Bovine viral diarrhea virus (BVDV) is a major pathogen that may be one of the main reasons for economic losses in the livestock industry. BVDV is a well-characterized member of Flaviviridae family with plus-stranded RNA viruses. Non-structural NS5B protein is RNA-dependent RNA polymerase, which is responsible for viral RNA synthesis and genome replication of BVDV. Therefore, the NS5B polymerase is a key target for the discovery of anti-BVDV drugs. A number of small-molecule inhibitors against the NS5B polymerase have been reported in literature of which we collected series molecules having various scaffold with their biological data determined by evident experimental conditions, methods and procedures. Then, we constructed database of 655 small-molecule NS5B inhibitors having definitive activity values, structural parameters, and physicochemical properties (such as molecular hydrophobicity, hydrophilicity, polarity, Hbond donors and H-bond acceptors) associated with their absorption and permeability through a cheminformatics approach. The database was opened to provide insight for allosteric NS5B inhibitors of BVDV with an accessible platform on the web (http://nabic.rda.go.kr/chemical genomic database/BVDV RNA dependent RNA polymerase inhibitors). This molecular information in the database would be useful in attempting to identify features and decision factors that enhance anti-BVDV activity or increase selectivity of the allosteric inhibitor. These anti-BVDV molecules could also be screening for the purpose of exploiting potent NS5B inhibitors in the same family (e.g., HCV, CSFV, YFV, WNV, and DENV).

Bromoviridae과 Cucumovirus속에 속하는 대표 바이러스인 오이모자이크바이러스 (Cucumber mosaic virus: CMV)는 많은 경제적으로 중요한 원예작물 및 관상식물들에 심한 손실을 초래하는 바이러스이다. 다중염기서열 비교는 현재까지 서브그룹1에 속하는 모든 CMV 계통들에서 3'말단부의 보전적 염기서열들이 존재하고 있음을 보여주었다. 이런 관찰에 기초하여, 우리는 CMV RNA3와 상동성을 가지는 162 bp 상보적 DNA를 포함하며 CMV감염에 대하여 식물 유래 RNA간섭 현상을 유도할 수 있는 도치된 반복 구조를 가지는 머리핀RNA (pIR-CMVNCR)를 발현시킬 수 있는 벡터를 제작하였다. 아그로박테리움을 이용하여 IR-CMVNCR의 일시 발현은 CMV 감염을 저해하였으며, 아그로박테리움이 접종된 식물의 상엽에서는 CMV 병징이 발현되지 않았다. 또한 RT-PCR결과는 아그로박테리움이 접종된 식물의 접종엽 및 상엽에서 CMV 서브유전자 4를 포함하는 CMV RNA들이 모두 검출이 되지 않았다. CMV 유래 작은 저해 RNA들의 축적이 관찰되었으며, 이의 결과의 의미는 아그로박테리움에 의해 IRCMVNCR을 일시 발현시킨 야생담배 (Nicotiana benthamiana)의 접종엽에서 RNA 간섭 현상이 유도되어 CMV 감염을 억제시키는 것으로 판명되었다.

Sacbood virus (SBV) is an infectious disease, resulting in failure to pupate and death and kSBV is a disease caused perish Apis cerana of 75% in South Korea. RNA dependent RNA Polymerase(RdRP) is one of polyprotein of viral genome and an enzyme that catalyzes the replication of RNA from an RNA templates and an essential protein encoded in the genomes of all RNA containing viruses with no DNA stages. In this study, recombinant construct with RdRP partial region of kSBV was used for sequence analysis to clarify about Korean SBV. As a result it could be determined that the virus develops by infection of Korean Apis cerana called kSBV. Also, we named Apis cerana-kSBV-region to the name of the unique region of gene that kSBV has. In comparison of the RdRP region of bee RNA virus on nucleotide sequence, its sequence from same species have less variability as well as each virus species has a certainty of RdRp region. It indicated that mutations of RdRP region of each virus species is able to be a useful indicator of honeybee virus detection.

Deformed wing virus(DWV) is one of infectious disease of honey bee that is caused to wings of immature or mutation and death at last. In this study 4 kinds of polyprotein of DWV are compared and then selected 2 kinds of polyprotein, RNA-dependent RNA polymerase(RdRP) and peptidase C3G, which has relatively higher homology than others. Analysis of both RdRP region and peptidase C3G of DWV deposited in Genbank of NCBI showed 99~100% and 95~97% of homology on genomic level, respectively whereas analysis of CRPV-capsid and RNA helicase showed 86~98% and 89~98% of homology, repectively. According to the result of gene analysis, two kinds of polyprotein are constructed and analyzed the homology, resulting in RdRP and Peptidase -C3G showed about 96% and 97% of homology, respectively. It indicated that both region is able to use for generation of specific antibody for the diagnosis of Deformed Wing Virus (DWV).

경산 묘목단지는 대단위 과수종묘를 생산하고 있어 경쟁력 강화를 위하여 무독묘 보증 생산이 요구되고 있다. 특히 생산규모가 큰 사과종묘에 대한 빠르고 정확한 바이러스 진단이 시급하다. 본 연구에서는 사과바이러스 진단을 위하여 다량의 시료를 동시 분쇄할 수 있는 bead beater를 이용하였으며 분쇄 bead는 저가의 산업용 glass bead (0.4 mm 직경)를 일회용으로 채택하였다. RNA추출을 위하여서는 guanidine thiocyanate 용액이 Trizol 용액보다 효과적인 것으로 나타났으며 silica membrane tube의 이용으로 RNA추출 간편성을 높일 수 있었다. 사과바이러스는 RT-PCR에 의하여 검증하였다.

The Cmr1 gene in peppers confers resistance to Cucumber mosaic virus isolate-P0 (CMV-P0). Cmr1 restricts the systemic spread of CMV-Fny, whereas this gene cannot block the spread of CMV-P1 to the upper leaves, resulting in systemic infection. To identify the virulence determinant of CMV-P1, six reassortant viruses and six chimeric viruses derived from CMV-Fny and CMV-P1 cDNA clones were used. Our results demonstrate that the helicase domain encoded by CMV-P1 RNA1 determines susceptibility to systemic infection. To identify the key amino acids determining systemic infection with CMV-P1, we then constructed amino acid substitution mutants. Of the mutants tested, amino acid residues at positions 865, 896, 957, and 980 in the 1a protein sequence of CMV-P1 affected the systemic infection. Virus localization studies with CMV-GFP clones and in situ localization of virus RNA revealed that these four amino acid residues together form the movement determinant for CMV-P1 movement from the epidermal cell layer to mesophyll cell layers. Quantitative real-time PCR revealed that CMV-P1 and a chimeric virus with four amino acid residues of CMV-P1 accumulated more genomic RNA in inoculated leaves than did CMV-Fny, indicating that those four amino acids are also involved in virus replication. These results demonstrate that the helicase domain is responsible for systemic infection by controlling virus replication and cell-to-cell movement. Whereas four amino acids are responsible for acquiring virulence in CMV-Fny, six amino acid (positions at 865, 896, 901, 957, 980 and 993) substitutions in CMV-P1 were required for complete loss of virulence in ‘Bukang’.

An isolate of barley yellow mosaic virus(BaYMV-HN) obtained from Haenam, Korea was compared with two BaYMV strains. BaYMV-Ⅱ-1 from Japan and BaYMV-G from Germany. The sequence of the 3'-terminal 3817nucleotides[excluding the poly (A) tail] of RNA 1 of BaYMV-HN was determined to start within a long open reading frame coding for a part of the NIa-VPg polymerase(26 amino acids). NIa-Pro polymerase (343 amino acids), NIb polymerase(528 amino acids) and the entire capsid protein(297 amino acids), which is followed by a noncoding region(NCR) of 235 nucelotides. In the partial ORFs, BaYMV-HN shows higher sequence homology with BaYMV-Ⅱ-1(99.5%) than BaYMV-G(92.7%). The 3' non-coding regions of BaYMV-HN(235nt) shows higher nucleotide sequence homology with BaYMV-G(235nt)(99.6%) than BaYMV-Ⅱ-1(231nt)(97.0%). The 3' NIa-Pro protein sequence of BaYMV-HN shows higher amino acid sequence homology with BaYMV-Ⅱ-1(95.0%) than BaYMV-G(93.6%), but, NIb protein sequence of BaYMV-HN shows same all amino acid sequence. The capsid protein sequence of BaYMV-HN(297aa) shows same with BaYMV-Ⅱ-1, and shows higher nucleotide sequence homology with BaYMV-UK (from United Kingdom)(97.3%) than BaYMV-G(96.9%) and G2(96.9%). Difference of capsid protein amino acid were 0-9 between the Japan, United Kingdom and Germany and were 2-6 between all Korean isolates. Many of the amino acid differences are located in the N-terminal regions of the capsid proteins from 1 to 74 amino acid positions.