• Parasites, Hosts and Diseases
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• v.55 no.2
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• pp.149-158
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• 2017

Variant surface antigens (VSAs) encoded by pir families are considered to be the key proteins used by many Plasmodium spp. to escape the host immune system by antigenic variation. This attribute of VSAs is a critical issue in the development of a novel vaccine. In this regard, a population genetic study of vir genes from Plasmodium vivax was performed in the Republic of Korea (ROK). Eighty-five venous blood samples and 4 of the vir genes, namely vir 27, vir 21, vir 12, and vir 4, were selected for study. The number of segregating sites (S), number of haplotypes (H), haplotype diversity (Hd), DNA diversity (${\pi}$ and ${\Theta}_w$), and Tajima's D test value were conducted. Phylogenetic trees of each gene were constructed. The vir 21 (S=143, H=22, Hd=0.827) was the most genetically diverse gene, and the vir 4 (S=6, H=4, Hd=0.556) was the opposite one. Tajima's D values for vir 27 (1.08530, P>0.1), vir 12 (2.89007, P<0.01), and vir 21 (0.40782, P>0.1) were positive, and that of vir 4 (-1.32162, P>0.1) was negative. All phylogenetic trees showed 2 clades with no particular branching according to the geographical differences and cluster. This study is the first survey on the vir genes in ROK, providing information on the genetic level. The sample sequences from vir 4 showed a clear difference to the Sal-1 reference gene sequence, whereas they were very similar to those from Indian isolates.

• Pediatric Infection and Vaccine
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• v.16 no.2
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• pp.199-204
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• 2009

Purpose : Various proteins encoded in the early region 3 (E3) of adenoviruses protect cells from being killed by cytotoxic T cells and death-inducing cytokines. We sought to find out whether the genetic heterogeneity of the E3 gene might contribute to the molecular diversity of adenoviruses. Methods : Sequences in the E3 region were analyzed for 14 adenovirus type 3 (Ad3) strains that were isolated from children with lower respiratory tract infections in the Seoul National University Children's Hospital during the period 1991-2000. Full-length adenoviral DNA was purified from the infected A549 cell lysates using a modified Hirt procedure. Results : There was 98% homology between 14 Korean Ad3 strains with a reference strain (M15952). Homology within the Korean Ad3 strains was 98.7%. Variation was found in the region of transcripts 20.1 kDa, 20.6 kDa, truncated 7.7 kDa, 10.3 kDa, 14.9 kDa, and 15.3 kDa. In particular, all 14 Korean strains showed a missense single point mutation at the start codon of the truncated 7.7 kDa. In addition, a deletion was found in the truncated 7.7 kDa region by 58 base pairs in 10 strains and 94 base pairs in 4 strains. Variations in amino acids were observed in the receptor internalization and degradation complex (10.3 kDa/14.9 kDa) which stimulates the clearance from the cell surface and subsequent degradation of the receptors for the Fas ligand and TRAIL, while no variations were observed in another immunoregulatory transcript, 19 kDa. Conclusion : Sequence analysis of the immunoregulatory region of adenovirus E3 shows that genetic heterogeneities are related to genome type patterns.

• Korean Journal of Veterinary Research
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• v.46 no.2
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• pp.107-117
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• 2006

This paper described the epidemiological characteristics of 2002 outbreak of classical swine fever (CSF) in Korea. A total of thirteen CSF-infected farms could be classified into two clusters according to the location and time of outbreak. Two farms located in the same county of Gangwon province and 11 farms located in several different districts of Incheon metropolitan/Gyeonggi province were identified as CSF-infected from April 16 to 30 and from October 7 to December 21 in 2002, respectively. As the result of epidemiological analysis, the two clusters of outbreaks were turned out to be independent epidemics which had different sources of virus introduction. Three farms were found to have been infected primarily; one located in Cheolwon county of Gangwon province and two located in Kangwha county of Incheon metropolitan area. The most likely factors of virus introduction into these primary infected farms were considered to be direct or indirect contact by foreign workers and/or owners of the infected farms who had come back from traveling in China before outbreaks. This was supported by the genetic typing of CSF viruses isolated from the pigs of infected farms. All the virus isolates of 2002 outbreak were found to be genetic type 2, whereas the viruses isolated before 2000 were type 3 and the reference strains, such as attenuated live vaccine virus (LOM strain) and high virulent challenge virus (ALD strain), were type 1. Accordingly, we concluded that the 2002 CSF outbreak must have been caused by a newly introduced virus from overseas and the type 3 virus must have been eradicated after the last outbreak of 1999 by the national CSF eradication campaign which were implemented since 1996. Based on the combined analysis of epidemiological data and genetic typing, the transmission routes of classical swine fever virus were found to be the movement of vehicles (60%) and persons (10%), neighbourhood spread (20%) and unknown (10%). It is expected that the analyzed data and findings of classical swine fever outbreak epidemic could be very useful to establish the disease control and eradication program for the country in the future.

• Korean Journal of Veterinary Service
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• v.44 no.2
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• pp.73-83
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• 2021

Although many swine farms continuously vaccinated to sow to prevent Porcine epidemic diarrhea(PED), PED has occurred annually in swine herds in Jeonbuk province, Korea. In the present study, the small intestine and feces samples from 17 farms where severe watery diarrhea and death of newborn piglets occurred in 2019 were collected, amplified by RT-PCR and determined the complete nucleotide sequences of the spike (S) glycoprotein genes of nine Jeonbuk PEDV isolates. The spike (S) glycoprotein is an important determinant for molecular characterization and genetic relationship of PEDV. These nine complete S gene isolates were compared with other PEDV reference strains to identify the molecular diversity, phylogenetic relationships and antigenicity analysis. 9 field strains share 98.5~100% homologies with each other at the nucleotide sequence level and 97.3~100% homologies with each other at the amino acid level. The nine Jeonbuk PEDV isolates were classified into G2b group including a genetic specific signal, S-indels (insertion and deletion of S gene). In addition, comparisons the neutralizing epitopes of S gene between 9 field strains and domestic vaccine strains of Korea mutated 12-15 amino acids with SM-98-1 (G1a group) and mutated 0-3 amino acids with QIAP1401 (G2b group). Therefore, the development of G2b-based live vaccines will have to be expedited to ensure effective prevention of endemic PED in Korea. In addition, we will need to be prepared with periodic updates of preventive vaccines based on the PEDV variants for the re-emergence of a virulent strain.

• Genomics & Informatics
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• v.20 no.2
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• pp.21.1-21.14
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• 2022

The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in hemagglutinin (HA) and neuraminidase (NA) genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, HA, and NA genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.

• Pediatric Infection and Vaccine
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• v.6 no.2
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• pp.219-233
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• 1999

Purpose : Respiratory syncytial virus(RSV) is the major cause of lower respiratory tract infection in infants and young children. This study was performed to analyze antigenic and genetic variation of G protein of subgroup A RSV. Methods : One hundred seventy-nine strains isolated at the Seoul National University Children's Hospital over 8 years-period from 1990 through 1998 were analysed for antigenic and genetic variability. Analysis was made by reactivity with monoclonal antibodies raised against RSV, and by restriction mapping and, for selected strains, nucleotide sequencing following amplification of full sequence of G gene by reverse transcription-polymerase chain reaction. Results : Restriction fragment analysis of the amplified G protein gene revealed 23 restriction patterns, 12 of which included more than 2 isolate, and the most frequent genetic type comprised 30% of the strains. Indirect immunofluorescent staining with monoclonal antibodies revealed 6 antigenic types with one predominant pattern accounting for 91% of the total strains. The most frequent antigenic type had 21 restriction patterns, and some viruses with same restiction pattern had different monoclonal antibody reaction pattern. Nucleotide sequence homology of subgroup A was 91~93% between reference(A2, Long) and Korean isolates, 93~99% among Korean isolates. Maximum-parsimony analysis demonstrated that Korean isolates were distinct from reference strains and subgroup A strains were clustered in 4 groups. Conclusion : The restriction analysis pattern of G protein gene identified greater diversity within subgroup A than was seen with the monoclonal analysis and a variety of antigenic and genetic types of RSV are circulating in Korea which are different from reference strains or strains isolated from other countries.

• The Journal of Korean Society of Virology
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• v.26 no.2
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• pp.251-258
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• 1996

The V3 loop, a hypervariable domain of envelope glycoprotein, has an essential role in viral infectivity and has a major epitope for type-specific neutralizing antibody. In order to investigate genetic diversity of V3 region of gp120 of human immunodeficiency virus type 1 (HIV-1) isolated from Korean patients, DNA sequences encoding the C2 to V3 region were amplified by nested polymerase chain reaction (PCR) from uncultured peripheral blood mononuclear cells obtained from 15 HIV-1 seropositive patients and nucleotide sequences were determined. All nucleotide sequences from fifteen patients were compared with 8 distinctive subtypes (A-H) and another subtype O. Phylogenetic analysis was carried out with PHYLIP ver 3.5 (Dnapars) program. Of the 15 isolates, 14 HIV-1 subjects were clustered with subtype B, while one was clustered with subtype C. Intra-subtype B distance at the nucleotide and deduced amino acid level were maximum 17.7% and 37.0%, respectively. Intra-patient distance at the nucleotide and deduced amino acid level were maximum 7.3% and 17.8%, respectively. Analysis of the nucleotide sequences revealed that Korean types have relatively well conserved sequences. These findings could be useful for assessing the source of infection and developing an AIDS vaccine.

• Journal of Microbiology and Biotechnology
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• v.30 no.3
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• pp.313-324
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• 2020

Coronavirus disease 2019 (COVID-19), which causes serious respiratory illness such as pneumonia and lung failure, was first reported in Wuhan, the capital of Hubei, China. The etiological agent of COVID-19 has been confirmed as a novel coronavirus, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is most likely originated from zoonotic coronaviruses, like SARS-CoV, which emerged in 2002. Within a few months of the first report, SARS-CoV-2 had spread across China and worldwide, reaching a pandemic level. As COVID-19 has triggered enormous human casualties and serious economic loss posing global threat, an understanding of the ongoing situation and the development of strategies to contain the virus's spread are urgently needed. Currently, various diagnostic kits to test for COVID-19 are available and several repurposing therapeutics for COVID-19 have shown to be clinically effective. In addition, global institutions and companies have begun to develop vaccines for the prevention of COVID-19. Here, we review the current status of epidemiology, diagnosis, treatment, and vaccine development for COVID-19.

• Pediatric Infection and Vaccine
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• v.21 no.3
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• pp.219-224
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• 2014

Invasive infection of the Streptococcus bovis group in a neonate is rare. In cases reported to date, the pathogen of neonatal S. bovis infections is usually Streptococcus gallolyticus subsp. pasteurianus (S. bovis biotype II/2). Streptococcus lutetiensis (S. bovis biotype II/1) was identified using 16S rRNA and tuf gene sequence analysis of the isolates from blood and cerebrospinal fluid (CSF) of a fever-presenting 28-day-old male. Blood culture analysis was performed using automatic equipment (VITEK 2) and identified Streptococcus infantarius supsp. infantarius, yet we were unable to get accurate results from the CSF culture. The fever subsided on the second day of hospitalization, and the patient was discharged without neurologic complication after 14 days of antibiotic therapy. In this case, we were able to accurately identify the pathogen using molecular genetic methods. To our knowledge, this is the first case of late onset neonatal bacteremia and meningitis caused by S. lutetiensis.

• Journal of Microbiology and Biotechnology
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• v.24 no.2
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• pp.217-224
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• 2014

Chicken are considered as the most important source of human infection by Campylobacter jejuni, which primarily arises from contaminated poultry meats. However, the genes expressed in vivo of the interaction between chicken and C. jejuni have not been screened. In this regard, in vivo-induced antigen technology (IVIAT) was applied to identify expressed genes in vivo during interaction between chicken and C. jejuni, a prevalent foodborne pathogen worldwide. Chicken sera were obtained by inoculating C. jejuni NCTC 11168 into Leghorn chickens through oral and intramuscular administration. Pooled chicken sera, adsorbed against in vitro-grown cultures of C. jejuni, were used to screen the inducible expression library of genomic proteins from sequenced C. jejuni NCTC 11168. Finally, 28 unique genes expressed in vivo were successfully identified after secondary and tertiary screenings with IVIAT. The genes were implicated in metabolism, molecular biosynthesis, genetic information processing, transport, regulation and other processes, in addition to Cj0092, with unknown function. Several potential virulence-associated genes were found to be expressed in vivo, including chuA, flgS, cheA, rplA, and Cj0190c. We selected four genes with different functions to compare their expression levels in vivo and in vitro using real-time RT-PCR. The results indicated that these selected genes were significantly upregulated in vivo but not in vitro. In short, the expressed genes in vivo may act as potential virulence-associated genes, the protein encoded by which may be meaningful vaccine candidate antigens for campylobacteriosis. IVIAT provides an important and efficient strategy for understanding the interaction mechanisms between Campylobacter and hosts.