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. 2020 Aug 13;16(8):e1008643.
doi: 10.1371/journal.ppat.1008643. eCollection 2020 Aug.

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon Baker  1 , Marius van den Beek  2 , Daniel Blankenberg  3 , Dave Bouvier  2 , John Chilton  2 , Nate Coraor  2 , Frederik Coppens  4   5 , Ignacio Eguinoa  4   5 , Simon Gladman  6   7 , Björn Grüning  8 , Nicholas Keener  2 , Delphine Larivière  2 , Andrew Lonie  6 , Sergei Kosakovsky Pond  9 , Wolfgang Maier  8 , Anton Nekrutenko  2 , James Taylor  1 , Steven Weaver  9
Affiliations

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon Baker et al. PLoS Pathog. .

Abstract

The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2.

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Conflict of interest statement

Dannon Baker, Dan Blankenberg, Nate Coroar, John Chilton, James Taylor, and Anton Nekrutenko are founders of and hold equity in GalaxyWorks, LLC. The results of the study discussed in this publication could affect the value of GalaxyWorks, LLC.

Figures

Fig 1
Fig 1. Distribution of nucleotide changes across SARS-CoV-2 genome.
AF, minor allele frequency; POS, position; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
Fig 2
Fig 2
Amino acid alignment of spike glycoprotein regions HR1 (A) and HR2 (B). The site of the Lys921Gln substitution observed by us in a SARS-CoV-2 isolate is highlighted with a black rectangle in panel A. Its corresponding salt bridge partner is highlighted with a black rectangle in panel B. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
Fig 3
Fig 3. Location of potential recombination breakpoints along the S gene (GARD analysis).
Fig 4
Fig 4. Analysis of branch-specific positive diversifying selection (aBSREL) along the branch leading to SARS-CoV-2 (MN988688).
SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
See this image and copyright information in PMC

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