• Journal of Preventive Medicine and Public Health
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• v.51 no.6
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• pp.326-328
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• 2018

As over 1000 new cases of HIV/AIDS occur in Korea annually, preventive health programs against HIV/AIDS are urgently needed. Since phylodynamic studies have been suggested as a way to understand how infectious diseases are transmitted and evolve, phylodynamic inferences can be a useful tool for HIV/AIDS research. In particular, phylodynamic models are helpful for dating the origins of an epidemic and estimating its basic reproduction number. Thus, the introduction of phylodynamics would be a highly valuable step towards controlling the HIV/AIDS epidemic in Korea.

• Korean Journal of Poultry Science
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• v.46 no.4
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• pp.263-269
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• 2019

Infectious bronchitis virus (IBV) is an acute respiratory disease, causing economic losses in poultry production. IBV commonly manifests respiratory disease symptoms and poor egg quality in poultry, affecting overall performance of both broilers and layers. IBV infection further predisposes poultry to secondary opportunistic bacterial infections. IBV undergoes rapid genetic evolution resulting in various new strains. There is no cross protection among IBV serotypes which makes full protection against wild-type IBV virtually impossible. In this study, recently isolated IBVs (K24/18, K29/18, K183/18) from Korean broiler farms were genetically analyzed based on S1 gene. According to the results, IBV isolates showed highest homology with QX-IBV. However, phylogenetic tree analysis revealed that isolates were divided into distinct sub-clusters within QX-IBV. To determine pathogenicity of IBV, day-old chicks were challenged with IBV through ocular route. After challenging the chicks, we executed microscopic examination, virus detection in their organs, and observation of clinical signs and mortality. We found that the K24/18, K29/18, K183/18 challenge groups showed 28%, 57%, and 42% mortality, respectively, with high microscopic trachea lesion scores, indicating that these QX-IBV-like strains are pathogenic to chicks and can therefore be a threat to poultry production.

• The Plant Pathology Journal
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• v.37 no.2
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• pp.152-161
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• 2021

Sugar beet (Beta vulgaris L.) is known as a key product for agriculture in several countries across the world. Beet soil-borne virus (BSBV) triggers substantial economic damages to sugar beet by reducing the quantity of the yield and quality of the beet sugars. We conducted the present study to report the complete genome sequences of two BSBV isolates in Turkey for the first time. The genome organization was identical to those previously established BSBV isolates. The tripartite genome of BSBV-TR1 and -TR3 comprised a 5,835-nucleotide (nt) RNA1, a 3,454-nt RNA2, and a 3,005-nt RNA3 segment. According to sequence identity analyses, Turkish isolates were most closely related to the BSBV isolate reported from Iran (97.83-98.77% nt identity). The BSBV isolates worldwide (n = 9) were phylogenetically classified into five (RNA-coat protein read through gene [CPRT], TGB1, and TGB2 segments), four (RNA-rep), or three (TGB3) lineages. In genetic analysis, the TGB3 revealed more genetic variability (Pi = 0.034) compared with other regions. Population selection analysis revealed that most of the codons were generally under negative selection or neutral evolution in the BSBV isolates studied. However, positive selection was detected at codon 135 in the TGB1, which could be an adaptation in order to facilitate the movement and overcome the host plant resistance genes. We expect that the information on genome properties and genetic variability of BSBV, particularly in TGB3, TGB1, and CPRT genes, assist in developing effective control measures in order to prevent severe losses and make amendments in management strategies.

• Journal of Veterinary Science
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• v.23 no.5
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• pp.63.1-63.14
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• 2022

Background: Chicken anemia virus (CAV) causes chicken infectious anemia, which results in immunosuppression; the virus has spread widely in chicken flocks in China. Objectives: The aim of this study was to understand recent CAV genetic evolution in chicken flocks in Guangxi Province, southern China. Methods: In total, 350 liver samples were collected from eight commercial broiler chicken farms in Guangxi Province in southern China from 2018 to 2020. CAV was detected by conventional PCR, and twenty CAV complete genomes were amplified and used for the phylogenetic analysis and recombination analysis. Results: The overall CAV-positive rate was 17.1%. The genetic analysis revealed that 84 CAVs were distributed in groups A, B, C (subgroups C1-C3) and D. In total, 30 of 47 Chinese CAV sequences from 2005-2020 belong to subgroup C3, including 15 CAVs from this study. There were some specific mutation sites among the intergenotypes in the VP1 protein. The amino acids at position 394Q in the VP1 protein of 20 CAV strains were consistent with the characteristics of a highly pathogenic strain. GX1904B was a putative recombinant. Conclusions: Subgroup C3 was the dominant genotype in Guangxi Province from 2018-2020. The 20 CAV strains in this study might be virulent according to the amino acid residue analysis. These data help improve our understanding of the epidemiological trends of CAV in southern China.

• The Plant Pathology Journal
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• v.40 no.1
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• pp.73-82
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• 2024

Gardenia (Gardenia jasminoides) is a popular and economically vital plant known for its ornamental and medicinal properties. Despite its widespread cultivation, there has been no documentation of plant viruses on gardenia yet. In the present study, gardenia leaves exhibiting symptoms of plant viral diseases were sampled and sequenced by both metatranscriptome and small RNA sequencing. As a consequence, bean common mosaic virus (BCMV) was identified in gardenia for the first time and named BCMV-gardenia. The full genome sequence of BCMV-gardenia is 10,054 nucleotides (nt) in length (excluding the poly (A) at the 3' termini), encoding a large polyprotein of 3,222 amino acids. Sequence analysis showed that the N-termini of the polyprotein encoded by BCMV-gardenia is less conserved when compared to other BCMV isolates, whereas the C-termini is the most conserved. Maximum likelihood phylogenetic analysis showed that BCMVgardenia was clustered closely with other BCMV isolates identified outside the leguminous plants. Our results indicated that the majority of BCMV-gardenia virus-derived small interfering RNAs (vsiRNAs) were 21 nt and 22 nt, with 21 nt being more abundant. The first nucleotide at the 5' termini of vsiRNAs derived from BCMV-gardenia preferred U and A. The ratio of vsiRNAs derived from sense (51.1%) and antisense (48.9%) strands is approaching, and the distribution of vsiRNAs along the viral genome is generally even, with some hot spots forming in local regions. Our findings could provide new insights into the diversity, evolution, and host expansion of BCMV and contribute to the prevention and treatment of this virus.

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.2 no.1
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• pp.53-58
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• 2002

In the construction of successful fuzzy models for nonlinear systems, the identification of an optimal fuzzy model system is an important and difficult problem. Traditionally, sGA(simple genetic algorithm) has been used to identify structures and parameters of fuzzy model because it has the ability to search the optimal solution somewhat globally. But SGA optimization process may be the reason of the premature local convergence when the appearance of the superior individual at the population evolution. Therefore, in this paper we propose a new method that can yield a successful fuzzy model using VmGA(virus messy genetic algorithms). The proposed method not only can be the countermeasure of premature convergence through the local information changed in population, but also has more effective and adaptive structure with respect to using changeable length string. In order to demonstrate the superiority and generality of the fuzzy modeling using VmGA, we finally applied the proposed fuzzy modeling methodof a complex nonlinear system.

• The Plant Pathology Journal
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• v.28 no.4
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• pp.381-389
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• 2012

Molecular characterization of Cucumber mosaic virus (CMV) was done by using samples from tomato and cucurbitaceous plants collected from different locations in the northwest region of Iran. After screening by enzyme-linked immunosorbent assay, 91 CMV-infected samples were identified. Biological properties of eight representative isolates were compared with each other revealing two distinct phenotypes on squash and tomato plants. Phylogenetic analyses based on nucleotide sequences of the coat protein (CP), movement protein (MP) and 2b of the new isolates, together with that of previously reported isolates, led to the placement of the Iranian isolates in subgroups IA and IB according to CP and MP genes, but in subgroup IA according to the 2b gene. These data suggest that reassortment may have been a major event in the evolution of CMV in Iran, and that the Iranian isolates are derived from a common recent ancestor that had passed through a bottleneck event.

• The Plant Pathology Journal
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• v.30 no.2
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• pp.195-199
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• 2014

Apple stem pitting virus (ASPV), of the Foveavirus genus in the family Betaflexiviridae, is one of the most common viruses of apple and pear trees. To examine variability of the coat protein (CP) gene from ASPV, eight isolates originating from 251 apple trees, which were collected from 22 apple orchards located in intensive apple growing areas of the North Gyeongsang and North Jeolla Provinces in Korea, were sequenced and compared. The nucleotide sequence identity of the CP gene of eight ASPV isolates ranged from 77.0 to 97.0%, while the amino acid sequence identity ranged from 87.7 to 98.5%. The N-terminal region of the viral CP gene was highly variable, whereas the C-terminal region was conserved. Genetic algorithm recombination detection (GARD) and single breakpoint recombination (SBP) analyses identified base substitutions between eight ASPV isolates at positions 54 and 57 and position 771, respectively. GABranch analysis was used to determine whether the eight isolates evolved due to positive selection. All values in the GABranch analysis showed a ratio of substitution rates at non-synonymous and synonymous sites (dNS/dS) below 1, suggestive of strong negative selection forces during ASPV CP history. Although negative selection dominated CP evolution in the eight ASPV isolates, SLAC and FEL tests identified four possible positive selection sites at codons 10, 22, 102, and 158. This is the first study of the ASPV genome in Korea.

• The Plant Pathology Journal
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• v.32 no.1
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• pp.33-46
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• 2016

In this study, the full-length nucleotide sequences of four Iranian PVY isolates belonging to $PVY^N$ strain were determined. The genome of Iranian PVY isolates were 9,703-9,707 nucleotides long encoding all potyviral cistrons including P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP with coding regions of 825, 1,395, 1,095, 156, 1,902, 156, 564, 732, 1,557 and 801 nucleotides in length, respectively. The length of pipo, embedded in the P3 cistron, was 231 nucleotides. Phylogenetic analysis showed that the Iranian isolates clustered with European recombinant NTN isolates in the N lineage. Recombination analysis demonstrated that Iranian $PVY^N$ isolates had a typical European $PVY^{NTN}$ genome having three recombinant junctions while $PVY^N$ and $PVY^O$ were identified as the parents. We used dN/dS methods to detect candidate amino acid positions for positive selection in viral proteins. The mean ${\omega}$ ratio differed among different genes. Using model M0, ${\omega}$ values were 0.267 (P1), 0.085 (HC-Pro), 0.153 (P3), 0.050 (CI), 0.078 (VPg), 0.087 (NIa-pro), 0.079 (NIb) and 0.165 (CP). The analysis showed different sites within P1, P3 and CP were under positive selection pressure, however, the sites varied among PVY populations. To the best of our knowledge, our analysis provides the first demonstration of population structure of $PVY^N$ strain in mid-Eurasia Iran using complete genome sequences and highlights the importance of recombination and selection pressure in the evolution of PVY.

• Molecules and Cells
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• v.21 no.1
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• pp.63-75
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• 2006

The 5′-region of Potato virus X (PVX) RNA, which contains an AC-rich, single-stranded region and stem-loop structure 1 (SL1), affects RNA replication and assembly. Using Systemic Evolution of Ligands by EXponential enrichment (SELEX) and the electrophoretic mobility shift assay, we demonstrate that SL1 interacts specifically with tobacco protoplast protein extracts (S100). The 36 nucleotides that correspond to the top region of SL1, which comprises stem C, loop C, stem D, and the tetra loop (TL), were randomized and bound to the S100. Remarkably, the wild-type (wt) sequence was selected in the second round, and the number of wt sequences increased as selection proceeded. All of the selected clones from the fifth round contained the wt sequence. Secondary structure predictions (mFOLD) of the recovered sequences revealed relatively stable stem-loop structures that resembled SL1, although the nucleotide sequences therein were different. Moreover, many of the clones selected in the fourth round conserved the TL and C-C mismatch, which suggests the importance of these elements in host protein binding. The SELEX clone that closely resembled the wt SL1 structure with the TL and C-C mismatch was able to replicate and cause systemic symptoms in plants, while most of the other winners replicated poorly only on inoculated leaves. The RNA replication level on protoplasts was also similarly affected. Taken together, these results indicate that the SL1 of PVX interacts with host protein(s) that play important roles related to virus replication.