Evaluation of Multiplex Rapid Antigen Test for the Detection of SARS-CoV-2 and Influenza A/B in Respiratory Samples.

BACKGROUND: There is little data about the performance of multiplex rapid antigen tests (RATs) on the detection of SARS-CoV-2, influenza A (Flu A), and influenza B (Flu B). This study is to evaluate the performance of Panbio COVID-19/Flu A&B rapid panel (Abbott Diagnostics, Korea) and analyze the factors influencing its sensitivity. METHODS: Nasopharyngeal swabs were collected and stored at the Korea University Anam hospital. In total, 400 residual samples from nasopharyngeal swabs were examined. The diagnostic accuracy of RAT was compared to that of RT-qPCR using the Allplex SARS-CoV-2/FluA/FluB/RSV Assay (Seegene, Seoul, South Korea). RESULTS: Panbio COVID-19/Flu A&B rapid panel showed the sensitivities of 88.0%, 92.0%, and 100% for SARS-CoV-2, Flu A, and Flu B, respectively, and specificities of 100% for all. The agreements with previously licensed single-plex RATs were shown to be high. In the analysis of variables affecting sensitivity, inappropriate sampling time after symptom onset (STASO) and high cycle threshold (Ct value) were shown to negatively affect the sensi-tivity. CONCLUSIONS: In conclusion, the multiplex RAT is useful for diagnosing SARS-CoV-2 and Flu A/B, but more clinical studies are needed.

Rapid Direct Identification of Microbial Pathogens and Antimicrobial Resistance Genes in Positive Blood Cultures Using a Fully Automated Multiplex PCR Assay.

This study assessed the performance of the BioFire Blood Culture Identification 2 (BCID2) panel in identifying microorganisms and antimicrobial resistance (AMR) profiles in positive blood cultures (BCs) and its influence on turnaround time (TAT) compared with conventional culture methods. We obtained 117 positive BCs, of these, 102 (87.2%) were correctly identified using BCID2. The discordance was due to off-panel pathogens detected by culture (n = 13), and additional pathogens identified by BCID2 (n = 2). On-panel pathogen concordance between the conventional culture and BCID2 methods was 98.1% (102/104). The conventional method detected 19 carbapenemase-producing organisms, 14 extended-spectrum beta-lactamase-producing Enterobacterales, 18 methicillin-resistant Staphylococcus spp., and four vancomycin-resistant Enterococcus faecium. BCID2 correctly predicted 53 (96.4%) of 55 phenotypic resistance patterns by detecting AMR genes. The TAT for BCID2 was significantly lower than that for the conventional method. BCID2 rapidly identifies pathogens and AMR genes in positive BCs.

Evaluation of a sterile, filter-based, in-house method for rapid direct bacterial identification and antimicrobial susceptibility testing using positive blood culture.

This study aimed to assess the performance of our in-house method for rapid direct bacterial identification (ID) and antimicrobial susceptibility testing (AST) using a positive blood culture (BC) broth. For Gram-negative bacteria, 4 mL of BC broth was aspirated and passed through a Sartorius Minisart syringe filter with a pore size of 5 µm. The filtrate was then centrifuged and washed. A small volume of the pellet was used for ID, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and for AST, using automated broth microdilution. For Gram-positive cocci, 4 mL of BC broth was passed through the Minisart syringe filter. Then, 4 mL of sterile distilled water was injected in the direction opposite to that of the filtration to collect the bacterial residue trapped in the filter. Compared with the conventional method performed with pure colonies on agar plates, 94.0% (234/249) were correctly identified using the in-house method, with rates of 91.4% (127/139) and 97.3% (107/110) for Gram-positive and Gram-negative isolates, respectively. Of 234 correctly identified isolates, 230 were assessed by AST. Categorical agreement and essential agreement were 93.3% and 94.5%, respectively, with a minor error rate of 3.8%, a major error rate of 3.4%, and a very major error rate of 1.6%. Our in-house preparation method showed good performance in rapid direct ID and AST using positive BC broths compared to the conventional method. This simple method can shorten the conventional turnaround time for ID and AST by at least 1 day, potentially contributing to better patient management.

HPLC-MS/MS Method Validation for Antifungal Agents in Human Serum in Clinical Application.

BACKGROUND: Therapeutic drug monitoring (TDM) of antifungal drugs is recommended. LC-MS/MS outperforms bioassay and high-performance liquid chromatography (HPLC) for TDM. In this study, we validated TDM for voriconazole, posaconazole, and itraconazole using HPLC-MS/MS with the multiple reaction monitoring (MRM) method. METHODS: For the validation of LC-MS/MS for antifungal TDM, accuracy, precision, linearity, carryover, lower limit of quantitation (LLOQ), ion suppression, and sample stability tests were performed according to the guidelines of the United States Food and Drug Administration (FDA) and the Clinical and Laboratory Standards Institute (CLSI). RESULTS: The LC-MS/MS triazole method showed that all analytes had biases less than 8.9% and coefficients of variation (CV) less than 7.7%. The linearity was validated over the ranges of 0.20 to 5.86 mg/L for voriconazole, 0.12 to 4.96 mg/L for posaconazole, 0.09 to 1.85 mg/L for itraconazole, and 0.12 to 2.38 mg/L for OH-itraconazole. Ion suppression and carryover were negligible. The lower limits of quantitation (LLOQs) for voriconazole, posaconazole, itraconazole, and OH-itraconazole were 0.114 mg/L, 0.206 mg/L, 0.118 mg/L, and 0.065 mg/L, respectively. Voriconazole, posaconazole, itraconazole, and OH-itraconazole can be stored at 4℃ for 4 - 7 days, according to sample stability. Sample preparation took < 15 minutes per batch, and analytical run time was 5 minutes per sample. CONCLUSIONS: We developed and validated a simple, reliable, and quick LC-MS/MS method for triazole antifungal agents TDM suitable for routine hospital practice.

Development and Validation of a U-HPLC-MS/MS Method for the Concurrent Measurement of four Immunosuppressants in Whole Blood.

BACKGROUND: This study aimed to develop and validate a U-HPLC-MS/MS method for simultaneous determination of four immunosuppressants in human whole blood. METHODS: The method was based on the injection of 20 µL of calibrators and controls pretreated with the liquid phase extraction method for chromatography separation and mass spectrometry determination. LPE offline was performed by adding 0.1 mol/L ZnSO4 and acetonitrile, while separation of target compounds was achieved within 2.5 minutes by a Zorbax Eclipse XDB-C8 column using ammonium acetate and ACN mixed with formic acid as solvents. RESULTS: The assay offers ng/mL detection limits (from 1.1 to 12.4 ng/mL), accuracy (% deviation from -4.4% to 5.6%), precision (CV less than 15% at all QC levels), and linearity (from 23.4 to 948 ng/mL for CsA, from 2.11 to 45.5 ng/mL for TAC, SIR and EVR). The recovery and matrix results were acceptable, and the carryover was less than 1%. The results of method comparison show that IA-based methods overestimated the concentration of drugs compared with the MS-based method. Comparing our MS-based method with external LC-MS/MS showed that the results were within 2 SDs. CONCLUSIONS: We have developed a reliable assay for the analysis of CsA, TAC, SIR and EVR in whole blood using U-HPLC-MS/MS.

Detection of Plasmodium vivax using Automated Hematology Analyzer in the Korean Army.

BACKGROUND: This study aimed to evaluate whether our equation model developed from the Sysmex hematology analyzer can discriminate patients with Plasmodium vivax (P. vivax) infection from those with acute febrile illness (AFI) and healthy controls. Besides, we compared our model with the previously studied models. METHODS: A total of 312 blood samples were collected from the P. vivax, AFI, and healthy control groups. All samples were tested for routine complete blood count conducted by using a Sysmex XE-2100 or XE-5000 analyzer. We compared the reportable and research parameters generated from the Sysmex analyzer among the three groups. The selected parameters that showed a significant difference between the P. vivax and the other group were included in the logistic regression analysis to develop our model (N-OIpv model). Moreover, we analyzed the CBC data according to the previous models, such as the presence of abnormal blue coded events in the WBC/BASO scattergram called the observer-interpretation (OIpv) model, and the previous equation model (N-OD1pv model) developed by Campuzano-Zuluaga et al. Results: The N-OIpv model, which consists of three parameters, such as mean cell volume, plateletcrit, and Lymph-X, showed the best performance for detection of malaria (97.4% accuracy). Also, this model can increase the sensitivity by about 11.9% to 18.1% compared with the OIpv and N-OD1pv models, respectively. CONCLUSIONS: We concluded that the N-OIpv model using the Sysmex hematology analyzer is a useful diagnostic tool in the routine laboratory workup for malaria.

USP37 Deubiquitinates CDC73 in HPT-JT Syndrome.

The CDC73/HRPT2 gene, a defect which causes hyperparathyroidism-jaw tumor (HPT-JT) syndrome, encodes CDC73/parafibromin. We aimed to investigate whether CDC73 would be a target for ubiquitin-proteasome degradation. We cloned full-length cDNAs encoding a family of 58 ubiquitin-specific deubiquitinating enzymes (DUBs), also known as ubiquitin-specific proteases (USPs). Use of the yeast two-hybrid system then enabled us to identify USP37 as interacting with CDC73. The biochemical interaction between the USP37 and CDC73 and their reciprocal binding domains were studied. Co-localization of CDC73 and USP37 was observed in cells. CDC73 was found to be polyubiquitinated, and polyubiquitination of CDC73 was prominent in mutants. CDC73 was deubiquitinated via K48-specific ubiquitin chains by USP37, but not by the catalytically inactive USP37C350S mutant. Observation of the binding between deletion mutants of CDC73 and USP37 revealed that the ß-catenin binding site of CDC73 and the ubiquitin-interacting motifs 2 and 3 (UIM2 and 3) of USP37 were responsible for the interaction between the two proteins. Moreover, these two enzymes co-existed within the nucleus of COS7 cells. We conclude that USP37 is a DUB for CDC73 and that the two proteins interact through specific domains, suggesting that USP37 is responsible for the stability of CDC73 in HPT-JT syndrome.

Radiogenomic Analysis of Breast Cancer by Using B-Mode and Vascular US and RNA Sequencing.

Background Radiogenomic investigations for breast cancer provide an understanding of tumor heterogeneity and discover image phenotypes of genetic variation. However, there is little research on the correlations between US features of breast cancer and whole-transcriptome profiling. Purpose To explore US phenotypes reflecting genetic alteration relevant to breast cancer treatment and prognosis by comparing US images of tumor with their RNA sequencing results. Materials and Methods From January to October 2016, B-mode and vascular US images in 31 women (mean age, 49 years ± 9 [standard deviation]) with breast cancer were prospectively analyzed. B-mode features included size, shape, echo pattern, orientation, margin, and calcifications. Vascular features were evaluated by using microvascular US and contrast agent-enhanced US: vascular index, vessel morphologic features, distribution, penetrating vessels, enhancement degree, order, margin, internal homogeneity, and perfusion defect. RNA sequencing was conducted with total RNA obtained from a surgical specimen by using next-generation sequencing. US features were compared with gene expression profiles, and ingenuity pathway analysis was used to analyze gene networks, enriched functions, and canonical pathways associated with breast cancer. The P value for differential expression was extracted by using a parametric F test comparing nested linear models. Results Thirteen US features were associated with various patterns of 340 genes (P < .05). Nonparallel orientation at B-mode US was associated with upregulation of TFF1 (log twofold change [log2FC] = 4.0; P < .001), TFF3 (log2FC = 2.5; P < .001), AREG (log2FC = 2.6; P = .005), and AGR3 (log2FC = 2.6; P = .003). Complex vessel morphologic structure was associated with upregulation of FZD8 (log2FC = 2.0; P = .01) and downregulation of IGF1R (log2FC = -2.0; P = .006) and CRIPAK (log2FC = -2.4; P = .01). The top networks with regard to orientation or vessel morphologic structure were associated with cell cycle, death, and proliferation. Conclusion Compared with RNA sequencing, B-mode and vascular US features reflected genomic alterations associated with hormone receptor status, angiogenesis, or prognosis in breast cancer. © RSNA, 2020 Online supplemental material is available for this article.

Analytical Performance of Two Enzymatic Methods for Glycated Albumin.

BACKGROUND: The measurement of glycemic control among patients with diabetes mellitus is important for predicting the risk of diabetic complications. Glycated hemoglobin (HbA1c) measurements have been used for long-term glycemic control in clinical practice. However, glycated albumin (GA) or glycated serum protein (GSP) is a more reliable indicator of glycemic control in the short term (2 - 4 weeks) and an alternative marker of HbA1c in clinical situations with changing red blood cell (RBC) lifespan. Here, we evaluated an analytical performance of the two enzymatic assays commercially available, Lucica GA-L and Autolab GA, for the determination of GA (%). METHODS: For each assay, the imprecision was evaluated based on CLSI EP05-A2. In total, serum samples of 283 subjects were simultaneously tested using the two enzymatic assays for method comparison according to CLSI EP09-A3. Some subjects collected the laboratory data for HbA1c. RESULTS: The GA (%) value of the Lucica GA-L assay showed highly reproducible results with within-run, between-run, and total coefficient of variations (CVs) below 2.4%. The Autolab GA assay also showed reliable results with within-run, between-run, and total CVs below 3.9%. The Lucica GA-L assay showed a very high correlation with the Autolab GA assay (r = 0.9993). However, at the median decision point (MDP, 14.3%), the estimated bias of the Autolab GA assay was 4.5%, exceeding the allowable bias (2.9%) accounting for the biological variation. For the correlation analysis between HbA1c and GA (%), the two assays demonstrated the same pattern, with no statistical differences between the two independent correlation coefficients. CONCLUSIONS: Both GA assays evaluated in this study showed good precision and excellent correlation, but the comparability at MDP did not meet the acceptance criteria.

Evaluation of Elecsys HTLV-I/II assay in comparison with ARCHITECT rHTLV-I/II assay with Korean samples.

BACKGROUND: The seroprevalence rate of human T-lymphotropic virus I and II (HTLV-I/II) in Korean blood donors has been known as 0.004%, and HTLV-I/II Ab screening test has been performed since 2008 in Korea. Korea Ministry of Food and Drug Safety (MFDS) approved two chemiluminescent microparticle immunoassays (CMIA) for testing HTLV-I/II antibody, ABBOTT PRISM HTLV-I/HTLV-II and ARCHITECT rHTLV-I/II. A multicenter performance evaluation study in Europe and Japan was carried out with the new electrochemiluminescence immunoassay (ECLIA) for HTLV-I/II antibody detection, Elecsys HTLV-I/II assay which launched in 2017, but not in Korea. We aimed to evaluate the clinical performance of Elecsys HTLV-I/II assay in comparison with ARCHITECT rHTLV-I/II for the detection of HTLV-I/II antibody with Korean samples. METHODS: For sensitivity evaluation, 100 HTLV-I/II-positive Korean standards from Korean Red Cross and two HTLV-II-positive samples that were purchased from Seracure were used. For the specificity, 500 potential donor specimens from Korea University Hospital healthcare center were used. All the samples were simultaneously analyzed by the two HTLV-I/II assays, Elecsys HTLV-I/II assay and ARCHITECT rHTLV-I/II assay. RESULTS: Elecsys HTLV-I/II assay and ARCHITECT rHTLV-I/II assay showed a complete agrement. Elecsys HTLV-I/II assay showed 100% sensitivity (95% CI: 96.38-100.0) and specificity (95% CI: 99.26-100.0). CONCLUSIONS: Elecsys HTLV-I/II assay is as reliable as ARCHITECT rTHLV-I/II assay, and can be used as a screening test for HTLV-I/II in Korea.

Comparison of three multiplex PCR assays for detection of respiratory viruses: Anyplex II RV16, AdvanSure RV, and Real-Q RV.

BACKGROUND: Due to its great sensitivity, the nucleic acid amplification test (NAAT) is widely used for detection of respiratory viruses (RV). However, few reports have described a direct comparison between multiplex RT-PCR assays for RV. The objective of this study was to perform a direct comparison of three multiplex RT-PCR assays for the detection of respiratory viruses. METHODS: A total of 201 respiratory samples (161 nasopharyngeal swab samples and 40 sputum samples) were tested with three commercial RV assays: Seegene Anyplex II RV16 (AP), LG AdvanSure RV (AD), and Biosewoom Real-Q RV (RQ). The additional tests for the discrepant results were conducted by repeat RV assay or monoplex PCR coupled direct sequencing. Data analysis using percent agreement, kappa, and prevalence-adjusted and bias-adjusted kappa (PABAK) values was performed for comparisons among the three RV assays. RESULTS: Of the 201 samples, AP, AD, and RQ detected 105 (52.2%), 99 (49.3%), and 95 (47.3%) positive cases respectively. The overall agreement, kappa, and PABAK values for the three assays ranged between 97%-98%, 0.76-0.86, and 0.93-0.96 respectively. The performance of the three assays was very similar, with 94%-100% agreement for all comparisons, each virus types. The additional testing of samples showed discrepant results demonstrating that AD assay had the highest rate of concordance with original results. CONCLUSIONS: We suggest that all multiplex assay would be suitable for the detection of for respiratory viruses in clinical setting.

Comparison between Saliva and Nasopharyngeal Swab Specimens for Detection of Respiratory Viruses by Multiplex Reverse Transcription-PCR.

Nasopharyngeal swabs (NPSs) are being widely used as specimens for multiplex real-time reverse transcription (RT)-PCR for respiratory virus detection. However, it remains unclear whether NPS specimens are optimal for all viruses targeted by multiplex RT-PCR. In addition, the procedure to obtain NPS specimens causes coughing in most patients, which possibly increases the risk of nosocomial spread of viruses. In this study, paired NPS and saliva specimens were collected from 236 adult male patients with suspected acute respiratory illnesses. Specimens were tested for 16 respiratory viruses by multiplex real-time RT-PCR. Among the specimens collected from the 236 patients, at least 1 respiratory virus was detected in 183 NPS specimens (77.5%) and 180 saliva specimens (76.3%). The rates of detection of respiratory viruses were comparable for NPS and saliva specimens (P = 0.766). Nine virus species and 349 viruses were isolated, 256 from NPS specimens and 273 from saliva specimens (P = 0.1574). Adenovirus was detected more frequently in saliva samples (P < 0.0001), whereas influenza virus type A and human rhinovirus were detected more frequently in NPS specimens (P = 0.0001 and P = 0.0289, respectively). The possibility of false-positive adenovirus detection from saliva samples was excluded by direct sequencing. In conclusion, neither of the sampling methods was consistently more sensitive than the other. We suggest that these cost-effective methods for detecting respiratory viruses in mixed NPS-saliva specimens might be valuable for future studies.

Fatal Graft-Versus-Host Disease Following Adult-To-Adult Living Donor Liver Transplantation From an HLA Nonhomozygous Donor.

The use of a human leukocyte antigen (HLA) homozygous donor to a haploidentical recipient is a well-documented cause of transfusion-associated graft-versus-host disease (GVHD). Several authors have reported that use of a graft from an HLA-homozygous donor with 1-way donor-recipient HLA matching led to an extremely high risk of developing GVHD in LDLT. We have experienced a fatal case of acute GVHD following adult-to-adult LDLT from a donor who was heterozygous at a single HLA locus. A 53-year-old female underwent LDLT for chronic hepatitis B and recurrent hepatocellular carcinoma. The donor was her 23-year-old son. The HLA phenotype of the donor was not homozygous (A24, -; B54, -; DR4, 9) and revealed one-way donor-dominant HLA matching at two loci with the recipient (A2, 24; B48, 54; DR4, 12). On the fortieth postoperative day, the patient showed erythematous skin lesions. Skin biopsy revealed typical findings of GVHD. Donor-derived chimerism was demonstrated by performing fluorescent in situ hybridization (FISH) using the recipient's skin tissue. As the clinical course deteriorated, etanercept was started in addition to broad-spectrum antibiotics but there was no improvement. As multi-organ failure progressed, the patient succumbed to death on the 54th postoperative day, which was 2 weeks after onset of GVHD. The prevention of GVHD is more important since the results of treatment have been disappointing. We have experienced a fatal case of acute GVHD following adult-to-adult LDLT from a HLA non-homozygous donor. HLA heterozygosity at a single locus does not preclude the possibility of developing GVHD following adult-to-adult LDLT.

Nontuberculous mycobacterial infection in a clinical presentation of Fitz-Hugh-Curtis syndrome: a case report with multigene diagnostic approach.

BACKGROUND: Fitz-Hugh-Curtis syndrome (FHCS) is caused by inflammation of perihepatic capsules associated with pelvic inflammatory disease. In recent years, infections with nontuberculous mycobacteria (NTM) have been increasingly occurring in immunocompromised and immunocompetent patients. However, NTM has never been reported in patients with FHCS. We present the first case of a patient with extrapulmonary NTM infection in a clinical presentation of FHCS. CASE PRESENTATION: A 26-year-old Korean woman presented with right upper quadrant and suprapubic pain. She was initially suspected to have FHCS. However, she was refractory to conventional antibiotic therapy. Laparoscopy revealed multiple violin-string adhesions of the parietal peritoneum to the liver and miliary-like nodules on the peritoneal surfaces. Diagnosis of NTM was confirmed by the polymerase chain reaction analysis results of biopsy specimens that showed caseating granulomas with positive acid-fast bacilli. Treatment with anti-NTM medications was initiated, and the patient's symptoms were considerably ameliorated. CONCLUSIONS: An awareness of NTM as potential pathogens, even in previously healthy adults, and efforts to exclude other confounding diseases are important to establish the diagnosis of NTM disease. NTM infection can cause various clinical manifestations, which in the present case, overlapped with the symptoms of perihepatic inflammation seen in FHCS.

Diabetes severity and the risk of depression: A nationwide population-based study.

BACKGROUND: In consideration of the substantial occurrence rates of diabetes mellitus (DM) and depression, it is imperative to identify patients with DM who are at an elevated risk of developing depression. Accordingly, this study aimed to examine whether the risk of depression escalated proportionally with the severity of diabetes. METHODS: 2,067,017 adults diagnosed with type 2 DM, with the exception of those diagnosed with depression either before or within one year of the index date, were identified from a nationwide population-based cohort in Korea. Severity scores for DM were established based on various factors, including insulin use, DM duration of at least 5 years, use of three or more oral hypoglycemic agents, the presence of chronic kidney disease (CKD), cardiovascular diseases (CVD), or diabetic retinopathy. Each of these attributes was assigned a score of one point for diabetes severity, and their cumulative sum was defined as a diabetes severity score, ranging from 0 to 6. RESULTS: During a median follow-up of 6.2 years, 407,047 cases of major depression were identified. Each component contributing to the DM severity score was significantly associated with an increased risk of depression (all P-values <0.001), with insulin use and the presence of CVD demonstrating the most significant correlation with depression risk. As the DM severity score increased, the risk of depression was observed to significantly escalate (P for trend <0.001). After adjusting for potential confounding variables, the hazard ratios (95% confidence intervals) of depression were 1.15 (1.14-1.16) in 1 point, 1.28 (1.27-1.29) in 2 points, 1.45 (1.43-1.47) in 3 points, 1.70 (1.67-1.73) in 4 points, 1.91 (1.84-1.98) in 5 points, and 2.01 (1.79-2.26) in 6 points, respectively. CONCLUSION: The results of this study indicate that diabetes severity is positively associated with an elevated risk of developing major depression. Based on these findings, it is feasible to consider targeting depression screening efforts towards individuals with higher diabetes severity scores.

Comparison of Neutralizing Activity between Vaccinated and Unvaccinated Hospitalized COVID-19 Patients Infected with Delta, Omicron BA.1, or Omicron BA.2 Variant.

BACKGROUND: Understanding the immune response to evolving viral strains is crucial for evidence-informed public health strategies. The main objective of this study is to assess the influence of vaccination on the neutralizing activity of SARS-CoV-2 delta and omicron infection against various SARS-CoV-2 variants. METHODS: A total of 97 laboratory-confirmed COVID-19 cases were included. To assess the influence of vaccination on neutralizing activity, we measured the neutralizing activity of SARS-CoV-2 delta or omicron (BA.1 or BA.2) infection against wild-type (WT), delta, BA.1, and BA.2, with the results stratified based on vaccination status. RESULTS: The neutralizing activity against the WT, delta, and omicron variants (BA.1 and BA.2) was significantly higher in the vaccinated patients than those in the unvaccinated patients. In the unvaccinated individuals infected with the delta variant, the decrease in binding to BA.1 and BA.2 was statistically significant (3.9- and 2.7-fold, respectively) compared to the binding to delta. In contrast, vaccination followed by delta breakthrough infection improved the cross-neutralizing activity against omicron variants, with only 1.3- and 1.2-fold decreases in BA.1 and BA.2, respectively. Vaccination followed by infection improved cross-neutralizing activity against WT, delta, and BA.2 variants in patients infected with the BA.1 variant, compared to that in unvaccinated patients. CONCLUSIONS: Vaccination followed by delta or BA.1 infection is associated with improved cross-neutralizing activity against different SARS-CoV-2 variants. The enhanced protection provided by breakthrough infections could have practical implications for optimizing vaccination strategies.

Molecular characterization of human respiratory syncytial virus in Seoul, South Korea, during 10 consecutive years, 2010-2019.

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections and hospitalization in infants and young children. Here, we analyzed the genetic diversity of RSV using partial G gene sequences in 84 RSV-A and 78 RSV- B positive samples collected in Seoul, South Korea, for 10 consecutive years, from 2010 to 2019. Our phylogenetic analysis revealed that RSV-A strains were classified into either the ON1 (80.9%) or NA1 (19.0%) genotypes. On the other hand, RSV-B strains demonstrated diversified clusters within the BA genotype. Notably, some sequences designated as BA-SE, BA-SE1, and BA-DIS did not cluster with previously identified BA genotypes in the phylogenetic trees. Despite this, they did not meet the criteria for the assignment of a new genotype based on recent classification methods. Selection pressure analysis identified three positive selection sites (amino acid positions 273, 274, and 298) in RSV-A, and one possible positive selection site (amino acid position 296) in RSV-B, respectively. The mean evolutionary rates of Korean RSV-A from 1999 to 2019 and RSV-B strains from 1991 and 2019 were estimated at 3.51 × 10-3 nucleotides (nt) substitutions/site/year and 3.32 × 10-3 nt substitutions/site/year, respectively. The population dynamics in the Bayesian skyline plot revealed fluctuations corresponding to the emergence of dominant strains, including a switch of the dominant genotype from NA1 to ON1. Our study on time-scaled cumulative evolutionary analysis contributes to a better understanding of RSV epidemiology at the local level in South Korea.

Performance Evaluation of Three Antibody Binding Assays, a Neutralizing Antibody Assay, and an Interferon-Gamma Release Assay for SARS-CoV-2 According to Vaccine Type in Vaccinated Group.

We evaluated the performance of SARS-CoV-2 assays in the vaccinated group using receptor-binding domain antibody assays (RBD Ab assay), neutralizing antibody assay (nAb assay), and interferon-gamma release assay (IGR assay). We also compared the performance of the SARS-CoV-2 assays based on vaccine type in a large population. We collected 1851 samples from vaccinated individuals with vector, mix-and-match (MM), and mRNA vaccines. The performance of the RBD Ab assays was assessed by SARS-CoV-2 IgG II Quant (Abbott Laboratories, Sligo, Ireland), SARS-CoV-2 IgG (Beckman Coulter, CA, USA), and anti-SARS-CoV-2 S (Roche Diagnostics GmbH, Mannheim, Germany). The nAb assay was assessed by cPass SARS-CoV-2 neutralization antibody detection kits (GenScript, NJ, USA). The IGR assay was assessed by QuantiFERON (Qiagen, Venlo, The Netherlands). Median values of the RBD Ab assays and nAb assay sequentially increased after the first and second vaccinations. RBD Ab assays and nAb assay showed very strong correlations. The median values of the RBD Ab, nAb, and IGR were higher in the mRNA vaccine group than in the vector and MM vaccine groups. The agreement and correlation among the RBD Ab assays, nAb assay, and IGR assay were higher in the mRNA vaccine group than in the vector and MM vaccine groups. We compared the performance of the RBD Ab assay, nAb assay, and IGR assay based on the vaccine types using the RBD Ab, nAb, and IGR assays. This study provides a better understanding of the assessment of humoral and cellular immune responses after vaccination.

A new allele, HLA-C*08:228, identified by sequence-based typing in a Korean individual.

The new allele C*08:228 showed one nucleotide difference from C*08:01:01 in codon 36 (TTC -> TTG).

Usefulness of Combining Sputum and Nasopharyngeal Samples for Viral Detection by Reverse Transcriptase PCR in Adults Hospitalized with Acute Respiratory Illness.

Nasopharyngeal swabs (NPS) or washings have traditionally been used to diagnose respiratory tract infections. Reverse transcriptase PCR (RT-PCR) is widely used for rapid viral detection using samples from the upper respiratory tract. However, RT-PCR is rarely applied to sputum samples, mainly due to the viscosity of sputum. Thus, we assessed the detection rates of respiratory viruses from NPS, sputum samples, and combined NPS and sputum samples using multiplex RT-PCR (Allplex respiratory panels I, II, and III; Seegene, Seoul, South Korea). Paired NPS and sputum samples were collected from 219 patients admitted to the hospital with acute respiratory illnesses from October to December 2019. RT-PCR was performed on each sample for virus detection. Combined samples for virus detection were produced using remnant NPS and sputum samples with a positive virus signal. Respiratory viral nucleic acid was identified in 92 (42%) of 219 patients. Among the 92 viral detections, 61 (28%) were detected by both NPS and sputum samples. Twenty-four (11%) were sputum positive/NPS negative, and seven (3%) were sputum negative/NPS positive. For the combined NPS-sputum samples (n = 92), all paired samples positive in both specimens (n = 61) were also positive in the combined NPS-sputum sample. Twenty-seven (87%) of the 31 discordant paired samples were positive in the combined samples. Out of the total of 103 viruses identified before combining the samples, the detection rate of the combined samples was 94% (97/103), which was higher than the detection rates of sputum (88%; 91/103) and NPS (71%; 73/103). Because additional tests incur additional costs, our findings suggest that combining samples instead of testing separate samples using RT-PCR is likely the most cost-effective method of viral testing for patients with acute respiratory illnesses. IMPORTANCE This study reveals that RT-PCR utilizing sputum significantly increased the detection rate for respiratory viral nucleic acids among adult patients admitted to the hospital, compared to nasopharyngeal swabs (NPS). Notably, combined samples of sputum and NPS maintained the majority of the improved sputum detection rate with only a few positive signal losses from NPS samples. In order to detect respiratory viruses in adult patients with acute respiratory illness, it is important to choose the optimal respiratory samples. This study helped to improve our understanding of this process.