Science, Open Data and the COVID-19 Pandemic

The speed of developments in science and technology to mitigate the COVID-19 pandemic is unprecedented in the history of science. Synthetic biology, a new branch of science, has contributed to containing and treating COVID-19 quickly.

DNA sequencing is crucial to fighting viruses like COVID-19. The sequence was available as early as Jan 10, 2020. On January 12th, a rapid-response team dispatched by the Chinese Centre for Disease Control and Prevention added three genome sequences in the open-access database, Global Initiative on Sharing All Influenza Data (GISAID). These sequences reveal the zoonotic origin of the novel coronavirus. It shares nearly 85% of the sequence identity of a known SARS-like coronavirus found in bats. As of March 21st, approximately 178 sequences of the virus from various parts of the world, including two from India, have been added to the GISAID.

The report from the International Health Regulations (2005) Emergency Committee underlines the importance of the release of full viral genome sequences to a public platform to diagnose and contain infections early. The first U.S. clinical trial of a COVID-19 vaccine has already started. More information on the virus is coming on a daily basis.

International collaboration

Deficiencies in data-sharing mechanisms, which were highlighted during the 2013–2016 Ebola virus outbreak in West Africa, raised the question of data access. It brought the issue to the forefront of the global health agenda. In September 2015, the World Health Organization reached an agreement on the need for open data-sharing, especially in a public health crisis like COVID-19. In 2018, the WHO facilitated the establishment of GISAID, promoting the international sharing of influenza virus sequences, including clinical and epidemiological data associated with human viruses, geographical data, and species-specific data associated with avian and other animal viruses. Such information would help researchers understand how the viruses evolve, spread, and potentially become pandemics.

As new generation sequencing technologies (NGS) have become more widely available and cheap, genetic sequence data has become central to mitigating outbreaks. Such data gives research groups and industries that synthesize viral genetic material to develop detection kits, monitor the disease, DNA printing, and vaccine development.

Modern science to the rescue

Synthetic biology, a set of techniques and technologies that ‘create’ life by using combinations of gene sequences, is now taking the world by storm. There are several ways in which synthetic biology advancements have contributed to fighting COVID-19.

Such achievements include the development of Centivax, a new kind of universal vaccine which can work against almost any virus and a detection assay, which uses precise DNA strands to accurately detect and measure the amount of pathogens in the bloodstream.

The vaccine development

The Coalition for Epidemic Preparedness Innovations (CEPI) is leading the effort to develop a vaccine for the 2019-nCoV. Although genetic sequencing is a quick process, making vaccines is as much art as is science. It involves finding a viral sequence that will reliably cause a protective immune-system memory that would not trigger an acute inflammatory response and disease-related symptoms.

Moderna’s mRNA-1273 funded by the U.S. National Institutes of Health (NIH) in collaboration with CEPI has begun trials. While the experimental vaccine remains unproven, the speed at which it was created is a positive indicator. According to Moderna, the vaccine was developed in 42 days of the company obtaining the virus’s genetic information. By comparison, it took researchers nearly twenty months to start trials for the SARS vaccine, an older coronavirus.

The University of Queensland in Brisbane, Australia, announced that they’re working on a vaccine that they hope to have ready within the next few months. The “molecular clamp” approach that Australian researchers have developed is designed to boost the immune system’s response while combating multiple viral infections.

Disease surveillance

Many RNA viruses, including the coronavirus, mutate frequently as it spreads through a population. Detecting multiple genes simultaneously reduces the risk of missing detection that could occur with a genomic variation. A software tool called Nextstrain can assess the origin of new viral infections. Such information is significant for healthcare workers who are trying to determine whether new infections are linked to international travel or local transmission. Genomic epidemiology can determine the virus’s origin and help inform decisions on travel restrictions, school closures, quarantines, and determine resource allocation to contain the outbreak.

To assist scientists in resource-limited areas who may not have the laboratory tools or training needed to perform analysis, a group called the ARTIC Network has been providing protocols and training to enable scientists globally to undertake disease surveillance and sequencing. They’re also developing a “lab-in-a-suitcase” that can be deployed to remote and resource-limited locations.

Open data sharing and samples

During the H7N9 influenza virus (bird flu), the U.S. alleged that several countries including China and Russia refused to share genetic information for more than a year, which slowed down the development of vaccines and treatments. Indonesia refused to share virus samples and data during the bird flu breakout fearing that pharmaceutical companies would make vaccines that would ultimately be unaffordable to their own people.

Initiatives like the GISAID were established to facilitate data sharing. This innovative approach has enabled GISAID to build a large database, which now hosts more than 650,000 flu virus sequences. GISAID ensures protection of the provider’s rights through an agreement governing the way individuals may access and use the virus data. To ensure transparency, GISAID’s platform also offers an electronic tracking system that enables individuals to see who has received virus samples from government laboratories and pharmaceutical companies.

The CBD to the rescue

The Convention on Biological Diversity (CBD) is a multilateral environmental agreement that focuses on issues of conservation and sustainable use of biological resources and the fair and equitable sharing of genetic resources. The CBD covers all biological diversity, except human genetic diversity. Under the CBD, countries negotiated and adopted an international protocol, the Nagoya Protocol (NP), on access to genetic resources and benefit-sharing. Article 8 of the protocol calls for special considerations while countries provide access to genetic resources and share the same, including for those related to food security, health, and related emergencies.

This is perhaps the most important and enabling clause of a multilateral agreement that has 124 countries as its signatories providing options for access to critical genetic resources and information. The access and benefit-sharing provisions under the protocol facilitated discussions within the WHO in coming up with fair provisions for sharing the genetic resources and related benefit-sharing components during the bird flu outbreak and to a significant extent supported initiatives such as the establishment of GISAID.

Ongoing discussions under the Nagoya Protocol currently focus on the issues related to digital sequence information (DSI) where the parties are negotiating how the genetic sequence information held in databases around the world should be accessed considering the need for sharing the benefits arising from such use. One sticky point during the ongoing discussion is the procedural requirements for seeking access to DSI and how benefits will be shared if the DSI-related information is commercialized.

Future needs challenges

The following are some future needs and a few emerging challenges in access to data and information, diagnostic capacities, and the treatment of infectious outbreaks.

The first one is the ongoing discussions for dealing with DSI under the Nagoya Protocol of CBD. The negotiations should be carefully steered before decisions are made during the next governing body meeting of the CBD that is scheduled to be held in 2020. While Article 8 (b) of the protocol requires countries to pay ‘due regard’ to present or imminent emergencies in providing access and sharing benefits, countries while developing national ABS frameworks need to ensure the procedural and institutional mechanisms to deal with ABS are simple and quick. Technical and institutional capacities need to be built for this at the national level.

The nature of public disclosure of sequence information, as witnessed during the current COVID-19 pandemic is a great example of the need for open-source data and information that can be used for developing diagnostics and treatment. Only time will determine how the commercialization of the products would span out and decisions would be made to share the benefits from using such data and information.

If used appropriately, the enabling provisions of the Nagoya Protocol can come to the rescue of future discussions on both access and sharing benefits. For this, the discussions under the DSI component of the Nagoya Protocol need to focus on decisions that are both facilitating and enabling.

The second challenge is the near absence of national policy frameworks on synthetic biology. The private sector is mainly dedicated to research and development. Based on the descriptions above on how technology is currently addressing COVID-19, it is important for countries to come up with policy frameworks that define future investments and collaborations using technology.

The third challenge is the need for building capacities and providing accessible and timely finances to deal with current challenges. The establishment of a global funding mechanism that combines technological capacities with finances is urgently needed and must be supported by governments, philanthropists, and the private sector.

If science can help us in such emergencies, policies should guide us in delivering positive outcomes.