• Genomics & Informatics
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• v.18 no.4
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• pp.44.1-44.7
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• 2020

The severity of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), greatly varies from patient to patient. In the present study, we explored and compared mutation profiles of SARS-CoV-2 isolated from mildly affected and severely affected COVID-19 patients in order to explore any relationship between mutation profile and disease severity. Genomic sequences of SARS-CoV-2 were downloaded from Global Initiative on Sharing Avian Influenza Data (GISAID) database. With the help of Genome Detective Coronavirus Typing Tool, genomic sequences were aligned with the Wuhan seafood market pneumonia virus reference sequence and all the mutations were identified. Distribution of mutant variants was then compared between mildly and severely affected groups. Among the numerous mutations detected, 14408C>T and 23403A>G mutations resulting in RNA-dependent RNA polymerase (RdRp) P323L and spike protein D614G mutations, respectively, were found predominantly in severely affected group (>82%) compared with mildly affected group (<46%, p < 0.001). The 241C>T mutation in the non-coding region of the genome was also found predominantly in severely affected group (p < 0.001). The 3037C>T, a silent mutation, also appeared in relatively high frequency in severely affected group compared with mildly affected group, but the difference was not statistically significant (p = 0.06). We concluded that spike protein D614G and RdRp P323L mutations in SARS-CoV-2 are associated with severity of COVID-19. Further studies will be required to explore whether these mutations have any impact on the severity of disease.

• IMMUNE NETWORK
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• v.20 no.5
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• pp.41.1-41.11
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• 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is a positive-sense single-stranded RNA (+ssRNA) that causes coronavirus disease 2019 (COVID-19). The viral genome encodes twelve genes for viral replication and infection. The third open reading frame is the spike (S) gene that encodes for the spike glycoprotein interacting with specific cell surface receptor - angiotensin converting enzyme 2 (ACE2) - on the host cell membrane. Most recent studies identified a single point mutation in S gene. A single point mutation in S gene leading to an amino acid substitution at codon 614 from an aspartic acid 614 into glycine (D614G) resulted in greater infectivity compared to the wild type SARS-CoV2. We were interested in investigating the mutation region of S gene of SARS-CoV2 from Korean COVID-19 patients. New mutation sites were found in the critical receptor binding domain (RBD) of S gene, which is adjacent to the aforementioned D614G mutation residue. This specific sequence data demonstrated the active progression of SARS-CoV2 by mutations in the RBD of S gene. The sequence information of new mutations is critical to the development of recombinant SARS-CoV2 spike antigens, which may be required to improve and advance the strategy against a wide range of possible SARS-CoV2 mutations.

• Pediatric Infection and Vaccine
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• v.31 no.1
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• pp.83-93
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• 2024

Purpose: Since the start of the coronavirus disease 2019 (COVID-19) pandemic, various variants of concern have emerged. We divided the representative COVID-19 mutation period into four waves and aimed to analyze the clinical and laboratory features of children with COVID-19 from pre-mutation wave to the middle of omicron wave. Methods: We retrospectively reviewed the medical records of hospitalized patients aged ≤19 years with laboratory confirmed COVID-19. Clinical and laboratory findings during pre-mutation (February 1st 2020 to September 30th 2020), alpha/beta (October 1st 2020 to May 31st 2021), delta (June 1st 2021 to October 31st 2021), and omicron (November 1st 2021 to May 31st 2022) waves were compared. Results: Among total 827 patients, 163 (19.7%) were asymptomatic, and the frequency of fever and cough was 320 (38.7%) and 399 (48.2%), respectively. The proportion of fever ≥38.5℃ was observed to be high during the omicron wave in the age group under 12 years. Lymphopenia was observed highly in the omicron wave in the age group under 12 years, and in the delta wave in the age group older than 12 years. Neutropenia was highly observed in the delta wave in the 0-4 years age group. Conclusions: There were distinct characteristics during all epidemic waves of COVID-19. Children with COVID-19 had more frequent persistent fever during delta wave and children during the omicron wave had a higher peak fever.

• Genomics & Informatics
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• v.19 no.3
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• pp.23.1-23.7
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• 2021

Currently, coronavirus disease 2019 (COVID-19) literature has been increasing dramatically, and the increased text amount make it possible to perform large scale text mining and knowledge discovery. Therefore, curation of these texts becomes a crucial issue for Bio-medical Natural Language Processing (BioNLP) community, so as to retrieve the important information about the mechanism of COVID-19. PubAnnotation is an aligned annotation system which provides an efficient platform for biological curators to upload their annotations or merge other external annotations. Inspired by the integration among multiple useful COVID-19 annotations, we merged three annotations resources to LitCovid data set, and constructed a cross-annotated corpus, LitCovid-AGAC. This corpus consists of 12 labels including Mutation, Species, Gene, Disease from PubTator, GO, CHEBI from OGER, Var, MPA, CPA, NegReg, PosReg, Reg from AGAC, upon 50,018 COVID-19 abstracts in LitCovid. Contain sufficient abundant information being possible to unveil the hidden knowledge in the pathological mechanism of COVID-19.

• 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.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.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.25 no.12
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• pp.1756-1761
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• 2021

Although the COVID-19 outbreak that occurred in Wuhan, Hubei around December 2019, seemed to be gradually decreasing, it was gradually increasing as of November 2020 and June 2021, and estimated confirmed cases were 192 million worldwide and approximately 184 thousand in South Korea. The Central Disaster and Safety Countermeasures Headquarters have been taking strong countermeasures by implementing level 4 social distancing. However, as the highly infectious COVID-19 variants, such as Delta mutation, have been on the rise, the number of daily confirmed cases in Korea has increased to 1,800. Therefore, the number of cumulative confirmed COVID-19 cases is predicted using ARIMA algorithms to emphasize the severity of COVID-19. In the process, differences are used to remove trends and seasonality, and p, d, and q values are determined and forecasted in ARIMA using MA, AR, autocorrelation functions, and partial autocorrelation functions. Finally, forecast and actual values are compared to evaluate how well it was forecasted.

• Journal of Microbiology and Biotechnology
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• v.30 no.7
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• pp.962-966
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• 2020

Monitoring the mutation dynamics of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in understanding its infectivity, virulence and pathogenicity for development of a vaccine. In an "age of mobility," the pandemic highlights the importance and vulnerability of regionalization and labor market interdependence in Southeast Asia. We intend to characterize the genetic variability of viral populations within the region to provide preliminary information for regional surveillance in the future. By analyzing 142 complete genomes from South East Asian (SEA) countries, we identified three central variants distinguished by nucleotide and amino acid changes.

• Journal of Life Science
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• v.33 no.2
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• pp.199-207
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• 2023

To prepare for the threat of a future epidemic in the post-COVID-19 era, research based on the one-health concept (i.e., the health of humans, animals, and the environment as "one") is essential. Cross-species infections are being identified as a result of the high infection rate and viral load of SARS-CoV-2 in humans. The possibility of transmission of SARS-CoV-2 from humans to mink has been determined. In addition, the transmission of SARS-CoV-2 from humans to cats through contact has been considered possible. The data so far show that livestock and poultry are less likely to be infected with SARS-CoV-2. However, if infections are established through a new mutation, the resulting diseases are expected to have enormous ripple effects on various fields, such as human food security, the economy, and trade. In addition, there are concerns about the endemic prospect of SARS-CoV-2 and the high accessibility of companion animals. This is because the evolution of the virus likely occurs in animal hosts. Once SARS-CoV-2 is established in other species, they might serve as intermediate hosts for the re-emergence of the virus in the human population. Thus, it is necessary to ensure a rapid response to future outbreaks by accumulating research data on the animal infection of SARS-CoV-2. These data can have implications for the development of animal models for vaccines and therapeutics against SARS-CoV-2. Therefore, in this study, epidemiological reviews were analyzed, and response strategies against SARS-CoV-2 infection in animals were presented using the One-health approach.

• Journal of agricultural medicine and community health
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• v.47 no.2
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• pp.61-66
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• 2022

Objectives: In the epidemiology of communicable diseases, the term epidemic period, also referred to as "wave" is often used in the general and academic milieu. A wave refers to a natural pattern of increase in the number of sick individuals, a defined peak, and then a decline in the number of cases. It implies a pattern of peaks and valleys after a particular peak is taken. The idea of epidemic waves is a useful tool for predicting the course as well as helping to accurately describe an epidemic. However, in many domestic and foreign news as well as in various research results in Korea, most of the reports either had no standard, were inaccurate, had a questionable classification of the period of the epidemic, or the basis for classification of a given wave was not presented. Methods: The author reviewed and organized related literature with epidemic wave. The author made several suggestions of an epidemic wave as follows. Results: To start with, it should be based on the number of incident cases in consideration of the size of the outbreak, then the period from the bottom to the peak and then reaching the next bottom; also, the period over a certain scale based on the number of incident cases; and the period according to the change in the major infection type (mutation-dominant species). In addition, according to the period of change in the vaccination rate (formation of herd immunity), as well as the content and duration of the intervention, that is, classification according to the applied quarantine stage. Furthermore, the classification of epidemic periods by the time-dependent reproduction number or time-varying reproduction number (Rt), and lastly the application of mathematical methodology. Conclusions: Therefore, classifying the epidemic period into generally known and accepted time frames is considered to be a very important task for future research analysis and development of intervention strategies.