New science used to combat COVID-19 disease

Read an article last week in Science Magazine (A completely new culture on doing research… ) on how the way science is done to combat disease has changed the last few years.

In the olden days (~3-5 years ago), disease outbreaks would generate a slew of research papers to be written, submitted for publication and there they would sit, until peer-reviewed, after which they might get published for the world to see for the first time. Estimates I’ve seen say that the scientific research publishing process takes anywhere from one month (very fast) to 4-8 months, assuming no major revisions are required.

With the emergence of the Zika virus and recent Ebola outbreaks, more and more biological research papers have become available through pre-print servers. These are web-sites which accept any research before publication (pre-print), posting the research for all to see, comment and understand.

Open science via pre-print

Most of these pre-print servers focus on specific areas of science. For example bioRxiv is a pre-print server focused on Biology and medRxiv is for health sciences. On the other hand, arXiv is a pre-print server for “physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics.” These are just a sampling of what’s available today.

In the past, scientific journals would not accept research that had been published before. But this slowly change as well. Now most scientific journals have policies gol pre-print publication and will also publish them if they deem it worthwhile, (see wikipedia article List of academic journals by pre-print policies).

As of today (9 March 2020) ,on biorXiv there are 423 papers with keyword=”coronavirus” and 52 papers with the keyword COVID-19, some of these may be the same. The newest (Substrate specificity profiling of SARS-CoV-2 Mpro protease provides basis for anti-COVID-19 drug design) was published on 3/7/2020. The last sentence in their abstract says “The results of our work provide a structural framework for the design of inhibitors as antiviral agents or diagnostic tests.” The oldest on bioRxiv is dated 23 January 2020. Similarly, there are 326 papers on medRxiv with the keyword “coronavirus”, the newest published 5 March 2020.

Pre-print research is getting out in the open much sooner than ever before. But the downside, is that pre-print papers may have serious mistakes or omissions in them as they are not peer-reviewed. So the cost of rapid openness is the possibility that some research may be outright wrong, badly done, or lead researchers down blind alleys.

However, the upside is any bad research can be vetted sooner, if it’s open to the world. We see similar problems with open source software, some of it can be buggy or outright failure prone. But having it be open, and if it’s popular, many people will see the problems (or bugs) and fixes will be rapidly created to solve them. With pre-print research, the comment list associated with a pre-print can be long and often will identify problems in the research.

Open science through open journals

In addition to pre-print servers , we are also starting to see the increasing use of open scientific journals such as PLOS to publish formal research.

PLOS has a number of open journals focused on specific arenas of research, such as PLOS Biology, PLOS Pathogyns, PLOS Medicine, etc.

Researchers or their institutions have to pay a nominal fee to publish in PLOS. But all PLOS publications are fully expert, peer-reviewed. But unlike research from say Nature, IEEE or other scientific journals, PLOS papers are free to anyone, and are widely available. (However, I just saw that SpringerNature is making all their coronavirus research free).

Open science via open data(sets)

Another aspect of scientific research that has undergone change of late is the sharing and publication of data used in the research.

Nature has a list of recommended data repositories. All these data repositories seem to be hosted by FAIRsharing at the University of Oxford and run by their Data Readiness Group. They list 1349 databases of which the vast majority (1250) are for the natural sciences with over 1380 standards used for data to be registered with FAIRsharing.

We’ve discussed similar data repositories in the past (please see Data banks, data deposits and data withdrawals, UK BioBank, Big open data leads to citizen science, etc). Having a place to store data used in research papers makes it easier to understand and replicate science.

Collaboration software

The other change to research activities is the use of collaborative software such as Slack. Researchers at UW Madison were already using Slack to collaborate on research but when Coronavirus went public, they Slack could help here too. So they created a group (or channel) under their Slack site called “Wu-han Clan” and invited 69 researchers from around the world. The day after they created it they held their first teleconference.

Other collaboration software exists today but Slack seems most popular. We use Slack for communications in our robotics club, blogging group, a couple of companies we work with, etc. Each has a number of invite-only channels, where channel members can post text, (data) files, links and just about anything else of interest to the channel.

Although I have not been invited to participate in Wu-han Clan (yet), I assume they usee Slack to discuss and vet (pre-print) research, discuss research needs, and other ways to avert the pandemic.

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So there you have it. Coronavirus scientific research is happening at warp speed compared to diseases of yore. Technologies to support this sped up research have all emerged over the last five to 10 years but are now being put to use more than ever before. Such technological advancement should lead to faster diagnosis, lower worldwide infection/mortality rates and a quicker medical solution.

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