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Viral Metagenomics

Overview of attention for book
Cover of 'Viral Metagenomics'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics
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    Chapter 2 Small RNA Isolation from Tissues of Grapevine and Woody Plants
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    Chapter 3 Double-Stranded RNA-Enriched Preparations to Identify Viroids by Next-Generation Sequencing
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    Chapter 4 Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing
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    Chapter 5 Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes
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    Chapter 6 Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples
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    Chapter 7 Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities
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    Chapter 8 Different Approaches to Discover Mycovirus Associated to Marine Organisms
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    Chapter 9 Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections
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    Chapter 10 The Use of High-Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen
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    Chapter 11 High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next-Generation Sequencing
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    Chapter 12 Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid
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    Chapter 13 DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method
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    Chapter 14 From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool
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    Chapter 15 Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs
  17. Altmetric Badge
    Chapter 16 Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches
Attention for Chapter 5: Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes
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Mentioned by

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3 tweeters

Citations

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4 Dimensions

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7 Mendeley
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Chapter title
Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes
Chapter number 5
Book title
Viral Metagenomics
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7683-6_5
Pubmed ID
Book ISBNs
978-1-4939-7682-9, 978-1-4939-7683-6
Authors

Marion Cornelissen, Astrid Gall, Antoinette van der Kuyl, Chris Wymant, François Blanquart, Christophe Fraser, Ben Berkhout

Abstract

We describe a detailed protocol for the manual workup of blood (plasma/serum) samples from individuals infected with the human immunodeficiency virus type 1 (HIV-1) for deep sequence analysis of the viral genome. The study optimizing the assay was performed in the context of the BEEHIVE (Bridging the Evolution and Epidemiology of HIV in Europe) project, which analyzes complete viral genomes from more than 3000 HIV-1-infected Europeans with high-throughput deep sequencing techniques. The goal of the BEEHIVE project is to determine the contribution of viral genetics to virulence. Recently we performed a pilot experiment with 125 patient plasma samples to identify the method that is most suitable for isolation of HIV-1 viral RNA for subsequent long-amplicon deep sequencing. We reported that manual isolation with the QIAamp Viral RNA Mini Kit (Qiagen) provides superior results over robotically extracted RNA. The latter approach used the MagNA Pure 96 System in combination with the MagNA Pure 96 Instrument (Roche Diagnostics), the QIAcube robotic system (Qiagen), or the mSample Preparation Systems RNA kit with automated extraction by the m2000sp system (Abbott Molecular). Here we present a detailed protocol for the labor-intensive manual extraction method that yielded the best results.

Twitter Demographics

The data shown below were collected from the profiles of 3 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 7 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 7 100%

Demographic breakdown

Readers by professional status Count As %
Lecturer > Senior Lecturer 1 14%
Lecturer 1 14%
Student > Bachelor 1 14%
Student > Ph. D. Student 1 14%
Researcher 1 14%
Other 0 0%
Unknown 2 29%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 3 43%
Psychology 1 14%
Chemistry 1 14%
Unknown 2 29%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 February 2019.
All research outputs
#12,286,397
of 21,190,873 outputs
Outputs from Methods in molecular biology
#3,080
of 11,951 outputs
Outputs of similar age
#142,793
of 294,198 outputs
Outputs of similar age from Methods in molecular biology
#5
of 5 outputs
Altmetric has tracked 21,190,873 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 11,951 research outputs from this source. They receive a mean Attention Score of 3.3. This one has gotten more attention than average, scoring higher than 73% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 294,198 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 50% of its contemporaries.
We're also able to compare this research output to 5 others from the same source and published within six weeks on either side of this one.