• Genomics & Informatics
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• 제20권2호
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• pp.22.1-22.9
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• 2022

The rise of newer coronavirus disease 2019 (COVID-19) variants has brought a challenge to ending the spread of COVID-19. The variants have a different fatality, morbidity, and transmission rates and affect vaccine efficacy differently. Therefore, the impact of each new variant on the spread of COVID-19 is of interest to governments and scientists. Here, we proposed mathematical SEIQRDVP and SEIQRDV3P models to predict the impact of the Omicron variant on the spread of the COVID-19 situation in South Korea. SEIQEDVP considers one vaccine level at a time while SEIQRDV3P considers three vaccination levels (only one dose received, full doses received, and full doses + booster shots received) simultaneously. The omicron variant's effect was contemplated as a weighted sum of the delta and omicron variants' transmission rate and tuned using a hyperparameter k. Our models' performances were compared with common models like SEIR, SEIQR, and SEIQRDVUP using the root mean square error (RMSE). SEIQRDV3P performed better than the SEIQRDVP model. Without consideration of the variant effect, we don't see a rapid rise in COVID-19 cases and high RMSE values. But, with consideration of the omicron variant, we predicted a continuous rapid rise in COVID-19 cases until maybe herd immunity is developed in the population. Also, the RMSE value for the SEIQRDV3P model decreased by 27.4%. Therefore, modeling the impact of any new risen variant is crucial in determining the trajectory of the spread of COVID-19 and determining policies to be implemented.

• Pediatric Infection and Vaccine
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• 제31권1호
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• pp.83-93
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• 2024

목적: 코로나19 판데믹이 시작된 이후, 다양한 주요 변이 바이러스가 출현했다. 코로나 19 판데믹 기간 동안 대표적인 주요 변이 바이러스 유행 시기를 네 가지로 나누고, 네 가지의 주요 변이 바이러스 시기로부터 임상적 그리고 혈액학적 검사의 특징을 파악하고자 하였다. 방법: 코로나19 확진으로 입원한 19세 이하 환자의 의무기록을 후향적으로 분석하였다. 변이전시기(2020년 2월 1일-2020년 9월 30일), 알파와 베타 변이 시기(2020년 10월 1일-2021년 5월 31일), 델타 변이 시기(2021년 6월 1일-2021년 10월 31일), 오미크론 변이 시기(2021년 11월 1일-2022년 5월 31일)를 비교하였다. 결과:대상환자 827명중에서 163명(19.7%)가무증상이었고, 발열과기침의빈도는각각 320명(38.7%), 399명(48.2%)이었다. 38.5℃ 이상의 발열이 있었던 경우는 12세 미만인 경우에 오미크론 변이 시기에 높게 관찰되었다. 혈액학적 검사에서 백혈구 감소증, 임파구 감소증 그리고 호중구 감소증은 각각 33%, 30.2%, 24.9%로 관찰되었다. 결론: 코로나 19의 주요 변이 바이러스 우세 시기에 다른 특징들이 있었다. 델타 변이 시기에 4일 이상의 발열이 지속되는 경우가 더 많았고, 오미크론 변이 시기에는 38.5℃ 이상의 발열을 가지는 경우가 많았다.

• Molecules and Cells
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• 제45권12호
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• pp.911-922
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• 2022

A structural protein of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), nucleocapsid (N) protein is phosphorylated by glycogen synthase kinase (GSK)-3 on the serine/arginine (SR) rich motif located in disordered regions. Although phosphorylation by GSK-3β constitutes a critical event for viral replication, the molecular mechanism underlying N phosphorylation is not well understood. In this study, we found the putative alpha-helix L/FxxxL/AxxRL motif known as the GSK-3 interacting domain (GID), found in many endogenous GSK-3β binding proteins, such as Axins, FRATs, WWOX, and GSKIP. Indeed, N interacts with GSK-3β similarly to Axin, and Leu to Glu substitution of the GID abolished the interaction, with loss of N phosphorylation. The N phosphorylation is also required for its structural loading in a virus-like particle (VLP). Compared to other coronaviruses, N of Sarbecovirus lineage including bat RaTG13 harbors a CDK1-primed phosphorylation site and Gly-rich linker for enhanced phosphorylation by GSK-3β. Furthermore, we found that the S202R mutant found in Delta and R203K/G204R mutant found in the Omicron variant allow increased abundance and hyper-phosphorylation of N. Our observations suggest that GID and mutations for increased phosphorylation in N may have contributed to the evolution of variants.

• Tuberculosis and Respiratory Diseases
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• 제86권2호
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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.