Genomic epidemiology of SARS-CoV-2 variants in South Korea between January 2020 and February 2023.

The Korea Disease Control and Prevention Agency (KDCA) has been conducting national genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). To monitor and characterize circulating SARS-CoV-2 variants in South Korea, 102,873 oropharyngeal/nasopharyngeal swab samples collected from patients with confirmed COVID-19 were sequenced, assigned lineages, and phylogenetically analyzed. Each wave followed a pattern of variants emerging first abroad and then spreading domestically. In 2020, B.41 lineage led the first wave, and B.1.497 dominated the second and third waves. In 2021, the fourth wave was driven by Delta (AY.69 and AY.122.5). In 2022, the fifth to seventh waves were dominated by Omicron sub-lineages BA.1/BA.1.1 and BA.2/BA.2.3, BA.5/BA.5.2, and BN.1, sequentially. The KDCA detected and monitored increasing variants in advance prior to large-scale epidemics, but the repeated emergence of new variants could threaten public health again. Therefore, it is important to continue to monitor and characterize emerging and circulating variants through national genomic surveillance.

Nosocomial outbreak of severe fever with thrombocytopenia syndrome among healthcare workers in a single hospital in Daegu, Korea.

BACKGROUND: In August 2020, 17 healthcare workers (HCWs) were simultaneously diagnosed with severe fever with thrombocytopenia syndrome (SFTS) at a university hospital in Daegu, Republic of Korea. METHODS: An epidemiologic investigation using questionnaires was conducted for all suspected HCWs who had viral infection symptoms or who had the possibility of exposure to the index patient. RESULTS: A total of 17 HCWs infected with the SFTS virus (SFTSV) (28.8%) were identified among the 59 HCWs who had contact with the patient. Operating a bag valve mask during cardiopulmonary resuscitation (CPR) (OR 7.50, 95% CI 1.75-41.07), cardiac massage during CPR (OR 12.00, 95% CI 1.76-241.94), exposure to the patient's body fluids (OR 7.43, 95% CI 1.91-34.69), and shorter individual hospital work experience periods (OR 6.79, 95% CI 1.70-32.10) were significantly associated with SFTS infection in the univariate analysis. However, exposure to body fluids was found to be the only statistically significant risk factor when multivariate analysis was conducted (OR 6.27. 95% CI 1.23-42.81, p = 0.036). CONCLUSIONS: This finding illustrates the importance of wearing appropriate personal protective equipment in treatment areas and when conducting any medical procedures, including CPR for patients with SFTS, and any procedure that involves potential exposure to body fluids.

Genetic Characterization of Middle East Respiratory Syndrome Coronavirus, South Korea, 2018.

We evaluated genetic variation in Middle East respiratory syndrome coronavirus (MERS-CoV) imported to South Korea in 2018 using specimens from a patient and isolates from infected Caco-2 cells. The MERS-CoV strain in this study was genetically similar to a strain isolated in Riyadh, Saudi Arabia, in 2017.

Serosurveillance of avian influenza A/H5N6 virus infection in poultry farmers, Gyeonggi Province, Republic of Korea, 2016-2017.

OBJECTIVES: Between November 20, 2016 and April 17, 2017, outbreaks of highly pathogenic avian influenza (HPAI) A/H5N6 occurred on poultry farms in Gyeonggi Province in the Republic of Korea. A serosurvey was conducted among poultry farmers to identify the transmission of HPAI A/H5N6 virus to humans. METHODS: A descriptive study of 870 poultry farmers in Gyeonggi Province in Korea was conducted during the 2016-2017 outbreaks. Serological testing was performed using a microneutralization (MN) assay for antibodies against influenza A/duck/ES2/Korea/2016 virus, which has antigenic properties similar to those of the HPAI A/H5N6 virus that caused this poultry outbreak. RESULTS: Overall, 523 exposed poultry farmers were assessed by serological testing. Consequently, all tested negative for HPAI A/H5N6 virus via MN assay. CONCLUSIONS: Based on serological assays, no transmission of HPAI A/H5N6 to humans was identified in this study cohort. Additional studies should be conducted to determine the possibility of poultry-to-human transmission of HPAI A/H5N6.

Development of infectious clones of a wild-type Korean rabies virus and evaluation of their pathogenic potential.

Most reverse genetic (RG) systems for rabies viruses (RVs) have been constructed on the genome background of laboratory-adapted strains. In this study, we developed an RG system using a Korean wild type (KGH) strain to investigate the pathogenic potential of different strains. We developed a RG system with the KGH strain for the first time. Following the complete genome sequencing of the KGH strain, pKGH infectious clones were constructed using the CMV/T7 promoter, and HamRz and HdvRz were introduced to allow self-cleavage of the synthesized RNA. We successfully recovered the rescued virus by constructing chimeric RVs in which we replaced a part of the construct with the partial gene from the fixed RC-HL strain. The rescued viruses formed clearer and countable plaques in an immunostaining plaque assay, with a distinct plaque morphology. Furthermore, compared with the chimeric RVs, the pKGH/RCinsΔ4 strain containing the KGH strain G protein exhibited a decreased efficiency of cell-to-cell spreading in BHK-21 cells and significantly reduced (100-1000 fold) replication kinetics. However, pKGH/RCinsΔ4 strain-infected mice revealed 100% morbidity at 11days post-infection, whereas other chimeric RV strains showed no mortality. Our RG system is a useful tool for studying differences in the cell-to-cell spreading efficiency and replication with respect to the different internalization patterns of street and fixed laboratory-adapted viruses.

Pathogenesis of novel reassortant avian influenza virus A (H5N8) Isolates in the ferret.

Outbreaks of avian influenza virus H5N8 first occurred in 2014, and spread to poultry farms in Korea. Although there was no report of human infection by this subtype, it has the potential to threaten human public health. Therefore, we evaluated the pathogenesis of H5N8 viruses in ferrets. Two representative Korean H5N8 strains did not induce mortality and significant respiratory signs after an intranasal challenge in ferrets. However, ferrets intratracheally infected with A/broiler duck/Korea/Buan2/2014 virus showed dose-dependent mortality. Although the Korean H5N8 strains were classified as the HPAI virus, possessing multiple basic amino acids in the cleavage site of the hemagglutinin sequence, they did not produce pathogenesis in ferrets challenged intranasally, similar to the natural infection route. These results could be useful for public health by providing the pathogenic characterization of H5N8 viruses.

Biological network inferences for a protection mechanism against familial Creutzfeldt-Jakob disease with E200K pathogenic mutation.

BACKGROUND: Human prion diseases are caused by abnormal accumulation of misfolded prion protein in the brain tissue. Inherited prion diseases, including familial Creutzfeldt-Jakob disease (fCJD), are associated with mutations of the prion protein gene (PRNP). The glutamate (E)-to-lysine (K) substitution at codon 200 (E200K) in PRNP is the most common pathogenic mutation causing fCJD, but the E200K pathogenic mutation alone is regarded insufficient to cause prion diseases; thus, additional unidentified factors are proposed to explain the penetrance of E200K-dependent fCJD. Here, exome differences and biological network analysis between fCJD patients with E200K and healthy individuals, including a non-CJD individual with E200K, were analysed to gain new insights into possible mechanisms for CJD in individuals carrying E200K. METHODS: Exome sequencing of the three CJD patients with E200K and 11 of the family of one patient (case1) were performed using the Illumina HiSeq 2000. The exome sequences of 24 Healthy Koreans were used as control. The bioinformatic analysis of the exome sequences was performed using the CLC Genomics Workbench v5.5. Sanger sequencing for variants validation was processed using a BigDye Terminator Cycle Sequencing Kit and an ABI 3730xl automated sequencer. Biological networks were created using Cytoscape (v2.8.3 and v3.0.2) and Pathway Studio 9.0 software. RESULTS: Nineteen sites were only observed in healthy individuals. Four proteins (NRXN2, KLKB1, KARS, and LAMA3) that harbour rarely observed single-nucleotide variants showed biological interactions that are associated with prion diseases and/or prion protein in our biological network analysis. CONCLUSION: Through this study, we confirmed that individuals can have a CJD-free life, even if they carry a pathogenic E200K mutation. Our research provides a possible mechanism that involves a candidate protective factor; this could be exploited to prevent fCJD onset in individuals carrying E200K.

Elevation of serum lactate dehydrogenase in patients with pectus excavatum.

INTRODUCTION: Pectus excavatum is the most common congenital chest wall deformity and the depression of the anterior chest wall, which compresses the internal organs. The aim of the present study is to investigate the effects of pectus excavatum on blood laboratory findings. MATERIAL AND METHODS: From March 2011 to December 2011, 71 patients with pectus excavatum who visited Seoul Saint Mary Hospital for Nuss procedure were reviewed and analyzed. The blood samples were routinely taken at the day before surgery and pectus bar removal was usually performed in 2 to 3 years after Nuss procedure. To investigate the effects on blood laboratory findings, preoperative routine blood laboratory data and postoperative changes of abnormal laboratory data were analyzed. RESULTS: Only lactate dehydrogenase (LDH), one of 26 separate routine laboratory tests, was abnormal and significantly elevated than normal value (age <10, p = 0.008; age ≥10, p < 0.001). However, there was no significant correlation between LDH levels and severities of pectus excavatum. The symmetric subgroup had significantly higher LDH level than the asymmetric subgroup (p < 0.001) and there was a significant decrease of LDH level after correction of deformity (p = 0.017). CONCLUSION: In conclusion, only LDH, one of the routine laboratory tests, was significantly elevated than normal value, which was thought to be caused by etiologies of pectus excavatum and the compression of the internal organs. Further studies on LDH including isoenzyme studies in patients with pectus excavatum will be needed, and these studies will provide a deeper and wider comprehension of pectus excavatum.

Molecular characterization of KGH, the first human isolate of rabies virus in Korea.

The complete genome sequence of the KGH strain of the first human rabies virus, which was isolated from a skin biopsy of a patient with rabies, whose symptoms developed due to bites from a raccoon dog in 2001. The size of the KGH strain genome was determined to be 11,928 nucleotides (nt) with a leader sequence of 58 nt, nucleoprotein gene of 1,353 nt, phosphoprotein gene of 894 nt, matrix protein gene of 609 nt, glycoprotein gene of 1,575 nt, RNA-dependent RNA polymerase gene of 6,384 nt, and trailer region of 69 nt. Sequence similarity was compared with 39 fully sequenced rabies virus genomes currently available, and the result showed 70.6-91.6 % at the nucleotide level, and 82.8-97.9 % at the amino acid level. The deduced amino acids in the viral protein were compared with those of other rabies viruses, and various functional regions were investigated. As a result, we found that the KGH strain only had a unique amino acid substitution that was identified to be associated either with host immune response and pathogenicity in the N protein, or with a related region regulating STAT1 in the P protein, and related to pathogenicity in G protein. Based on phylogenetic analyses using the complete genome of 39 rabies viruses, the KGH strain was determined to be closely related with the NNV-RAB-H strain and transplant rabies virus serotype 1, which are Indian isolates, and was confirmed to belong to the Arctic-like 2 clade. The KGH strain was most closely related to the SKRRD0204HC and SKRRD0205HC strain when compared with Korean animal isolates, which was separated around the same time and place, and belonged to the Gangwon III subgroup.

The association between prion proteins and Aß1₋42 oligomers in cytotoxicity and apoptosis.

Misfolding of prion protein (PrP to PrPSc) can cause neurodegenerative prion diseases. As a glycosylphosphatidylinositol (GPI)-anchored membrane protein, the normal form of PrP (PrPC) can function as a receptor for ligands in the extracellular space. PrPC was suggested to be involved in memory, synaptic neuronal communication, and anti-oxidation as a neuroprotective agent. The recently identified interaction between PrPC and Aß(1-42) oligomers suggested another role for PrP as a receptor for Aß(1-42) oligomers, thereby influencing cytotoxicity and apoptosis. Here, the association between PrPC and Aß(1-42) oligomers was investigated by visualizing protein localization in neuronal cells by immunocytochemistry. Aß(1-42) oligomer-induced cytotoxicity was tested in respective expressions of PrPC by using mouse neuroblastoma-2a (N2a) cells, the prion protein overexpressed cells (L2-2B1), and a Prnp-null mouse hippocampal cell line (HpL 3-4). Moreover, apoptotic proteins such as caspase-8 were used to assess the effect of PrPC on Aß(1-42) oligomer-mediated apoptosis. In L2-2B1 and HpL 3-4 cells, the difference in the cytotoxicity of Aß(1-42) oligomers could be clearly distinguished. In addition, Aß(1-42) oligomers induced mitochondria dysfunction, reactive oxygen species (ROS) generation, and calcium influx PrPC-dependently. Apoptosis, related to mitochondria dysfunction, was further investigated to determine the cytotoxic pathway; the results suggest that PrPC could be involved in both the intrinsic and extrinsic apoptotic pathways. Finally, cells with abundant PrPC expression seemed to be more susceptible to Aß(1-42) oligomer toxicity, suggesting the importance of the level of PrPC expression in the induction of apoptosis.

Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

BACKGROUND: Polymorphisms of the human prion protein gene (PRNP) contribute to the genetic determinants of Creutzfeldt-Jakob disease (CJD). Numerous polymorphisms in the promoter regions as well as the open reading frame of PRNP were investigated. Greater than 90% of Korean, Chinese, and Japanese carry the homozygote 129 MM codon. In Korea, polymorphisms have not been comprehensively studied, except codons 129 and 219 in PRNP among Korean CJD cases. Although polymorphisms at codons 129 and 219 play an important role in susceptibility to sporadic CJD, patients with other polymorphisms in PRNP exhibited critical distinctions of clinical symptoms. METHODS: The genetic analyses of PRNP were carried out among probable CJD patients in comparison with the results from magnetic resonance imaging (MRI) and electroencephalogram (EEG). RESULTS: The molecular analyses revealed that three mutations at codons D178N, E200K, and M232R in heterozygosity. Patients with the D178N and M232R mutations had a 129MM codon, whereas the patient with the E200K mutation showed 129MV heterozygosity. They all revealed strong 14-3-3 positive signals. The 67-year-old patient with the D178N-129M mutation showed progressive gait disturbance and dysarthria was in progress. The 58-year-old patient with the E200K mutation coupled to the 129MV codon had gait disturbance, dysarthria, agitation, and ataxic gait, and progressed rapidly to death 3 months from the first onset of symptoms. The 65-year-old patient with the M232R mutation showed rapidly progressive memory decline and gait disturbance, and died within 16 months after onset of symptoms. CONCLUSION: Despite differences in ethnicity, the clinical and pathological outcomes were similar to the respective mutations around the world, except absence of insomnia in D178N-129M subject.

The effect of thoracosopic thoracic sympathetomy on pulmonary function and bronchial hyperresponsiveness.

BACKGROUND: Endoscopic thoracic sympathectic denervation (ESD) is a procedure used in primary hyperhidrosis and upper extremity ischemia. Bronchial tone is affected by the sympathetic and parasympathetic nervous systems and bronchial asthma is associated with an imbalance between them. The aim of this study was to evaluate the effects of ESD on pulmonary function and bronchial hyperresponsiveness (BHR). PATIENTS AND METHODS: Fifty-eight patients with primary hyperhidrosis (n = 54) or upper limb ischemia (n = 4) were included. Spirometry and bronchial provocation test with methacholine was performed before and 4 weeks after ESD. RESULTS: Forced expiratory volume in 1 second (FEV(1)) and forced vital capacity (FVC) were significantly decreased early after ESD (from 4.67 +/- 0.84 L and 4.36 +/- 0.85 L to 4.12 +/- 0.78 L and 3.84 +/- 0.82 L, respectively), although no patient complained of an aggravation of respiratory symptoms. Twelve patients (21%) had a positive response to methacholine provocation preoperatively, and all remained positive post surgery. The provocative concentration of methacholine, which brought about a 20% decrease in the FEV(1) in the patients, was not significantly changed after surgery (from 5.1 +/- 4.3 to 4.6 +/- 4.6). Of 46 patients who had a negative result for methacholine challenge preoperatively, 12 (26%) became positive after surgery. In terms of the level of sympathectomy, T3 sympathectomy significantly increased the ratio of patients exhibiting a positive response to methacholine (from 19% to 34%, respectively) (p < 0.005). CONCLUSIONS: Thoracic sympathectomy can adversely affect lung function early after surgery, although the clinical significance is uncertain. It may also exert an influence on the development of bronchial hyperresponsiveness, especially when performed at the T3 level.

Coordinate regulation of bovine prion protein gene promoter activity by two Sp1 binding site polymorphisms.

Relationships between insertion/deletion (Ins/Del) polymorphisms of the bovine prion protein gene (PRNP) promoter and bovine spongiform encephalopathy (BSE) susceptibility have been reported. Our previous study has shown that polymorphisms of -6C-->T included in the specific protein 1 (Sp1) site in the 5'-flanking region of bovine PRNP influence the promoter activity of bovine PRNP. The present study shows that 12 and 23bp Ins/Del polymorphisms in the upstream region and an additional polymorphism (-47C-->A) in the Sp1 binding site coordinately affect the promoter activity. Reporter gene assays demonstrated that the bovine PRNP promoter containing -47A and 23bp Del/12bp Ins or 23bp Ins/12bp Ins showed lower promoter activity compared with other haplotypes (23bp Del/12bp Ins or 23bp Ins/12bp Del with -47C) or the wild-type haplotype (23bp Del/12bp Del with -47C). Furthermore, gel shift assays showed that the binding activity of Sp1 to the PRNP promoter was influenced by both polymorphisms with corresponding effects on the promoter activity. The coordinate regulation of the bovine PRNP promoter suggests the two Sp1 binding site polymorphisms control Sp1 binding to the PRNP promoter and its activity.

Late-onset olfactory deficits and mitral cell loss in mice lacking prion protein with ectopic expression of Doppel.

Several lines of prion protein gene (Prnp)-knockout mice such as ZrchI, ZrchII, Npu, Ngsk and Rcm0 have been generated. Of these, ZrchII, Ngsk and Rcm0 exhibit late-onset ataxia due to ectopic expression of Doppel (Dpl); a result of damage to the splicing acceptor of Prnp exon 3. Recently, we developed another line of Prnp-/- mice (Rikn), which was generated by gene targeting with more nucleotides by replacing intron 2 with the pgk-neo gene (cf. Ngsk Prnp-/- mice) and showed not only ataxia but also a lower olfactory sensitivity than the other Prnp-/- mouse line ZrchI at over 60 weeks of age. The histopathology of the elderly Rikn Prnp-/- mice showed mitral cell loss concomitantly observed with gliosis of astrocytes. Western blot analysis showed that Dpl was detected in the cerebrum, cerebellum and olfactory bulb of Rikn Prnp-/- mice, where aberrant histopathology was observed. Thus, mitral cell loss and gliosis induced by ectopic Dpl expression were probably associated with the late-onset olfactory deficits in Rikn Prnp-/- mice.

Reduced response of splenocytes after mitogen-stimulation in the prion protein (PrP) gene-deficient mouse: PrPLP/Doppel production and cerebral degeneration.

Splenocytes of wild-type (Prnp(+/+)) and prion protein gene-deficient (Prnp(-/-)) mice were treated with various activation stimuli such as T cell mitogen concanavalin A (ConA), phorbol 12-myristate 13-acetate (PMA)+ionomycin (Io), or B cell mitogen lipopolysaccharide (LPS). Cellular prion protein (PrP(C)) expression was enhanced following ConA stimulation, but not PMA+Io or LPS in Prnp(+/+) splenocytes. Rikn Prnp(-/-) splenocytes elicited lower cell proliferations than Prnp(+/+) or Zrch I Prnp(-/-) splenocytes after LPS stimulation and showed sporadic nerve cells in the cerebral cortex and deeper structure. Around the degenerated nerve cells, mild vacuolation in the neuropil was observed. This neural alteration correlated well to the suppressed response of B cells in the spleen. The finding that discrete lesions within the central nervous systems induced marked modulation of immune function probably indicates the existence of a delicately balanced neural-endocrine network by PrP(C) and PrPLP/Doppel.

Modification of thoracoscopic surgery for spontaneous pneumothorax.

Morbidity, use of analgesics, postoperative drainage, and hospital stay are reduced after video-assisted thoracoscopic surgery for pneumothorax. However, some surgeons prefer a minithoracotomy because the rate of recurrence after thoracoscopic surgery is 5%-10%. A modified thoracoscopic bullectomy is described, which has the advantages of both conventional video-assisted thoracoscopic surgery and a minithoracotomy. Of 69 patients who underwent surgery for pneumothorax from January 2002 to February 2003, 13 were treated by conventional video-assisted thoracoscopic surgery and 21 by the modified thoracoscopic bullectomy. The mean ages were 20.6 years in the conventional group and 23.0 years in the modified group, with follow-up of 25.8 +/- 1.8 months in the conventional group and 20.6 +/- 1.3 months in the modified group. The duration of operation was similar in both groups (49.3 +/- 16.0 vs. 44.2 +/- 19.2 min). Significantly fewer staples were used in the modified group (1.62 +/- 0.74 vs. 2.92 +/- 1.19). The duration of chest tube drainage and postoperative hospital stay were significantly reduced in the modified group. The modified thoracoscopic bullectomy is an effective procedure for the treatment of primary spontaneous pneumothorax.

Fusion of Doppel to octapeptide repeat and N-terminal half of hydrophobic region of prion protein confers resistance to serum deprivation.

Our previous studies have shown an essential role played by the octapeptide repeat region (OR) and the N-terminal half of hydrophobic region (HR) in the anti-apoptotic activity of prion protein (PrP). As PrP-like protein Doppel (Dpl), which structurally resembles an N-terminally truncated PrP, did not show any anti-apoptotic activity, we examined apoptosis of HpL3-4 cells expressing Dpl fused to various lengths of the N-terminal region of PrP to investigate whether the PrP/Dpl fusion proteins retain anti-apoptotic function. HpL3-4 cells expressing Dpl fused to PrP(1-124) with the OR and N-terminal half of HR of PrP showed anti-apoptotic function, whereas Dpl fused to PrP(1-95) with OR did not rescue cells from apoptotic cell death induced by serum deprivation. These results indicate that the OR and N-terminal half of HR of PrP retains anti-apoptotic activity similar to full-length PrP.

BSE situation and establishment of Food Safety Commission in Japan.

Eight major policies were implemented by Japanese Government since Oct. 2001, to deal with bovine spongiform encephalopathy (BSE). These are; 1) Surveillance in farm by veterinarian, 2) Prion test at healthy 1.3mi cows/yr, by veterinarian, 3) Elimination of specified risk material (SRM), 4) Ban of MBM for production, sale use, 5) Prion test for fallen stocks, 6) Transparent information and traceability, 7) New Measures such as Food Safety Basic Law, and 8) Establish of Food Safety Commission in the Cabinet Office. At this moment, the extent of SRM risk has only been indicated by several reports employing tests with a limited sensitivity. There is still a possibility that the items in the SRM list will increase in the future, and this indiscriminately applies to Japanese cattle as well. Although current practices of SRM elimination partially guarantee total food safety, additional latent problems and imminent issues remain as potential headaches to be addressed. If the index of SRM elimination cannot guarantee reliable food safety, we have but to resort to total elimination of tissues from high risk-bearing and BSE-infected animals. However, current BSE tests have their limitations and can not yet completely detect highrisk and/or infected animals. Under such circumstances, tissues/wastes and remains of diseased, affected fallen stocks and cohort animals have to be eliminated to prevent BSE invading the human food chain systems. The failure to detect any cohort should never be allowed to occur, and with regular and persistent updating of available stringent records, we are at least adopting the correct and useful approach as a reawakening strategy to securing food safety. In this perspective, traceability based on a National Identification System is required.