Serial Intervals and Household Transmission of SARS-CoV-2 Omicron Variant, South Korea, 2021.

To clarify transmissibility of the severe acute respiratory syndrome coronavirus 2 Omicron variant, we determined serial intervals and secondary attack rates among household contacts in South Korea. Mean serial interval for 12 transmission pairs was 2.9 days, and secondary attack rate among 25 households was 50.0%, raising concern about a rapid surge in cases.

Time from Exposure to Diagnosis among Quarantined Close Contacts of SARS-CoV-2 Omicron Variant Index Case-Patients, South Korea.

To determine optimal quarantine duration, we evaluated time from exposure to diagnosis for 107 close contacts of severe acute respiratory syndrome coronavirus 2 Omicron variant case-patients. Average time from exposure to diagnosis was 3.7 days; 70% of diagnoses were made on day 5 and 99.1% by day 10, suggesting 10-day quarantine.

Importation and Transmission of SARS-CoV-2 B.1.1.529 (Omicron) Variant of Concern in Korea, November 2021.

In November 2021, 14 international travel-related severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (omicron) variant of concern (VOC) patients were detected in South Korea. Epidemiologic investigation revealed community transmission of the omicron VOC. A total of 80 SARS-CoV-2 omicron VOC-positive patients were identified until December 10, 2021 and 66 of them reported no relation to the international travel. There may be more transmissions with this VOC in Korea than reported.

Serotype Distribution and Antimicrobial Susceptibilities of Invasive Streptococcus pneumoniae Isolates from Adults in Korea from 1997 to 2012.

In Republic of Korea, a 7-valent pneumococcal conjugated vaccine (PCV7) was licensed for use in infants in 2003, and 13-valent PCV (PCV13) replaced it since 2010. We investigated trends in serotype distribution and antibiotic susceptibility of pneumococcal isolates from adult patients with invasive pneumococcal diseases (IPD). Invasive pneumococcal isolates from adult patients of ≥ 16 years of age were collected from 1997 to 2012. Serotypes of the isolates were determined by the Quellung reaction. Distribution of serotypes was analyzed according to the vaccine types. Antibiotic susceptibility was tested by using E-test strips. A total of 272 invasive pneumococcal isolates were included. The most common serotypes were serotype 19F (8.5%, 23/272), and serotype 3 (8.1%, 22/272), and 24.6% (67/272) of the isolates were of non-vaccine serotypes. Of the 272 isolates, 2.6% (7/272) were penicillin MICs of ≥ 4 µg/mL. The proportion of the PCV13 serotypes decreased from 63.3% (50/79) in 1997-2003 to 48.6% (17/35) in 2011-2012, whereas that of non-vaccine serotypes was 26.6% (21/79) and 25.7% (9/35), respectively, for the same periods. The proportion of the PCV13 serotypes showed a decreasing trend among adult patients with IPD over the study period.

Predictors of positive tuberculin skin test in neonates exposed to pulmonary tuberculosis.

BACKGROUND: Neonates are at risk of nosocomial tuberculosis (TB) infection from health care workers (HCWs) in neonatal care facilities, which can progress to severe TB diseases. Tuberculin skin test (TST) is commonly used for TB diagnosis, but its accuracy in neonates is influenced by various factors, including bacilli Calmette-Guérin (BCG) vaccination. This study aimed to identify predictors of positive TSTs in neonates exposed to HCWs with pulmonary TB. METHODS: A retrospective observational study was conducted to compare the frequency of predictors between TST-positive and TST-negative neonates. Demographic, epidemiological, and clinical data of neonates exposed to TB, along with that of HCW and household contacts, were collected retrospectively through contact investigations with the Korean National TB Surveillance System (KNTSS) database. TSTs using 2 tuberculin units of purified protein derivative RT23 were performed on exposed neonates at the end of preventive TB treatment. Firth logistic regression was performed to identify predictors of TST positivity. RESULTS: Contact investigations revealed that 152 neonates and 54 HCWs were exposed to infectious TB index cases in 3 neonatal care facilities. Of 152 exposed neonates, 8 (5.3%) had positive TST results. Age of 6 days or more at the initial exposure is a statistically significant predictor of positive TST (Firth coefficient 2.1, 95% confidence interval 0.3-3.9, P = 0.024); BCG vaccination showed no statistical significance in both univariable and multivariable analysis. Sex, prematurity, exposure duration, duration from initial exposure to contact investigation, and isoniazid preventive treatment duration were not significant predictors. CONCLUSION: Age at the initial exposure is a significant predictor of positive TST in neonates exposed to active pulmonary TB. Given the complexities of TST interpretation, including false positives due to BCG vaccination, careful risk assessment is necessary for appropriate decision-making and resource allocation in the management of neonatal TB exposure.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry identification of peptide citrullination site using Br signature.

Enzymatic conversion of arginine to citrulline by peptidyl arginine deiminase is associated with peptide presentation and development of autoimmunity in rheumatoid arthritis. In order to facilitate identification of the citrullination site, citrulline residue was modified using 4-bromophenyl glyoxal, and 194Da mass increase and incorporation of the Br signature were confirmed by MALDI-TOF MS. Using this approach, we identified four and five citrullination sites of bovine serum albumin and bovine fibrinogen, respectively. MALDI-TOF/TOF MS was used to unambiguously identify two citrullination sites from bovine fibrinogen.

Controlled nuclear import of the transcription factor NTL6 reveals a cytoplasmic role of SnRK2.8 in the drought-stress response.

Controlled proteolytic activation of membrane-anchored transcription factors provides an adaptation strategy that guarantees rapid transcriptional responses to abrupt environmental stresses in both animals and plants. NTL6 is a plant-specific NAC [NAM/ATAF1/2/CUC2] transcription factor that is expressed as a dormant plasma membrane-associated form in Arabidopsis. Proteolytic processing of NTL6 is triggered by abiotic stresses and ABA (abscisic acid). In the present study, we show that NTL6 is linked directly with SnRK (Snf1-related protein kinase) 2.8-mediated signalling in inducing a drought-resistance response. SnRK2.8 phosphorylates NTL6 primarily at Thr142. NTL6 phosphorylation by SnRK2.8 is required for its nuclear import. Accordingly, a mutant NTL6 protein, in which Thr142 was mutated to an alanine, was poorly phosphorylated and failed to enter the nucleus. In accordance with the role of SnRK2.8 in drought-stress signalling, transgenic plants overproducing either NTL6 or its active form 6ΔC (35S:NTL6 and 35S:6ΔC) exhibited enhanced resistance to water-deficit conditions such as those overproducing SnRK2.8 (35S:SnRK2.8). In contrast, NTL6 RNAi (RNA interference) plants were susceptible to dehydration as observed in the SnRK2.8-deficient snrk2.8-1 mutant. Furthermore, the dehydration-resistant phenotype of 35S:NTL6 transgenic plants was compromised in 35S:NTL6 X snrk2.8-1 plants. These observations indicate that SnRK2.8-mediated protein phosphorylation, in addition to a proteolytic processing event, is important for NTL6 function in inducing a drought-resistance response.

Structure-based design and biochemical evaluation of sulfanilamide derivatives as hepatitis B virus capsid assembly inhibitors.

Virus capsid structure is essential in virion maturation and durability, so disrupting capsid assembly could be an effective way to reduce virion count and cure viral diseases. However, currently there is no known antiviral which affects capsid inhibition, and only a small number of assembly inhibitors were experimentally successful. In this present study, we aimed to find hepatitis B virus (HBV) capsid assembly inhibitor which binds to the HBV core protein and changes protein conformation. Several candidate molecules were found to bind to certain structure in core protein with high specificity. Furthermore, these molecules significantly changed the protein conformation and reduced assembly affinity of core protein, leading to decrease of the number of assembled capsid or virion, both in vitro and in vivo. In addition, prediction also suggests that improvements in inhibition efficiency could be possible by changing functional groups and ring structures.

Helicobacter pylori proinflammatory protein up-regulates NF-kappaB as a cell-translocating Ser/Thr kinase.

There has been considerable interest in virulence genes in the plasticity region of Helicobacter pylori, but little is known about many of these genes. JHP940, one of the virulence factors encoded by the plasticity region of H. pylori strain J99, is a proinflammatory protein that induces tumor necrosis factor-alpha and interleukin-8 secretion as well as enhanced translocation of NF-κB in cultured macrophages. Here we have characterized the structure and function of JHP940 to provide the framework for better understanding its role in inflammation by H. pylori. Our work demonstrates that JHP940 is the first example of a eukaryotic-type Ser/Thr kinase from H. pylori. We show that JHP940 is catalytically active as a protein kinase and translocates into cultured human cells. Furthermore, the kinase activity is indispensable for indirectly up-regulating phosphorylation of NF-κB p65 at Ser276. Our results, taken together, contribute significantly to understanding the molecular basis of the role of JHP940 in inflammation and subsequent pathogenesis caused by H. pylori. We propose to rename the jhp940 gene as ctkA (cell translocating kinase A).

Widespread Household Transmission of SARS-CoV-2 B.1.1.529 (Omicron) Variant from Children, South Korea, 2022.

The role that children play in the transmission of the omicron variant is unclear. Here we report an outbreak that started in young children attending various pediatric facilities, leading to extensive household transmission that affected 75 families with 88 confirmed case-patients in 3 weeks. Tailored social and public health measures directed towards children and pediatric facilities are warranted with the emergence of highly transmissible omicron variant to mitigate the impact of coronavirus diseases 2019 (COVID-19).

Ventilation strategies based on an aerodynamic analysis during a large-scale SARS-CoV-2 outbreak in an acute-care hospital.

BACKGROUND: This study aimed to investigate ventilation strategies to prevent nosocomial transmission of coronavirus disease 2019 (COVID-19). METHODS: We conducted a retrospective epidemiological investigation of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in a teaching hospital (February-March 2021). The largest outbreak ward was studied, and measurements were taken to determine the pressure difference and air change per hour (ACH) of the rooms. Airflow dynamics were assessed using an oil droplet generator, indoor air quality sensor, and particle image velocimetry in the index patient's room, corridor, and opposite rooms, by varying the opening and closing of windows and doors. RESULTS: During the outbreak, 283 COVID-19 cases were identified. The SARS-CoV-2 spread occurred sequentially from the index room to the nearest room, especially the opposite. The aerodynamic study demonstrated that droplet-like particles in the index room diffused through the corridor and the opposite room through the opening door. The mean ACH of the rooms was 1.44; the air supply volume was 15.9% larger than the exhaust volume, forming a positive pressure. Closing the door prevented diffusion between adjacent rooms facing each other, and natural ventilation reduced the concentration of particles within the ward and minimised their spread to adjacent rooms. CONCLUSIONS: Spread of droplet-like particles between rooms could be attributed to the pressure difference between the rooms and corridor. To prevent spread of SARS-CoV-2 between rooms, increasing the ACH in the room by maximising ventilation and minimising the positive pressure through supply/exhaust control and closing the room door are essential.

De novo analysis of protein N-terminal sequence utilizing MALDI signal enhancing derivatization with Br signature.

De novo analysis of protein N-terminal sequence is important for identification of N-terminal proteolytic processing such as N-terminal methionine or signal peptide removal, or for the genome annotation of uncharacterized proteins. We introduce a de novo sequencing method of protein N terminus utilizing matrix-assisted laser desorption/ionization (MALDI) signal enhancing picolinamidination with bromine isotopic tag incorporated to the N terminus. The doublet signature of bromine in the tandem mass (MS/MS) spectrum distinguished N-terminal ion series from C-terminal ion series, facilitating de novo N-terminal sequencing of protein. The dual advantage of MALDI signal enhancement by the basic picolinamidine and b-ion selection aided by Br signature is demonstrated using a variety of peptides. The N-terminal sequences of myoglobin and hemoglobin as model proteins were determined by incorporating the Br tag to the N terminus of the proteins and obtaining a series of b-ions with Br signature by MS/MS analysis after chymotryptic digestion of the tagged proteins. The N-terminal peptide was selected for MS/MS analysis from the chymotryptic digest based on the Br signature in the mass spectrum. Identification of phosphorylation site as well as N-terminal sequencing of a phosphopeptide was straightforward.

A low risk of nosocomial transmission of subclinical tuberculosis to neonates in a postpartum care center under COVID-19 control measures.

We report the results of investigating and managing a tuberculosis (TB) exposure in apostpartum care center. Among the contacts exposed to a nursing assistant with subclinical TB,5 of 44 neonates (11.4%) had positive tuberculin skin tests (TSTs) at 3 months of age, and all theTST-positive neonates received the Bacille Calmette-Guérin vaccination. Seven of 28 healthcareworkers (25.0%) and 1 of 3 household contacts (33.3%) were positive in the initial or repeatedinterferon-gamma release assay. None of the contacts developed TB disease during the studyperiod. Annual TB examinations of healthcare personnel at a postpartum care center under theTuberculosis Prevention Act in South Korea enabled the early detection of subclinical TB, whichreduced the risk of transmission to neonates under strict coronavirus disease 2019 preventionmeasures.

An outbreak of SARS-CoV-2 reinfection in a long-term care facility in South Korea.

We report a cluster of 12 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection in a long-term care facility in South Korea. There were two outbreaks of SARS-CoV-2 infection in the facility at the beginning and end of October 2021, respectively. All residents in the facility were screened for SARS-CoV-2 infection using RT-PCR as part of the investigation of the second outbreak. Twelve residents, who had infection confirmed during the first outbreak, were found to be re-positive for RT-PCR test at the second outbreak. 8 Of 12 RT-PCR re-positive cases were confirmed as reinfections based on investigation through the whole genome sequencing, viral culture, and serological analysis, despite of the short interval between the first and second outbreaks (29-33 days) and a history of full vaccination for 7 of the 12 re-positive cases. This study suggests that decreased immunity and underlying health condition in older adults makes them susceptible to reinfection, highlighting the importance of prevention and control measures regardless of vaccination status in long-term care settings.

Crystal structures of Pseudomonas aeruginosa guanidinobutyrase and guanidinopropionase, members of the ureohydrolase superfamily.

Pseudomonas aeruginosa guanidinobutyrase (GbuA) and guanidinopropionase (GpuA) catalyze the hydrolysis of 4-guanidinobutyrate and 3-guanidinopropionate, respectively. They belong to the ureohydrolase superfamily, which includes arginase, agmatinase, proclavaminate amidinohydrolase, and formiminoglutamase. In this study, we have determined the crystal structures of GbuA and GpuA from P. aeruginosa to provide a structural insight into their substrate specificity. Although GbuA and GpuA share a common structural fold of the typical ureohydrolase superfamily, they exhibit significant variations in two active site loops. Mutagenesis of Met161 of GbuA and Tyr157 of GpuA, both of which are located in the active site loop 1 and predicted to be involved in substrate recognition, significantly affected their enzymatic properties, implying their important roles in catalysis.

C-terminal de novo sequencing of peptides using oxazolone-based derivatization with bromine signature.

Due to almost identical chemical properties of C-terminal and side-chain carboxylic groups, selective C-terminal derivatization has been difficult. Although oxazolone-based C-terminal derivatization is the only selective C-terminal modification available, it has not been used widely because of its low derivatization efficiency. In this paper, an improved oxazolone chemistry for incorporation of Br signature to C-terminus is reported. MS/MS analysis of the brominated peptides led to a series of y ions with Br signature, facilitating de novo C-terminal sequencing.

Proteolytic processing of an Arabidopsis membrane-bound NAC transcription factor is triggered by cold-induced changes in membrane fluidity.

Changes in membrane fluidity are the earliest cellular events that occur in plant cells upon exposure to cold. This subsequently triggers physiological processes, such as calcium influx and reorganization of actin cytoskeletons, and induces expression of cold-responsive genes. The plasma-membrane-anchored NAC (NAM/ATAF/CUC) transcription factor NTL6 is of particular interest. Cold triggers proteolytic activation of the dormant NTL6 protein, which in turn elicits pathogen-resistance responses by inducing a small group of cold-inducible PR (pathogenesis-related) genes in Arabidopsis. In the present study, we show that proteolytic processing of NTL6 is regulated by cold-induced remodelling of membrane fluidity. NTL6 processing was stimulated rapidly by cold. The protein stability of NTL6 was also enhanced by cold. The effects of cold on NTL6 processing and protein stability were significantly reduced in cold-acclimatized plants, supporting the regulation of NTL6 processing by membrane fluidity. Consistent with this, although NTL6 processing was stimulated by pharmacological agents that reduce membrane fluidity and thus mimic cold, it was inhibited when plants were treated with a 18:3 unsaturated fatty acid, linolenic acid. In addition, the pattern of NTL6 processing was changed in Arabidopsis mutants with altered membrane lipid compositions. Assays employing chemicals that inhibit activities of the proteasome and proteases showed that NTL6 processing occurs via the regulated intramembrane proteolysis mechanism. Interestingly, a metalloprotease inhibitor blocked the NTL6 processing. These observations indicate that a metalloprotease activity is responsible for NTL6 processing in response to cold-induced changes in membrane fluidity.

Usefulness of routine lumbar puncture in non-HIV patients with latent syphilis of unknown duration.

OBJECTIVES: To evaluate the usefulness of routine lumbar puncture in non-HIV patients with untreated latent syphilis. METHODS: We conducted a prospective study in Seoul National University Bundang Hospital from May 2003 to December 2005. Participants in routine health check-ups of the healthcare system were screened for serological evidence of syphilis by the Treponema pallidum particle agglutination (TPPA) test. Lumbar puncture was performed, with consent, on untreated latent syphilitic patients. Neurosyphilis was defined as positivity for cerebrospinal fluid Venereal Disease Research Laboratory (CSF VDRL) or pleocytosis with positivity for CSF TPPA or elevation of CSF protein with IgG index exceeding 0.85. RESULTS: Of 21 507 participants, 282 (1.4%) had serological evidence of syphilis. 117 (41%) of these had a history of syphilis treatment and 2 were seropositive for HIV. Among the 163 non-HIV patients with untreated latent syphilis, 70 (43%) underwent lumbar puncture. All the patients had VDRL titres less than 1:16. Abnormal neurological signs or symptoms were present in eight (11%) patients. CSF abnormalities were seen in 57 (81%), but no patient (0%, 95% CI 0 to 6.2) was diagnosed with neurosyphilis. CONCLUSIONS: The estimated prevalence of neurosyphilis among non-HIV patients with untreated latent syphilis and serum VDRL <1:16, was below 6.2%.

Incidence of atazanavir-associated hyperbilirubinemia in Korean HIV patients: 30 months follow-up results in a population with low UDP-glucuronosyltransferase1A1*28 allele frequency.

Hyperbilirubinemia is frequently observed in Caucasian HIV patients treated with atazanavir. UDP-glucuronosyltransferase 1A1 polymorphism, UGT1A1*28, which is associated with atazanavir-induced hyperbilirubinemia, is less common in Asians than in Caucasians. However, little is known about the incidence of atazanavir-associated hyperbilirubinemia in Asian populations. Our objective was to investigate the incidence of and tolerability of atazanavir-associated hyperbilirubinemia in Korean HIV patients. The prevalence and cumulative incidence of atazanavir-associated hyperbilirubinemia and UGT1A1*28 allele frequency was investigated in 190 Korean HIV-infected patients treated with atazanavir 400 mg per day. The UGT1A1*28 were examined by direct sequencing of DNA from peripheral whole blood. The UGT1A1*28 allele frequency was 11%. The cumulative incidence of any grade of hyperbilirubinemia was 77%, 89%, 98%, and 100%, at 3, 12, 24, and 30 months, respectively. The cumulative incidence of severe (grade 3-4) hyperbilirubinemia was 21%, 41%, 66%, and 75%, at 3, 12, 24, and 30 months, respectively. However, the point prevalence of severe hyperbilirubinemia did not increase with time and remained around 25%. Our data suggest that atazanavir-associated hyperbilirubinemia is common but transient in a population with low UGT1A1*28 allele frequency.

Spectrum of intracranial parenchymal lesions in patients with human immunodeficiency virus infection in the Republic of Korea.

The incidence of specific intracranial parenchymal lesions of HIV-infected patients varies considerably between countries. In the Republic of Korea, the number of HIV-infected patients is increasing, but little is known regarding the spectrum of intracranial parenchymal lesions in these patients. The aim of the present study was to obtain this information. To identify HIV patients with intracranial parenchymal lesions, the electronic database of radiological reports for 1,167 HIV-infected patients, seen from 1999 to 2008 at the Seoul National University Hospital, were reviewed. Neuroradiologic studies were performed on 165 of these patients, and intracranial parenchymal lesions were detected in 40 (3.4%) of them. Thirty-seven were male, and median age was 41 yr (range, 26-61). At the time of the diagnosis of intracranial parenchymal lesions, median CD4(+) lymphocyte count was 40 cells/microL (range 5-560) and in 33 (82.5%) patients, it was less than 200 cells/microL. Progressive multifocal leukoencephalopathy (12 patients) is the most frequent intracranial parenchymal lesions, followed by intracranial tuberculoma (7 patients), primary central nervous system lymphoma (7 patients), intracranial cryptococcoma (4 patients), Toxoplasma encephalitis (4 patients), and disseminated non-tuberculous mycobacterial infection (3 patients).