| Title |
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
|
|---|---|
| Published in |
Genome Medicine, September 2015
|
| DOI | 10.1186/s13073-015-0220-9 |
| Pubmed ID | |
| Authors |
Alexander L. Greninger, Samia N. Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, Jerome Bouquet, Sneha Somasekar, Jeffrey M. Linnen, Roger Dodd, Prime Mulembakani, Bradley S. Schneider, Jean-Jacques Muyembe-Tamfum, Susan L. Stramer, Charles Y. Chiu |
| Abstract |
We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, web-based pipeline for real-time bioinformatics analysis on a computational server or laptop (MetaPORE). At titers ranging from 10(7)-10(8) copies per milliliter, reads to EBOV from two patients with acute hemorrhagic fever and CHIKV from an asymptomatic blood donor were detected within 4 to 10 min of data acquisition, while lower titer HCV virus (1 × 10(5) copies per milliliter) was detected within 40 min. Analysis of mapped nanopore reads alone, despite an average individual error rate of 24 % (range 8-49 %), permitted identification of the correct viral strain in all four isolates, and 90 % of the genome of CHIKV was recovered with 97-99 % accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hr sample-to-answer turnaround time, and in a timeframe amenable to actionable clinical and public health diagnostics. |
X Demographics
The data shown below were collected from the profiles of 95 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 20 | 21% |
| United Kingdom | 14 | 15% |
| Denmark | 3 | 3% |
| Finland | 3 | 3% |
| France | 2 | 2% |
| Spain | 2 | 2% |
| Myanmar | 1 | 1% |
| Germany | 1 | 1% |
| Australia | 1 | 1% |
| Other | 6 | 6% |
| Unknown | 42 | 44% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 45 | 47% |
| Scientists | 41 | 43% |
| Science communicators (journalists, bloggers, editors) | 5 | 5% |
| Practitioners (doctors, other healthcare professionals) | 4 | 4% |
Mendeley readers
The data shown below were compiled from readership statistics for 989 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Brazil | 7 | <1% |
| United Kingdom | 6 | <1% |
| Germany | 5 | <1% |
| United States | 5 | <1% |
| Spain | 2 | <1% |
| Japan | 2 | <1% |
| Korea, Republic of | 2 | <1% |
| Sweden | 1 | <1% |
| Israel | 1 | <1% |
| Other | 7 | <1% |
| Unknown | 951 | 96% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 205 | 21% |
| Student > Ph. D. Student | 165 | 17% |
| Student > Master | 140 | 14% |
| Student > Bachelor | 110 | 11% |
| Other | 46 | 5% |
| Other | 148 | 15% |
| Unknown | 175 | 18% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 276 | 28% |
| Biochemistry, Genetics and Molecular Biology | 226 | 23% |
| Medicine and Dentistry | 73 | 7% |
| Immunology and Microbiology | 61 | 6% |
| Computer Science | 39 | 4% |
| Other | 110 | 11% |
| Unknown | 204 | 21% |
Attention Score in Context
This research output has an Altmetric Attention Score of 220. 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 28 November 2023.
All research outputs
#177,595
of 25,711,518 outputs
Outputs from Genome Medicine
#28
of 1,608 outputs
Outputs of similar age
#2,242
of 286,999 outputs
Outputs of similar age from Genome Medicine
#2
of 26 outputs
Altmetric has tracked 25,711,518 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 99th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,608 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 26.7. This one has done particularly well, scoring higher than 98% of its peers.
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We're also able to compare this research output to 26 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 92% of its contemporaries.