• Genomics & Informatics
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• 제18권4호
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• pp.43.1-43.13
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• 2020

The coronavirus disease 2019 is a contagious disease and had caused havoc throughout the world by creating widespread mortality and morbidity. The unavailability of vaccines and proper antiviral drugs encourages the researchers to identify potential antiviral drugs to be used against the virus. The presence of RNA binding domain in the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be a potential drug target, which serves multiple critical functions during the viral life cycle, especially the viral replication. Since vaccine development might take some time, the identification of a drug compound targeting viral replication might offer a solution for treatment. The study analyzed the phylogenetic relationship of N protein sequence divergence with other 49 coronavirus species and also identified the conserved regions according to protein families through conserved domain search. Good structural binding affinities of a few natural and/or synthetic phytocompounds or drugs against N protein were determined using the molecular docking approaches. The analyzed compounds presented the higher numbers of hydrogen bonds of selected chemicals supporting the drug-ability of these compounds. Among them, the established antiviral drug glycyrrhizic acid and the phytochemical theaflavin can be considered as possible drug compounds against target N protein of SARS-CoV-2 as they showed lower binding affinities. The findings of this study might lead to the development of a drug for the SARS-CoV-2 mediated disease and offer solution to treatment of SARS-CoV-2 infection.

• 한국동물위생학회지
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• 제45권3호
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• pp.211-219
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• 2022

Bovine viral diarrhea (BVD) is one of the problematic wasting diseases in cattle leading to huge economic losses. This study was conducted to investigate the prevalence of BVD including transient and persistent infection from cattle farms in Gyeongsangnam-do. A total of 2,667 blood samples from 24 farms were collected and the sera were subjected to ELISA to detect BVD virus (BVDV) antigen, E^rns. 5' untranslated region (5'-UTR) of BVDV-positive samples was sequenced to identify the genotype, and compared with isolates previously reported elsewhere. There were fourteen BVDV-positive calves from 2,667 samples (positive rate: 0.52%) from first ELISA testing followed by eight persistently infected out of eleven BVDV-positive samples (72.73%) in secondary ELISA that was conducted in at least four weeks suggesting the circulation of BVDV in the area. Sequencing analysis exhibited that thirteen BVDV-positive samples were identified as BVDV-1b and one sample was BVDV-2a. Phylogenetic analysis revealed that the BVDV-1b-positive samples showed the highest homology in nucleotide sequence to Korean isolates collected from Sancheong, Gyeongsangnam-do, while the BVDV-2a-positive sample (21GN7) was more similar to reference strains collected outside South Korea. This study will provide the recent fundamental data on BVD prevalence in Gyeongsangnam-do to be referred in developing strategies to prevent BVDV in South Korea.

• The Plant Pathology Journal
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• 제35권1호
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• pp.41-50
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• 2019

Sugarcane bacilliform viruses (SCBV), which belong to the genus Badnavirus, family Caulimoviridae, are an important DNA virus complex that infects sugarcane. To explore the genetic diversity of the sugarcane-infecting badnavirus complex in China, we tested 392 sugarcane leaf samples collected from Fujian, Yunnan, and Hainan provinces for the occurrence of SCBV by polymerase chain reaction (PCR) assays using published primers SCBV-F and SCBV-R that target the reverse transcriptase/ribonuclease H (RT/RNase H) regions of the viral genome. A total of 111 PCR-amplified fragments (726 bp) from 63 SCBV-positive samples were cloned and sequenced. A neighbor-joining phylogenetic tree was constructed based on the SCBV sequences from this study and 34 published sequences representing 18 different phylogroups or genotypes (SCBV-A to -R). All SCBV-tested isolates could be classified into 20 SCBV phylogenetic groups from SCBV-A to -T. Of nine SCBV phylogroups reported in this study, two novel phylogroups, SCBV-S and SCBV-T, that share 90.0-93.2% sequence identity and show 0.07-0.11 genetic distance with each other in the RT/RNase H region, are proposed. SCBV-S had 57.6-92.2% sequence identity and 0.09-0.66 genetic distance, while SCBV-T had 58.4-90.0% sequence identity and 0.11-0.63 genetic distance compared with the published SCBV phylogroups. Additionally, two other Badnavirus species, Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV), which originally clustered in phylogenetic groups SCBV-E and SCBV-F, respectively, are first reported in China. Our findings will help to understand the level of genetic heterogeneity present in the complex of Badnavirus species that infect sugarcane.

• 한국어병학회지
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• 제26권3호
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• pp.149-161
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• 2013

바이러스성 출혈성 패혈증을 일으키는 VHSV는 국내의 넙치양식에 심각한 피해를 주고 있다. 본 연구에서는 우리나라에서 분리한 8종의 VHSV 분리주들의 glycoprotein (G)의 염기서열을 분석하여 Korean VHSV 분리주들과 기보고된 일본 및 중국의 분리주들을 계통발생학적으로 비교하여 G-protein의 8 부위(G34, C528, A755, T834, T951, T1147, T1221, T1336)에서 국내 VHSV 분리주들의 특이적인 서열을 확인하였고, 전 세계적으로 분리된 VHSV의 분리주들과의 비교결과 8 부위 중 3 부위 (A755, T834, T1221)의 국내VHSV 분리주 특이적 염기서열들을 확인하였다. 또한 중국 유래 VHSV 분리주의 특이적 염기서열 11 부위 (C498, C545, C548, C642, G648, T678, A738, C804, C834, G851, C1139)와 일본 유래 VHSV 분리주의 특이적 염기서열 1부위 (C179)를 확인하였다. 이상의 연구결과는 국내 특이적인 염기서열을 확보하여, 구역화된 수산생물 질병의 예찰, 모니터링 및 질병 관리에 유용하게 사용될 것으로 사료된다.

• 농업과학연구
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• 제45권1호
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• pp.38-42
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• 2018

Demand for tomatoes has been increasing every year as people desire more healthy food. In Korea, tomatoes are mainly grown in the Chungnam, Chunnam and Kyungnam provinces. Recently, reports of whitefly-transmitted viral diseases have increased due to newly emerging whitefly pressures caused by climate change in Korea. Specifically, in 2017, the main tomato growing areas, Buyeo and Nonsan in Chungnam, showed damage typical of viral infection; therefore, we investigated viral diseases in these areas. We collected samples with virus-like symptoms and found that not only whitefly transmitted Tomato yellow leaf curl virus (TYLCV) and Tomato chlorosis virus (ToCV) were detected but also Tomato mosaic virus (ToMV, for which no specific vector is known) and Tomato spotted wilt virus (TSWV, transmitted by thrips). The ToMV-infected samples were mostly co-infected with either TYLCV or ToCV. Mixed infections of different combinations of TYLCV, ToCV and ToMV were detected with the mixed infection of two whitefly-transmitted viruses (TYLCV and ToCV) causing the most severe symptoms. According to the CP sequence of each virus, the 100% identities were shown to be Mexico/ABG73017.1 (TYLCV), Greece/CDG34553.1 (ToCV), China/AKN79752 (TSWV), and Australia/NP078449.1 (ToMV). Based on the sequence data, we presumed that these tomato infecting viruses were transmitted through insects and seeds introduced from neighboring countries.

• 대한바이러스학회지
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• 제28권1호
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• pp.31-38
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• 1998

In Korea, all domestic made test systems for detecting antibodies in HIV-1 contain the antigens from human immunodeficiency type 1 (HIV-1) subtype B. However, because HIV-1 subtype O is significantly different in amino acid sequences from all other subtypes of HIV-1, there has been a need for developing a test for detecting antibodies in subtype O. For this purpose, the entire nucleotide sequence corresponding to the extracellular domain of the transmembrane glycoprotein of HIV-1 subtype O was synthesized with consideration of Escherichia coli condon usage. Various regions of the extracellular domain were cloned into E. coli expression vectors and tested for levels of protein production. The nucleotide sequence, named ECTM, that can encode a 129 amino acid-long peptide, was found to be expressed at a high level in E. coli. The protein of approximately 17 kDa specifically reacted with sera from individuals infected with HIV-1 subtype O. The ECTM protein was purified to near homogeneity by the CM-T gel chromatography, using concentrated, denatured inclusion bodies. In Western blot analysis, the purified viral antigen reacted with sera from individuals infected with subtype O more efficiently than subtype B. The enzyme linked immunoabsorbent assay (ELISA) system was developed using the subtype O viral protein and compared with the commercially available kit lacking the antigens from subtype O. The ELISA kit containing the subtype O antigen ECTM alone efficiently reacted with sera from individuals infected with subtype O. The subtype O antigen-containing kit produced a positive absorbence even when sera were diluted 512-fold, suggesting a high sensitivity. The commercially available kit also reacted with subtype O sera, but produced a negative result at a dilution of 8-fold. Our results suggest that the currently available kit may not be able to efficiently detect subtype O sera and that the viral protein developed in this study may be added to the current system to maximize the detection of sera from individuals infected with subtype O.

• 한국어병학회지
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• 제10권2호
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• pp.87-95
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• 1997

새우의 갑각에 흰점을 유발하는 특징을 가진 WSBV는 Baculovirus의 일종으로 여러 종류의 새우에 높은 치사율을 보이는 병원체로서 새우양식에 막대한 피해를 주고 있다. 본 연구에서는 국내에서 양식중인 대하에 질병을 유발한 WSBV의 특성을 알아내고자 치사한 새우로부터 바이러스의 게놈을 클로닝하여 재조합클론(E3)을 분자생물학적으로 분석하였다. E3의 염기서열을 분석한 결과, 이 클론은 AcNPV를 포함한 지금까지 알려진 어떠한 바이러스와도 뚜렷한 상동성(60%)을 보이지 않아 WSBV가 기존의 바이러스와 구분되는 새로운 바이러스임을 알 수 있다. E3의 염기서열에 기초하여 한쌍의 PCR 프라이머를 작성하였다. 병든 새우로부터 분리한 DNA를 30회 증폭한 결과, 예상크기의 산물을 얻을 수 있어 이 방법은 바이러스의 감염여부를 알아낼 수 있는 진단법으로도 활용가능하다.

• Journal of Microbiology and Biotechnology
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• 제8권6호
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• pp.676-684
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• 1998

Baculovirus transfer and expression vectors with Hyphantria cunea nuclear polyhedrosis virus (HcNPV) were constructed. An initial transfer vector, pHcEV, constructed using HcNPV was previously reported (Park et al. 1993. J. Kor. Soc. Viral. 23: 141-151). Herein, the size of the vector was properly reduced, and a functionally perfect vector was constructed and named pHcEV-IV (6.7 kb). The vector has a 2.2-kb HcNPV DNA sequence in the 5'-flanking region of the vector's polyhedrin gene promoter. The 1.8-kb HcNPV DNA sequence, poly A signal sequence, T3 primer sequence, and 13 multicloning site sequences, in order, were ligated in front of the translation start codon of the polyhedrin gene. The cloning indicating marker lacZ gene was inserted into the pHcEV-IV, named pHcEV-IV-lacZ, and transferred into the wild-type virus. Recombinant expression virus, lacZ-HcNPV, was constructed by replacing the lacZ gene in the pHcEV-IV-lacZ with the polyhedrin gene of the wild-type virus. The recombinant virus was isolated from blue plaques that produce $\beta$-galactosidase without polyhedra. The lacZ gene insertion was confirmed by Southern hybridization analysis. The expression of the lacZ gene in Spodoptera frugiperda cells infected with the lacZ-HcNPV was examined by SDS-PAGE and colorimetric assay. One 116-kDa LacZ protein band appeared on the PAGE. The production rate of the $\beta$-galactosidase was approximately 50 international units (IU) per min per ml between 2 to 5 days postinfection (p.i.). The highest activity occurred at five days p.i. was 170 IU/min/$m\ell$. The enzyme activity first appeared about 20 h p.i. as measured by colorimetric assay.

• 한국잠사학회:학술대회논문집
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• 한국잠사학회 1997년도 Progress and Future Development of Sericultural Science and Technology 40th Anniversary Commemoration Symposium
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• pp.73-101
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• 1997

Baculoviruses are characterized by large double-stranded circular DNA genomes and rod-shaped enveloped virions. Bombyx mori nucleopolyhedrovirus(BmNPV) is a major pathogen, which causes severe damage in sericulture. Currently, BmNPV is recogtnized as an improtant tool in molecular biology, especially for expression of useful genes in B.mori cells and silkworm larvae. Our laboratories have focused on the studies of the molecular mechanisms of BmNPV replication and the application of BmNPV to agriculture and medicine. The entire nucleotide sequence of the BmNPV genome has recently determined. The BmNPV genome possessed 135 putative genes and 7 homologous repeated sequence (hrs) regions. Relatively little space, a few to a few hundred base-pairs, was observed between the open reading frames and hrs. Termination codons often overlapped. These results showed a compactly packde BmNPV genome. Based on comparative sequence analyses, we speculated that the ancestor of BmNPV was a baculovirus similar to Autographa californica NPV(AcNPV). The function of the BmNPV genes were characterized by gene deletion analysis; p35 was found to be involved in blocking apoptosis and cysteine proteinase was found to be involved in horizontal virus transmission by degrading viral-infected larval host. By AcNPV and BmNPV coinfection experiments, we identified a BmNPV gene involved in expanding host specificity of AcNPV. The identified gene was likely encoded a DNA helicase based on the amino acid sequence analysis; a few amino acid substitutions in the putative DNA helicase gene resulted in the expansion of host range of AcNPV. These findings indicate that BmNPV evolved within a short period from an AcNPV-like ancestral virus due to rapid evolution including specific amino acid substitutions and gene deletions/insertions.

• Pediatric Infection and Vaccine
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• 제7권1호
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• pp.83-93
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• 2000

목 적 : Urabe AM-9 볼거리 백신주는 무균성 뇌막염의 발생 빈도가 높은 것으로 알려져 있다. 백신 접종 후 무균성 뇌막염을 일으키는 경우 Urabe AM-9 백신주의 hemagglutinin-neuraminidase(HN) 유전자의 염기서열 1081번의 G가 A로 치환되어 335번째 아미노산이 glutamic acid에서 lysine으로 바뀌게 됨에 따라 야생형의 mumps 바이러스와 동일한 작용을 나타내는 것으로 알려져 있다. 이에 국내에서 사용중인 Urabe AM-9 백신주의 안전성 여부를 조사하기 위해 일부 백신주와 야생 분리주의 HN 유전자의 염기서열 분석을 실시하였다. 방 법 : 국내에서 사용되고있는 Urabe AM-9주 백신 2종류와 1998~1999년에 볼거리 환자로부터 분리된 야생 분리주를 이용하여 RT-PCR 방법에 의해 HN 유전자를 증폭시킨 후 염기 및 아미노산 서열 분석을 실시하였다. 결 과 : 백신주와 야생 분리주 모두 HN 343, 1476, 1570번 위치에서의 염기 변이는 없었으나 1081번 위치 염기는 모두 야생주와 같은 Lysine/AAA form으로 나타났으며 변이주인 Glutamic acid/GAA와의 혼합 양상은 관찰되지 않았다. HN 1470번 위치의 염기는 백신주 중 계대 배양시 C에서 A로 치환되었으며, HN 1727번 위치 염기는 모두 A에서 G로 치환된 것으로 나타났다. 결 론 : 국내에서 사용중인 2종류의 Urabe AM-9 백신주와 야생 분리주 모두 1081번 위치의 염기가 야생주와 같은 무균성 뇌막염을 일으킬 생물학적 가능성이 있는 것으로 나타났으며, 국내에서도 상기 백신주를 사용한 후 무균성 뇌막염이 발생하고 있을 개연성이 매우 크다고 사료되며 직접적인 연관성에 대한 보완 연구를 위하여 정확하고 믿을만한 자료에 의한 실제 부작용 실태를 파악하여야 한다.