High-resolution phylogeographical surveillance of Hantaan orthohantavirus using rapid amplicon-based Flongle sequencing, Republic of Korea.

Orthohantaviruses, etiological agents of hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome, pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) outbreaks are particularly endemic in Gyeonggi Province in northern area of the Republic of Korea (ROK). Small mammals were collected from three regions in the Gyeonggi Province during 2017 and 2018. Serological and molecular prevalence of HTNV was 25/201 (12.4%) and 10/25 (40%), respectively. A novel nanopore-based diagnostic assay using a cost-efficient Flongle chip was developed to rapidly and sensitively detect HTNV infection in rodent specimens within 3 h. A rapid phylogeographical surveillance of HTNV at high-resolution phylogeny was established using the amplicon-based Flongle sequencing. In total, seven whole-genome sequences of HTNV were newly obtained from wild rodents collected in Paju-si (Gaekhyeon-ri) and Yeoncheon-gun (Hyeonga-ri and Wangnim-ri), Gyeonggi Province. Phylogenetic analyses revealed well-supported evolutionary divergence and genetic diversity, enhancing the resolution of the phylogeographic map of orthohantaviruses in the ROK. Incongruences in phylogenetic patterns were identified among HTNV tripartite genomes, suggesting differential evolution for each segment. These findings provide crucial insights into on-site diagnostics, genome-based surveillance, and the evolutionary dynamics of orthohantaviruses to mitigate hantaviral outbreaks in HFRS-endemic areas in the ROK.

Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus.

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.

Clinical impact of massive transfusion protocol implementation in non-traumatic patients.

BACKGROUND: Massive transfusion protocol (MTP) has been used to provide plasma and packed red blood cells (pRBCs) rapidly. MTP also has been adapted for non-traumatic patients. The effects of hospital-wide MTP implementation on clinical outcomes were reviewed. METHODS: This was a retrospective study of patients who received massive transfusion before and after MTP implementation, between August 2010 and May 2018. Massive transfusion was defined as 10 or more units of pRBCs within 24 h. Recipients of massive transfusion were divided into periods before and after MTP implementation. The 24 -h death rate, thirty-day death rate and several laboratory findings were investigated. RESULTS: Eighty patients whose massive transfusion occurred before MTP implementation and 63 patients whose massive transfusion occurred after MTP implementation were compared. No statistically significant difference was found in 24 -h death rate (15.0% vs. 23.8%, p = 0.181), or 30-day death rate (43.8% vs. 36.5%, p = 0.381). Use of an anti-fibrinolytic agent was more frequent in patients after the MTP implementation (31.3% vs. 55.6%, p = 0.003). A statistically significant difference was found in the lowest body temperature of the two groups during the 24 -h period (34.7 °C vs. 35.6 °C, p < 0.001). Transfusion ratio of plasma to pRBC was numerically improved after the MTP implementation (1:1.91 vs. 1:1.58, p = 0.173). Earlier initiation of pRBC transfusion was achieved after implementation (51 min vs. 40 min, p = 0.042). CONCLUSIONS: MTP implementation showed improved coagulation profiles, but did not show a statistically significant death-rate reduction in non-traumatic patients.

Multiplex PCR-Based Next-Generation Sequencing and Global Diversity of Seoul Virus in Humans and Rats.

Seoul virus (SEOV) poses a worldwide public health threat. This virus, which is harbored by Rattus norvegicus and R. rattus rats, is the causative agent of hemorrhagic fever with renal syndrome (HFRS) in humans, which has been reported in Asia, Europe, the Americas, and Africa. Defining SEOV genome sequences plays a critical role in development of preventive and therapeutic strategies against the unique worldwide hantavirus. We applied multiplex PCR-based next-generation sequencing to obtain SEOV genome sequences from clinical and reservoir host specimens. Epidemiologic surveillance of R. norvegicus rats in South Korea during 2000-2016 demonstrated that the serologic prevalence of enzootic SEOV infections was not significant on the basis of sex, weight (age), and season. Viral loads of SEOV in rats showed wide dissemination in tissues and dynamic circulation among populations. Phylogenetic analyses showed the global diversity of SEOV and possible genomic configuration of genetic exchanges.

Febrile Respiratory Illness Associated with Human Adenovirus Type 55 in South Korea Military, 2014-2016

An outbreak of febrile respiratory illness associated with human adenovirus (HAdV) occurred in the South Korea military during the 2014-15 influenza season and thereafter. Molecular typing and phylogenetic analysis of patient samples identified HAdV type 55 as the causative agent. Emergence of this novel HAdV necessitates continued surveillance in military and civilian populations.

Construction of Bacillus thuringiensis Simulant Strains Suitable for Environmental Release.

For a surrogate bacterium to be used in outdoor studies, it is important to consider environmental and human safety and ease of detection. Recently, Bacillus thuringiensis, a popular bioinsecticide bacterium, has been gaining attention as a surrogate bacterium for use in biodefense. In this study, we constructed simulant strains of B. thuringiensis with enhanced characteristics for environmental studies. Through transposon mutagenesis, pigment genes were inserted into the chromosome, producing yellow-colored colonies for easy detection. To prevent persistence of spores in the environment, a genetic circuit was designed to produce a spore without sporulation capability. Two loxP sites were inserted, one on each side of the spo0A gene, which encodes a sporulation master regulator, and a sporulation-dependent Cre expression cassette was inserted into the chromosome. This genetic circuit successfully deleted spo0A during sporulation, producing spores that lacked the spo0A gene. In addition, two major α/ß-type small acid-soluble spore protein (SASP) genes, predicted by synteny analysis, were deleted. The spores of the mutant strain showed increased UV-C sensitivity and quickly lost viability when tested in a solar simulator. When the spores of the mutant strain were administered to the lungs of BALB/c mice, cells were quickly removed from the body, suggesting enhanced in vivo safety. All strains constructed in this study contain no antibiotic resistance markers and all heterologous genes were inserted into the chromosome, which are useful features for simulants to be released into the environment.IMPORTANCEB. thuringiensis has recently been receiving increasing attention as a good spore simulant in biodefense research. However, few studies were done to properly address many important features of B. thuringiensis as a simulant in environmental studies. Since spores can persist in the environment for years after release, environmental contamination is a big problem, especially when genetically engineered strains are used. To solve these problems, we report here the development of B. thuringiensis simulant strains that are capable of forming yellow colonies for easy detection, incapable of forming spores more than once due to a genetic circuit, and lacking in two major SASP genes. The genetic circuit to produce a spore without sporulation capability, together with the deletion of SASP genes, ensures the environmental and human safety of the simulant strains developed in this study. All of these features will allow wider use of B. thuringiensis as a simulant for Bacillus anthracis in environmental release studies.

Whole-genome sequence analysis of Zika virus, amplified from urine of traveler from the Philippines.

Zika virus (ZIKV) (genus Flavivirus, family Flaviviridae) is an emerging pathogen associated with microcephaly and Guillain-Barré syndrome. The rapid spread of ZIKV disease in over 60 countries and the large numbers of travel-associated cases have caused worldwide concern. Thus, intensified surveillance of cases among immigrants and tourists from ZIKV-endemic areas is important for disease control and prevention. In this study, using Next Generation Sequencing, we reported the first whole-genome sequence of ZIKV strain AFMC-U, amplified from the urine of a traveler returning to Korea from the Philippines. Phylogenetic analysis showed geographic-specific clustering. Our results underscore the importance of examining urine in the diagnosis of ZIKV infection.

Classification and regression tree model for predicting tracheostomy in patients with traumatic cervical spinal cord injury.

PURPOSE: In patients with cervical spinal cord injury (CSCI), respiratory compromise and the need for tracheostomy are common. The purpose of this study was to identify common risk factors for tracheostomy following traumatic CSCI and develop a decision tree for tracheostomy in traumatic CSCI patients without pulmonary function test. METHODS: Data of 105 trauma patients with CSCI admitted in our institution from April, 2008 to February, 2014 were retrospectively analyzed. Patients who underwent tracheostomy were compared to those who did not. Stepwise logistic regression analysis and classification and regression tree model were used to predict the risk factors for tracheostomy. RESULTS: Tracheostomy was performed in 20% of patients with traumatic CSCI on median hospital day 4. Patients who underwent tracheostomy tended to be more severely injured (higher Injury Severity Score, lower Glasgow Coma Score, and lower systolic blood pressure on admission) which required more frequent intubation in the emergency room (ER) with a higher rate of complete CSCI compared to those who did not. Upon multiple logistic analysis, Age ≥ 55 years (OR: 6.86, p = 0.037), Car accident (OR: 5.8, p = 0.049), injury above C5 (OR: 28.95, p = 0.009), ISS ≥ 16 (OR: 12.6, p = 0.004), intubation in the ER (OR: 23.87, p = 0.001), and complete CSCI (OR: 62.14, p < 0.001) were significant predictors for the need of tracheostomy after CSCI. These factors can predict whether a new patient needs future tracheostomy with 91.4% accuracy. CONCLUSIONS: Age ≥ 55 years, injury above C5, ISS ≥ 16, Car accident, intubation in the ER, and complete CSCI were independently associated with tracheostomy after CSCI. CART analysis may provide an intuitive decision tree for tracheostomy.

Detection of Hantaan virus RNA from anti-Hantaan virus IgG seronegative rodents in an area of high endemicity in Republic of Korea.

Hantaan virus (HTNV), of the family Bunyaviridae, causes hemorrhagic fever with renal syndrome (HFRS) in humans. Although the majority of epidemiologic studies have found that rodents are seropositive for hantavirus-specific immunoglobulin, the discovery of hantavirus RNA in seronegative hosts has led to an investigation of the presence of HTNV RNA in rodents captured in HFRS endemic areas. HTNV RNA was detected in seven (3.8%) of 186 anti-HTNV IgG seronegative rodents in Republic of Korea (ROK) during 2013-2014. RT-qPCR for HTNV RNA revealed dynamic virus-host interactions of HTNV in areas of high endemicity, providing important insights into the epidemiology of hantaviruses.

Spontaneous intracranial haemorrhage in critically ill patients with malignancies.

PURPOSE: Limited data are available on the intracranial haemorrhage (ICH) developed in critically ill cancer patients during their stay in the intensive care unit (ICU). METHODS: All consecutive patients who underwent brain CT for suspicion of spontaneous intracerebral haemorrhage (ICH) with acute neurologic symptoms or signs developed during their ICU stay were retrospectively evaluated to identify predictors of ICH. RESULTS: Over the study period, a total of 273 patients underwent brain CT scanning for suspicion of ICH, with altered mentality in 202 (74 %), seizure in 43 (16 %), and hemiparesis in 34 (13 %). However, only 49 (18 %) patients had a final diagnosis of ICH. The most common type of haemorrhage was intracerebral in 34 patients (69 %), followed by subarachnoidal haemorrhage in 17 (35 %). In multiple logistic regression analysis, anisocoric pupils or abnormal pupil reflex (adjusted OR 7.939; 95 % CI, 2.315-27.228) was an independent predictor of ICH. In addition, higher positive end-expiratory pressure (adjusted OR 1.204; 95 % CI, 1.065-1.361) was significantly associated with ICH. However, platelet count was inversely associated with ICH (adjusted OR 0.993; 95 % CI 0.988-0.999). CONCLUSION: Brain CT scanning should be performed even in critically ill cancer patients, especially with risk factors and acute neurologic changes.

Clinical usefulness of capnographic monitoring when inserting a feeding tube in critically ill patients: retrospective cohort study.

BACKGROUND: It is not rare for a small-bore feeding tube to be inserted incorrectly into the respiratory system in critically ill patients. Thus, monitoring is necessary to prevent respiratory malplacement of the tube. We investigated the utility of capnographic monitoring to prevent respiratory complications due to feeding tube mispositioning in critically ill patients. METHODS: This study was a pre and post-interventional study, including 445 feeding tube placements events studied retrospectively in the medical and surgical intensive care units of the Samsung Medical Center. We compared outcomes between time periods before and after capnographic monitoring and documented any respiratory complications. RESULTS: Feeding tubes were inserted in 275 cases without capnographic monitoring. Capnographic monitoring was performed in 170 cases. Sixteen patients (4%) had respiratory complications of all tube placements. Feeding tube was inserted into the trachea in 11 (2%) patients and for a pneumothorax in five (1%) patients. Fourteen cases of respiratory complications were detected in the control group (14/275, 5%, 10 tracheal insertions and four pneumothoraxes). Two respiratory complications were detected in the capnographic monitoring group (2/170, 1%, one tracheal insertion and one pneumothorax). Respiratory complications were detected less frequently in the capnographic monitoring group than that in the control group (P = 0.035). CONCLUSIONS: Capnographic monitoring is simple, easy to learn, and may be useful to prevent respiratory complications when placing a feeding tube in a critically ill patient.

Effect of Early Intervention on Long-Term Outcomes of Critically Ill Cancer Patients Admitted to ICUs.

OBJECTIVES: The objective of this observational study was to evaluate whether early intervention was associated with improved long-term outcomes in critically ill patients with cancer. DESIGN: Retrospective analysis with prospectively collected data. SETTING: A university-affiliated, tertiary referral hospital. PATIENTS: Consecutive critically ill cancer patients who were managed by a medical emergency team before ICU admission between January 2010 and December 2012. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: During the study period, 525 critically ill cancer patients were admitted to the ICU with respiratory failure (41.7%) and severe sepsis or septic shock (40.6%) following medical intervention by a medical emergency team. Of 356 ICU survivors, 161 (45.2%) received additional treatment for cancer after ICU discharge. Mortality was 66.1% at 6 months and 72.8% at 1 year. Median time from physiological derangement to intervention before ICU admission was significantly shorter in 1-year survivors (1.3 hr; interquartile range, 0.5-4.8 hr) than it was in nonsurvivors (2.9 hr; interquartile range, 0.8-9.6 hr) (p< 0.001). Additionally, the early intervention (≤ 1.5 hr) group had a lower 30-day mortality rate than the late intervention (> 1.5 hr) group (29.0% vs 55.3%; p < 0.001) and a similar difference in mortality rate was observed up to 1 year. Other factors associated with 1-year mortality were illness severity, performance status, malignancy status, presence of more than three abnormal physiological variables, time from derangement to ICU admission, and the need for mechanical ventilation. Even after adjusting for potential confounding factors, early intervention was significantly associated with 1-year mortality (adjusted hazard ratio, 0.456; 95% CI, 0.348-0.597; p < 0.001). CONCLUSION: Early intervention for clinical derangement on general wards was significantly associated with long-term outcomes in critically ill cancer patients.

Risk factors for acquisition of multidrug-resistant bacteria in patients with anastomotic leakage after colorectal cancer surgery.

PURPOSE: The risk factors for acquiring an infection with multidrug-resistant (MDR) bacteria in patients with anastomotic leakage after colorectal cancer surgery are poorly understood. We evaluated the risk factors associated with the initial acquisition of MDR pathogens in patients with anastomotic leakage after colorectal cancer surgery. METHODS: This study was a retrospective review of prospectively collected data at a university affiliated-tertiary referral hospital in South Korea. From January 2009 to April 2013, a total of 6767 consecutive patients with colorectal cancer who underwent surgery were registered. Of these patients, 190 (2.8%) were diagnosed with anastomotic leakage. Finally, 143 (2.1%) patients with culture test results were included in this study. RESULTS: Of the 143 enrolled patients, 46 (32.2%) were classified in the MDR group. The use of antibiotics for more than 5 days before diagnosis of anastomosis site leakage (p = 0.016) and diabetes mellitus (p = 0.028) was identified as independent risk factors for MDR acquisition by multivariate analysis. The rate of adequate initial empirical antibiotic therapy in the MDR group was lower than in the non-MDR group (35 vs. 75%, p < 0.001). Furthermore, the duration of antibiotic administration after the leak was longer in the MDR group (p = 0.013). Patients in the MDR group also had a longer hospital stay (p = 0.012). CONCLUSIONS: The length of antibiotic administration before the diagnosis of anastomotic leakage and diabetes mellitus were risk factors associated with the acquisition of MDR bacteria in patients with anastomotic leakage after colorectal cancer surgery.

Predictors of neurological outcomes after successful extracorporeal cardiopulmonary resuscitation.

BACKGROUND: Extracorporeal cardiopulmonary resuscitation (ECPR) refers to use of extracorporeal membrane oxygenation (ECMO) in cardiopulmonary arrest. Although ECPR can increase survival rates after cardiac arrest, it can also result in poor post-resuscitation neurological status. Thus, we investigated predictors of good neurological outcomes after successful ECPR. METHODS: A total of 227 patients underwent ECPR from May 2004 to June 2013 at Samsung Medical Center. Successful ECPR was defined as survival more than 24 hours after ECPR. Neurological outcomes were assessed at discharge using the Glasgow-Pittsburgh Cerebral Performance Categories scale (CPC). CPC 1 and 2 were classified as good and CPC 3 to 5 were classified as poor neurological outcomes. Excluded were 22 patients who did not survive more than 24 hours after ECPR and 90 patients who died from unknown causes or causes other than brain death or whose neurological status could not be assessed at discharge. Multiple logistic regression analysis was used to identify independent predictors of neurological outcomes. RESULTS: Included were 115 patients with a mean age of 58 (range 45-66) years and 80 men (70%). Cardiopulmonary resuscitation (CPR) was performed at non-hospital sites for 19 (17%) patients and bystander CPR was performed in 9 of 19 cases (47%). Cardiac etiology was verified in 74 (64%) patients and therapeutic hypothermia was performed in 9 patients (8%); 68 (59%) had good neurological outcomes and 47 (41%) did not and 24 patients died from brain death. Neurological outcomes were affected by hemoglobin levels before ECMO (P = 0.02), serum lactic acid (P < 0.001) before ECMO insertion, and interval from cardiac arrest to ECMO (P = 0.04). CONCLUSIONS: Low hemoglobin or high serum lactic acid levels before ECMO, and prolonged interval from cardiac arrest to ECMO predicted poor neurological outcomes after successful ECPR. Early institution of ECMO and a low threshold for blood transfusion might improve neurological outcomes for patients who survive ECPR.

Molecular characterization of SARS-CoV-2 from the saliva of patients in the Republic of Korea in 2020.

Background and aims: Despite global vaccination efforts, the number of confirmed cases of coronavirus disease 2019 (COVID-19) remains high. To overcome the crisis precipitated by the ongoing pandemic, characteristic studies such as virus diagnosis, isolation, and genome analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are necessary. Herein, we report the isolation and molecular characterization of SARS-CoV-2 from the saliva of patients who had tested positive for COVID-19 at Proving Ground in Taean County, Republic of Korea, in 2020. Methods: We analyzed the whole-genome sequence of SARS-CoV-2 isolated from the saliva samples of patients through next-generation sequencing. We also successfully isolated SARS-CoV-2 from the saliva samples of two patients by using cell culture, which was used to study the cytopathic effects and viral replication in Vero E6 cells. Results: Whole-genome sequences of the isolates, SARS-CoV-2 ADD-2 and ADD-4, obtained from saliva were identical, and phylogenetic analysis using Bayesian inference methods showed SARS-CoV-2 GH clade (B.1.497) genome-specific clustering. Typical coronavirus-like particles, with diameters of 70-120 nm, were observed in the SARS-CoV-2 infected Vero E6 cells using transmission electron microscopy. Conclusion: In conclusion, this report provides insights into the molecular diagnosis, isolation, genetic characteristics, and diversity of SARS-CoV-2 isolated from the saliva of patients. Further studies are needed to explore and monitor the evolution and characteristics of SARS-CoV-2 variants.

A Portable Diagnostic Assay, Genetic Diversity, and Isolation of Seoul Virus from Rattus norvegicus Collected in Gangwon Province, Republic of Korea.

Seoul virus (SEOV), an etiological agent for hemorrhagic fever with renal syndrome, poses a significant public health threat worldwide. This study evaluated the feasibility of a mobile Biomeme platform for facilitating rapid decision making of SEOV infection. A total of 27 Rattus norvegicus were collected from Seoul Metropolitan City and Gangwon Province in Republic of Korea (ROK), during 2016-2020. The serological and molecular prevalence of SEOV was 5/27 (18.5%) and 2/27 (7.4%), respectively. SEOV RNA was detected in multiple tissues of rodents using the Biomeme device, with differences in Ct values ranging from 0.6 to 2.1 cycles compared to a laboratory benchtop system. Using amplicon-based next-generation sequencing, whole-genome sequences of SEOV were acquired from lung tissues of Rn18-1 and Rn19-5 collected in Gangwon Province. Phylogenetic analysis showed a phylogeographical diversity of rat-borne orthohantavirus collected in Gangwon Province. We report a novel isolate of SEOV Rn19-5 from Gangwon Province. Our findings demonstrated that the Biomeme system can be applied for the molecular diagnosis of SEOV comparably to the laboratory-based platform. Whole-genome sequencing of SEOV revealed the phylogeographical diversity of orthohantavirus in the ROK. This study provides important insights into the field-deployable diagnostic assays and genetic diversity of orthohantaviruses for the rapid response to hantaviral outbreaks in the ROK.

Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea.

BACKGROUND: Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK). PRINCIPAL FINDINGS: A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nanopore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S segments) sub-genotypes, indicating a natural reassortment between sub-genotypes. CONCLUSION/SIGNIFICANCE: Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.

Evaluating mortality and recovery of extreme hyperbilirubinemia in critically ill patients by phasing the peak bilirubin level: A retrospective cohort study.

BACKGROUND: Hyperbilirubinemia is a devastating complication in patients admitted to an intensive care unit (ICU). The sequential organ failure assessment (SOFA) score classifies hyperbilirubinemia without further detailed analyses for bilirubin increase above 12 mg/dL. We evaluated whether the level of bilirubin increase in patients with extreme hyperbilirubinemia (total bilirubin ≥ 12 mg/dL) affects and also helps estimate mortality or recovery. METHODS: A retrospective cohort analysis comprising 427 patients with extreme hyperbilirubinemia admitted to the ICU of Samsung Medical Center, Seoul, Korea between 2011 and 2015 was conducted. Extreme hyperbilirubinemia was classified into four grades: grade 1 (12-14.9 mg/dL), grade 2 (15-19.9 mg/dL), grade 3 (20-29.9 mg/dL), and grade 4 (≥ 30 mg/dL). These grades were then assessed for their association with hospital mortality and recovery from hyperbilirubinemia to SOFA grade (point) 2 or below (total bilirubin < 6 mg/dL). The influences of various factors, some of which caused extreme hyperbilirubinemia, while others induced bilirubin recovery, were assessed. RESULTS: A total of 427 patients (mean age: 59.8 years, male: 67.0%) were evaluated, and the hospital mortality for these patients was very high (76.1%). Extreme hyperbilirubinemia was observed in 111 (grade 1, 26.0%), 99 (grade 2, 23.2%), 131 (grade3, 30.7%), and 86 (grade 4, 20.1%) patients with mortality rates of 62.2%, 71.7%, 81.7%, and 90.7%, respectively (p < 0.001). The peak bilirubin value correlated with the mortality (odds ratio [OR], 1.09; 95% confidence interval [CI], 1.04-1.15, p < 0.001). Compared to those with grade 1 extreme hyperbilirubinemia, the mortality rate gradually increased as the grade increased (OR [95% CI]: 1.92 [0.70-5.28], 3.55 [1.33-9.48], and 12.47 [3.07-50.59] for grades 2, 3 and 4, respectively). The main causes of extreme hyperbilirubinemia were infection including sepsis and hypoxic hepatitis. The recovery from hyperbilirubinemia was observed in 110 (25.8%) patients. Mortality was lower for those who recovered from hyperbilirubinemia than for those who did not (29.1% vs. 92.4%, p < 0.001). The favorable factors of bilirubin recovery were albumin and ursodeoxycholic acid (UDCA). CONCLUSIONS: This study determined that the level of extreme hyperbilirubinemia is an important prognostic factor in critically ill patients. We expect the results of this study to help predict the clinical course of and determine the optimal treatment for extreme hyperbilirubinemia.

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

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.

Genomic investigation of the coronavirus disease-2019 outbreak in the Republic of Korea.

The South Korean government effectively contained the coronavirus disease-2019 (COVID-19) outbreak primarily associated with a religious group. We conducted SARS-CoV-2 whole genome sequencing of 66 cases to investigate connections among the initial South Korean cases and the religious group outbreak. We assessed the accuracy of genomic investigation by comparing the whole genome sequences with comprehensive contact tracing records. Five transmission clusters were estimated among the 15 initial cases. The six close-contact cases and two potential exposure pairs identified by contact tracing showed two or fewer nucleotide base differences. Additionally, we identified two transmission clusters that were phylogenetically distinct from the initial clusters, sharing common G11083T, G26144T, and C14805T markers. The strain closest to the two additional clusters was identified from a pair of identical sequences isolated from individuals who traveled from Wuhan to Italy. Our findings provide insights into the origins of community spread of COVID-19.