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Article ; Online: Adaptation and validation of a quantitative vanA/vanB DNA screening assay on a high-throughput PCR system.

Giersch, Katja / Tanida, Konstantin / Both, Anna / Nörz, Dominik / Heim, Denise / Rohde, Holger / Aepfelbacher, Martin / Lütgehetmann, Marc

Scientific reports

2024 Volume 14, Issue 1, Page(s) 3523

Abstract: Vancomycin resistant enterococci (VRE) are a leading cause of ICU-acquired bloodstream infections in Europe. The bacterial load in enteral colonization may be associated with a higher probability of transmission. Here, we aimed to establish a ... ...

Abstract	Vancomycin resistant enterococci (VRE) are a leading cause of ICU-acquired bloodstream infections in Europe. The bacterial load in enteral colonization may be associated with a higher probability of transmission. Here, we aimed to establish a quantitative vanA/vanB DNA real-time PCR assay on a high-throughput system. Limits of detection (LOD), linear range and precision were determined using serial bacterial dilutions. LOD was 46.9 digital copies (dcp)/ml for vanA and 60.8 dcp/ml for vanB. The assay showed excellent linearity between 4.7 × 10
MeSH term(s)	Humans ; Vancomycin-Resistant Enterococci/genetics ; Predictive Value of Tests ; Real-Time Polymerase Chain Reaction ; DNA ; DNA, Bacterial/genetics ; DNA, Bacterial/analysis ; Bacterial Proteins/genetics ; Gram-Positive Bacterial Infections/microbiology ; Anti-Bacterial Agents
Chemical Substances	DNA (9007-49-2) ; DNA, Bacterial ; Bacterial Proteins ; Anti-Bacterial Agents
Language	English
Publishing date	2024-02-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-54037-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Analytical and clinical validation of a multiplex PCR assay for detection of

Pflüger, Lisa Sophie / Nörz, Dominik / Grunwald, Moritz / Pfefferle, Susanne / Giersch, Katja / Christner, Martin / Weber, Beatrice / Aepfelbacher, Martin / Rohde, Holger / Lütgehetmann, Marc

Microbiology spectrum

2024 Volume 12, Issue 3, Page(s) e0275623

Abstract: For effective infection control measures ... ...

Abstract	For effective infection control measures for
MeSH term(s)	Humans ; Lymphogranuloma Venereum/diagnosis ; Neisseria gonorrhoeae/genetics ; Chlamydia trachomatis/genetics ; Multiplex Polymerase Chain Reaction ; Serotyping ; Prospective Studies ; Gonorrhea/diagnosis ; Sensitivity and Specificity
Language	English
Publishing date	2024-02-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.02756-23
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Article ; Online: Clinical evaluation of a fully automated, laboratory-developed multiplex RT-PCR assay integrating dual-target SARS-CoV-2 and influenza A/B detection on a high-throughput platform.

Nörz, Dominik / Hoffmann, Armin / Aepfelbacher, Martin / Pfefferle, Susanne / Lütgehetmann, Marc

Journal of medical microbiology

2021 Volume 70, Issue 2

Abstract: Introduction. ...

Abstract	Introduction.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing/methods ; High-Throughput Screening Assays/methods ; Humans ; Influenza A virus/genetics ; Influenza A virus/isolation & purification ; Influenza B virus/genetics ; Influenza B virus/isolation & purification ; Influenza, Human/diagnosis ; Influenza, Human/virology ; Limit of Detection ; Molecular Diagnostic Techniques/methods ; Multiplex Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity
Language	English
Publishing date	2021-01-06
Publishing country	England
Document type	Evaluation Study ; Journal Article
ZDB-ID	218356-0
ISSN	1473-5644 ; 0022-2615
ISSN (online)	1473-5644
ISSN	0022-2615
DOI	10.1099/jmm.0.001295
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Article ; Online: Comparison of four commercial EBV DNA quantitative tests to a new test at an early stage of development.

Stelzl, Evelyn / Kessler, Harald H / Parulekar, Amit D / Bier, Carolin / Nörz, Dominik / Schneider, Tanja / Kumar, Suchitra / Simon, Christian O / Lütgehetmann, Marc

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2023 Volume 161, Page(s) 105400

Abstract: Background: Regular screening for Epstein-Barr virus (EBV) DNA using quantitative RT-PCR is recommended for early intervention in at-risk patients. Harmonization of quantitative RT-PCR assays is critical to avoid misinterpretation of results. Here, we ... ...

Abstract	Background: Regular screening for Epstein-Barr virus (EBV) DNA using quantitative RT-PCR is recommended for early intervention in at-risk patients. Harmonization of quantitative RT-PCR assays is critical to avoid misinterpretation of results. Here, we compare quantitative results of the cobas® EBV assay to four commercial RT-qPCR assays. Methods: The cobas EBV, EBV R-Gene, artus EBV RG PCR, RealStar EBV PCR kit 2.0 and Abbott EBV RealTime assays were compared for analytic performance using a 10-fold dilution series of EBV reference material, normalized to the WHO standard. For clinical performance, their quantitative results were compared using anonymized, leftover EBV-DNA-positive EDTA plasma samples. Results: For analytic accuracy, the cobas EBV deviated -0.0097 log Conclusion: The cobas EBV showed the closest correlation to the reference material, followed closely by EBV R-Gene and Abbott EBV RealTime. Values obtained are stated in IU/mL, facilitating comparison across testing sites and potentially improving utilization of guidelines for diagnosis, monitoring, and treatment of patients.
MeSH term(s)	Humans ; Herpesvirus 4, Human/genetics ; Epstein-Barr Virus Infections/diagnosis ; Polymerase Chain Reaction/methods ; DNA, Viral/genetics ; Viral Load/methods ; Sensitivity and Specificity
Chemical Substances	DNA, Viral
Language	English
Publishing date	2023-02-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2023.105400
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Article: Screening for Monkeypox Infection in Asymptomatic High-Risk-Behaviour Men Having Sex with Men (MSM).

Pestel, Julia / Matthews, Hanna / Schmiedel, Stefan / Hüfner, Anja / Jordan, Sabine / Scheiter, Robin Luca / Lütgehetmann, Marc / Nörz, Dominik / Degen, Olaf

Infectious disease reports

2022 Volume 14, Issue 5, Page(s) 794–797

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2022-10-17
Publishing country	Switzerland
Document type	Journal Article
ISSN	2036-7430
ISSN	2036-7430
DOI	10.3390/idr14050081
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Article ; Online: Modifying a Diagnostic SARS-CoV-2 Spike PCR to Turn a Del69/70 Dropout into a Discriminatory On-Target Assay.

Nörz, Dominik / Pfefferle, Susanne / Grunwald, Moritz / Fischer, Nicole / Aepfelbacher, Martin / Lütgehetmann, Marc

The Journal of molecular diagnostics : JMD

2021 Volume 23, Issue 6, Page(s) 777–778

MeSH term(s)	COVID-19 ; Humans ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2021-04-13
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2021.03.007
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Zs.A 5146: Show issues

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Article ; Online: Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7.

Nörz, Dominik / Grunwald, Moritz / Olearo, Flaminia / Fischer, Nicole / Aepfelbacher, Martin / Pfefferle, Susanne / Lütgehetmann, Marc

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2021 Volume 141, Page(s) 104894

Abstract: Background: New SARS-CoV-2 variants with increased transmissibility, like B.1.1.7, first detected in England or B.1.351, first detected in South Africa, have caused considerable concern worldwide. In order to contain the spread of these lineages, it is ... ...

Abstract	Background: New SARS-CoV-2 variants with increased transmissibility, like B.1.1.7, first detected in England or B.1.351, first detected in South Africa, have caused considerable concern worldwide. In order to contain the spread of these lineages, it is of utmost importance to have rapid, sensitive and high-throughput detection methods at hand. Methods: A set of RT-qPCR assays was modified for a diagnostic SARS-CoV-2 multiplex assay including detection of the del-HV69/70 and N501Y mutations on the cobas6800 platform. Analytical sensitivity was assessed for both wild-type SARS-CoV-2 and B.1.1.7 lineage by serial dilution. For clinical performance, a total of 176 clinical samples were subjected to the test and results compared to a commercial manual typing-PCR assay and next generation sequencing as gold standard. Results: The multiplex assay was highly sensitive for detection of SARS-CoV-2 RNA in clinical samples, with an LoD of 6.16 cp/ml (CI: 4.00-8.31). LoDs were slightly higher for detection of the HV69/70 deletion (85.92, CI: 61-194.41) and the N501Y SNP (105.99 cp/ml, CI: 81.59 - 183.66). A total of 176 clinical samples were tested with the assay, including 50 samples containing SARS-CoV-2 of the B.1.1.7 lineage, one containing B.1.351 and 85 non-B.1.1.7/B.1.351 lineage, of which three also harbored a HV69/70 deletion. All were correctly identified by the multiplex assay. Conclusion: We describe here a highly sensitive, fully automated multiplex PCR assay for the simultaneous detection of the del-HV69/70 and N501Y mutations that can distinguish between B.1.1.7 and other lineages. The assay allows for high-throughput screening for currently relevant variants in clinical samples prior to sequencing.
MeSH term(s)	COVID-19 ; High-Throughput Screening Assays ; Humans ; RNA, Viral ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-06-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2021.104894
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Zs.A 3790: Show issues

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Article ; Online: New Postmortem Perspective on Emerging SARS-CoV-2 Variants of Concern, Germany.

Heinrich, Fabian / Huter, Tobias / Mertens, Sophie / Lange, Philine / Vering, Jessica / Heinemann, Axel / Nörz, Dominik Sebastian / Hoffmann, Armin / Aepfelbacher, Martin / Ondruschka, Benjamin / Krasemann, Susanne / Lütgehetmann, Marc

Emerging infectious diseases

2023 Volume 29, Issue 3, Page(s) 652–656

Abstract: We performed autopsies on persons in Germany who died from COVID-19 and observed higher nasopharyngeal SARS-CoV-2 viral loads for variants of concern (VOC) compared with non-VOC lineages. Pulmonary inflammation and damage appeared higher in non-VOC than ... ...

Abstract	We performed autopsies on persons in Germany who died from COVID-19 and observed higher nasopharyngeal SARS-CoV-2 viral loads for variants of concern (VOC) compared with non-VOC lineages. Pulmonary inflammation and damage appeared higher in non-VOC than VOC lineages until adjusted for vaccination status, suggesting COVID-19 vaccination may mitigate pulmonary damage.
MeSH term(s)	Humans ; Autopsy ; SARS-CoV-2 ; COVID-19 Vaccines ; COVID-19 ; Germany
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2023-02-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2903.221297
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Zs.A 4778: Show issues

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Article ; Online: Sotrovimab in Hospitalized Patients with SARS-CoV-2 Omicron Variant Infection: a Propensity Score-Matched Retrospective Cohort Study.

Woo, Marcel S / Brehm, Thomas Theo / Fischer, Marlene / Heyer, Andreas / Wichmann, Dominic / Jordan, Sabine / Nörz, Dominik / Lütgehetmann, Marc / Addo, Marylyn M / Lohse, Ansgar W / Schmiedel, Stefan / Kluge, Stefan / Schulze Zur Wiesch, Julian

Microbiology spectrum

2022 Volume 11, Issue 1, Page(s) e0410322

Abstract: ... In ... ...

Abstract	In vitro
MeSH term(s)	Humans ; SARS-CoV-2 ; Retrospective Studies ; Propensity Score ; COVID-19 ; Antibodies, Neutralizing
Chemical Substances	sotrovimab (1MTK0BPN8V) ; Antibodies, Neutralizing
Language	English
Publishing date	2022-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.04103-22
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Article: Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants

Nörz, Dominik / Grunwald, Moritz / Tang, Hui Ting / Weinschenk, Celine / Günther, Thomas / Robitaille, Alexis / Giersch, Katja / Fischer, Nicole / Grundhoff, Adam / Aepfelbacher, Martin / Pfefferle, Susanne / Lütgehetmann, Marc

Viruses. 2022 Mar. 15, v. 14, no. 3

2022

Abstract: Background: The recently emerged SARS-CoV-2 B.1.1.529 lineage and its sublineages (Omicron variant) pose a new challenge to healthcare systems worldwide due to its ability to efficiently spread in immunized populations and its resistance to currently ... ...

Abstract	Background: The recently emerged SARS-CoV-2 B.1.1.529 lineage and its sublineages (Omicron variant) pose a new challenge to healthcare systems worldwide due to its ability to efficiently spread in immunized populations and its resistance to currently available monoclonal antibody therapies. RT-PCR-based variant tests can be used to screen large sample-sets rapidly and accurately for relevant variants of concern (VOC). The aim of this study was to establish and validate a multiplex assay on the cobas 6800/8800 systems to allow discrimination between the two currently circulating VOCs, Omicron and Delta, in clinical samples. Methods: Primers and probes were evaluated for multiplex compatibility. Analytic performance was assessed using cell culture supernatant of an Omicron variant isolate and a clinical Delta variant sample, normalized to WHO-Standard. Clinical performance of the multiplex assay was benchmarked against NGS results. Results: In silico testing of all oligos showed no interactions with a high risk of primer-dimer formation or amplification of human DNA/RNA. Over 99.9% of all currently available Omicron variant sequences are a perfect match for at least one of the three Omicron targets included in the multiplex. Analytic sensitivity was determined as 19.0 IU/mL (CI95%: 12.9–132.2 IU/mL) for the A67V + del-HV69-70 target, 193.9 IU/mL (CI95%: 144.7–334.7 IU/mL) for the E484A target, 35.5 IU/mL (CI95%: 23.3–158.0 IU/mL) for the N679K + P681H target and 105.0 IU/mL (CI95%: 80.7–129.3 IU/mL) for the P681R target. All sequence variances were correctly detected in the clinical sample set (225/225 Targets). Conclusion: RT-PCR-based variant screening compared to whole genome sequencing is both rapid and reliable in detecting relevant sequence variations in SARS-CoV-2 positive samples to exclude or verify relevant VOCs. This allows short-term decision-making, e.g., for patient treatment or public health measures.
Keywords	DNA ; RNA ; Severe acute respiratory syndrome coronavirus 2 ; cell culture ; clinical examination ; computer simulation ; decision making ; genome ; health services ; humans ; monoclonal antibodies ; patients ; public health ; risk
Language	English
Dates of publication	2022-0315
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14030608
Database	NAL-Catalogue (AGRICOLA)

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