Emil A. Sørensen
A5008328962- Genomics and Phylogenetic Studies
- SARS-CoV-2 and COVID-19 Research
- Bacteriophages and microbial interactions
- Microbial Community Ecology and Physiology
- COVID-19 epidemiological studies
- SARS-CoV-2 detection and testing
- Animal Virus Infections Studies
- Plant Virus Research Studies
- Historical and Archaeological Studies
- COVID-19 diagnosis using AI
- Botany and Plant Ecology Studies
- Virology and Viral Diseases
- Environmental DNA in Biodiversity Studies
- RNA and protein synthesis mechanisms
- Protist diversity and phylogeny
- Lichen and fungal ecology
Aalborg University
2019-2024
Ecologie Microbienne Lyon
2020
Long-read Oxford Nanopore sequencing has democratized microbial genome and enables the recovery of highly contiguous genomes from isolates or metagenomes. However, to obtain near-finished it been necessary include short-read polishing correct insertions deletions derived homopolymer regions. Here, we show that R10.4 can be used generate metagenomes without reference polishing.
New lineages of SARS-CoV-2 are potential concern due to higher transmissibility, risk 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 factors, such as age primary case viral load remains poorly understood. Here, we used comprehensive administrative data Denmark, comprising full population (January 11 February 7, 2021), estimate household transmissibility. This...
Abstract Background In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of world. Denmark, comprehensive and real-time test, contact-tracing, sequencing efforts were applied to sustain epidemic control. Here, we use these data investigate transmissibility, introduction, onward transmission in Denmark. Methods We analyzed a set 60,178 genomes generated from high-throughput by Danish COVID-19 Genome Consortium, representing 34% all positive cases...
Abstract High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, we report a high-throughput approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies or Pacific Biosciences CCS sequencing, yielding high accuracy single-molecule consensus sequences regions. Our generates and >10,000 bp in length mean error-rate 0.0049-0.0006% chimera rate <0.022%.
ABSTRACT Long-read Oxford Nanopore sequencing has democratized microbial genome and enables the recovery of highly contiguous genomes from isolates or metagenomes. However, to obtain near-perfect it been necessary include short-read polishing correct insertions deletions derived homopolymer regions. Here, we show that R10.4 can be used generate metagenomes without shortread reference polishing.
Summary The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes natural and human associated environments. Recent large-scale metagenome surveys record variety of microbial life oceans 1 , wastewater 2 gut 3,4 earth 5,6 with compilations encompassing thousands public datasets 7–13 . So far, microbiome studies either miss functional information or consistency sample processing, although they may cover locations, these are missing...
Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding SARS-CoV-2 emergence spread. We examined the drivers molecular evolution spread 291,791 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, up to 80% PCR-positive samples between March November, viral genome set is broadly whole-epidemic representative. identify consistent rise diversity over time, with notable spikes upon importation novel variants (e.g., Delta...
Abstract In early 2021, the SARS-CoV-2 lineage B.1.1.7 became dominant across large parts of world. Denmark, comprehensive and real-time test, contact-tracing, sequencing efforts were applied to sustain epidemic control. Here, we use these data investigate transmissibility, introduction, onward transmission in Denmark. a period with stable restrictions, estimated an increased transmissibility 58% (95% CI: [56%,60%]) relative other lineages. Epidemiological phylogenetic analyses revealed that...
This protocol describes the preparation of long read amplicon libraries nCoV-2019 for sequencing with Oxford Nanopore MinION platform. The is based on samples rRNA extracts virus. Sequences primers can be found under guidelines, currently using V3.1 from CJ020. ARTIC Networks and modified to our lab at Aalborg Univeristy. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w
Abstract Genomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery genomes from environmental samples at scale. However, expanding the genome catalogue soils sediments been challenging due enormous complexity these environments. Here, we performed deep, Nanopore 154 soil sediment collected across Denmark through an optimised bioinformatics pipeline, recovered 15,314 novel species, including 4,757...