An improved reverse transcription loop-mediated isothermal amplification assay for sensitive and specific detection of serotype O foot-and-mouth disease virus.

A sensitive and specific swarm primer-based reverse transcription loop-mediated isothermal amplification (sRT-LAMP) assay for the detection of serotype O foot-and-mouth disease virus (FMDV) was developed and evaluated. The assay specifically amplified the VP3 gene of serotype O FMDV, but did not amplify the VP3 gene of other serotype FMDVs or any other viruses. The limit of detection of the assay was 102 TCID50/mL or 103 RNA copies/µL, which is 100 times lower than that of the RT-LAMP assay without swarm primers. The new assay is 10 times more sensitive than reverse transcription-polymerase chain reaction (RT-PCR) and is comparable to the sensitivity of real time RT-PCR (qRT-PCR). Evaluation of the assay using different serotypes of FMDV strains showed 100% agreement with the RT-PCR results. The previously reported serotype O FMDV-specific RT-LAMP assay did not detect 20 out of 22 strains of serotype O FMDVs, probably due to multiple mismatches between the primer and template sequences, showing that it is not suitable for detecting the serotype O FMDVs circulating in Pool 1 region countries, including Korea. In contrast, the developed sRT-LAMP assay with improved primers can rapidly and accurately diagnose serotype O FMDVs circulating in Pool 1 region countries and will be a useful alternative to RT-PCR and qRT-PCR.

Detection and genetic characterization of porcine circovirus 3 from aborted fetuses and pigs with respiratory disease in Korea.

A novel porcine circovirus 3 (PCV3) was first detected in pigs showing porcine dermatitis and nephropathy syndrome, reproductive failure, and multisystemic inflammation in the USA. Herein, we report on PCV3 as a potential etiological agent of clinical signs, reproductive failure and respiratory distress on Korean pig farms, based on in situ hybridization, pathological, and molecular findings. Confirmation of the presence of PCV3 may increase co-infection with other causative agents of disease in Korean pig herds, indicating the need for further systemic investigation of pathogenicity and of multiple infections with PCV2 genotypes and bacteria, and the development of an effective PCV3 vaccine.

Loop-mediated isothermal amplification assay for the rapid and visual detection of novel porcine circovirus 3.

A loop-mediated isothermal amplification (LAMP) assay using hydroxynaphthol blue was developed for the rapid and visual detection of the capsid gene of porcine circovirus 3 (PCV3). The amplification could be completed in 40 min at 62°C, and the results could be visually detected by the naked eye. The assay specifically amplified PCV3 DNA and not other porcine viral nucleic acids. The limit of detection of the assay was 50 PCV3 DNA copies, which was comparable to that of the real-time polymerase chain reaction (qPCR) and lower than that of conventional PCR. In the clinical evaluation, the PCV3 detection rate of the LAMP assay was higher than that of PCR and agreed 100% with that of qPCR. These results indicate that the LAMP assay will be a valuable tool for the rapid, sensitive, and specific detection of PCV3 in clinical samples.

Molecular analysis of the hexon, penton base, and fiber-2 genes of Korean fowl adenovirus serotype 4 isolates from hydropericardium syndrome-affected chickens.

Fowl adenovirus serotype 4 (FAdV-4) is the causative agent of hydropericardium syndrome (HPS), a highly pathogenic disease in poultry. In the present study, hexon, penton base, and fiber-2 genes encoding major capsid proteins were analyzed in four FAdV-4 isolates from HPS-affected chickens in Korea. Nucleotide sequences of the entire hexon (2811 bases), penton base (1578 bases), and fiber-2 (1425 bases) genes from the Korean isolates were 97.5-99.3, 99.1-99.7, and 95.5-99.0 % identical, respectively, to those of foreign FAdV-4 isolates. In the N-terminal tail region of fiber-2, the KRP motif predicted to be the nuclear localization signal was identified in the Korean isolates, whereas KRP/A was detected in other isolates. The VYPF motif in fiber-2, which is known to interact with the penton base, was present in the same region of all FAdV-4 isolates that were compared. Amino acid variations in fiber-2 for HPS and non-HPS isolates revealed that D219 and T300 were conserved among ten HPS isolates from five countries, including Korea. T380 in fiber-2, previously found in HPS isolates, corresponded to A380 in the Korean isolates, indicating that T380 is not relevant for increased virulence. Phylogenetic analysis showed that the four Korean FAdV-4 isolates were more related to MX-SHP95, a Mexican FAdV-4 isolate of HPS origin, than to FAdV-4 isolates of Indian and Chinese origin, suggesting that the genetic relationship among FAdV-4 isolates is independent of geographic distribution. The molecular features of these genes will provide valuable information for vaccine development against HPS in the future.

Uracil-DNA glycosylase-treated reverse transcription loop-mediated isothermal amplification for rapid detection of avian influenza virus preventing carry-over contamination.

Here, we describe a uracil-DNA glycosylase (UNG)-treated reverse transcription loop-mediated isothermal amplification (uRT-LAMP) for the visual detection of all subtypes of avian influenza A virus (AIV). The uRT-LAMP assay can prevent unwanted amplification by carryover contamination of the previously amplified DNA, although the detection limit of the uRT-LAMP assay is 10-fold lower than that of the RT-LAMP without a UNG treatment. To the best of our knowledge, this is the first successful application of deoxyuridine triphosphate/UNG strategy in RT-LAMP for AIV detection, and the assay can be applied for the rapid, and reliable diagnosis of AIVs, even in contaminated samples.

Evaluation of single nucleotide polymorphisms of pvmdr1 and microsatellite genotype in Plasmodium vivax isolates from Republic of Korea military personnel.

BACKGROUND: Chloroquine has been administered to the soldiers of the Republic of Korea as prophylaxis against vivax malaria. Recent increase in the number of chloroquine-resistant parasites has raised concern over the chemoprophylaxis and treatment of vivax malaria. METHODS: To monitor the development of chloroquine-resistant parasites in the Republic of Korea, analyses of single nucleotide polymorphisms (SNPs) of pvmdr1 and microsatellite markers were performed using samples collected from 55 South Korean soldiers infected with Plasmodium vivax. RESULTS: Four SNPs, F1076L, T529, E1233, and S1358, were identified. Among these, S1358 was detected for the first time in Korea. The microsatellite-based study revealed higher genetic diversity in samples collected in 2012 than in 2011. CONCLUSIONS: Taken together, the results indicate that P. vivax with a newly identified SNP of pvmdr1 has been introduced into the Korean P. vivax population. Therefore, continuous monitoring for chloroquine-resistant parasites is required for controlling vivax malaria in the Republic of Korea.

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.

Expression of VP2 gene protein of infectious bursal disease virus detected in Korea.

The VP2 gene DNA (1.4 kb in approximate) of a very virulent infectious bursal disease virus (vvIBDV) Chinju strain detected in Chinju, Korea was cloned into the bacmid, a baculovirus shuttle vector, through transposition of the gene from initially cloned pFastBacHTa plasmid, a baculovirus expression vector, and was subsequently expressed in Spodoptera frugiperda (Sf) cells. Biological properties of the expressed VP2 subunit protein were characterized to aid in the development of genetically engineered diagnostic reagents and vaccines against the vvIVDV. When the VP2 DNA-recombinant bacmid was transfected and propagated in the Sf cells, the cells showed no occlusion formation, which is a positive evidence for the insertion of the VP2 DNA into the polyhedrin gene of the bacmid, whereas the occlusions were observed in the cells infected by the Autographa californica nuclear polyhedrosis virus, a wild baculovirus. The expression of VP2 DNA was identified by strong positive reaction in fluorescent antibody test using chicken anti-IBDV serum. The VP2 protein was determined as a polypeptide band with Mr of 48 kDa by the sodium dodecyl-polyacrylamide gel electrophoresis for the lysate of the Sf cells infected with the recombinant bacmid. The VP2 protein was successfully purified from the cell lysate by Ni-NTA affinity chromatography. The expressed VP2 subunit protein reacted specifically with chicken anti-IBDV serum in Western blotting.

Cloning and sequence analysis of the spike gene of porcine epidemic diarrhea virus Chinju99.

The spike (S) gene of the porcine epidemic diarrhea virus (PEDV) Chinju99 which was previously isolated in Chinju, Korea was cloned and sequenced to aid in the development of genetically engineered vaccines and diagnostic reagents against PEDV. The nucleotide sequence encoding the entire S gene open reading frame (ORF) of Chinju99 was 4,152 bases long encoding 1,383 amino acids. It consisted of 1,001 adenine (24.1%), 849 cytosine (20.4%), 877 guanine (21.1%) and 1425 thymine (34.3%) residues. The Chinju99 S ORF nucleotide sequence was 94.5% homologous with that of the Br1/87 and CV777 strains, respectively. The Chinju99 S protein had 92.8% amino acid identity with that of Br1/87 and CV777, respectively. The amino acid sequence contained 27 potential sites for asparagine (N)-linked glycosylation and there was a stretch of highly hydrophobic residues at position 1,325-1,350.

Cloning and sequence analysis of the nucleocapsid gene of porcine epidemic diarrhea virus Chinju99.

The nucleocapsid (N) gene of the porcine epidemic diarrhea virus (PEDV) Chinju99 which was previously isolated in Chinju, Korea was cloned and sequenced to establish the information for the development of genetically engineered diagnostic reagents. Also, sequences of the nucleotides and deduced amino acids of the Chinju99 N gene were analyzed by alignment with those of CV777 and Brl/87. The nucleotide sequence encoding the entire N gene open reading frame (ORF) of Chinju99 was 1326 bases long and encoded a protein of 441 amino acids with predicted M(r) of 49 kDa. It consisted of 405 adenine (30.5%), 293 cytosine (22.1%), 334 guanines (25.2%) and 294 thymines (22.2%) residues. The Chinju99 N ORF nucleotide sequence was 96.5% and 96.4% homologous with that of the CV777 and Brl/87, respectively. The Chinju99 N protein revealed 96.8% amino acid identity with that of Brl/87 and CV777, respectively. The amino acid sequence contained seven potential sites for threonine (T)- or serine (S)-linked phosphorylation by each protein kinase C and casein kinase II.

Cloning and nucleotide analysis of segment A gene of infectious bursal disease virus detected in Korea.

A strain of infectious bursal disease virus (IBDV) was detected from bursal tissues of chicks which suffered from infectious bursal disease (IBD) in Chinju, Korea and provisionally named as Chinju strain. A full-length cDNA clone for segment A gene of the virus was constructed, and complete nucleotide sequence of the gene including noncoding region was determined and analyzed by comparison with that of other IBDV strains. The segment A gene of Chinju strain consisted of 3,269 nucleotides including 862 adenine (26.4%), 917 cytosine (28.0%), 854 guanine (26.1%) and 636 thymine (19.5%). There were regions for two open reading frames (ORFs), ORF1 encoding the VP5 with ATG codon at nucleotides 98-100 and ORF2 encoding the polyprotein of VP2, VP4 and VP3 in the nucleotides 132-3,170. In deduced translation the ORF2 encoded 1,012 amino acids. The full nucleotide sequence of segment A gene and amino acid sequence of ORF2 of the Chinju strain showed 98-99% homology with those of the very virulent IBDVs (vvIBDVs) such as HK46, OKYM, UK661, UPM97/ 61, D6948 and BD3/99. In phylogenetic analysis of nucleotide and amino acid sequences, the Chinju strain was also related closely to the vvIBDVs. Hence, it was suggested that the Chinju strain is a vvIBDV. The nucleotide and amino acid sequences of the Chinju strain with pertinent information can be useful for the development of genetically engineered vaccines and diagnostic reagents against vvIBDV.

Indirect method for prediction of hemagglutination inhibition antibody titers to Newcastle disease virus in chickens by titration of antibodies in egg yolk.

Attempts were made to establish methods for indirect prediction of hemagglutination inhibition (HI) antibody titers to Newcastle disease virus (NDV) in sera of laying hens and day-old chicks by determining if these are correlated to HI titers in egg yolks. For this purpose, geometric means of HI antibody titers in sera from 60 hens, yolks from 60 matched eggs, and sera from 180 day-old chicks of an identical vaccination program were measured and plotted. There was a significant correlation between HI antibody titers in yolks (X) and hens (Y), with a linear regression of Y = 23.24 + 0.47X and a correlation coefficient of r = 0.65. The linear regression between HI antibody titers in yolks (X) and chicks (Y) was Y = 6.33 + 0.36X (r = 0.58). Immunity to NDV in hens and their offspring can be maintained effectively, and the proper time for the vaccination or booster can be determined by reference to HI titers predicted from the linear regression in the present study. The approach of testing egg yolk for HI titers provides a feasible alternative to determining HI titers from blood samples and eliminates stress in birds during blood sampling.