• Genomics & Informatics
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• 제19권4호
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• pp.48.1-48.10
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• 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes small envelope protein (E) that plays a major role in viral assembly, release, pathogenesis, and host inflammation. Previous studies demonstrated that pyrazine ring containing amiloride analogs inhibit this protein in different types of coronavirus including SARS-CoV-1 small envelope protein E (SARS-CoV-1 E). SARS-CoV-1 E has 93.42% sequence identity with SARS-CoV-2 E and shared a conserved domain NS3/small envelope protein (NS3_envE). Amiloride analog hexamethylene amiloride (HMA) can inhibit SARS-CoV-1 E. Therefore, we performed molecular docking and dynamics simulations to explore whether amiloride analogs are effective in inhibiting SARS-CoV-2 E. To do so, SARS-CoV-1 E and SARS-CoV-2 E proteins were taken as receptors while HMA and 3-amino-5-(azepan-1-yl)-N-(diaminomethylidene)-6-pyrimidin-5-ylpyrazine-2-carboxamide (3A5NP2C) were selected as ligands. Molecular docking simulation showed higher binding affinity scores of HMA and 3A5NP2C for SARS-CoV-2 E than SARS-CoV-1 E. Moreover, HMA and 3A5NP2C engaged more amino acids in SARS-CoV-2 E. Molecular dynamics simulation for 1 ㎲ (1,000 ns) revealed that these ligands could alter the native structure of the proteins and their flexibility. Our study suggests that suitable amiloride analogs might yield a prospective drug against coronavirus disease 2019.

• 생명과학회지
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• 제30권8호
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• pp.731-741
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• 2020

코로나바이러스감염증-19(COVID-19)는 SARS-CoV-2에 의해 발병된다. 지금까지 인간에게 감염되는 7 가지 종류의 코로나 바이러스가 보고되었다. 그 중, HCoV-229E, HCoV-OC43, HCoV-NL63, 그리고 HCoV-HKU1 등 4종류의 코로나바이러스는 감기와 같은 단순 호흡기 질환을 유발한다고 보고되었다. 반면, SARS-CoV는 2002년에, MERS-CoV는 2012년에 각각 대유행을 일으킨 바 있다. 가장 최근에는 2019년 12월 중국 우한에서 처음 보고된 SARS-CoV-2가 전세계적인 대유행의 원인이 되고 있다. 이러한 SARS-CoV-2를 진단하고, 치료하고, 예방하기 위해서는 신속 정확한 진단키트, 치료제, 그리고 안전한 백신의 개발의 필수적으로 요구된다. 이러한 강력한 도구들을 개발하기 위해서는 SARS-CoV-2의 표현형, 유전자형, 그리고 생활주기 등의 연구가 선행되어야 한다. SARS-CoV-2의 진단기술은 현재 크게 두가지의 큰 분야인 분자진단과 면역혈청학적 진단으로 구분할 수 있다. 분자진단의 경우 SARS-CoV-2의 유전체를 대상으로 하며, 면역혈청학적 진단은 SARS-CoV-2의 항원 단백질 혹은 SARS-CoV-2에 대한 항체를 대상으로 한다. 본 총설에서는 SARS-CoV-2의 표현형, 유전체 구조, 그리고 유전자 발현에 대해서 정리하고, SARS-CoV-2에 대한 다양한 진단 기술 등에 대한 기초지식을 제공하고자 한다.

• 대한의생명과학회지
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• 제27권4호
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• pp.283-290
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• 2021

Severe acute respiratory syndrome coronavirus (SARS-CoV2) is a major coronavirus that infects humans with human Coronavirus (HuCoV)-229E, HCoV-OC43, HCoV-HKU1, HCoV-NL63, Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle east respiratory syndrome coronavirus (MERS-CoV). SARS-CoV2 is currently a global pandemic pathogen. In this study, we developed conventional RT-PCR based diagnostic system for the detection of SARS-CoV2 which is relatively inexpensive but has high stability and a wide range of users. Three conventional RT-PCR primer sets capable of forming specific band sizes by targeting the ORF1ab [232 nucleotide (nt)], E (200 nt) and N (288 nt) genes of SARS-CoV2 were developed, respectively, and it were confirmed to be about 10~100 times higher detection sensitivity than the previously reported methods. In addition, a standard positive control that can generate specific amplicons by reacting with the developed RT-PCR primers and verify the false-positiv from contamination of the laboratory was produced. Therefore, the diagnostic system that uses the RT-PCR method is expected to be used to detect SARS-CoV2.

• Journal of Veterinary Science
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• 제22권1호
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• pp.12.1-12.11
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• 2021

Background: Bats have been considered natural reservoirs for several pathogenic human coronaviruses (CoVs) in the last two decades. Recently, a bat CoV was detected in the Republic of Korea; its entire genome was sequenced and reported to be genetically similar to that of the severe acute respiratory syndrome CoV (SARS-CoV). Objectives: The objective of this study was to compare the genetic sequences of SARS-CoV, SARS-CoV-2, and the two Korean bat CoV strains 16BO133 and B15-21, to estimate the likelihood of an interaction between the Korean bat CoVs and the human angiotensin-converting enzyme 2 (ACE2) receptor. Methods: The phylogenetic analysis was conducted with the maximum-likelihood (ML) method using MEGA 7 software. The Korean bat CoVs receptor binding domain (RBD) of the spike protein was analyzed by comparative homology modeling using the SWISS-MODEL server. The binding energies of the complexes were calculated using PRODIGY and MM/GBGA. Results: Phylogenetic analyses of the entire RNA-dependent RNA polymerase, spike regions, and the complete genome revealed that the Korean CoVs, along with SARS-CoV and SARS-CoV-2, belong to the subgenus Sarbecovirus, within BetaCoVs. However, the two Korean CoVs were distinct from SARS-CoV-2. Specifically, the spike gene of the Korean CoVs, which is involved in host infection, differed from that of SARS-CoV-2, showing only 66.8%-67.0% nucleotide homology and presented deletions within the RBD, particularly within regions critical for cross-species transmission and that mediate interaction with ACE2. Binding free energy calculation revealed that the binding affinity of Korean bat CoV RBD to hACE2 was drastically lower than that of SARS-CoV and SARS-CoV-2. Conclusions: These results suggest that Korean bat CoVs are unlikely to bind to the human ACE2 receptor.

• IMMUNE NETWORK
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• 제21권5호
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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.

• IMMUNE NETWORK
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• 제21권1호
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• pp.2.1-2.11
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• 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes coronavirus disease 2019 (COVID-19), an ongoing pandemic disease. In the current review, we describe SARS-CoV-2-specific CD4⁺ and CD8⁺ T-cell responses in acute and convalescent COVID-19 patients. We also discuss the relationships between COVID-19 severity and SARS-CoV-2-specific T-cell responses and summarize recent reports regarding SARS-CoV-2-reactive T cells in SARS-CoV-2-unexposed individuals. These T cells may be cross-reactive cells primed by previous infection with human common-cold coronaviruses. Finally, we outline SARS-CoV-2-specific T-cell responses in the context of vaccination. A better understanding of SARS-CoV-2-specific T-cell responses is needed to develop effective vaccines and therapeutics.

• IMMUNE NETWORK
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• 제21권1호
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• pp.3.1-3.16
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• 2021

Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading worldwide since its outbreak in December 2019, and World Health Organization declared it as a pandemic on March 11, 2020. SARS-CoV-2 is highly contagious and is transmitted through airway epithelial cells as the first gateway. SARS-CoV-2 is detected by nasopharyngeal or oropharyngeal swab samples, and the viral load is significantly high in the upper respiratory tract. The host cellular receptors in airway epithelial cells, including angiotensin-converting enzyme 2 and transmembrane serine protease 2, have been identified by single-cell RNA sequencing or immunostaining. The expression levels of these molecules vary by type, function, and location of airway epithelial cells, such as ciliated cells, secretory cells, olfactory epithelial cells, and alveolar epithelial cells, as well as differ from host to host depending on age, sex, or comorbid diseases. Infected airway epithelial cells by SARS-CoV-2 in ex vivo experiments produce chemokines and cytokines to recruit inflammatory cells to target organs. Same as other viral infections, IFN signaling is a critical pathway for host defense. Various studies are underway to confirm the pathophysiological mechanisms of SARS-CoV-2 infection. Herein, we review cellular entry, host-viral interactions, immune responses to SARS-CoV-2 in airway epithelial cells. We also discuss therapeutic options related to epithelial immune reactions to SARS-CoV-2.

• Genomics & Informatics
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• 제18권3호
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• pp.30.1-30.7
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• 2020

The novel coronavirus pandemic that has originated from China and spread throughout the world in three months. Genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) predecessor, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) play an important role in understanding the concept of genetic variation. In this paper, the genomic data accessed from National Center for Biotechnology Information (NCBI) through Molecular Evolutionary Genetic Analysis (MEGA) for statistical analysis. Firstly, the Bayesian information criterion (BIC) and Akaike information criterion (AICc) are used to evaluate the best substitution pattern. Secondly, the maximum likelihood method used to estimate of transition/transversions (R) through Kimura-2, Tamura-3, Hasegawa-Kishino-Yano, and Tamura-Nei nucleotide substitutions model. Thirdly and finally nucleotide frequencies computed based on genomic data of NCBI. The results indicate that general times reversible model has the lowest BIC and AICc score 347,394 and 347,287, respectively. The transition/transversions bias for nucleotide substitutions models varies from 0.56 to 0.59 in MEGA output. The average nitrogenous bases frequency of U, C, A, and G are 31.74, 19.48, 28.04, and 20.74, respectively in percentages. Overall the genomic data analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV highlights the close genetic relationship.

• Journal of Microbiology
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• 제44권1호
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• pp.83-91
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• 2006

The sudden appearance and potential lethality of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) in humans has resulted in a focusing of new attention on the determination of both its origins and evolution. The relationship existing between SARS-CoV and other groups of coronaviruses was determined via analyses of phylogenetic trees and comparative genomic analyses of the coronavirus genes: polymerase (Orflab), spike (S), envelope (E), membrane (M) and nucleocapsid (N). Although the coronaviruses are traditionally classed into 3 groups, with SARS-CoV forming a $4^{th}$ group, the phylogenetic position and origins of SARS-CoV remain a matter of some controversy. Thus, we conducted extensive phylogeneitc analyses of the genes common to all coronavirus groups, using the Neighbor-joining, Maximum-likelihood, and Bayesian methods. Our data evidenced largely identical topology for all of the obtained phylogenetic trees, thus supporting the hypothesis that the relationship existing between SARS-CoV and group 2 coronavirus is a monophyletic one. Additional comparative genomic studies, including sequence similarity and protein secondary structure analyses, suggested that SARS-Co V may bear a closer relationship with group 2 than with the other coronavirus groups. Although our data strongly suggest that group 2 coronaviruses are most closely related with SARS-CoV, further and more detailed analyses may provide us with an increased amount of information regarding the origins and evolution of the coronaviruses, most notably SARS-CoV.

• IMMUNE NETWORK
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• 제21권2호
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• pp.12.1-12.17
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• 2021

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the emergence of SARS-CoV-2 in the human population in late 2019, it has spread on an unprecedented scale worldwide leading to the first coronavirus pandemic. SARS-CoV-2 infection results in a wide range of clinical manifestations from asymptomatic to fatal cases. Although intensive research has been undertaken to increase understanding of the complex biology of SARS-CoV-2 infection, the detailed mechanisms underpinning the severe pathogenesis and interactions between the virus and the host immune response are not well understood. Thus, the development of appropriate animal models that recapitulate human clinical manifestations and immune responses against SARS-CoV-2 is crucial. Although many animal models are currently available for the study of SARS-CoV-2 infection, each has distinct advantages and disadvantages, and some models show variable results between and within species. Thus, we aim to discuss the different animal models, including mice, hamsters, ferrets, and non-human primates, employed for SARS-CoV-2 infection studies and outline their individual strengths and limitations for use in studies aimed at increasing understanding of coronavirus pathogenesis. Moreover, a significant advantage of these animal models is that they can be tailored, providing unique options specific to the scientific goals of each researcher.