Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Full-genome sequences of severe Fever with thrombocytopenia syndrome virus, isolated from South Korea in 2014.

ABSTRACT: Here, we present the full-length genome sequencing of severe fever with thrombocytopenia syndrome (SFTS) virus, isolated from South Korea in 2014. The five Korean strains were compared by phylogenetic analysis with full SFTS genome sequences of two neighboring nations, China and Japan.

SUBMITTER: Yun MR

PROVIDER: S-EPMC4400419 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Full-genome sequences of severe Fever with thrombocytopenia syndrome virus, isolated from South Korea in 2014.

Yun Mi-Ran MR Park Sun-Whan SW Kwon TaeSoo T Lee SangHyun S Yoo Won Gi WG Choi WooYoung W Lee Won-Ja WJ Kim Dae-Won DW

Genome announcements 20150416 2

Here, we present the full-length genome sequencing of severe fever with thrombocytopenia syndrome (SFTS) virus, isolated from South Korea in 2014. The five Korean strains were compared by phylogenetic analysis with full SFTS genome sequences of two neighboring nations, China and Japan. ...[more]

PMID: 25883276

Similar Datasets

Severe fever with thrombocytopenia syndrome, South Korea, 2012.

Project description:We report a retrospectively identified fatal case of severe fever with thrombocytopenia syndrome (SFTS) in South Korea from 2012. SFTS virus was isolated from the stored blood of the patient. Phylogenetic analysis revealed this isolate was closely related to SFTS virus strains from China and Japan.

| S-EPMC3837670 | biostudies-literature

Severe fever with thrombocytopenia syndrome virus, South Korea, 2013.

Project description:During 2013, severe fever with thrombocytopenia syndrome was diagnosed in 35 persons in South Korea. Environmental temperature probably affected the monthly and regional distribution of case-patients within the country. Phylogenetic analysis indicated that the isolates from Korea were closely related to isolates from China and Japan.

| S-EPMC4214315 | biostudies-literature

Severe Fever with Thrombocytopenia Syndrome Virus in Dogs, South Korea.

Project description:Of 103 serum samples collected from dogs in South Korea, 3 (2.9%) were positive for severe fever with thrombocytopenia syndrome virus (SFTSV) and 22 (21.4%) were positive for antibodies against SFTSV. A dog-derived isolate of SFTSV clustered with many South Korea SFTSV strains in the Japanese clade.

| S-EPMC6346443 | biostudies-literature

Severe Fever with Thrombocytopenia Syndrome in South Korea, 2013-2015.

Project description:BackgroundSevere fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease that was recently identified in China, South Korea and Japan. The objective of the study was to evaluate the epidemiologic and clinical characteristics of SFTS in South Korea.Methods/principal findingsSFTS is a reportable disease in South Korea. We included all SFTS cases reported to the Korea Centers for Disease Control and Prevention (KCDC) from January 2013 to December 2015. Clinical information was gathered by reviewing medical records, and epidemiologic characteristics were analyzed using both KCDC surveillance data and patient medical records. Risk factors for mortality in patients with SFTS were assessed. A total of 172 SFTS cases were reported during the study period. SFTS occurred throughout the country, except in urban areas. Hilly areas in the eastern and southeastern regions and Jeju island (incidence, 1.26 cases /105 person-years) were the main endemic areas. The yearly incidence increased from 36 cases in 2013 to 81 cases in 2015. Most cases occurred from May to October. The overall case fatality ratio was 32.6%. The clinical progression was similar to the 3 phases reported in China: fever, multi-organ dysfunction, and convalescence. Confusion, elevated C-reactive protein, and prolonged activated partial thromboplastin times were associated with mortality in patients with SFTS. Two outbreaks of nosocomial SFTS transmission were observed.ConclusionsSFTS is an endemic disease in South Korea, with a nationwide distribution and a high case-fatality ratio. Confusion, elevated levels of C-reactive protein, and prolonged activated partial thromboplastin times were associated with mortality in patients with SFTS.

| S-EPMC5226827 | biostudies-literature

Prognostic Factors of Severe Fever with Thrombocytopenia Syndrome in South Korea.

Project description:Severe fever with thrombocytopenia syndrome (SFTS), a tick-borne infectious disease, is difficult to differentiate from other common febrile diseases. Clinically distinctive features and climate variates associated with tick growth can be useful predictors for SFTS. This retrospective study (2013-2019) demonstrated the role of climatic factors as predictors of SFTS and developed a clinical scoring system for SFTS using climate variables and clinical characteristics. The presence of the SFTS virus was confirmed using reverse transcription polymerase chain reaction (RT-PCR) tests. In the univariate analysis, the SFTS-positive group was significantly associated with higher mean ambient temperature and humidity compared with the SFTS-negative group (22.5 °C vs. 18.9 °C; 77.9% vs. 70.7%, all p < 0.001). In the multivariate analysis, poor oral intake (Odds ratio [OR] 5.87, 95% CI: 2.42-8.25), lymphadenopathy (OR 7.20, 95% CI: 6.24-11.76), mean ambient temperature ≥ 20 °C (OR 4.62, 95% CI: 1.46-10.28), absolute neutrophil count ≤ 2000 cells/μL (OR 8.95, 95% CI: 2.30-21.25), C-reactive protein level ≤ 1.2 mg/dL (OR 6.42, 95% CI: 4.02-24.21), and creatinine kinase level ≥ 200 IU/L (OR 5.94, 95% CI: 1.42-24.92) were significantly associated with the SFTS-positive group. This study presents the risk factors, including ambient temperature and clinical characteristics, that physicians should consider when suspecting SFTS.

| S-EPMC7822455 | biostudies-literature

Seroprevalence of Severe Fever with Thrombocytopenia Syndrome Phlebovirus in Domesticated Deer in South Korea.

Project description:Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV) has a wide host range. Not only has it been found in humans, but also in many wild and domesticated animals. The infection of breeding deer on farms is a particularly worrisome public health concern due to the large amount of human contact and the diverse use of deer products, including raw blood. To investigate the prevalence of breeding domesticated deer, we examined the SFTSV infection rate on deer farms in South Korea from 2015 to 2017. Of the 215 collected blood samples, 0.9% (2/215) were found to be positive for viral RNA by PCR, and sequence analysis showed the highest homology with the KADGH human isolate. Both SFTSV-specific recombinant N and Gn protein-based ELISAs revealed that 14.0% (30/215) and 7.9% (17/215) of collected blood specimens were positive for SFTSV antibody. These results demonstrate that the breeding farm deer are exposed to SFTSV and could be a potential infection source for humans through direct contact or consumption of byproducts.

| S-EPMC6814664 | biostudies-literature

Severe fever with thrombocytopenia syndrome virus in ticks collected from humans, South Korea, 2013.

Project description:We investigated the infection rate for severe fever with thrombocytopenia syndrome virus (SFTSV) among ticks collected from humans during May-October 2013 in South Korea. Haemaphysalis longicornis ticks have been considered the SFTSV vector. However, we detected the virus in H. longicornis, Amblyomma testudinarium, and Ixodes nipponensis ticks, indicating additional potential SFTSV vectors.

| S-EPMC4111194 | biostudies-literature

Estimating severe fever with thrombocytopenia syndrome transmission using machine learning methods in South Korea.

Project description:Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne infectious disease in China, Japan, and Korea. This study aimed to estimate the monthly SFTS occurrence and the monthly number of SFTS cases in the geographical area in Korea using epidemiological data including demographic, geographic, and meteorological factors. Important features were chosen through univariate feature selection. Two models using machine learning methods were analyzed: the classification model in machine learning (CMML) and regression model in machine learning (RMML). We developed a novel model incorporating the CMML results into RMML, defined as modified-RMML. Feature importance was computed to assess the contribution of estimating the number of SFTS cases using modified-RMML. Aspect to the accuracy of the novel model, the performance of modified-RMML was improved by reducing the MSE for the test data as 12.6-52.2%, compared to the RMML using five machine learning methods. During the period of increasing the SFTS cases from May to October, the modified-RMML could give more accurate estimation. Computing the feature importance, it is clearly observed that climate factors such as average maximum temperature, precipitation as well as mountain visitors, and the estimation of SFTS occurrence obtained from CMML had high Gini importance. The novel model incorporating CMML and RMML models improves the accuracy of the estimation of SFTS cases. Using the model, climate factors, including temperature, relative humidity, and mountain visitors play important roles in transmitting SFTS in Korea. Our findings highlighted that the guidelines for mountain visitors to prevent SFTS transmissions should be addressed. Moreover, it provides important insights for establishing control interventions that predict early identification of SFTS cases.

| S-EPMC8575988 | biostudies-literature

Genetic and pathogenic diversity of severe fever with thrombocytopenia syndrome virus (SFTSV) in South Korea.

Project description:To investigate nationwide severe fever with thrombocytopenia syndrome virus (SFTSV) infection status, we isolated SFTSVs from patients with suspected severe fever with thrombocytopenia syndrome (SFTS) in 207 hospitals throughout South Korea between 2013 and April 2017. A total of 116 SFTSVs were isolated from 3137 SFTS-suspected patients, with an overall 21.6% case fatality rate. Genetic characterization revealed that at least 6 genotypes of SFTSVs were co-circulating in South Korea, with multiple reassortments among them. Of these, the genotype B-2 strains were the most prevalent, followed by the A and F genotypes. Clinical and epidemiologic investigations revealed that genotype B strains were associated with the highest case fatality rate, while genotype A caused only one fatality among 10 patients. Further, ferret infection studies demonstrated varying clinical manifestations and case mortality rates with different strains of SFTSV, which suggests this virus could exhibit genotype-dependent pathogenicity.

| S-EPMC7098714 | biostudies-literature

Severe Fever with Thrombocytopenia Syndrome Virus in Ticks and SFTS Incidence in Humans, South Korea.

Project description:During 2016-2018, we collected 3,193 ticks from rural areas in South Korea to investigate the prevalence of severe fever with thrombocytopenia syndrome virus (SFTSV). We detected SFTSV in ticks at an infection rate (IR) of 11.1%. We noted increases in the human IR associated with the monthly SFTSV IR in ticks.

| S-EPMC7454071 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data