Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020

Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.

Discovery of mesoscopic nematicity wave in iron-based superconductors

[Figure: see text].

Transverse bunch-by-bunch feedback system for time-resolved experiments at PLS-II

A description of the upgraded bunch-by-bunch feedback system for time-resolved experiments at Pohang Light Source II (PLS-II) is provided. The bunch-by-bunch feedback system has been upgraded to increase the single-bunch current in the hybrid fill pattern of the PLS-II facility. The project is part of the SPring-8 and PLS-II collaboration. The main features of the upgrade are to employ a single 500 MHz analog-to-digital converter (ADC) instead of the previous four 125 MHz interleaved ADCs for 500 MHz rate, to replace a single-loop two-dimensional feedback with two independent one-dimensional feedback loops, to implement the tune measurement function with a single bunch, and mainly to implement single-bunch and stretcher control. The realization of a 400 mA hybrid fill pattern including a 10 mA single bunch demonstrates the precision of the upgraded bunch-by-bunch feedback system.

Sumoylation of transcription factor ETV1 modulates its oncogenic potential in prostate cancer

The transcription factor ETS variant 1 (ETV1) is capable of promoting prostate tumorigenesis. We demonstrate that ETV1 can be posttranslationally modified by covalent attachment of small ubiquitin-like modifier 1 (SUMO1) onto four different lysine residues. In human embryonic kidney 293T cells, mutation of these sumoylation sites stimulated the transactivation potential of ETV1 at the matrix metalloproteinase 1 (MMP1), but not Yes-associated protein 1 gene promoter, while ETV1 protein stability and intracellular localization remained unchanged. In stark contrast, sumoylation-deficient ETV1 was repressed in its ability to stimulate the MMP1 promoter and to cooperate with a histone demethylase, JmjC domain-containing 2A (JMJD2A), in LNCaP prostate cancer cells. Mutation of sumoylation sites enhanced the ability of ETV1 to interact with the histone deacetylase (HDAC) 1, but had basically no impact on complex formation with HDAC3 or JMJD2A. Further, compared to non-sumoylated ETV1, its sumoylated forms were less able to bind to the transcription factor, SMAD family member 4. Lastly, in contrast to wild-type ETV1, sumoylation-deficient ETV1 repressed LNCaP cell growth. Altogether, these data suggest that sumoylation modulates ETV1 function in a cell type-specific manner, possibly by altering the spectrum of transcriptional cofactors being recruited. Notably, SUMO pathway components SUMO1, ubiquitin-like modifier activating enzyme 2 and ubiquitin conjugating enzyme 9 were upregulated in prostate tumors, implying that enhanced sumoylation indeed promotes ETV1's oncogenic activity during prostate cancer formation.

The complete mitochondrial genome of Anneissia pinguis (Crinoidea, Articulata, Comatulidae), from South Korea

In this study, the complete mitochondrial genome sequence of Anneissia pinguis was examined by next-generation sequencing analysis. The complete mitogenome of A. pinguis has 15,912 bp in length and 37 genomes consist of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (D-loop). Both gene orders and characteristics were in accordance with other species belonging to the phylum Echinodermata. Phylogenetic analysis revealed the establishment of molecular taxonomic relationship in class Crinoidea based on complete mitogenome.

AB0760 HIGH SERUM IGA LEVELS HAVE LIMITED CLINICAL SIGNIFICANCE IN PATIENTS WITH IGG4-RELATED DISEASE DIAGNOSED BY EXPERTS

Background:

While the diagnostic and classification criteria for IgG4-related disease (IgG4-RD) have been recently developed [1-3], it is known that, without appropriate exclusions, some non-IgG4-RDs may meet these criteria. In particular, hyper IL-6 syndromes, including Castleman disease, can be misdiagnosed as IgG4-RD. Some clinical findings, including elevated serum levels of C-reactive protein (CRP) or IgA, have been suggested to be useful for differentiating hyper IL-6 syndromes from IgG4-RD [4]. However, since few clinical studies have focused on IgG4-RD with high serum IgA levels, its clinical significance has not been well known.

Objectives:

This study aimed to clarify the clinical significance of high serum IgA levels in patients with IgG4-RD.

Methods:

We retrospectively investigated the clinical features of 170 patients with IgG4-RD on the basis of the presence or absence of elevated serum IgA levels (>410 mg/dL) at the time of diagnosis. The diagnosis of IgG4-RD was made by experts on the basis of the fulfillment of the comprehensive diagnostic criteria and/or each organ-specific diagnostic criteria.

Results:

Elevated serum IgA levels were observed in 18 patients (10.6%). In the patients with elevated serum IgA levels, serum CRP levels were higher (1.14 ± 1.18 vs. 0.31 ± 0.63 mg/dL, p=0.003) and the prevalence of relapse during the clinical course was lower (5.6% vs. 27.6%, p=0.046) than in those without elevated serum IgA levels. However, there were no significant differences in the other clinical features including the number of involved organs (2.4 ± 1.3 vs. 2.8 ± 1.6, p=0.443) and inclusion scores of the ACR/EULAR classification criteria (32 ± 14 vs. 36 ± 17, p=0.374). To evaluate the influence of serum IgA elevation on relapse, we performed Cox regression analysis, which showed that the elevated serum IgA levels had no significant association with lower incidence of relapse but a tendency of it (hazard ratio 0.997, 95% confidence interval 0.994-1.000, p=0.055) during the clinical course. In addition, a prompt improvement in the IgG4-RD responder index [5] during the clinical course was seen in the patients with serum IgA elevation, suggesting a similar good response to glucocorticoids as in those without it.

Conclusion:

The findings of the present study suggest that IgG4-RD patients with high serum IgA levels can be diagnosed and treated in the same way as those without it, although they may be characterized by mild serum CRP elevation.

References:

[1]Wallace ZS et al. The 2019 American College of Rheumatology/European League Against Rheumatism classification criteria for IgG4-related disease. Ann Rheum Dis. 2020;79:77-87.

[2]Umehara H et al. The 2020 Revised Comprehensive Diagnostic (RCD) Criteria for IgG4-RD. Mod Rheumatol. 2020 Dec 4:1-14. doi: 10.1080/14397595.2020.1859710. Online ahead of print.

[3]Umehara H et al. Current approach to the diagnosis of IgG4-related disease - Combination of comprehensive diagnostic and organ - specific criteria. Mod Rheumatol. 2017;27:381-91.

[4]Sato Y et al. Systemic IgG4-related lymphadenopathy: A clinical and pathologic comparison to multicentric Castleman’s disease. Mod Pathol.2009;22:589-99.

[5]Carruthers MN et al. Development of an IgG4-RD Responder Index. Int J Rheumatol. 2012;2012:259408.

Disclosure of Interests:

None declared

POS1348 MORTALITY AND ITS RELATED FACTORS IN PATIENTS WITH IGG4-RELATED DISEASE: A JAPANESE SINGLE-CENTER STUDY

Background:

In recent years, IgG4-related disease (IgG4-RD) has become a widely recognized disorder. However, mortality and its related factors in this disease are not well known.

Objectives:

This study aimed to clarify mortality and its related factors in patients with IgG4-RD.

Methods:

We retrospectively reviewed the medical records of patients with IgG4-RD diagnosed by experts based on fulfillment of the Japanese comprehensive diagnostic criteria and/or the 2019 ACR/EULAR classification criteria for IgG4-RD at a single center in Japan. Using the collected data, we calculated the crude mortality rate and the standardized mortality ratio (SMR) using national Japan mortality statistics and investigated the cause of death. We performed Cox regression analyses to assess mortality-related factors.

Results:

A total of 179 patients with IgG4-RD were included: 124 were male (69.3%); the median age was 68 years (interquartile range [IQR] 60-75 years); and the median follow-up from diagnosis was 47 months (IQR 17-84). Ten patients (5.6%) in our cohort died during the follow-up period. Five died of malignancy, one of respiratory failure, two of infectious pneumonia, one of sudden cardiac event, and one of suspected aortic aneurysmal rupture. The crude mortality rate was 11.1 per 1,000 person-years. According to national Japan mortality statistics, 11.6 age- and sex-matched deaths were expected to occur within the follow-up period, resulting in a SMR of 0.86 (95% confidence interval [CI] 0.41-1.59). Univariate Cox regression analyses indicated that the number of affected organs at diagnosis (hazard ratio [HR] 1.45, 95% CI 1.02-2.05), serum creatinine levels at diagnosis (HR 1.82, 95% CI 1.06-3.12), and the presence of malignancy during the clinical course (HR 3.93, 95% CI 1.10-14.02) had a significant impact on the time to death, whereas the other factors including age at diagnosis and serum C-reactive protein and IgG4 levels at diagnosis did not.

Conclusion:

Our findings suggest that the mortality rate of patients with IgG4-RD does not significantly differ from that of the Japanese general population. Multi-organ involvement and renal dysfunction at diagnosis as well as malignancy during the clinical course may be associated with higher mortality. An appropriate clinical evaluation for the early detection of these risk factors is required at first diagnosis and during long-term follow-up.

Disclosure of Interests:

None declared

The complete mitochondrial genome of Anneissia intermedia (Crinoidea: Comatulida: Comatulidae)

Anneissia intermedia (A.H. Clark, 1916) is a common crinoid found in waters along the coastlines of China, Japan, and Korea. In this study, we determined the complete mitogenome of A. intermedia. The genome was found to be 15,874 bp in length and consists of 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. With the exception of Antedon mediterranea, the gene order and genetic characteristics of the A. intermedia mitogenome are identical with those of the mitogenomes of other crinoids. The complete mitogenome of A. intermedia will contribute to enhance our understanding of the phylogeny of crinoids.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Application of chitosan as a natural disinfectant against porcine epidemic diarrhoea virus

Porcine epidemic diarrhoea virus (PEDV) is one of the major pathogens causing acute enteritis, which is characterised by vomiting and watery diarrhoea and commonly leads to high rates of mortality and morbidity in suckling piglets. Chitosan has been regarded as a promising natural disinfectant. In this study, the disinfectant effect and mammalian-cell toxicity of chitosan were evaluated against PEDV using Vero cells. A 0.01% solution of chitosan was determined to be an effective disinfectant. In addition, no evidence of toxicity was observed during the cell toxicity test; on the contrary, chitosan promoted cell proliferation. In conclusion, chitosan is a promising candidate for an effective and safe disinfectant against PEDV as well as other coronaviruses.

Characterization of Extended-Spectrum β-Lactamase-Producing and AmpC β-Lactamase-Producing Enterobacterales Isolated from Companion Animals in Korea

The emergence of extended-spectrum cephalosporin (ESC)-resistant Gram-negative bacteria is of great concern in both human and veterinary medicine. The aim of this study was to investigate ESC-resistant bacterial isolates from companion animals in South Korea between 2017 and 2019. Isolates with ESC resistance genes, which were identified by PCR, were assessed for genetic relatedness by multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). In total, 91 ESC-resistant Escherichia coli, Klebsiella spp., Serratia spp., and Enterobacter cloacae isolates harbored the bla_TEM gene. Among other ESC resistance genes, bla_CTX-M-15, bla_CIT, and bla_CTX-M-55 were predominantly detected in E. coli isolates, whereas bla_SHV and bla_DHA were more frequently detected in Klebsiella pneumoniae isolates. In addition, all bla_EBC-positive isolates were classified as E. cloacae. From the MLST results, bla_CTX-M-9-carrying ST131, bla_CIT-carrying ST405, and bla_CTX-M-1-carrying ST3285 strains were dominant among E. coli isolates. ST273 and ST275 strains harboring bla_SHV were frequently detected in K. pneumoniae isolates. Various sequence types were obtained in E. cloacae and Klebsiella oxytoca isolates. All isolates demonstrated unique PFGE profiles (<57–98% similarity) and were unlikely to be derived from a single clone. The present study reveals the presence and wide genetic distribution of ESC-resistant bacterial species in South Korean companion animals.

An automated approach to determine antibody endpoint titers for COVID-19 by an enzyme-linked immunosorbent assay

While a variety of therapeutic options continue to emerge for COVID-19 treatment, convalescent plasma (CP) has been used as a possible treatment option early in the pandemic. One of the most significant challenges with CP therapy, however, both when defining its efficacy and implementing its approach clinically, is accurately and efficiently characterizing an otherwise heterogenous therapeutic treatment. Given current limitations, our goal is to leverage a SARS antibody testing platform with a newly developed automated endpoint titer analysis program to rapidly define SARS-CoV-2 antibody levels in CP donors and hospitalized patients. A newly developed antibody detection platform was used to perform a serial dilution enzyme-linked immunosorbent assay (ELISA) for immunoglobulin (Ig)G, IgM, and IgA SARS-CoV-2 antibodies. Data were then analyzed using commercially available software, GraphPad Prism, or a newly developed program developed in Python called TiterScape, to analyze endpoint titers. Endpoint titer calculations and analysis times were then compared between the two analysis approaches. Serial dilution analysis of SARS-CoV-2 antibody levels revealed a high level of heterogeneity between individuals. Commercial platform analysis required significant time for manual data input and extrapolated endpoint titer values when the last serial dilution was above the endpoint cutoff, occasionally producing erroneously high results. By contrast, TiterScape processed 1008 samples for endpoint titer results in roughly 14 minutes compared with the 8 hours required for the commercial software program analysis. Equally important, results generated by TiterScape and Prism were highly similar, with differences averaging 1.26 ± 0.2 percent (mean ± SD). The pandemic has created unprecedented challenges when seeking to accurately test large numbers of individuals for SARS-CoV-2 antibody levels with a rapid turnaround time. ELISA platforms capable of serial dilution analysis coupled with a highly flexible software interface may provide a useful tool when seeking to define endpoint titers in a high-throughput manner. Immunohematology 2021;37:33-43. While a variety of therapeutic options continue to emerge for COVID-19 treatment, convalescent plasma (CP) has been used as a possible treatment option early in the pandemic. One of the most significant challenges with CP therapy, however, both when defining its efficacy and implementing its approach clinically, is accurately and efficiently characterizing an otherwise heterogenous therapeutic treatment. Given current limitations, our goal is to leverage a SARS antibody testing platform with a newly developed automated endpoint titer analysis program to rapidly define SARS-CoV-2 antibody levels in CP donors and hospitalized patients. A newly developed antibody detection platform was used to perform a serial dilution enzyme-linked immunosorbent assay (ELISA) for immunoglobulin (Ig)G, IgM, and IgA SARS-CoV-2 antibodies. Data were then analyzed using commercially available software, GraphPad Prism, or a newly developed program developed in Python called TiterScape, to analyze endpoint titers. Endpoint titer calculations and analysis times were then compared between the two analysis approaches. Serial dilution analysis of SARS-CoV-2 antibody levels revealed a high level of heterogeneity between individuals. Commercial platform analysis required significant time for manual data input and extrapolated endpoint titer values when the last serial dilution was above the endpoint cutoff, occasionally producing erroneously high results. By contrast, TiterScape processed 1008 samples for endpoint titer results in roughly 14 minutes compared with the 8 hours required for the commercial software program analysis. Equally important, results generated by TiterScape and Prism were highly similar, with differences averaging 1.26 ± 0.2 percent (mean ± SD). The pandemic has created unprecedented challenges when seeking to accurately test large numbers of individuals for SARS-CoV-2 antibody levels with a rapid turnaround time. ELISA platforms capable of serial dilution analysis coupled with a highly flexible software interface may provide a useful tool when seeking to define endpoint titers in a high-throughput manner. Immunohematology 2021;37:33–43.

Characteristics of Aerococcus viridans isolated from porcine fetuses in Korean farms

Swine abortion caused by viruses as well as bacteria has caused many economic losses in domestic farms over the years; however, bacterial abortion has not yet been studied in Korea. Several bacterial species were isolated from aborted fetuses (n = 103) for which the cause of death was not viral abortion. Among them, we focused on Aerococcus viridans, which had the highest positive rate within three provinces (Gangwon, Jeonnam and Gyeongnam). A total of 16 isolates were identified as A. viridans by matrix‐assisted laser desorption ionization‐time of flight mass spectrometry (MALDI‐TOF MS), and 13 were characterized by both antibiotic resistance and 16S rRNA gene analysis. Based on antibiotic susceptibility testing result, eight antimicrobials could not effectively eliminate the present isolation (more than 40% of isolates can resist these antibiotics), while all except two strains were susceptible to trimethoprim/sulfamethoxazole. Molecular analysis indicated genetic variation among these strains. This study is the first report detecting A. viridans from aborted fetuses in Korean domestic farms.

A new species of the genus Henricia (Asteroidea, Spinulosida, Echinasteridae) from South Korea

A new species of the genus Henricia Gray, 1840 that belongs to the family Echinasteridae is described from South Korea. Henriciaepiphysialissp. nov. has epiphyseal ossicles at the ends of the abactinal and lateral plates, and the abactinal and lateral spines form a hooked crown. The partial sequence of the mitochondrial COXI gene (537 bp) of H.epiphysialissp. nov. was obtained, and the new species was morphologically and genetically compared with other related Henricia species.

Evaluation of adverse plaque characteristics in coronary computed tomography angiography using combined near infrared spectroscopy

Background/Introduction

Coronary computed tomography angiography (CCTA) has developed rapidly, enabling the evaluation of coronary stenosis as well as plaque characteristics. However, it is not clear whether the adverse plaque characteristics found in CCTA are really vulnerable plaques. Near-infrared spectroscopy (NIRS) is able to quantify cholesterol within coronary arteries by the lipid core burden index (LCBI).

Purpose

The purpose of this study was to determine whether positive remodeling (PR), low attenuated plaque (LAP) and spotty calcificaiton (SC) found in CCTA have high LCBI values in NIRS.

Methods

The study was single center, prospective, and cross-sectional. A total of 84 patients who underwent NIRS during percutaneous coronary intervention after CCTA imaging for coronary artery disease were studied. PR, LAP and SC were identified in the plaques visible on CCTA, and LCBI and maxLCBI (4mm) were measured by NIRS on the same plaque.

Results

In the presence of PR and LAP in the plaque, the maxLCBI (4mm) [PR: 468±161 vs. 319±214, p=0.032, LAP: 475±178 vs. 278±191, p=0.006] and LCBI [PR: 190±74 vs. 132±104, p=0.044, LAP: 182±96 vs. 124±93, p=0.038] values were significantly higher than those in the plaque without PR and LAP. However, with and without SC, there was no significant difference between the maxLCBI (4mm) [474±181 vs. 336±208] and LCBI [183±77 vs. 142±102, p=0.127] values.

Conclusion

Among the adverse plaque characteristics found in CCTA, PR and LAP were clearly correlated with maxLCBI (4mm) and LCBI measured by NIRS, but SC was less correlated.

APC vs. LCBI

Funding Acknowledgement

Type of funding source: None

Investigation of the damping wiggler effect and application on the PAL fourth-generation storage ring

An investigation of the damping wiggler effect to reduce the emittance in the Pohang Accelerator Laboratory (PAL), a fourth-generation storage ring (4GSR) that uses a multi-bend achromat, is presented. A 4GSR lattice which has reduced emittance and increased dynamic aperture to amplify the synergy with two existing light sources (PLS-II and PAL-XFEL) at PAL is described.