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  1. Article ; Online: Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays.

    Fung, Becky / Gopez, Allan / Servellita, Venice / Arevalo, Shaun / Ho, Coral / Deucher, Anne / Thornborrow, Ed / Chiu, Charles / Miller, Steve

    Journal of clinical microbiology

    2020  Volume 58, Issue 9

    Abstract: Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material ... ...

    Abstract Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85 to 499 copies/ml, depending on the extraction method and thermocycler used. These results can help to inform the assay choice for testing approaches to manage the current COVID-19 outbreak.
    MeSH term(s) Betacoronavirus/genetics ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Clinical Laboratory Techniques/statistics & numerical data ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Humans ; Limit of Detection ; Molecular Diagnostic Techniques/methods ; Molecular Diagnostic Techniques/statistics & numerical data ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; RNA, Viral/analysis ; RNA, Viral/genetics ; SARS-CoV-2
    Chemical Substances RNA, Viral
    Keywords covid19
    Language English
    Publishing date 2020-08-24
    Publishing country United States
    Document type Comparative Study ; Journal Article
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.01535-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1188: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme.

    Fasching, Clare L / Servellita, Venice / McKay, Bridget / Nagesh, Vaishnavi / Broughton, James P / Sotomayor-Gonzalez, Alicia / Wang, Baolin / Brazer, Noah / Reyes, Kevin / Streithorst, Jessica / Deraney, Rachel N / Stanfield, Emma / Hendriks, Carley G / Fung, Becky / Miller, Steve / Ching, Jesus / Chen, Janice S / Chiu, Charles Y

    Journal of clinical microbiology

    2022  Volume 60, Issue 7, Page(s) e0026122

    Abstract: Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here, we present the development and ... ...

    Abstract Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here, we present the development and validation of a rapid COVID-19 variant DETECTR assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene. This assay targets the L452R, E484K/Q/A, and N501Y mutations, at least one of which is found in nearly all major variants. In a comparison of three different Cas12 enzymes, only the newly identified enzyme CasDx1 was able to accurately identify all targeted SNP mutations. An analysis pipeline for CRISPR-based SNP identification from 261 clinical samples yielded a SNP concordance of 97.3% and agreement of 98.9% (258 of 261) for SARS-CoV-2 lineage classification, using SARS-CoV-2 whole-genome sequencing and/or real-time RT-PCR as test comparators. We also showed that detection of the single E484A mutation was necessary and sufficient to accurately identify Omicron from other major circulating variants in patient samples. These findings demonstrate the utility of CRISPR-based DETECTR as a faster and simpler diagnostic method compared with sequencing for SARS-CoV-2 variant identification in clinical and public health laboratories.
    MeSH term(s) COVID-19/diagnosis ; COVID-19 Testing ; CRISPR-Cas Systems ; Clinical Laboratory Techniques/methods ; Humans ; Mutation ; SARS-CoV-2/genetics ; Sensitivity and Specificity
    Language English
    Publishing date 2022-06-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.00261-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1188: Show issues Location:
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  3. Article: Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays

    Fung, Becky / Gopez, Allan / Servellita, Venice / Arevalo, Shaun / Ho, Coral / Deucher, Anne / Thornborrow, Ed / Chiu, Charles / Miller, Steve

    J. clin. microbiol

    Abstract: Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material ... ...

    Abstract Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85 to 499 copies/ml, depending on the extraction method and thermocycler used. These results can help to inform the assay choice for testing approaches to manage the current COVID-19 outbreak.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #638997
    Database COVID19

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  4. Article ; Online: Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays.

    Fung, Becky / Gopez, Allan / Servellita, Venice / Arevalo, Shaun / Ho, Coral / Deucher, Anne / Thornborrow, Ed / Chiu, Charles / Miller, Steve

    Journal of clinical microbiology, vol 58, iss 9

    2020  

    Abstract: Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material ... ...

    Abstract Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85 to 499 copies/ml, depending on the extraction method and thermocycler used. These results can help to inform the assay choice for testing approaches to manage the current COVID-19 outbreak.
    Keywords Humans ; Pneumonia ; Viral ; Coronavirus Infections ; RNA ; Clinical Laboratory Techniques ; Molecular Diagnostic Techniques ; Limit of Detection ; Pandemics ; Betacoronavirus ; SARS-CoV-2 ; Microbiology ; Biological Sciences ; Agricultural and Veterinary Sciences ; Medical and Health Sciences ; covid19
    Publishing date 2020-08-24
    Publisher eScholarship, University of California
    Publishing country us
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays

    Fung, Becky / Gopez, Allan / Servellita, Venice / Arevalo, Shaun / Ho, Coral / Deucher, Anne / Thornborrow, Ed / Chiu, Charles / Miller, Steve

    Journal of Clinical Microbiology

    2020  Volume 58, Issue 9

    Abstract: ABSTRACT Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material ... ...

    Abstract ABSTRACT Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85 to 499 copies/ml, depending on the extraction method and thermocycler used. These results can help to inform the assay choice for testing approaches to manage the current COVID-19 outbreak.
    Keywords Microbiology (medical) ; covid19
    Language English
    Publisher American Society for Microbiology
    Publishing country us
    Document type Article ; Online
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.01535-20
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1188: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Impacts of Antimalarial Drugs on

    Hemming-Schroeder, Elizabeth / Umukoro, Emuejevuoke / Lo, Eugenia / Fung, Becky / Tomás-Domingo, Pedro / Zhou, Guofa / Zhong, Daibin / Dixit, Amruta / Atieli, Harrysone / Githeko, Andrew / Vardo-Zalik, Anne / Yan, Guiyun

    The American journal of tropical medicine and hygiene

    2018  Volume 98, Issue 3, Page(s) 692–699

    Abstract: Antimalarial drug resistance has threatened global malaria control since chloroquine (CQ)- ... ...

    Abstract Antimalarial drug resistance has threatened global malaria control since chloroquine (CQ)-resistant
    MeSH term(s) Adolescent ; Antimalarials/administration & dosage ; Antimalarials/therapeutic use ; Child ; Chloroquine/therapeutic use ; Drug Combinations ; Drug Resistance/genetics ; Genetic Markers ; Haplotypes ; Humans ; Kenya ; Malaria, Falciparum/drug therapy ; Mutation ; Plasmodium falciparum/drug effects ; Plasmodium falciparum/genetics ; Time Factors
    Chemical Substances Antimalarials ; Drug Combinations ; Genetic Markers ; Chloroquine (886U3H6UFF)
    Language English
    Publishing date 2018-01-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2942-7
    ISSN 1476-1645 ; 0002-9637
    ISSN (online) 1476-1645
    ISSN 0002-9637
    DOI 10.4269/ajtmh.17-0763
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Ud II Zs.61: Show issues Location:
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  7. Article ; Online: Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.

    Miller, Steve / Naccache, Samia N / Samayoa, Erik / Messacar, Kevin / Arevalo, Shaun / Federman, Scot / Stryke, Doug / Pham, Elizabeth / Fung, Becky / Bolosky, William J / Ingebrigtsen, Danielle / Lorizio, Walter / Paff, Sandra M / Leake, John A / Pesano, Rick / DeBiasi, Roberta / Dominguez, Samuel / Chiu, Charles Y

    Genome research

    2019  Volume 29, Issue 5, Page(s) 831–842

    Abstract: Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we ...

    Abstract Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of 0.2-313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, spiked phages used as internal controls were reliable indicators of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, and 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, encephalitis, and/or myelitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.
    MeSH term(s) Child ; Computational Biology ; Encephalitis/cerebrospinal fluid ; Encephalitis/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Meningitis, Aseptic/cerebrospinal fluid ; Meningitis, Aseptic/diagnosis ; Metagenomics/methods ; Myelitis/cerebrospinal fluid ; Myelitis/diagnosis ; Sensitivity and Specificity ; Viruses/isolation & purification
    Language English
    Publishing date 2019-04-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Validation Study
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.238170.118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3729: Show issues Location:
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