Seong-Hee Kim

Multiplex real-time RT-PCR for the simultaneous detection and quantification of transmissible gastroenteritis virus and porcine epidemic diarrhea virus

Abstract Transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) are major etiological agents of diarrhea and death in piglets. Multiplex real-time reverse transcriptase (RT)-PCR was developed for simultaneous differential quantification of each virus in a single reaction tube, using Cy5- and FAM-labeled TaqMan-probes based on sequences from the TGEV and PEDV nucleocapsid genes. The copy numbers for transcripts of TGEV and PEDV were quantified using this assay over a range from 9×107 to 9×101 copies and 7×107 to 7×101 copies, respectively. The variability of the intra-assay and inter-assay were evaluated using standard solutions of each transcript, with coefficients of variation (CV) less than 3.43 and 3.33%, respectively. Piglets were experimentally infected with virulent TGEV and PEDV, and the amounts of virus from the onset of diarrhea were measured. Samples obtained from farms experiencing PED or TGE were quantified between 102 and 105 RNA copies. In conclusion, this assay provides an effective etiological diagnostic tool for detecting and quantifying viral loads. The assay may also prove useful for detecting infections, ultimately leading to better disease control on farms.

Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea.

Abstract Porcine epidemic diarrhea virus (PEDV) has plagued the domestic swine industry in Korea causing significant economic impacts on pig production nationwide. In the present study, we determined the complete nucleotide sequences of the spike (S) glycoprotein genes of seven Korean PEDV isolates. The entire S genes of all isolates were found to be nine nucleotides longer in length than other PEDV reference strains. This size difference was due to the combined presence of notable 15bp insertion and 6bp deletion within the N-terminal region of the S1 domain of the Korean isolates. In addition, the largest number of amino acid variations was accumulated in the S1 N-terminal region, leading to the presence of hypervariability in the isolates. Sequence comparisons at the peptide level of the S proteins revealed that all seven Korean isolates shared diverse similarities ranging from a 93.6% to 99.6% identity with each other but exhibited a 92.2% to 93.7% identity with other reference strains. Collectively, the sequence analysis data indicate the diversity of the PEDV isolates currently prevalent in Korea that represents a heterogeneous group. Phylogenetic analyses showed two separate clusters, in which all Korean field isolates were grouped together in the second cluster (group 2). The results indicate that prevailing isolates in Korea are phylogenetically more closely related to each other rather than other reference strains. Interestingly, the tree topology based on the nucleotide sequences representing the S1 domain or the S1 N-terminal region most nearly resembled the full S gene-based phylogenetic tree. Therefore, our data implicates a potential usefulness of the partial S protein gene including the N-terminal region in unveiling genetic relatedness of PEDV isolates.

Generation of a porcine alveolar macrophage cell line for the growth of porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus (PRRSV) has a marked tropism for cells of the monocyte-macrophage lineage and accordingly, replicates in fully differentiated alveolar macrophages in the natural host. Despite the identification of several putative receptors for PRRSV on porcine alveolar macrophages (PAM), only CD163 was found to be able to make non-permissive cells susceptible to PRRSV, indicating a requirement for CD163 in productive infection. Interestingly, the preliminary experiments revealed that the immortalized PAM cell line, which was previously shown to fail to support PRRSV replication, does not express detectable levels of CD163. These data suggest that there may be a correlation between the CD163 undetectable expression level and PRRSV non-susceptibility in the continuous PAM cell line. In this study, therefore, it was attempted to stably transfect non-permissive PAM cells with CD163 cDNA to generate cell lines constitutively expressing CD163 and to evaluate their permissivity to PRRSV. The newly established PAM cell lines were demonstrated to express robust levels of CD163 and to be fully permissive for both type 1 and 2 PRRSV strains. This PRRSV-permissive PAM cell line will be a valuable tool not only to facilitate virus propagation but also to advance in vitro studies on virus pathogenesis.

An outbreak of highly pathogenic H5N1 avian influenza in Korea, 2008

In spite of intensive surveillance programs for the control of HPAI, an outbreak of highly pathogenic avian influenza (HPAI) H5N1 in Korea in April 2008 caused serious damage to poultry farms, as did previous outbreaks in 2003/2004 and 2006/2007. Six viruses were selected from the Korean 2008 isolates for genetic analysis, and all eight gene segments from each of the influenza viruses were sequenced. A phylogenetic analysis showed that all of the viruses were of the same virus type and that the hemagglutinin (HA) gene was clustered with that of clade 2.3.2 viruses. However, the internal and neuraminidase (NA) genes were closely related to those of the clade 2.3.4 viruses (recent human and bird isolates from Southeast Asia).

Complete genomic characterization of a European type 1 porcine reproductive and respiratory syndrome virus isolate in Korea.

Porcine reproductive and respiratory syndrome virus (PRRSV) isolates belonging to the European genotype 1 have recently emerged in South Korea, suggesting potential problems for disease control. In the present study, we attempted to determine the complete nucleotide sequence of the first Korean type 1 PRRSV isolate, designated KNU-07. The full-length genome of KNU-07 was found to be 15,038 nucleotides in length, which was 60 nucleotides shorter than the type 1 prototype strain Lelystad due to a notable 60-bp deletion within the nonstructural protein 2 (NSP2). The KNU-07 genome was shown to consist of a 221-nucleotide (nt) 5′ untranslated region (UTR), a 14,703-nt protein-coding region, and a 114-nt 3′ UTR, followed by a 42-73-bp poly(A) tail. A nucleotide sequence comparison of the KNU-07 genome with 20 complete PRRSV genomes revealed a 10.5–13.3% and 39.5–40.3% divergence from type 1 and type 2 strains, respectively, at the genome level, indicating a high similarity to the virus strains commonly identified as the European genotype. In order to investigate genetic variation and to understand the molecular evolution of the type 1 isolate in Korea, extensive phylogenetic analyses were performed using the ORF5 and ORF7 nucleotide sequences of published type 1 PRRSV isolates. The data further indicated that the newly emerging type 1 isolate KNU-07 belongs to the recently proposed pan-European subtype 1. Taken together, the results of this study describe the genomic characterization of the type 1 PRRSV isolated in South Korea, suggesting a recent introduction of the virus typical for this genotype that has commonly appeared worldwide.

Sero-survey on Aino, Akabane, Chuzan, bovine ephemeral fever and Japanese encephalitis virus of cattle and swine in Korea.

Vector-borne arboviruses produce mild to severe symptoms in domestic animals. Bovine ephemeral fever (BEF), Akabane, Aino, and Chuzan virus have been primarily attributed to reproductive disorders or febrile diseases in cattle, and Japanese encephalitis virus (JEV) is mainly associated with reproductive failures in swine. We investigated antibody titers from domestic swine against four bovine arboviruses (BEF, Akabane, Aino, and Chuzan virus) and from cattle against JEV in Korea. While the positive rates for Akabane and BEF were 37.4% and 15.7%, the positive incidence of Chuzan and Aino were relatively low, with positive rates of 3.04% and 0.4%, respectively, based on a virus neutralization assay. Antibody titers against more than one virus were also frequently detected in domestic swine. The incidence of JEV was 51.3% among domestic cattle. In addition, one positive case was detected in the thoracic fluids from 35 aborted calves, based on the hemagglutination inhibition test. Our results indicate that swine are susceptible hosts of bovine arboviruses without showing clinical symptoms in a natural environment. Moreover, we confirmed that JEV could be associated with reproductive failure in pregnant cattle, as were other vector-borne bovine arboviruses assessed in this study.

A molecular analysis of European porcine reproductive and respiratory syndrome virus isolated in South Korea.

In a situation where European genotype of porcine reproductive and respiratory syndrome virus (PRRSV) has recently emerged in South Korea, this study aims to understand variations in and relatedness among 25 European (EU) genotype 1 PRRSV isolates obtained from Korean pig farms during the period ranging from 2006 to 2009 for their sequences of nonstructural protein 2 (NSP2), open reading frames (ORF) 5 and 7, which, in turn, were compared with those of published Korean type 1 PRRSV isolates (CP6874, IV3140 and KNU07) and other EU PRRSV strains. The sequence data revealed that all Korean type 1 isolates were found to possess notable 19 amino acid deletions within NSP2 between positions 748 and 766. Based on the complete ORF5 sequences, the results showed that the Korean isolates amounted to 82.0-99.5% in amino acid identity with one another, while sharing a lower level of amino acid identity ranging from 71.6% to 92.0% with EU genotype strains isolated in other geographic areas. According to an amino acid sequence comparison of ORF7, the level of identity among the Korean type 1 isolates was found to range from 86.7% to 100%. Phylogenetic analyses based on ORF5 and ORF7 sequences indicated that the Korean type 1 isolates belonged to the pan-European subtype 1; in ORF5 phylogeny, they form three distinct clusters from other EU genotype PRRSV strains. In conclusion, those findings suggest that the Korean type 1 PRRSV may have undergone a high degree of variations since EU genotype virus was first detected.

Genetic relatedness of H6 subtype avian influenza viruses isolated from wild birds and domestic ducks in Korea and their pathogenicity in animals

We report the genetic characterization of H6 avian influenza (AI) viruses isolated from domestic ducks and wild birds in Korea between April 2008 and April 2009. A phylogenetic analysis showed that the H6N1 viruses of wild birds and domestic ducks were of the same genotype (K-1) and were similar to the H6N1 virus isolated from a live poultry market in 2003, as six of the eight gene segments of those viruses had a common source. However, the H6N2 viruses of domestic poultry were separated into four genotypes (K-2a, K-2b, K-2c and K-2d) by at least a triple reassortment between influenza viruses of low pathogenicity from Korean poultry (H9N2 and H3N2) and viruses from aquatic birds. In an experimental infection of animals, certain H6 AI viruses replicated well in chickens and mice without pre-adaptation, indicating that H6 virus pathogenicity has the potential to be altered due to multiple reassortments, and that these reassortments could result in interspecies transmission to mammals.

Human telomerase reverse transcriptase-immortalized porcine monomyeloid cell lines for the production of porcine reproductive and respiratory syndrome virus.

Porcine reproductive and respiratory syndrome virus (PRRSV) shows highly restricted cell tropism and targets subpopulations of differentiated macrophages such as porcine alveolar macrophages (PAM) in the natural host. Although primary PAM cells would be ideal for in vitro virus production, they are not only difficult and expensive for establishment but cannot be frozen reliably for long-term storage and use. Apart from PAM cells, African green monkey kidney derived Marc-145 cells are used commonly for virus propagation. However, concerns have been raised regarding a possible modification of specific epitopes associated with virus neutralization because of distinct virus entry between PAM and Marc-145 cells. In order to overcome these problems, the present study was aimed to generate immortalized porcine monocyte/macrophage cell lines and to evaluate their potential for PRRSV production. Primary PAM cells were transfected stably with the human telomerase reverse transcriptase (hTERT) cDNA by a retrovirus vector so that constitutive expression of the hTERT protein allows cells to proliferate indefinitely. The newly immortalized PAM clones were shown to exert functional telomerase activity, indicating sustained expression of hTERT. In addition, telomerase-immortalization of PAMs did not affect expression levels of the native CD163 receptor on their surface. It was further demonstrated that these continuous PAM cell lines are fully permissive for the efficient growth of both type 1 and 2 PRRSV strains. The findings suggest that the hTERT-immortalized PAM cell lines can enable us to facilitate the continued use of PAMs for virus isolation and production and to provide a promising tool for viral pathogenesis and immune function studies.

Molecular characterization of a Korean bovine parainfluenza virus type 3 isolate

Bovine parainfluenza virus type 3 (BPIV-3) was isolated from Korean native cattle that presented clinical signs of mild pneumonia. The complete genome of a representative isolate (12Q061) was sequenced. The newly identified strain, which was found to be distinct from the previously reported genotypes A (BPIV-3a) and B (BPIV-3b) and closely related to the Chinese strain SD0835, was tentatively classified as genotype C (BPIV-3c). Our results suggest a relationship between BPIV-3 genetic variation and the geographic location of its isolation. Identification of these new BPIV-3 genotypes may facilitate the development of improved diagnostic methods and vaccines. This is to our knowledge the first report of the identification and molecular characterization of BPIV-3 in Korea.