How open source is helping to fight Covid-19

By Marilyn de Villiers
Johannesburg, 16 Mar 2020

An open-source project, Netstrain, which harnesses scientific and public health information about the genetic data of known infection-causing pathogens, is being used to track the transmission of the coronavirus, Covid-19.

And another open source project, #OpenCovid19Initiatve, has been set up to develop and share open source methodologies that will enable the safe testing for the presence of Covid-19 (scientific name SARS-CoV-2) using multiple approaches.

By mapping the genetic mutations of the Covid-19 virus, the Netstrain software tool, which is also used to track such common viruses as mumps, measles and tuberculosis, is able to track the Covid-19 virus movement around the world. It can determine whether all people in the world with coronavirus have been infected by the same strain of the virus, and if not, where new cases of the virus are coming from.

While this type of information won’t stop the spread of the virus, or predict where it is going next, it does enable health authorities to determine whether the new cases that are arriving in their countries are the result of international travel, or whether the virus is being transmitted locally. This will have an effect on decisions around travel restrictions, school closures, whether or not to cancel public cultural and sporting events, quarantine requirements and so on.

Mutating genetic code

Netstrain analysis to date clearly shows that the virus’s genetic code has mutated since it was first identified in China in December last year. The mutations are not significant – so far they do not appear to have changed the actual biology of the virus itself – but they are enough to identify its origins. It is clear that in many regions, different 'strains' of Covid-19 are infecting people.

However, while all the sequenced data in the latest available Netstrain analysis includes a common 'ancestor' that emerged between mid-November and mid-December 2019, the Covid-19 that reached Italy was actually introduced at least twice (from different sources). From there, it spread through the Italian community. This then led to a cluster of mutated virus sequences in six countries, where cases appear to have exported from Italy.

The #OpenCovid19Initiative brings together a group of concerned individuals around a non-profit organisation, Just One Giant Lab (JOGL), which operates out of Paris, France. JOGL’s goal is to create an open platform for scientific collaboration on a wide range of issues facing humanity.

On its Web site, JOGL maintains that humanity has far too many problems to expect traditional institutions to fix in a conventional manner. It therefore wants to offer anyone the opportunity to challenge themselves by launching or contributing to collaborative initiatives that are focused on some of humanity’s most urgent and important problems.

One of these is clearly the Covid-19 pandemic. The group is therefore seeking to create an open source method that will enable better management of the cases spreading across the world.

To date, the group has collected a variety of resources and has started hosting conference calls to discuss best practices for testing for the virus.