• IMMUNE NETWORK
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• v.21 no.5
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• pp.32.1-32.14
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• 2021

Over two hundred twenty-eight million cases of coronavirus disease 2019 (COVID-19) in the world have been reported until the 21^st of September 2021 after the first rise in December 2019. The virus caused the disease called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Over 4 million deaths blame COVID-19 during the last one year and 8 months in the world. Currently, four SARS-CoV-2 variants of concern are mainly focused by pandemic studies with limited experiments to translate the infectivity and pathogenicity of each variant. The SARS-CoV-2 α, β, γ, and δ variant of concern was originated from United Kingdom, South Africa, Brazil/Japan, and India, respectively. The classification of SARS-CoV-2 variant is based on the mutation in spike (S) gene on the envelop of SARS-CoV-2. This review describes four SARS-CoV-2 α, β, γ, and δ variants of concern including SARS-CoV-2 ε, ζ, η, ι, κ, and B.1.617.3 variants of interest and alert. Recently, SARS-CoV-2 δ variant prevails over different countries that have 3 unique mutation sites: E156del/R158G in the N-terminal domain and T478K in a crucial receptor binding domain. A particular mutation in the functional domain of the S gene is probably associated with the infectivity and pathogenesis of the SARS-CoV-2 variant.

• Clinical and Experimental Vaccine Research
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• v.11 no.3
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• pp.285-289
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• 2022

Various vaccines have been developed to fight severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 pandemic. However, new variants of SARS-CoV-2 undermine the effort to fight SARS-CoV-2. Here, we produced S proteins harboring the receptor-binding domain (RBD) of the Omicron variant in plants. Plant-produced S proteins together with adjuvant CIA09A triggered strong immune responses in mice. Antibodies in serum inhibited interaction of recombinant human angiotensin-converting enzyme 2 with RBD of the Omicron variant, but not RBD of other variants. These results suggest that antibodies induced by RBD of the Omicron variant are highly specific for the Omicron RBD, but not for that of other variants.

• Clinical and Experimental Vaccine Research
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• v.11 no.2
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• pp.173-183
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• 2022

The coronavirus disease 2019 pandemic has not ended, and several variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continue to emerge. The emergence of new variants is worrying because higher transmission leads to spikes in infections, vaccine efforts, and other therapeutic developments. Existing literature reports that with new variants affecting vaccine efficacy, hospitalization and risk of a recurrent infection increase. In this review article, we describe the latest variants of SARS-CoV-2, and the impact of each new variant on the efficacy of the developed vaccines reported in the literature and findings. The report concludes that the emergence of a variant that completely evades the immune response and reduces neutralizing antibodies.

• IMMUNE NETWORK
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• v.22 no.6
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• pp.48.1-48.13
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• 2022

With the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, which are randomly mutated, the dominant strains in regions are changing globally. The development of preclinical animal models is imperative to validate vaccines and therapeutics against SARS-CoV-2 variants. The objective of this study was to develop a non-human primate (NHP) model for SARS-CoV-2 Delta variant infection. Cynomolgus macaques infected with Delta variants showed infectious viruses and viral RNA in the upper (nasal and throat) and lower respiratory (lung) tracts during the acute phase of infection. After 3 days of infection, lesions consistent with diffuse alveolar damage were observed in the lungs. For cellular immune responses, all macaques displayed transient lymphopenia and neutrophilia in the early stages of infection. SARS-CoV-2 Delta variant spike protein-specific IgM, IgG, and IgA levels were significantly increased in the plasma of these animals 14 days after infection. This new NHP Delta variant infection model can be used for comparative analysis of the difference in severity between SARS-CoV-2 variants of concern and may be useful in the efficacy evaluation of vaccines and universal therapeutic drugs for mutations.

• Nuclear Engineering and Technology
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• v.56 no.6
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• pp.2421-2427
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• 2024

In this research, the Omicron variant of the SARS-CoV-2 virus was simulated and exposed to electron radiation with up to 20 keV energy. Absorbed energy was measured for spike protein, nucleocapsid protein, and envelope of the virus. Simulations were performed by Geant4-DNA in a water environment at temperature of 20 ℃ and pressure of 1 atm. Since the viral RNA is kept inside the nucleocapsid protein, damage to this area could destroy the viral RNA strand and create an inactive virus. Our findings showed that electron beams with an energy of 2.5 keV could cause a maximum absorption dose and consequently maximum damage to the nucleocapsid and effectively be used for inactivation virus.

• IMMUNE NETWORK
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• v.21 no.6
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• pp.38.1-38.8
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• 2021

Recently, a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (B.1.1.529) Omicron variant originated from South Africa in the middle of November 2021. SARS-CoV-2 is also called coronavirus disease 2019 (COVID-19) since SARS-CoV-2 is the causative agent of COVID-19. Several studies already suggested that the SARS-CoV-2 Omicron variant would be the fastest transmissible variant compared to the previous 10 SARS-CoV-2 variants of concern, interest, and alert. Few clinical studies reported the high transmissibility of the Omicron variant but there is insufficient time to perform actual experiments to prove it, since the spread is so fast. We analyzed the SARS-CoV-2 Omicron variant, which revealed a very high rate of mutation at amino acid residues that interact with angiostatin-converting enzyme 2. The mutation rate of COVID-19 is faster than what we prepared vaccine program, antibody therapy, lockdown, and quarantine against COVID-19 so far. Thus, it is necessary to find better strategies to overcome the current crisis of COVID-19 pandemic.

• Clinical and Experimental Vaccine Research
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• v.12 no.2
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• pp.116-120
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• 2023

Purpose: In Japan, the data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody titers after the booster dose of the coronavirus disease 2019 (COVID-19) vaccine are insufficient. The aim of this study is to evaluate changes in SARS-CoV-2 antibody titers before, 1, 3, and 6 months after the booster dose of the BNT162b2 COVID-19 vaccine among health care workers. Materials and Methods: A total of 268 participants who received the booster dose of the BNT162b2 vaccine were analyzed. SARS-CoV-2 antibody titers were measured before (baseline) and at 1, 3, and 6 months after the booster dose. Factors associated with changes in SARS-CoV-2 antibody titers at 1, 3, and 6 months were analyzed. Cutoff values at baseline were calculated to prevent infection of the omicron variant of COVID-19. Results: The SARS-CoV-2 antibody titers at baseline, and 1, 3, and 6 months were 1,018.3 AU/mL, 21,396.5 AU/mL, 13,704.6 AU/mL, and 8,155.6 AU/mL, respectively. Factors associated with changes in SARS-CoV-2 antibody titers at 1 month were age and SARS-CoV-2 antibody titers at baseline, whereas changes in SARS-CoV-2 antibody titers at 3 and 6 months were associated with the SARS-CoV-2 antibody titers at 1 month. The cutoff values of the SARS-CoV-2 antibody titers at baseline were 515.4 AU/mL and 13,602.7 AU/mL at baseline and 1 month after the booster dose, respectively. Conclusion: This study showed that SARS-CoV-2 antibody titers increase rapidly at 1 month after the booster dose of the BNT162b2 vaccine and begin to decrease from 1 to 6 months. Hence, another booster may be needed as soon as possible to prevent infection.

• BMB Reports
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• v.56 no.12
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• pp.669-674
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• 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to various clinical symptoms including anemia. Lipocalin-2 has various biological functions, including defense against bacterial infections through iron sequestration, and it serves as a biomarker for kidney injury. In a human protein array, we observed increased lipocalin-2 expression due to parental SARS-CoV-2 infection in the Calu-3 human lung cancer cell line. The secretion of lipocalin-2 was also elevated in response to parental SARS-CoV-2 infection, and the SARS-CoV-2 Alpha, Beta, and Delta variants similarly induced this phenomenon. In a Calu-3 implanted mouse xenograft model, parental SARSCoV-2 and Delta variant induced lipocalin-2 expression and secretion. Additionally, the iron concentration increased in the Calu-3 tumor tissues and decreased in the serum due to infection. In conclusion, SARS-CoV-2 infection induces the production and secretion of lipocalin-2, potentially resulting in a decrease in iron concentration in serum. Because the concentration of iron ions in the blood is associated with anemia, this phenomenon could contribute to developing anemia in COVID-19 patients.

• Tuberculosis and Respiratory Diseases
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• v.86 no.2
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• pp.142-149
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• 2023

Background: Coronavirus disease 2019 (COVID-19) is an ongoing global public health threat and different variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified. This study aimed to analyse the factors associated with negative conversion of polymerase chain reaction (PCR) and prognosis in critically ill patients according to the SARS-CoV-2 variant. Methods: This study retrospectively analysed 259 critically ill patients with COVID-19 who were admitted to the intensive care unit of a tertiary medical center between January 2020 and May 2022. The Charlson comorbidity index (CCI) was used to evaluate comorbidity, and a negative PCR test result within 2 weeks was used to define negative PCR conversion. The cases were divided into the following three variant groups, according to the documented variant of SARS-CoV-2 at the time of diagnosis: non-Delta (January 20, 2020-July 6, 2021), Delta (July 7, 2021- January 1, 2022), and Omicron (January 30, 2022-April 24, 2022). Results: The mean age of the 259 patients was 67.1 years and 93 (35.9%) patients were female. Fifty (19.3%) patients were smokers, and 50 (19.3%) patients were vaccinated. The CCI (hazard ratio [HR], 1.555; p<0.001), vaccination (HR, 0.492; p=0.033), and Delta variant (HR, 2.469; p=0.002) were significant factors for in-hospital mortality. The Delta variant (odds ratio, 0.288; p=0.003) was associated with fewer negative PCR conversion; however, vaccination (p=0.163) and remdesivir (p=0.124) treatments did not. Conclusion: The Delta variant of SARS-CoV-2 is associated with lower survival and negative PCR conversion. Contrary to expectations, vaccination and remdesivir may not affect negative PCR conversion in critically ill patients with COVID-19.

• Proceedings of the Korean Society of Computer Information Conference
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• 2021.07a
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• pp.283-284
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• 2021

최근 SARS-CoV-2 백신들의 예방접종이 진행됨에 따라 코로나 19 팬데믹의 종결이 예상되고 있다. 하지만 계속해서 출현 중인 변종 바이러스들은 팬데믹 종결의 위험요소로 남아있다. 본 논문에서는 사전학습된 단백질 BERT와 단백질-단백질 상호작용 모델을 활용한 SARS-CoV-2 스파이크 단백질의 변이 예측 분석 알고리즘을 제안한다. 제안하는 기술은 변이 단백질 서열의 예측과 변이 단백질과 human ACE2 수용체의 친화도에 따른 자연선택으로 이루어진다. 이를 통해 시간이 지나며 나타날 수 있는 변종 바이러스들을 시뮬레이션 할 수 있어 변종 바이러스들의 해결에 기여할 것으로 기대된다.