Investigation of SARS-CoV-2 lineages and mutations circulating in a university-affiliated hospital in South Korea analyzed using Oxford Nanopore MinION sequencing

Objectives: Despite the introduction of vaccines, treatments, and massive diagnostic testing, the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to overcome barriers that had slowed its previous spread. As the virus evolves towards increasing fitness, it is critical to continue monitoring the occurrence of new mutations that could evade human efforts to control them. Methods: We performed whole-genome sequencing using Oxford Nanopore MinION sequencing on 58 SARS-CoV-2 isolates collected during the ongoing coronavirus disease 2019 pandemic at a tertiary hospital in South Korea and tracked the emergence of mutations responsible for massive spikes in South Korea. Results: The differences among lineages were more pronounced in the spike gene, especially in the receptor-binding domain (RBD), than in other genes. Those RBD mutations could compromise neutralization by antibodies elicited by vaccination or previous infections. We also reported multiple incidences of Omicron variants carrying mutations that could impair the diagnostic sensitivity of reverse transcription-polymerase chain reaction-based testing. Conclusion: These results provide an understanding of the temporal changes of variants and mutations that have been circulating in South Korea and their potential impacts on antigenicity, therapeutics, and diagnostic escape of the virus. We also showed that the utilization of the nanopore sequencing platform and the ARTIC workf low can provide convenient and accurate SARS-CoV-2 genomic surveillance even at a single hospital.ope

Laboratory Diagnosis of Carbapenemase-producing Enterobacterales

Carbapenem-resistant enterobacterales (CREs) are pathogens of special concern in healthcareassociated infections. Enterobacterales become resistant to carbapenems through several mechanisms, including carbapenemase enzyme production. Enterobacterales that produce carbapenemase are known as carbapenemase-producing enterobacterales (CPEs). Genes encoding carbapenemase are usually found on plasmids that can transmit horizontally between strains, which could explain the rapid spread of carbapenem resistance. Timely and accurate laboratory tests of CPE are necessary to prevent and treat these infections. Various phenotypic tests, such as the modified Hodge test, modified carbapenem inactivation method (mCIM) with or without EDTA-CIM (eCIM), chromogenic agar test, carba NP, immunoassay, mass spectrometry, and molecular tests are available. In this study, we discussed the importance of CRE and CPE control in the COVID-19 pandemic era and summarized several laboratory CPE detection methods currently utilized in clinical microbiology laboratories.ope

Clinical Evaluation of BioFire COVID-19 Test, BioFire Respiratory Panel 2.1, and Cepheid Xpert Xpress SARS-CoV-2 Assays for Sample-to-Answer Detection of SARS-CoV-2

Background: Due to the extreme infectivity of SARS-CoV-2, sample-to-answer SARS-CoV-2 reverse transcription (RT) polymerase chain reaction (PCR) assays are urgently needed in order to facilitate infectious disease surveillance and control. The purpose of this study was to evaluate three sample-to-answer SARS-CoV-2 RT-PCR assays—BioFire COVID-19 Test, BioFire RP 2.1, and Cepheid Xpert Xpress SARS-CoV-2—using clinical samples. Methods: A total of 77 leftover nasopharyngeal swab (NP) swabs (36 positives and 41 negatives) confirmed by reference SARS-CoV-2 RT real-time (q) PCR assay were collected. The clinical sample concordance, as specified by their respective emergency use authorizations (EUAs), in comparison to the reference SARS-CoV-2 RT-qPCR assay, was assessed. Results: The results showed that all three sample-to-answer SARS-CoV-2 RT-PCR assays provided perfectly concordant results consistent with the reference SARS-CoV-2 RT-qPCR assay. The BioFire COVID-19 Test exhibited the best turnaround time (TAT) compared to the other assays, regardless of the test results, using one-way analysis of variance followed by Scheffe’s post hoc test (p < 0.001). The Xpert Xpress SARS-CoV-2 showed a shorter average TAT (mean ± standard deviation, 49.9 ± 3.1 min) in the positive samples compared to that (55.7 ± 2.5 min) of the negative samples. Conclusions: Our evaluation demonstrates that the BioFire COVID-19 Test, BioFire RP 2.1, and Cepheid Xpert Xpress SARS-CoV-2 assays compare favorably to the reference SARS-CoV-2 RT-qPCR assay, along with a 100% concordance in assay results for clinical samples and an acceptable analytical performance at their guaranteed limits of detection. The addition of a widely used simultaneous sample-to-answer SARS-CoV-2 RT-PCR assay will contribute to the number of medical laboratories able to test for COVID-19. © 2023 by the authors.ope

Guidelines for Mobile Laboratories for Molecular Diagnostic Testing of COVID-19

With the rapid spread of the coronavirus disease (COVID-19), the need for rapid testing and diagnosis and consequently, the demand for mobile laboratories have increased. Despite this need, there are no clear guidelines for the operation, maintenance, or quality control of mobile laboratories. We provide guidelines for the operation, management, and quality control of mobile laboratories, and specifically for the implementation and execution of COVID-19 molecular diagnostic testing. These practical guidelines are primarily based on expert opinions and a laboratory accreditation inspection checklist. The scope of these guidelines includes the facility, preoperative evaluation, PCR testing, internal and external quality control, sample handling, reporting, laboratory personnel, biosafety level, and laboratory safety management. These guidelines are useful for the maintenance and operation of mobile laboratories not only in normal circumstances but also during public health crises and emergencies.ope

Korean National Healthcare-associated Infections Surveillance System, Intensive Care Unit Module Report: Summary of Data from July 2020 through June 2021

Background: The Korean National Healthcare-associated Infections Surveillance System (KONIS) is a nationwide surveillance network established by the Korean Society for Healthcare-Associated Infection and Prevention in July 2006 to perform healthcare-associated infection surveillance using standardized methods. This report presents the annual data of the intensive care unit (ICU) module of the KONIS system between July 2020 and June 2021. Methods: We performed prospective surveillance of healthcare-associated infections (HAIs), including urinary tract infections (UTIs), bloodstream infections (BSIs), and pneumonia (PNEU), at 339 ICUs in 257 hospitals using the KONIS database. HAI rates and device-associated infection (DAI) rates were calculated as the numbers of infections per 1,000 patient days (PD) and device days (DD), respectively. Device utilization was calculated as the ratio (DUR) of device days to patient days. Results: A total of 4,435 HAIs were found during the study period: 1,645 UTIs (1,589 cases were urinary catheter-associated), 1,994 BSIs (1,753 were central line-associated), and 796 PNEUs (383 were ventilator-associated). The rate of urinary catheter-associated UTIs (CAUTI) was 1.30 cases per 1,000 DD (95% confidence interval [CI], 1.24-1.36) and DUR was 0.74 (95% CI, 0.739-0.741). The rate of central line-associated BSIs was 2.21/1,000 DD (95% CI, 2.11-2.31) and DUR was 0.48 (95% CI, 0.479-0.481). The rate of ventilator-associated PNEUs was 0.79/1,000 DD (95% CD, 071-0.87) and DUR was 0.29 (95% CI, 0.289-0.291). Conclusion: The overall DAI rate was similar to that of the previous year’s data; however, the rate of VAP showed a trend of decline. Furthermore, all DURs were reduced. Therefore, continuous infection surveillance may reduce infection rates and device use.ope

Nationwide Survey for Current Status of Laboratory Diagnosis of Clostridioides difficile Infection in Korea

Background: The interest in Clostridioides difficile infection (CDI) has increased, and the choice of assays became wider since the first national survey in Korea on CDI diagnosis in 2015. We conducted a survey of the domestic CDI assays with more varied questions to understand the current situation in Korea. Methods: In April 2018, about 50 questions on the current status of CDI assays and details on implementation and perceptions were written, and a survey questionnaire was administered to laboratory medicine specialists in 200 institutions. Results: One-hundred and fifty institutions responded to the questionnaire, of which 90 (60.0%) including one commercial laboratory, performed CDI assays. The toxin AB enzyme immunoassay (toxin AB EIA), nucleic acid amplification test (NAAT), and C. difficile culture, glutamate dehydrogenase assay, alone or in combination with other assays, were used in 75 (84.3%), 52 (58.4%), 35 (36.0%), and 23 (25.8%), respectively, and 65 (73.0%) institutions performed a combination of two or more assays. The sensitivity of toxin AB EIA was more negatively perceived, and that on specificity was more positively perceived. The perception of sensitivity and specificity of NAAT was mostly positive. Perception on the algorithm test projected it as useful but in need of countermeasures. Sixty-three (73.3%) institutions responded that they performed surveillance on CDI. Conclusion: This study provides useful evidence on the current status of CDI laboratory diagnosis in Korea as well as on items that require improvement and is thought to aid in standardizing and improving the CDI laboratory diagnosis in Korea.ope

Concerns Regarding Validity of the Use of Bean Extract-Based Gargle for COVID-19 Diagnosis

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Rates of Coinfection Between SARS-CoV-2 and Other Respiratory Viruses in Korea

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Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay

The sensitivity of molecular diagnostics could be affected by nucleotide variants in pathogen genes, and the sites affected by such variants should be monitored. We report a single-nucleotide variant (SNV) in the nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., G29179T, which impairs the diagnostic sensitivity of the Xpert Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, CA, USA). We observed significant differences between the threshold cycle (Ct) values for envelope (E) and N genes and confirmed the SNV as the cause of the differences using Sanger sequencing. This SNV, G29179T, is the most prevalent in Korea and is associated with the B.1.497 virus lineage, which is dominant in Korea. Clinical laboratories should be aware of the various SNVs in the SARS-CoV-2 genome and consider their potential effects on the diagnosis of coronavirus disease 2019.ope

Clinical Performance of the Standard Q COVID-19 Rapid Antigen Test and Simulation of its Real-World Application in Korea

The rapid antigen test (RAT) for coronavirus disease (COVID-19) represents a potent diagnostic method in situations of limited molecular testing resources. However, considerable performance variance has been reported with the RAT. We evaluated the clinical performance of Standard Q COVID-19 RAT (SQ-RAT; SD Biosensor, Suwon, Korea), the first RAT approved by the Korean Ministry of Food and Drug Safety. In total, 680 nasopharyngeal swabs previously tested using real-time reverse-transcription PCR (rRT-PCR) were retested using SQ-RAT. The clinical sensitivity of SQ-RAT relative to that of rRT-PCR was 28.7% for all specimens and was 81.4% for specimens with RNA-dependent RNA polymerase gene (RdRp) threshold cycle (Ct) values ≤23.37, which is the limit of detection of SQ-RAT. The specificity was 100%. The clinical sensitivity of SQ-RAT for COVID-19 diagnosis was assessed based on the Ct distribution at diagnosis of 33,294 COVID-19 cases in Korea extracted from the laboratory surveillance system of Korean Society for Laboratory Medicine. The clinical sensitivity of SQ-RAT for COVID-19 diagnosis in the Korean population was 41.8%. Considering the molecular testing capacity in Korea, use of the RAT for COVID-19 diagnosis appears to be limited.ope