPCR/GIHE and RTqPCR/AMC. Among 11 samples, RT-qPCR/AMC exclusively detected SFTSV. In four samples, both assays yielded negative results. Amplicon-based MinION sequencing enabled nearly whole-genome sequencing of SFTSV in samples N39 and N50. Among 11 discordant samples, five contained significant SFTSV reads, aligning with the RT-qPCR/AMC findings. However, another six samples showed insufficient viral reads in accordance with the negativity observed in RT-qPCR/GIHE. The phylogenetic pattern of SFTSV demonstrated N39 formed a genetic lineage with genotype A in all segments. SFTSV N50 grouped with the B-1 sub-genotype for L segment and B-2 sub-genotype for the M and S segments, indicating genetic reassortment.
Conclusion
The study demonstrates the robust sensitivity of amplicon-based MinION sequencing for the direct detection of SFTSV in clinical samples containing ultralow copies of viral genomes. Next-generation sequencing holds potential in resolving SFTSV diagnosis discrepancies, enhancing understanding of diagnostic capacity, and risk assessment for emerging SFTSV.
3.Amplicon-Based MinION Sequencing Complements Severe Fever With Thrombocytopenia Syndrome (SFTS) Diagnosis via Real-Time RT-PCR in Patients With Suspected SFTS
Sara P. PRAYITNO ; Yeong Geon CHO ; Eun Sil KIM ; Kyungmin PARK ; Seonghyeon LEE ; Augustine NATASHA ; Jieun PARK ; Jin-Won SONG ; Yang Soo KIM ; Seung Soon LEE ; Won-Keun KIM
Journal of Korean Medical Science 2025;40(19):e69-
Background:
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a lethal threat.Increasing Severe fever with thrombocytopenia syndrome (SFTS) risk in Asia and the United States stems from the spread of natural host, Haemaphysalis longicornis. Rapid and accurate SFTSV molecular diagnosis is crucial for treatment decisions, reducing fatality risk.
Methods:
Blood samples from 17 suspected SFTS patients at Chuncheon Sacred Heart Hospital (September-December 2022) were collected. SFTSV was diagnosed using two reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays from Gangwon Institute of Health and Environment (RT-qPCR/GIHE) and Asan Medical Center (RT-qPCR/AMC). To address RT-qPCR disparities, amplicon-based MinION sequencing traced SFTSV genomic sequences in clinical samples.
Results:
In two samples (N39 and N50), SFTSV was detected in both RT-qPCR/GIHE and RTqPCR/AMC. Among 11 samples, RT-qPCR/AMC exclusively detected SFTSV. In four samples, both assays yielded negative results. Amplicon-based MinION sequencing enabled nearly whole-genome sequencing of SFTSV in samples N39 and N50. Among 11 discordant samples, five contained significant SFTSV reads, aligning with the RT-qPCR/AMC findings. However, another six samples showed insufficient viral reads in accordance with the negativity observed in RT-qPCR/GIHE. The phylogenetic pattern of SFTSV demonstrated N39 formed a genetic lineage with genotype A in all segments. SFTSV N50 grouped with the B-1 sub-genotype for L segment and B-2 sub-genotype for the M and S segments, indicating genetic reassortment.
Conclusion
The study demonstrates the robust sensitivity of amplicon-based MinION sequencing for the direct detection of SFTSV in clinical samples containing ultralow copies of viral genomes. Next-generation sequencing holds potential in resolving SFTSV diagnosis discrepancies, enhancing understanding of diagnostic capacity, and risk assessment for emerging SFTSV.
4.Amplicon-Based MinION Sequencing Complements Severe Fever With Thrombocytopenia Syndrome (SFTS) Diagnosis via Real-Time RT-PCR in Patients With Suspected SFTS
Sara P. PRAYITNO ; Yeong Geon CHO ; Eun Sil KIM ; Kyungmin PARK ; Seonghyeon LEE ; Augustine NATASHA ; Jieun PARK ; Jin-Won SONG ; Yang Soo KIM ; Seung Soon LEE ; Won-Keun KIM
Journal of Korean Medical Science 2025;40(19):e69-
Background:
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a lethal threat.Increasing Severe fever with thrombocytopenia syndrome (SFTS) risk in Asia and the United States stems from the spread of natural host, Haemaphysalis longicornis. Rapid and accurate SFTSV molecular diagnosis is crucial for treatment decisions, reducing fatality risk.
Methods:
Blood samples from 17 suspected SFTS patients at Chuncheon Sacred Heart Hospital (September-December 2022) were collected. SFTSV was diagnosed using two reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays from Gangwon Institute of Health and Environment (RT-qPCR/GIHE) and Asan Medical Center (RT-qPCR/AMC). To address RT-qPCR disparities, amplicon-based MinION sequencing traced SFTSV genomic sequences in clinical samples.
Results:
In two samples (N39 and N50), SFTSV was detected in both RT-qPCR/GIHE and RTqPCR/AMC. Among 11 samples, RT-qPCR/AMC exclusively detected SFTSV. In four samples, both assays yielded negative results. Amplicon-based MinION sequencing enabled nearly whole-genome sequencing of SFTSV in samples N39 and N50. Among 11 discordant samples, five contained significant SFTSV reads, aligning with the RT-qPCR/AMC findings. However, another six samples showed insufficient viral reads in accordance with the negativity observed in RT-qPCR/GIHE. The phylogenetic pattern of SFTSV demonstrated N39 formed a genetic lineage with genotype A in all segments. SFTSV N50 grouped with the B-1 sub-genotype for L segment and B-2 sub-genotype for the M and S segments, indicating genetic reassortment.
Conclusion
The study demonstrates the robust sensitivity of amplicon-based MinION sequencing for the direct detection of SFTSV in clinical samples containing ultralow copies of viral genomes. Next-generation sequencing holds potential in resolving SFTSV diagnosis discrepancies, enhancing understanding of diagnostic capacity, and risk assessment for emerging SFTSV.
5.Hepatic Artery Occlusion after Liver Transplantation in Patients with Doppler Ultrasound Abnormality: Increasing Sensitivity of Contrast-Enhanced Ultrasound Diagnosis
Jin Sil KIM ; Kyoung Won KIM ; Sang Hyun CHOI ; So Yeong JEONG ; Jae Hyun KWON ; Gi Won SONG ; Sung Gyu LEE
Korean Journal of Radiology 2019;20(3):459-468
OBJECTIVE: To investigate whether diagnostic performance of contrast-enhanced ultrasound (CEUS) could be improved with modified criteria to diagnose significant hepatic artery occlusion (HAO) and to determine the role of CEUS in patients with a tardus-parvus hepatic artery (HA) pattern on Doppler US. MATERIALS AND METHODS: Among 2679 adult liver transplantations performed over 7 years, HAO was suspected in 288 recipients, based on Doppler ultrasound. Among them, 130 patients underwent CEUS. After excluding two technical failures, 128 CEUS images were retrospectively reviewed to search for abnormal findings, such as no HA enhancement, abnormal HA enhancement (delayed, faint, and discontinuous enhancement), and perfusion defect in the liver parenchyma. The performance CEUS abnormalities were assessed in the patients overall and in subgroups based on Doppler ultrasound abnormality (group A, no flow; group B, tardus-parvus pattern) and were compared based on the area under the receiver operating characteristic curve (AUC). RESULTS: HAO were diagnosed in 41 patients by surgery, angiography, or follow-up abnormality. By using the conventional criterion (no HA enhancement) to diagnose HAO in patients overall, the sensitivity, specificity, and AUC were 58.5%, 100%, and 0.793, respectively. Modified criteria for HAO (no HA enhancement, abnormal enhancement, or parenchymal perfusion defect) showed statistically significantly increased sensitivity (97.6%, 40/41) and AUC (0.959) (p < 0.001), although the specificity (95.4%, 83/87) was slightly decreased. The sensitivity and specificity of the modified criteria in Groups A and B were 97.1% (33/34) and 95.7% (22/23), and 100% (7/7) and 95.3% (61/64), respectively. CONCLUSION: Modified criteria could improve diagnostic performance of CEUS for HAO, particularly by increasing sensitivity. CEUS could be useful for diagnosing HAO even in patients with a tardus-parvus HA pattern on Doppler US, using modified criteria.
Adult
;
Angiography
;
Area Under Curve
;
Contrast Media
;
Diagnosis
;
Follow-Up Studies
;
Hepatic Artery
;
Humans
;
Liver Transplantation
;
Liver
;
Perfusion
;
Retrospective Studies
;
ROC Curve
;
Sensitivity and Specificity
;
Ultrasonography
6.Endothelium Independent Effect of Pelargonidin on Vasoconstriction in Rat Aorta.
Young Sil MIN ; Hyuk Jun YOON ; Hyun Dong JE ; Jong Hyuk LEE ; Seong Su YOO ; Hyun Sub SHIM ; Hak Yeong LEE ; Hyen Oh LA ; Uy Dong SOHN
Biomolecules & Therapeutics 2018;26(4):374-379
In this study, we investigated the effects of pelargonidin, an anthocyanidin found in many fruits and vegetables, on endothelium-independent vascular contractility to determine the underlying mechanism of relaxation. Isometric contractions of denuded aortic muscles from male rats were recorded, and the data were combined with those obtained in western blot analysis. Pelargonidin significantly inhibited fluoride-, thromboxane A2-, and phorbol ester-induced vascular contractions, regardless of the presence or absence of endothelium, suggesting a direct effect of the compound on vascular smooth muscles via a different pathway. Pelargonidin significantly inhibited the fluoride-dependent increase in the level of myosin phosphatase target subunit 1 (MYPT1) phosphorylation at Thr-855 and the phorbol 12,13-dibutyrate-dependent increase in the level of extracellular signal-regulated kinase (ERK) 1/2 phosphorylation at Thr202/Tyr204, suggesting the inhibition of Rho-kinase and mitogen-activated protein kinase kinase (MEK) activities and subsequent phosphorylation of MYPT1 and ERK1/2. These results suggest that the relaxation effect of pelargonidin on agonist-dependent vascular contractions includes inhibition of Rho-kinase and MEK activities, independent of the endothelial function.
Animals
;
Anthocyanins
;
Aorta*
;
Blotting, Western
;
Endothelium*
;
Fluorides
;
Fruit
;
Humans
;
Isometric Contraction
;
Male
;
Muscle, Smooth, Vascular
;
Muscles
;
Myosin-Light-Chain Phosphatase
;
Phosphorylation
;
Phosphotransferases
;
Protein Kinases
;
Rats*
;
Relaxation
;
rho-Associated Kinases
;
Vasoconstriction*
;
Vegetables
7.A Comparison of Substantia Nigra T1 Hyperintensity in Parkinson's Disease Dementia, Alzheimer's Disease and Age-Matched Controls: Volumetric Analysis of Neuromelanin Imaging.
Won Jin MOON ; Ju Yeon PARK ; Won Sung YUN ; Ji Yeong JEON ; Yeon Sil MOON ; Heejin KIM ; Ki Chang KWAK ; Jong Min LEE ; Seol Heui HAN
Korean Journal of Radiology 2016;17(5):633-640
OBJECTIVE: Neuromelanin loss of substantia nigra (SN) can be visualized as a T1 signal reduction on T1-weighted high-resolution imaging. We investigated whether volumetric analysis of T1 hyperintensity for SN could be used to differentiate between Parkinson's disease dementia (PDD), Alzheimer's disease (AD) and age-matched controls. MATERIALS AND METHODS: This retrospective study enrolled 10 patients with PDD, 18 patients with AD, and 13 age-matched healthy elderly controls. MR imaging was performed at 3 tesla. To measure the T1 hyperintense area of SN, we obtained an axial thin section high-resolution T1-weighted fast spin echo sequence. The volumes of interest for the T1 hyperintense SN were drawn onto heavily T1-weighted FSE sequences through midbrain level, using the MIPAV software. The measurement differences were tested using the Kruskal-Wallis test followed by a post hoc comparison. RESULTS: A comparison of the three groups showed significant differences in terms of volume of T1 hyperintensity (p < 0.001, Bonferroni corrected). The volume of T1 hyperintensity was significantly lower in PDD than in AD and normal controls (p < 0.005, Bonferroni corrected). However, the volume of T1 hyperintensity was not different between AD and normal controls (p = 0.136, Bonferroni corrected). CONCLUSION: The volumetric measurement of the T1 hyperintensity of SN can be an imaging marker for evaluating neuromelanin loss in neurodegenerative diseases and a differential in PDD and AD cases.
Aged
;
Alzheimer Disease*
;
Dementia*
;
Humans
;
Magnetic Resonance Imaging
;
Mesencephalon
;
Neurodegenerative Diseases
;
Parkinson Disease*
;
Parkinsonian Disorders
;
Retrospective Studies
;
Substantia Nigra*
8.A Case of Complete Remission in Patient with Extrahepatic Metastasis after Curative Resection of Hepatocellular Carcinoma by Radiotherapy, Lung Resection and Systemic Chemotherapy.
Yeong Jin KIM ; Hye Won LEE ; Ji Hoon LEE ; Jin Sil SUNG ; Do Young KIM
Journal of Liver Cancer 2016;16(1):63-66
Surgical resection is mainstay treatment of hepatocellular carcinoma (HCC). However, its prognosis is poor, because of the high incidence of HCC recurrence (cumulative 5-year HCC recurrence rate of 70-80%). The most common site of HCC recurrence is the remnant liver, and extrahepatic recurrence occurs in 6.7-13.5% of patients. Because the tumor characteristics in extrahepatic recurrence are usually multiple and aggressive, the optimal treatment modality has not yet been determined. We report a case of complete remission and long term survival over 60 months in patient with extrahepatic metastasis after curative resection of HCC by aggressive treatment, which include lung resection for lung metastasis, radiotherapy for mediastinal lymph node metastasis, and systemic chemotherapy.
Carcinoma, Hepatocellular*
;
Drug Therapy*
;
Humans
;
Incidence
;
Liver
;
Lung*
;
Lymph Nodes
;
Metastasectomy
;
Neoplasm Metastasis*
;
Prognosis
;
Radiotherapy*
;
Recurrence
9.Clinical Characteristics of the Development of Pneumothorax in Mechanically Ventilated Patients in Intensive Care Units.
Wan Chul KIM ; Su Jin LIM ; Kyong Young KIM ; Seung Jun LEE ; Yu Ji CHO ; Yi Yeong JEONG ; Mi Jung PARK ; Kyoung Nyeo JEON ; Jong Deog LEE ; Young Sil HWANG ; Ho Cheol KIM
The Korean Journal of Critical Care Medicine 2014;29(1):13-18
BACKGROUND: Pneumothorax (PTX) can occur as a complication of positive pressure ventilation in mechanically ventilated patients. METHODS: We retrospectively reviewed the clinical characteristics of patients who developed PTX during mechanical ventilation (MV) in the intensive care unit (ICU). RESULTS: Of the 326 patients admitted (208 men and 118 women; mean age, 65.3 +/- 8.74 years), 15 (4.7%) developed PTX, which was MV-associated in 11 (3.3%) cases (6 men and 5 women; mean age, 68.3 +/- 9.12 years) and procedure-associated in 4. Among the patients with MV-associated PTX, the underlying lung diseases were acute respiratory distress syndrome in 7 patients, interstitial lung disease in 2 patients, and chronic obstructive pulmonary disease in 2 patients. PTX diagnosis was achieved by chest radiography alone in 9 patients and chest computed tomography alone in 2 patients. Nine patients were using assist-control mode MV with the mean applied positive end-expiratory pressure, 9 +/- 4.6 cmH2O and the mean tidal volume, 361 +/- 63.7 ml at the diagnosis of PTX. Two patients died as a result of MV-associated PTX and their systolic pressure was below 80 mmHg and heart rates were less than 80/min. Ten patients were treated by chest tube insertion, and 1 patient was treated by percutaneous pigtail catheter insertion. CONCLUSIONS: PTX can develop in patients undergoing MV, and may cause death. Early recognition and treatment are necessary to prevent hemodynamic compromise in patients who develop PTX.
Blood Pressure
;
Catheters
;
Chest Tubes
;
Diagnosis
;
Female
;
Heart Rate
;
Hemodynamics
;
Humans
;
Intensive Care Units*
;
Critical Care*
;
Lung Diseases
;
Lung Diseases, Interstitial
;
Male
;
Pneumothorax*
;
Positive-Pressure Respiration
;
Pulmonary Disease, Chronic Obstructive
;
Radiography
;
Respiration, Artificial
;
Respiratory Distress Syndrome, Adult
;
Retrospective Studies
;
Thorax
;
Tidal Volume
10.Development of Acute Respiratory Failure on Initiation of Anti-Tuberculosis Medication in Patients with Pulmonary Tuberculosis: Clinical and Radiologic Features of 8 Patients and Literature Review.
Su Jin LIM ; Donghoon LEW ; Haa Na SONG ; You Eun KIM ; Seung Jun LEE ; Yu Ji CHO ; Yi Yeong JEONG ; Mi Jung PARK ; Kyoung Nyeo JEON ; Ho Cheol KIM ; Jong Deog LEE ; Young Sil HWANG
The Korean Journal of Critical Care Medicine 2013;28(2):108-114
BACKGROUND: Acute respiratory failure can occur paradoxically on initiation of anti-tuberculosis (TB) treatment in patients with pulmonary TB. This study is aimed to analyze the clinical features of anti-TB treatment induced acute respiratory failure. METHODS: We reviewed the clinical and radiological characteristics of 8 patients with pulmonary tuberculosis (5 men and 3 women; mean age, 55 +/- 15.5 years) who developed acute respiratory failure following initiation of anti-TB medication and thus required mechanical ventilation (MV) in the intensive care unit (ICU). RESULTS: The interval between initiation of anti-TB medication and development of MV-requiring acute respiratory failure was 2-14 days (mean, 4.4 +/- 4.39 days), and the duration of MV was 1-18 days (mean, 7.1 +/- 7.03 days). At admission, body temperature and serum levels of lactate dehydrogenase and C-reactive protein were increased. Serum levels of protein, albumin and creatinine were 5.8 +/- 0.98, 2.3 +/- 0.5 and 1.8 +/- 2.58 mg/ml, respectively. Radiographs characterized both lung involvements in all patients. Consolidation with the associated nodule was noted in 7 patients, ground glass opacity in 2, and cavitary lesion in 4. Micronodular lesion in the lungs, suggesting miliary tuberculosis lesion, was noted in 1 patient. At ICU admissions, the ranges of the APACHE II and SOFA scores were 17-38 (mean, 28.2 +/- 7.26) and 6-14 (mean, 10.1 +/- 2.74). The mean lung injury score was 2.8 +/- 0.5. Overall, 6 patients died owing to septic shock and multiorgan failure. CONCLUSIONS: On initiation of treatment for pulmonary TB, acute respiratory failure can paradoxically occur in patients with extensive lung parenchymal involvement and high mortality.
APACHE
;
Body Temperature
;
C-Reactive Protein
;
Creatinine
;
Glass
;
Humans
;
Intensive Care Units
;
L-Lactate Dehydrogenase
;
Lung
;
Lung Injury
;
Male
;
Respiration, Artificial
;
Respiratory Insufficiency
;
Shock, Septic
;
Tuberculosis, Miliary
;
Tuberculosis, Pulmonary

Result Analysis
Print
Save
E-mail