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A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Overview of attention for article published in Virology Journal, April 2017
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (78th percentile)
  • High Attention Score compared to outputs of the same age and source (90th percentile)

Mentioned by

blogs
1 blog
twitter
2 tweeters

Citations

dimensions_citation
66 Dimensions

Readers on

mendeley
102 Mendeley
citeulike
3 CiteULike
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Title
A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses
Published in
Virology Journal, April 2017
DOI 10.1186/s12985-017-0741-5
Pubmed ID
Authors

Kiril M. Dimitrov, Poonam Sharma, Jeremy D. Volkening, Iryna V. Goraichuk, Abdul Wajid, Shafqat Fatima Rehmani, Asma Basharat, Ismaila Shittu, Tony M. Joannis, Patti J. Miller, Claudio L. Afonso

Abstract

Next-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral nucleic acids without utilization of target-specific primers provides advantages over traditional sequencing methods and allows detection of unsuspected variants and co-infecting agents. However, NGS is not widely used for small RNA viruses because of incorrectly perceived cost estimates and inefficient utilization of freely available bioinformatics tools. In this study, we have utilized NGS-based random sequencing of total RNA combined with barcode multiplexing of libraries to quickly, effectively and simultaneously characterize the genomic sequences of multiple avian paramyxoviruses. Thirty libraries were prepared from diagnostic samples amplified in allantoic fluids and their total RNAs were sequenced in a single flow cell on an Illumina MiSeq instrument. After digital normalization, data were assembled using the MIRA assembler within a customized workflow on the Galaxy platform. Twenty-eight avian paramyxovirus 1 (APMV-1), one APMV-13, four avian influenza and two infectious bronchitis virus complete or nearly complete genome sequences were obtained from the single run. The 29 avian paramyxovirus genomes displayed 99.6% mean coverage based on bases with Phred quality scores of 30 or more. The lower and upper quartiles of sample median depth per position for those 29 samples were 2984 and 6894, respectively, indicating coverage across samples sufficient for deep variant analysis. Sample processing and library preparation took approximately 25-30 h, the sequencing run took 39 h, and processing through the Galaxy workflow took approximately 2-3 h. The cost of all steps, excluding labor, was estimated to be 106 USD per sample. This work describes an efficient multiplexing NGS approach, a detailed analysis workflow, and customized tools for the characterization of the genomes of RNA viruses. The combination of multiplexing NGS technology with the Galaxy workflow platform resulted in a fast, user-friendly, and cost-efficient protocol for the simultaneous characterization of multiple full-length viral genomes. Twenty-nine full-length or near-full-length APMV genomes with a high median depth were successfully sequenced out of 30 samples. The applied de novo assembly approach also allowed identification of mixed viral populations in some of the samples.

Twitter Demographics

The data shown below were collected from the profiles of 2 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 102 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 <1%
Netherlands 1 <1%
Unknown 100 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 27 26%
Researcher 16 16%
Student > Master 10 10%
Student > Bachelor 8 8%
Student > Postgraduate 5 5%
Other 18 18%
Unknown 18 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 23 23%
Biochemistry, Genetics and Molecular Biology 18 18%
Veterinary Science and Veterinary Medicine 14 14%
Immunology and Microbiology 8 8%
Engineering 5 5%
Other 10 10%
Unknown 24 24%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. 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 03 May 2017.
All research outputs
#3,699,470
of 22,963,381 outputs
Outputs from Virology Journal
#358
of 3,057 outputs
Outputs of similar age
#66,840
of 309,929 outputs
Outputs of similar age from Virology Journal
#5
of 54 outputs
Altmetric has tracked 22,963,381 research outputs across all sources so far. Compared to these this one has done well and is in the 83rd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,057 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 25.7. This one has done well, scoring higher than 88% 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 309,929 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 78% of its contemporaries.
We're also able to compare this research output to 54 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 90% of its contemporaries.