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Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark

Michaelsen, Thomas Y. ; Bennedbæk, Marc ; Christiansen, Lasse E. ; [weitere]

Springer Science and Business Media LLC ; 2022

In: Genome Medicine Vol. 14, No. 1 ( 2022-12)

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In: Genome Medicine, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2022-12)

Kurzfassung: In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transmissibility, introduction, and onward transmission of B.1.1.7 in Denmark. Methods We analyzed a comprehensive set of 60,178 SARS-CoV-2 genomes generated from high-throughput sequencing by the Danish COVID-19 Genome Consortium, representing 34% of all positive cases in the period 14 November 2020 to 7 February 2021. We calculated the transmissibility of B.1.1.7 relative to other lineages using Poisson regression. Including all 1976 high-quality B.1.1.7 genomes collected in the study period, we constructed a time-scaled phylogeny, which was coupled with detailed travel history and register data to outline the introduction and onward transmission of B.1.1.7 in Denmark. Results In a period with unchanged restrictions, we estimated an increased B.1.1.7 transmissibility of 58% (95% CI: [56%, 60%]) relative to other lineages. Epidemiological and phylogenetic analyses revealed that 37% of B.1.1.7 cases were related to the initial introduction in November 2020. The relative number of cases directly linked to introductions varied between 10 and 50% throughout the study period. Conclusions Our findings corroborate early estimates of increased transmissibility of B.1.1.7. Both substantial early expansion when B.1.1.7 was still unmonitored and continuous foreign introductions contributed considerably to case numbers. Finally, our study highlights the benefit of balanced travel restrictions and self-isolation procedures coupled with comprehensive surveillance efforts, to sustain epidemic control in the face of emerging variants.

Materialart: Online-Ressource

ISSN: 1756-994X

URL: Article

DOI: 10.1186/s13073-022-01045-7

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2022

ZDB Id: 2484394-5

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Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load

Lyngse, Frederik Plesner ; Mølbak, Kåre ; Skov, Robert Leo ; [weitere]

Springer Science and Business Media LLC ; 2021

In: Nature Communications Vol. 12, No. 1 ( 2021-12-13)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-12-13)

Kurzfassung: New lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and risk factors, such as age of primary case and viral load remains poorly understood. Here, we used comprehensive administrative data from Denmark, comprising the full population (January 11 to February 7, 2021), to estimate household transmissibility. This study included 5,241 households with primary cases; 808 were infected with lineage B.1.1.7 and 4,433 with other lineages. Here, we report an attack rate of 38% in households with a primary case infected with B.1.1.7 and 27% in households with other lineages. Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5–1.7 times that of primary cases infected with other lineages. The increased transmissibility of B.1.1.7 was multiplicative across age and viral load.

Materialart: Online-Ressource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-021-27202-x

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2021

ZDB Id: 2553671-0

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A comparison of glycemic control, water retention, and musculoskeletal effects of balaglitazone and pioglitazone in diet-induced obese rats

Henriksen, Kim ; Byrjalsen, Inger ; Nielsen, Rasmus H. ; [weitere]

Elsevier BV ; 2009

In: European Journal of Pharmacology Vol. 616, No. 1-3 ( 2009-8), p. 340-345

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In: European Journal of Pharmacology, Elsevier BV, Vol. 616, No. 1-3 ( 2009-8), p. 340-345

Materialart: Online-Ressource

ISSN: 0014-2999

URL: Article

DOI: 10.1016/j.ejphar.2009.06.051

Sprache: Englisch

Verlag: Elsevier BV

Publikationsdatum: 2009

ZDB Id: 1483526-5

SSG: 15,3

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Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Singleton, Caitlin M. ; Petriglieri, Francesca ; Kristensen, Jannie M. ; [weitere]

Springer Science and Business Media LLC ; 2021

In: Nature Communications Vol. 12, No. 1 ( 2021-03-31)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-03-31)

Kurzfassung: Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with 〉 13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

Materialart: Online-Ressource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-021-22203-2

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2021

ZDB Id: 2553671-0

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Degradation of the Organic Phase of Bone by Osteoclasts: A Secondary Role for Lysosomal Acidification

Henriksen, Kim ; Sørensen, Mette G ; Nielsen, Rasmus H ; [weitere]

Wiley ; 2005

In: Journal of Bone and Mineral Research Vol. 21, No. 1 ( 2005-09-06), p. 58-66

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In: Journal of Bone and Mineral Research, Wiley, Vol. 21, No. 1 ( 2005-09-06), p. 58-66

Materialart: Online-Ressource

ISSN: 0884-0431

URL: Article

DOI: 10.1359/JBMR.050905

RVK:

XA 52230

Sprache: Englisch

Verlag: Wiley

Publikationsdatum: 2005

ZDB Id: 2008867-X

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A microarray analysis of full depth knee cartilage of ovariectomized rats

Bay-Jensen, Anne C ; Nielsen, Rasmus H ; Segovia-Silvestre, Toni ; [weitere]

Springer Science and Business Media LLC ; 2011

In: BMC Research Notes Vol. 4, No. 1 ( 2011-12)

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In: BMC Research Notes, Springer Science and Business Media LLC, Vol. 4, No. 1 ( 2011-12)

Materialart: Online-Ressource

ISSN: 1756-0500

URL: Article

DOI: 10.1186/1756-0500-4-63

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2011

ZDB Id: 2413336-X

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Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

McIlroy, Simon J. ; Kirkegaard, Rasmus H. ; Dueholm, Morten S. ; [weitere]

Frontiers Media SA ; 2017

In: Frontiers in Microbiology Vol. 8 ( 2017-06-23)

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In: Frontiers in Microbiology, Frontiers Media SA, Vol. 8 ( 2017-06-23)

Materialart: Online-Ressource

ISSN: 1664-302X

URL: Article

DOI: 10.3389/fmicb.2017.01134

Sprache: Unbekannt

Verlag: Frontiers Media SA

Publikationsdatum: 2017

ZDB Id: 2587354-4

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The impact of immigration on microbial community composition in full-scale anaerobic digesters

Kirkegaard, Rasmus H. ; McIlroy, Simon J. ; Kristensen, Jannie M. ; [weitere]

Springer Science and Business Media LLC ; 2017

In: Scientific Reports Vol. 7, No. 1 ( 2017-08-24)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2017-08-24)

Kurzfassung: Anaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. Hence, we investigated microbial communities of thirty-two full-scale anaerobic digesters over a six-year period using 16S rRNA gene amplicon sequencing. Sampling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent. This observation indicates that a failure to consider immigration will interfere with correlation analysis and give an inaccurate picture of the growing microbial community. Furthermore, several abundant OTUs could not be classified to genus level with commonly applied taxonomies, making inference of their function unreliable and comparison to other studies problematic. As such, the existing MiDAS taxonomy was updated to include these abundant phylotypes. The communities of individual digesters surveyed were remarkably similar – with only 300 OTUs representing 80% of the total reads across all plants, and 15% of these identified as non-growing and possibly inactive immigrating microbes. By identifying abundant and growing taxa in anaerobic digestion, this study paves the way for targeted characterisation of the process-important organisms towards an in-depth understanding of the microbiology.

Materialart: Online-Ressource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-017-09303-0

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2017

ZDB Id: 2615211-3

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Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

Karst, Søren M ; Dueholm, Morten S ; McIlroy, Simon J ; [weitere]

Springer Science and Business Media LLC ; 2018

In: Nature Biotechnology Vol. 36, No. 2 ( 2018-2), p. 190-195

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In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 36, No. 2 ( 2018-2), p. 190-195

Materialart: Online-Ressource

ISSN: 1087-0156 , 1546-1696

URL: Article

DOI: 10.1038/nbt.4045

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2018

ZDB Id: 1494943-X

ZDB Id: 1311932-1

SSG: 12

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Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

Albertsen, Mads ; Karst, Søren M. ; Ziegler, Anja S. ; [weitere]

Public Library of Science (PLoS) ; 2015

In: PLOS ONE Vol. 10, No. 7 ( 2015-7-16), p. e0132783-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 10, No. 7 ( 2015-7-16), p. e0132783-

Materialart: Online-Ressource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0132783

DOI: 10.1371/journal.pone.0132783.g001

DOI: 10.1371/journal.pone.0132783.g002

DOI: 10.1371/journal.pone.0132783.g003

DOI: 10.1371/journal.pone.0132783.g004

DOI: 10.1371/journal.pone.0132783.g005

DOI: 10.1371/journal.pone.0132783.g006

DOI: 10.1371/journal.pone.0132783.s001

DOI: 10.1371/journal.pone.0132783.s002

DOI: 10.1371/journal.pone.0132783.s003

DOI: 10.1371/journal.pone.0132783.s004

DOI: 10.1371/journal.pone.0132783.s005

DOI: 10.1371/journal.pone.0132783.s006

DOI: 10.1371/journal.pone.0132783.s007

DOI: 10.1371/journal.pone.0132783.s008

DOI: 10.1371/journal.pone.0132783.s009

DOI: 10.1371/journal.pone.0132783.s010

DOI: 10.1371/journal.pone.0132783.s011

Sprache: Englisch

Verlag: Public Library of Science (PLoS)

Publikationsdatum: 2015

ZDB Id: 2267670-3

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