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Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

Overview of attention for article published in Biology Direct, January 2016
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  • Average Attention Score compared to outputs of the same age and source

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Citations

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Title
Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome
Published in
Biology Direct, January 2016
DOI 10.1186/s13062-016-0105-x
Pubmed ID
Authors

Dingchen Li, Zongwei Li, Zhe Zhou, Zhen Li, Xinyan Qu, Peisong Xu, Pingkun Zhou, Xiaochen Bo, Ming Ni

Abstract

Next-generation sequencing (NGS) enables the recovery of pathogen genomes from clinical samples without the need for culturing. Depletion of host/microbiota components (e.g., ribosomal RNA and poly-A RNA) and whole DNA/cDNA amplification are routine methods to improve recovery results. Using mixtures of human and influenza A virus (H1N1) RNA as a model, we found that background depletion and whole transcriptome amplification introduced biased distributions of read coverage over the H1N1 genome, thereby hampering genome assembly. Influenza serotyping was also affected by pretreatments. We propose that direct sequencing of noncultured samples without pretreatment is a favorable option for pathogen genome recovery applications. This article was reviewed by Sebastian Maurer-Stroh.

X Demographics

X Demographics

The data shown below were collected from the profiles of 5 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 62 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Malaysia 1 2%
United States 1 2%
Germany 1 2%
Unknown 59 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 18 29%
Student > Ph. D. Student 17 27%
Student > Master 6 10%
Student > Postgraduate 4 6%
Student > Doctoral Student 3 5%
Other 8 13%
Unknown 6 10%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 15 24%
Agricultural and Biological Sciences 12 19%
Immunology and Microbiology 9 15%
Veterinary Science and Veterinary Medicine 5 8%
Medicine and Dentistry 3 5%
Other 8 13%
Unknown 10 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 4. 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 14 January 2016.
All research outputs
#6,964,541
of 22,837,982 outputs
Outputs from Biology Direct
#249
of 487 outputs
Outputs of similar age
#113,314
of 395,131 outputs
Outputs of similar age from Biology Direct
#9
of 18 outputs
Altmetric has tracked 22,837,982 research outputs across all sources so far. This one has received more attention than most of these and is in the 68th percentile.
So far Altmetric has tracked 487 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.7. This one is in the 47th percentile – i.e., 47% of its peers scored the same or lower than it.
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 395,131 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 70% of its contemporaries.
We're also able to compare this research output to 18 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 50% of its contemporaries.