COVID 19 and Open Science - OpenSourceSarsCoV2/LivingResourceReview GitHub Wiki

In late 2019, reports began to emerge from Wuhan, China concerning cases of pneumonia of an unknown origin. Shortly thereafter, Chinese authorities identified this to be a novel type of coronavirus disease (now known as coronavirus disease 2019; COVID-19) caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), with the outbreak being declared by the World Health Organization (WHO) as a public health emergency of international concern. Over the next two months, increasing numbers of COVID-19 cases were reported in countries outside China at an alarming rate, prompting the WHO to declare COVID-19 a global pandemic in March 2020 [1]. To date, according to the WHO COVID-19 Situation Dashboard [2], there have been more than 10 million cases worldwide, in over 200 countries, resulting in around 500 thousand deaths. As COVID-19 is caused by a novel coronavirus, there are no established methods for its treatment, and measures such as social distancing and self-isolation have become crucial to prevent further spread. The urgency to overcome this pandemic is furthered by the devastating effect on the world economy that has been seen as a result of the prolonged implementation of these measures [3].

The enormous impact of this disease has resulted in significant activity towards new therapeutics, particularly for the development of a new vaccine. Much of this work is taking place in the private sector, alongside the usual requirement in that sector for secrecy. However, there has in parallel been a significant push for a more open approach because it is understood that openness leads to research acceleration. Broadly speaking, these initiatives can be grouped together as three types: 1) open access (the availability of research publications that are free to access and, often, re-use), 2) open data (the same, but with data) and 3) open source (in which broader community participation is allowed via liberal licence terms). There are many well-known and frequently-described advantages of openness (e.g. reduction of duplication of effort, faster communication of important outcomes) that nevertheless compete with a need for secrecy for many researchers, arising from the need for protected intellectual property or a perceived competitive advantage. These motivations for secrecy seem, in a time of crisis, to be lessened, and the increased prevalence of open initiatives relating to COVID-19 research has been striking.

Open science in biomedical research has gained increased traction over the past decade [4,5] from screening projects (e.g., CO-ADD [6]) and the sharing of physical samples (e.g., SGC probes [7], MMV Boxes [8]) through to fully-fledged drug discovery (e.g., Open Source Malaria [9], MycetOS [10]) and development (e.g., M4K Pharma [11]) campaigns. For COVID-19, data are being generated and shared (e.g. protein target structures, fragment hits), and initiatives have been created to identify and fast-track candidate compounds into clinical use. Even the lengthy process of drug approval is thought to be something that can be shortened: the urgency of the current situation and the use of open science has opened the possibility of reducing the timeline significantly to as little as 1.5 years [12] (though the fastest vaccine to be developed, for the 2014-2016 Ebola virus epidemic, took 5 years) [13,14].

This article collates the key open science resources and initiatives currently available for COVID-19 research. The three previously mentioned categories will be used to group the resources and a brief description of each will be given. This article forms the basis of a “living” collection of open science resources for COVID-19. As more resources become available, anyone may update the repository and discuss those additions.

References

[1] WHO Director-General’s Open Remarks at the Media Briefing on COVID-19 – 11 March 2020. 2020; Accessed 9 June, 2020. https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020

[2] WHO Coronavirus Disease (COVID-19) Dashboard. 2020; Accessed 9 June, 2020. https://covid19.who.int

[3] Gopinath G: The Great Lockdown: Worst Economic Downturn Since the Great Depression. 2020; Accessed 24 June, 2020. https://blogs.imf.org/2020/04/14/the-great-lockdown-worst-economic-downturn-since-the-great-depression/

[4] McKiernan EC, Bourne PE, Brown CT, et al.: Point of View: How Open Science Helps Researchers Succeed. eLife 2016; 5: e16800. doi: 10.7554/eLife.16800

[5] Shaw DL: Is Open Science the Future of Drug Development? Yale J. Biol. Med. 2017; 90(1): 147-151.

[6] Zuegg J, Hansford KA, Elliott AG, et al.: How to Stimulate and Facilitate Early Stage Antibiotic Discovery. ACS Infect. Dis. 2020; 6(6): 1302-1304. doi: 10.1021/acsinfecdis.0c00163

[7] Müller S, Ackloo S, Arrowsmith CH, et al.: Science Forum: Donated Chemical Probes for Open Science. eLife 2018; 7: e34311. doi: 10.7554/eLife.34311

[8] Van Voorhis WC, Adams JH, Adelfio R, et al.: Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. PLoS Pathog. 2016; 12(7): e1005763. doi: 10.1371/journal.ppat.1005763

[9] Williamson AE, Ylioja PM, Robertson MN, et al.: Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles. ACS Cent. Sci. 2016; 2(10): 687-701. doi: 10.1021/acscentsci.6b00086

[10] Lim W, Melse Y, Konings M, et al.: Addressing the Most Neglected Diseases Through an Open Research Model: The Discovery of Fenarimols as Novel Drug Candidates for Eumycetoma. PLoS Negl. Trop. Dis. 2018; 12(4): e0006437. doi: 10.1371/journal.pntd.0006437

[11] Morgan MR, Roberts OG, Edwards AM: Ideation and Implementation of an Open Science Drug Discovery Business Model − M4K Pharma [version 1; peer review: 2 approved, 1 approved with reservations]. Wellcome Open Res. 2018; 3: 154. doi: 10.12688/wellcomeopenres.14947.1

[12] Lurie N, Saville M, Hatchett R, et al.: Developing Covid-19 Vaccines at Pandemic Speed. N. Engl. J. Med. 2020; 382: 1969-1973. doi: 10.1056/NEJMp2005630

[13] WHO Prequalifies Ebola Baccine, Paving the Way for its use in High-Risk Countries. 2019; Accessed 9 June, 2020. https://www.who.int/news-room/detail/12-11-2019-who-prequalifies-ebola-vaccine-paving-the-way-for-its-use-in-high-risk-countries

[14] Herder M, Graham JE, Gold R: From Discovery to Delivery: Public Sector Development of the rVSV - ZEBOV Ebola Vaccine. J. Law Biosci. 2020; lsz019. doi: 10.1093/jlb/lsz019