• Genomics & Informatics
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• v.20 no.2
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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.

• Journal for History of Mathematics
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• v.36 no.6
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• pp.105-113
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• 2023

We will suggest a train model to explain the weekly periodic character of Covid19 in South Korea on the first half of 2022, the period of the Omicron variant outbreak. In the model, the daily new infected individuals board a train, divided into 4 compartments. The train moves at night by the length of one compartment. Then the infected are quarantined during the daytime after their compartment reaches the quarantine area. Then it remains empty on the 5-th night after boarding. The parameters of the model are fitted with the daily measured quarantine populations and generate the simulated quarantine populations that hit the real weekly and global peaks.

• 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.

• IMMUNE NETWORK
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• v.23 no.4
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• pp.33.1-33.13
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• 2023

Vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been acknowledged as an effective mean of preventing infection and hospitalization. However, the emergence of highly transmissible SARS-CoV-2 variants of concern (VOCs) has led to substantial increase in infections among children and adolescents. Vaccine-induced immunity and longevity have not been well defined in this population. Therefore, we aimed to analyze humoral and cellular immune responses against ancestral and SARS-CoV-2 variants after two shots of the BNT162b2 vaccine in healthy adolescents. Although vaccination induced a robust increase of spike-specific binding Abs and neutralizing Abs against the ancestral and SARS-CoV-2 variants, the neutralizing activity against the Omicron variant was significantly low. On the contrary, vaccine-induced memory CD4⁺ T cells exhibited substantial responses against both ancestral and Omicron spike proteins. Notably, CD4⁺ T cell responses against both ancestral and Omicron strains were preserved at 3 months after two shots of the BNT162b2 vaccine without waning. Polyfunctionality of vaccine-induced memory T cells was also preserved in response to Omicron spike protein. The present findings characterize the protective immunity of vaccination for adolescents in the era of continuous emergence of variants/subvariants.

• The Journal of Industrial Distribution & Business
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• v.13 no.6
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• pp.9-18
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• 2022

Purpose: The government around the world is still highlighting the effect of the new variant of Covid-19. The government continues to make efforts to restore the economy through several programs, one of them is National Economic Recovery. This program is expected to increase public and investor confidence in handling Covid-19. This study aims to capture public sentiment on the economic growth rate in Indonesia, especially during the third wave of the omicron variant of the covid-19 virus, that is at the time in the fourth quarter of 2021. Research design, data, and methodology: The approach used in this research is to collect crowdsourcing data from twitter, in the range of 1st to 10th October 2021. The analysis is done by building model using Deep Learning Neural Network method. Results: The result of the sentiment analysis is that most of the tweets have a neutral sentiment on the Economic Growth discussion. Several central figures who discussed were Minister of Coordinating for the Economy of Indonesia, Minister of State-Owned Enterprises. Conclusions: Data from social media can be used by the government to capture public responses, especially public sentiment regarding economic growth. This can be used by policy makers, for example entrepreneurs to anticipate economic movements under certain conditions.

• 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.

• Pediatric Infection and Vaccine
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• v.29 no.2
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• pp.61-69
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• 2022

Coronavirus disease 2019 (COVID-19) has been a global pandemic for over 2 years. During the Omicron (B.1.1.529) variant-predominant period in South Korea, confirmed cases among children and adolescents surged. This review found that, although younger children may be less susceptible to COVID-19 than adolescents, more research is needed on the role of children and adolescents in the disease's spread. Detailed epidemiological information about the transmissibility of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain in children and adolescents is currently scarce, and more research is needed on the role of children and adolescents in disease's spread. There may be a difference in the proportion of cases with severe disease requiring hospitalization depending on the dominant mutant strain; however, COVID-19 generally presents with a mild-to-moderate course in children aged 5-11 years old.

• Molecules and Cells
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• v.45 no.12
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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.

• The Journal of Korean Medicine
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• v.44 no.4
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• pp.182-192
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• 2023

Coronavirus disease 2019 (COVID-19) cases surged across South Korea during the omicron-variant wave. We aimed to report the effectiveness of herbal medicine administered through telemedicine consultations as an adjunctive therapy for COVID-19. Patients with confirmed COVID-19 who were self-isolating at home were provided telephone consultations through a Korean Medicine clinic between January and March 2022. On the basis of their dominant symptoms, the patients were prescribed Eunkyo-san for seven days. Patients were asked to evaluate the severity of their COVID-19 symptoms before and after treatment by numeric rating scale. Of ten patients, more than half of them reported cough, fever, headache, and sore throat on the first telephone consultation. Patients reported that all symptoms related to COVID-19 disappeared completely on the second consultation. No severe adverse events were identified. The results of this case series suggest that Eunkyo-san administration can be a beneficial adjunctive therapy for patients with COVID-19.

• Genomics & Informatics
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• v.21 no.4
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• pp.50.1-50.9
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• 2023

Vaccine development is one of the key efforts to control the spread of coronavirus disease 2019 (COVID-19). However, it has become apparent that the immunity acquired through vaccination is not permanent, known as the waning effect. Therefore, monitoring the proportion of the population with immunity is essential to improve the forecasting of future waves of the pandemic. Despite this, the impact of the waning effect on forecasting accuracies has not been extensively studied. We proposed a method for the estimation of the effective immunity (EI) rate which represents the waning effect by integrating the second and booster doses of COVID-19 vaccines. The EI rate, with different periods to the onset of the waning effect, was incorporated into three statistical models and two machine learning models. Stringency Index, omicron variant BA.5 rate (BA.5 rate), booster shot rate (BSR), and the EI rate were used as covariates and the best covariate combination was selected using prediction error. Among the prediction results, Generalized Additive Model showed the best improvement (decreasing 86% test error) with the EI rate. Furthermore, we confirmed that South Korea's decision to recommend booster shots after 90 days is reasonable since the waning effect onsets 90 days after the last dose of vaccine which improves the prediction of confirmed cases and deaths. Substituting BSR with EI rate in statistical models not only results in better predictions but also makes it possible to forecast a potential wave and help the local community react proactively to a rapid increase in confirmed cases.