Complete genome sequence of Middle East respiratory syndrome coronavirus KOR/KNIH/002_05_2015, isolated in South Korea

The full genome sequence of a Middle East respiratory syndrome coronavirus (MERS-CoV) was identified from cultured and isolated in Vero cells. The viral genome sequence has high similarity to 53 human MERS-CoVs, ranging from 99.5% to 99.8% at the nucleotide level. © 2015 Kim et al.

Efficacy and Tolerability of Peginterferon Alpha Plus Ribavirin in the Routine Daily Treatment of Chronic Hepatitis C Patients in Korea: A Multi-Center, Retrospective Observational Study

Background/Aims: We aimed to evaluate the efficacy and safety of peginterferon plus ribavirin for chronic hepatitis C (CHC) patients under real life setting in Korea. Methods: We retrospectively analyzed the medical records of 758 CHC patients treated with peginterferon plus ribavirin between 2000 and 2008 from 14 university hospitals in the Gyeonggi-Incheon area in Korea. Results: Hepatitis C virus (HCV) genotype 1 was detected in 61.2% of patients, while genotype 2 was detected in 35.5%. Baseline HCV RNA level was >= 6x10(5) IU/mL in 51.6% of patients. The sustained virological response (SVR) rate was 59.6% regardless of genotype; 53.6% in genotype 1 and 71.4% in genotype 2/3. On multivariate analysis, male gender (p=0.011), early virological response (p<0.001), genotype 2/3 (p<0.001), HCV RNA <6x10(5) IU/mL (p=0.005) and adherence to the drug >80% of the planned dose (p<0.001) were associated with SVR. The rate of premature discontinuation was 35.7%. The main reason for withdrawal was intolerance to the drug due to common adverse events or cytopenia (48.2%). Conclusions: Our data suggest that the efficacy of peginterferon and ribavirin therapy in Koreans is better in Koreans than in Caucasians for the treatment of CHC, corroborating previous studies that have shown the superior therapeutic efficacy of this regimen in Asians.This study was supported by the Korean Association for the Study of the Liver in 2009

Development of a multiplexed opsonophagocytic killing assay (MOPA) for group B Streptococcus

Group B Streptococcus (GBS) is a leading cause of sepsis in infants as well as chorioamnionitis in pregnant women. Opsonophagocytic killing assays (OPAs) are an essential technique in vaccine studies of encapsulated bacteria for estimating serotype-specific functional antibody levels in vitro. Here, we developed a three-fold multiplexed OPA (MOPA) to enable practical, large-scale assessment of GBS vaccine immunogenicity, including against serotypes Ia, III, and V. First, three target bacteria strains resistant to streptomycin, spectinomycin, or kanamycin were generated by natural selection through exposure to increasing antibiotic concentrations. Since a high level of nonspecific killing (NSK) of serotype V was observed in a 12.5% baby rabbit complement (BRC) solution, the BRC concentration was optimized. The final GBS-MOPA BRC concentration was 9%, which resulted in less than 20% NSK. The specificity was measured by preabsorbing serum with inactivated GBS. The opsonic index (OI) of preabsorbed serum with the homologous serotype GBS was significantly reduced in all three serotypes tested. The accuracy of the MOPA was compared with that of a single OPA (SOPA) with 35 serum samples. The OIs of the MOPA correlated well with those of the SOPA, and the r2 values were higher than 0.950 for all three serotypes. The precision of the MOPA assay was assessed in five independent experiments with five serum samples. The inter-assay precision of the GBS-MOPA was 12.5% of the average coefficient of variation. This is the first report to develop and standardize a GBS-MOPA, which will be useful for GBS vaccine development and evaluation

Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections

<div><p>Human rhinoviruses (HRVs), in the <i>Enterovirus</i> genus within the family <i>Picornaviridae</i>, are a highly prevalent cause of acute respiratory infection (ARI). Enteroviruses are genetically highly variable, and recombination between serotypes is known to be a major contribution to their diversity. Recently it was reported that recombination events in HRVs cause the diversity of HRV-C. This study analyzed parts of the viral genes spanning the 5′ non- coding region (NCR) through to the viral protein (VP) encoding sequences of 105 HRV field isolates from 51 outpatient cases of Acute Respiratory Infectious Network (ARINET) and 54 inpatient cases of severe lower respiratory infection (SLRI) surveillance, in order to identify recombination in field samples. When analyzing parts of the 5′NCR and VP4/VP2 encoding sequences, we found intra- and interspecies recombinants in field strains of HRV-A and -C. Nineteen cases of recombination events (18.1%) were found among 105 field strains. For HRV-A, there were five cases (4.8%) of intraspecies recombination events and three cases (2.8%) of interspecies recombination events. For HRV-C, there were four cases (3.8%) of intraspecies recombination events and seven cases (6.7%) of interspecies recombination events. Recombination events were significantly more frequently observed in the ARINET samples (18 cases) than in the SLRI samples (1 case; <i>P</i>< 0.0001). The recombination breakpoints were located in nucleotides (nt) 472–554, which comprise stem-loop 5 in the internal ribosomal entry site (IRES), based on the HRV-B 35 sequence (accession no. FJ445187). Our findings regarding genomic recombination in circulating HRV-A and -C strains suggest that recombination might play a role in HRV fitness and could be a possible determinant of disease severity caused by various HRV infections in patients with ARI. </p> </div

Phylogenetic analysis of field HRVs of ARINET and SLRI based on the VP4/VP2 and the 5′ NCR sequences.

<p>The phylogenetic trees were constructed using the Neighbor-Joining method in the program MEGA 4 and HEV-D 68 (accession no. AY426531) was designated as outgroup [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068081#B35" target="_blank">35</a>]. The distances of trees were computed using the Maximum Composite Likelihood method [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068081#B42" target="_blank">42</a>], and the units are the number of base substitutions per site. The intraspecies recombination strains of HRV-A, interspecies recombination strains of HRV-A, intraspecies recombination strains of HRV-C and interspecies recombination strains of HRV-C are labeled using white circles, black circles, white squares and black squares, respectively.</p

Prediction of the recombination breakpoints.

<p>Recombination breakpoints located in SL5 of the IRES (nt 472–554) were identified using RDP. The conserved nucleotides of each field strain are indicated by stars, and gray boxes show the recombination sites of each strain. The breakpoints were mainly scattered in a conserved region of SL5 (nt 515–554).</p

Analysis of recombination events in the 5′ NCR–VP2 sequences of HRV field isolates.

<p>The diagrams show the results of bootscan analysis in RDP. (<b>A</b>) KA08-3505 is a representative intraspecies recombinant of HRV-A which consists of the 5′ NCR sequence of HRV-A 78 and the VP sequence of HRV-A 12. (<b>B</b>) KA08-4374 is a representative interspecies recombination strain of HRV-A. The recombination event occurred between two different parent viruses: the 5′ NCR sequence of HRV-C subtype 35 and the VP sequence of HRV-A 41. (<b>C</b>) KL0809-374 was identified as an intraspecies recombination strain of HRV-C combining HRV-A 46 and HRV-C strain CL-170085. (<b>D</b>) KA08-4189 has undergone an interspecies recombination between two HRV-C viruses: the 5′ NCR sequence of HRV-C isolate LZ508 and the VP sequence of HRV-C isolate LZY101.</p