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Book ; Online ; Thesis: Epidemiology and Ecology of Bacillus cereus biovar anthracis in Taï National Park, Côte d’Ivoire

Zimmermann, Fee [Verfasser]

2019

Author's details	Fee Zimmermann
Keywords	Landwirtschaft, Veterinärmedizin ; Agriculture, Veterinary Science
Subject code	sg630
Language	English
Publisher	Freie Universität Berlin
Publishing place	Berlin
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article: In vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCR

Zimmermann, Fee / Urban, Maria / Krüger, Christian / Walter, Mathias / Wölfel, Roman / Zwirglmaier, Katrin

Journal of virological methods. 2022 Jan., v. 299

2022

Abstract: A number of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous commercial assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 ... ...

Abstract	A number of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous commercial assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 pandemic progresses, the virus accrues mutations, which in some cases – as seen with the B.1.1.7 variant – can outperform and push back other strains of SARS-CoV-2. If mutations occur in primer or probe binding sites, this can impact RT-qPCR results and impede SARS-CoV-2 diagnostics. Here we tested the effect of primer mismatches on RT-qPCR performance in vitro using synthetic mismatch in vitro transcripts. The effects of the mismatches ranged from a shift in ct values from -0.13 to +7.61. Crucially, we found that a mismatch in the forward primer has a more detrimental effect for PCR performance than a mismatch in the reverse primer. Furthermore, we compared the performance of the original Charité RdRP primer set, which has several ambiguities, with a primer version without ambiguities and found that without ambiguities the ct values are ca. 3 ct lower. Finally, we investigated the shift in ct values observed with the Seegene Allplex kit with the B.1.1.7 SARS-CoV-2 variant and found a three-nucleotide mismatch in the forward primer of the N target.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; diagnostic techniques ; markets ; oligodeoxyribonucleotides ; pandemic ; viruses
Language	English
Dates of publication	2022-01
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2021.114352
Database	NAL-Catalogue (AGRICOLA)

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Article: Analysis of Sporulation in

Gummelt, Constanze / Dupke, Susann / Howaldt, Sabine / Zimmermann, Fee / Scholz, Holger C / Laue, Michael / Klee, Silke R

Pathogens (Basel, Switzerland)

2023 Volume 12, Issue 12

Abstract: ... Bacillus ... ...

Abstract	Bacillus cereus
Language	English
Publishing date	2023-12-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens12121442
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: In vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCR.

Zimmermann, Fee / Urban, Maria / Krüger, Christian / Walter, Mathias / Wölfel, Roman / Zwirglmaier, Katrin

Journal of virological methods

2021 Volume 299, Page(s) 114352

Abstract	A number of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous commercial assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 pandemic progresses, the virus accrues mutations, which in some cases - as seen with the B.1.1.7 variant - can outperform and push back other strains of SARS-CoV-2. If mutations occur in primer or probe binding sites, this can impact RT-qPCR results and impede SARS-CoV-2 diagnostics. Here we tested the effect of primer mismatches on RT-qPCR performance in vitro using synthetic mismatch in vitro transcripts. The effects of the mismatches ranged from a shift in ct values from -0.13 to +7.61. Crucially, we found that a mismatch in the forward primer has a more detrimental effect for PCR performance than a mismatch in the reverse primer. Furthermore, we compared the performance of the original Charité RdRP primer set, which has several ambiguities, with a primer version without ambiguities and found that without ambiguities the ct values are ca. 3 ct lower. Finally, we investigated the shift in ct values observed with the Seegene Allplex kit with the B.1.1.7 SARS-CoV-2 variant and found a three-nucleotide mismatch in the forward primer of the N target.
MeSH term(s)	Binding Sites ; COVID-19 ; Humans ; Mutation ; RNA, Viral/genetics ; SARS-CoV-2 ; Sensitivity and Specificity
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-11-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2021.114352
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 1565: 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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Article: In-Depth Analysis of Bacillus anthracis 16S rRNA Genes and Transcripts Reveals Intra- and Intergenomic Diversity and Facilitates Anthrax Detection.

Braun, Peter / Zimmermann, Fee / Walter, Mathias C / Mantel, Sonja / Aistleitner, Karin / Stürz, Inga / Grass, Gregor / Stoecker, Kilian

mSystems

2022 Volume 7, Issue 1, Page(s) e0136121

Abstract: Analysis of 16S rRNA (rRNA) genes provides a central means of taxonomic classification of bacterial species. Based on presumed sequence identity among species of the Bacillus cereus sensu lato group, the 16S rRNA genes of B. anthracis have been ... ...

Abstract	Analysis of 16S rRNA (rRNA) genes provides a central means of taxonomic classification of bacterial species. Based on presumed sequence identity among species of the Bacillus cereus sensu lato group, the 16S rRNA genes of B. anthracis have been considered unsuitable for diagnosis of the anthrax pathogen. With the recent identification of a single nucleotide polymorphism in some 16S rRNA gene copies, specific identification of B. anthracis becomes feasible. Here, we designed and evaluated a set of
Language	English
Publishing date	2022-01-25
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/msystems.01361-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: In vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCR

Zimmermann, Fee / Urban, Maria / Krueger, Christian / Walter, Mathias / Woelfel, Roman / Zwirglmaier, Katrin

bioRxiv

Abstract	A number of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous commercial assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 pandemic progresses, the virus accrues mutations, which in some cases - as seen with the B.1.1.7 variant - can outperform and push back other strains of SARS-CoV-2. If mutations occur in primer or probe binding sites, this can impact RT-qPCR results and impede SARS-CoV-2 diagnostics. Here we tested the effect of primer mismatches on RT-qPCR performance in vitro using synthetic mismatch in vitro transcripts. The effects of the mismatches ranged from a shift in ct values from -0.13 to +7.61. Crucially, we found that a mismatch in the forward primer has a more detrimental effect for PCR performance than a mismatch in the reverse primer. Furthermore, we compared the performance of the original Charite RdRP primer set, which has several ambiguities, with a primer version without ambiguities and found that without ambiguities the ct values are ca. 3 ct lower. Finally, we investigated the shift in ct values observed with the Seegene Allplex kit with the B.1.1.7 SARS-CoV-2 variant and found a three-nucleotide mismatch in the forward primer of the N target.
Keywords	covid19
Language	English
Publishing date	2021-06-07
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.06.07.447338
Database	COVID19

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Article ; Online: First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region.

Kouriba, Bourema / Dürr, Angela / Rehn, Alexandra / Sangaré, Abdoul Karim / Traoré, Brehima Y / Bestehorn-Willmann, Malena S / Ouedraogo, Judicael / Heitzer, Asli / Sogodogo, Elisabeth / Maiga, Abderrhamane / Walter, Mathias C / Zimmermann, Fee / Wölfel, Roman / Antwerpen, Markus H

Viruses

2020 Volume 12, Issue 11

Abstract: We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, ... ...

Abstract	We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on March 2, 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequencing data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates, from which 21 whole genome sequences were generated. Our analysis shows that both the early A (19B) and the later observed B (20A/C) clade are present in Mali, indicating multiple and independent introductions of SARS-CoV-2 to the Sahel region.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; COVID-19 ; Child ; Child, Preschool ; Coronavirus Infections/epidemiology ; Female ; Genetic Variation/genetics ; Genome, Viral/genetics ; Genomics ; Humans ; Male ; Mali/epidemiology ; Middle Aged ; Pandemics ; Phylogeny ; Pneumonia, Viral/epidemiology ; RNA, Viral/genetics ; SARS-CoV-2 ; Whole Genome Sequencing ; Young Adult
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-11-02
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v12111251
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region

Viruses. 2020 Nov. 02, v. 12, no. 11

2020

Abstract	We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on 2 March 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequencing data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates, from which 21 whole genome sequences were generated. Our analysis shows that both the early A (19B) and the later observed B (20A/C) clade are present in Mali, indicating multiple and independent introductions of SARS-CoV-2 to the Sahel region.
Keywords	COVID-19 infection ; Sahel ; Severe acute respiratory syndrome coronavirus 2 ; genetic variation ; humans ; nucleotide sequences ; pandemic ; patients ; phylogeny ; screening ; sequence analysis ; viruses ; China ; Mali
Language	English
Dates of publication	2020-1102
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v12111251
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: First phylogenetic analysis of Malian SARS-CoV-2 sequences provide molecular insights into the genomic diversity of the Sahel region

Kouriba, Bourema / Duerr, Angela / Rehn, Alexandra / Sangare, Abdoul Karim / Traoure, Brehima Youssouf / Bestehorn-Willmann, Malena S / Ouedraogo, Judicael LJ / Heitzer, Asli / Sogodogo, Elisabeth / Maiga, Abderrhamane / Walter, Mathias C / Zimmermann, Fee / Woelfel, Roman / Antwerpen, Markus H

medRxiv

Abstract: We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occuring in the Wuhan region, China, in December 2019. From China the virus has spread to 188 countries and regions worldwide, reaching ...

Abstract	We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occuring in the Wuhan region, China, in December 2019. From China the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on the 2nd of March 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequence data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening of 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates from which 21 whole genome sequences were generated. Our analysis shows that both, the early A (19B) and the fast evolving B (20A/C) clade, are present in Mali indicating multiple and independent introductions of the SARS-CoV-2 to the Sahel region.
Keywords	covid19
Language	English
Publishing date	2020-09-25
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.09.23.20165639
Database	COVID19

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Article: First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region

Kouriba, Bourema Dürr Angela Rehn Alexandra Sangaré Abdoul Karim Traoré Brehima Y. / Bestehorn-Willmann, Malena S. / Ouedraogo, Judicael Heitzer Asli Sogodogo Elisabeth Maiga Abderrhamane Walter Mathias C. / Zimmermann, Fee Wölfel Roman Antwerpen Markus H.

Viruses

Abstract: We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019 From China, the virus has spread to 188 countries and regions worldwide, ... ...

Abstract	We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019 From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on March 2, 2020 Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequencing data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available Screening 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates, from which 21 whole genome sequences were generated Our analysis shows that both the early A (19B) and the later observed B (20A/C) clade are present in Mali, indicating multiple and independent introductions of SARS-CoV-2 to the Sahel region
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #896394
Database	COVID19

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