Why Scientists and Citizens are Turning to Open Science To Combat COVID-19

Publicado en Coder stories

01 abr 2020

9 min

Why Scientists and Citizens are Turning to Open Science To Combat COVID-19
Hannah H. Kim

Freelance writer

In early March, a worker at Nasa’s Ames Research Center tested positive for COVID-19, causing the Silicon Valley-based facility to issue a mandatory policy for all employees to work from home. Unable to access the campus’s lab, Matteo Bori, an external researcher for the center’s astrobiology department, decided he would instead use his engineering knowledge and own design lab to provide resources for healthcare professionals working on the front line.

Bori’s extended family lives in Milan, Italy, and he had already heard firsthand from them about the shortage of medical supplies. So back home in California, Bori consulted a neighbor, a registered nurse, about the supplies most needed by healthcare professionals and designed a homemade mask and biocontainment suit that could be replicated by hobbyists with products found at their local hardware stores. He sent prototypes to local hospitals and released his designs online to teach others how to make them for their local hospitals. “We should not have gotten to a point where we have to MacGyver a solution, but we are at that point,” he says.

Bori is part of Open Source COVID19 Medical Supplies (OSCMS), a Facebook group that aims to collect and disseminate specialist knowledge from around the world to address the pandemic’s supply-chain crisis. It is one example of how the public is turning to open science—a movement to develop transparent and accessible scientific knowledge through collaborative networks—to fight coronavirus.

Institutions scramble as coronavirus cases rise

As the novel coronavirus spreads across the globe, institutions in some countries in the West are struggling with two-fold containment challenges: a widespread lack of accessible testing and a critical shortage of medical supplies for doctors, nurses, and other frontline medical workers.

South Korea demonstrated to the world how efficient and wide-scale testing could significantly curtail the number of infections, but the rollout and availability of COVID-19 tests in countries such as the US and UK have been hindered by policy and procedural failings.

Meanwhile, hospitals are running out of protective equipment for their staff, including face masks and shields, surgical gowns, and hand sanitizer. Trade data reported by the associated press indicates how the medical-supply shortage has resulted, in large part, from a reduction in imports from China. A decline in shipments started in mid-February, when China itself was battling with the coronavirus outbreak, resulting in the shuttering of factories.

By the time the number of active cases of people with coronavirus had started to decline there, state governors in the US were expressing an urgent need for federal action to help them get medical supplies and protective equipment. In short, nobody was getting enough of either.

In Europe, which had become the epicenter of the pandemic by mid-March, private factories started stepping in to produce protective medical supplies. In France, LVMH, the luxury-goods conglomerate, announced plans to produce hand sanitizer at its factories that normally produce perfumes and cosmetics, while the British government emphasized urgency for companies such as Rolls-Royce to produce simplified ventilators as it started preparing for an influx of patients that could overwhelm the nation’s healthcare capacities.

The public organizes around open science to respond to the crisis

While institutions buckle under mounting pressure to contain the virus, individuals around the world have instigated grassroots efforts to share knowledge and contribute resources to fight the pandemic.

“I’ve seen critical-care protocols develop in a matter of weeks, things that usually take months or years to finalize before a board. But in this case, there is no time,” says Victoria Jaqua, a Texas-based radiologic technologist. “Doctors are leaning heavily on the Hippocratic oath and fighting this as hard as they can with limited resources and no vaccine.”

In northern Italy, where hospitals were running out of space and equipment to provide care for all its coronavirus patients, a group of engineers and experts who work in digital manufacturing recreated respirator valves using a 3D printer. When they started looking into responding to the need, the valve’s official manufacturer refused to release the designs, but they were able to work together to reverse engineer it and offer a supply of valves to a hospital near Brescia that was particularly affected.

It was San Francisco-based roboticist Gui Cavalcanti who started the OSCMS Facebook group, which grew to more than 35,000 members within 14 days. Cavalcanti explained over a phone call how the focus of the group is for designers, manufacturers, and other specialists to understand the disease and how it’s treated. The aim is to document and distribute their designs for protective medical equipment that can be made with publicly accessible supplies and be locally distributed.

The group has also organized into a more concentrated network that Cavalcanti describes as a “flash NGO,” consisting of manufacturing networks, doctors, medical transcribers, researchers, and administrative volunteers. One function of the group is to review the open-sourced designs for quality and safety, the goal being to be able to recommend them to the public.

The group’s second function is organizational: to connect hospitals to local manufacturing resources, and to be a resource for local groups to produce supplies for hospitals effectively, without overwhelming the hospitals with communication and donations. The key for communities to mount an effective supply-chain response, says Cavalcanti, is to “appoint a low number of people to activate a larger collective.” Collective leaders can then “get in contact with local hospitals and get ready to respond.”

Open science accelerates vaccine research

As the world races to contain the fast-moving coronavirus, clinical trials for a vaccine have begun at the Kaiser Permanente Washington Health Research Institute, following Massachusetts-based biotech company Moderna Therapeutics’ development and shipment of its first batch of the COVID-19 vaccine to the US National Institutes of Health (NIH) in late February.

The unprecedented speed at which researchers have created a potential vaccine for human trials—only 42 days after the virus’s genetic sequence was released by Chinese researchers—is one result of the scientific community’s efforts to work together through open-science methodologies.

Under ordinary circumstances, scientific research is distributed through journals by a lengthy peer-review and curation process that is time intensive. Access to research can also be inhibited by paywalls or scientists’ organization affiliations. However, the urgency of the coronavirus pandemic has prompted researchers around the world to work together and share information, using tools such as real-time virus-tracking software and open-access research databases.

The global research community has made a “commitment to make COVID-19 data freely available,” says Dr. Naval Asija, a general practice physician and medical writer based in India. Asija points to the pledge that was made by a group of leading journals and academic organizations on January 31, 2020, to make all peer-reviewed COVID-19 studies immediately and openly available for researchers throughout the pandemic.

During past outbreaks, both state and private actors’ assertion of proprietary knowledge has worked to the detriment of the global health community’s efforts to combat viral disease. For instance, in 2007, that community was embroiled in controversy when Indonesia declared “viral sovereignty” regarding H5N1 influenza samples collected within their borders. The Indonesian government resumed sharing viral samples when the World Health Organization (WHO) made a commitment to work toward equitable access to vaccines between developed and developing countries.

In 2016, the WHO released a policy statement on data sharing in the context of public health emergencies “to permit analyses that allow the furthest possible understanding of the emergency.” The following year, researchers published an editorial in the WHO’s bulletin, stating, “The experiences from the 2013–2016 Ebola virus disease outbreak and the 2015 Zika virus outbreak demonstrated the importance of research in public emergencies and the difficulties associated with sharing research findings rapidly and outside conventional scientific publications.”

In light of progress with accessible data, however, researchers have raised concerns. Without a rigorous, peer-reviewed selection process, some unfounded COVID-19 studies have been rapidly shared, causing misinformation to circulate. For example, also on January 31, researchers at the Indian Institutes of Technology shared a first draft of a paper on bioRxiv, an online server that allows biologists to share early research and gain feedback through a crowdsourced, peer-review process. According to reporting by Fred Hutch news services, the researchers implied that coronavirus’s sequencing could be laboratory generated. While the claims were quickly invalidated by the scientific community, conspiracy theories had already started circulating online about how “scientists had confirmed” that the virus may have been intentionally created.

Accessing reputable data may be the first step for researchers to take when collaborating against a viral disease, but synthesizing all the information available is a formidable challenge in itself.

“As there are thousands of biomedical journals in multiple languages, compiling bits of information on all aspects of the disease can be difficult and pose a challenge to researchers,” says Asija. In an effort to provide a comprehensive resource of COVID-19 medical research papers, the WHO has taken the initiative to organize the latest scientific findings into a global database.

The COVID-19 Open Research Dataset is another example of a free resource, and has more than 44,000 scholarly articles about coronavirus and C-19. It was released by a group of organizations including the Allen Institute for AI, Chan Zuckerberg Initiative, Georgetown University’s Center for Security and Emerging Technology, Microsoft, and the National Library of Medicine. The White House joined these organizations’ call to action for AI experts to use the COVID-19 Open Research Dataset to develop text and data-mining techniques that could help the scientific community answer questions relating to coronavirus.

Researchers organize open-source coronavirus-testing methodologies

The current public-health crisis has activated urgency among open-science initiatives. As a movement, open science aims to make scientific research and data accessible to the larger community by openly publishing findings and allowing the public to participate in the research process.

Previous open-science initiatives, such as the Paris-based project EchOpen, have already helped to improve healthcare. Between 2014 and 2017, EchOpen utilized the efforts of more than 400 community members over 3 years to transform the unwieldy ultrasound scanner into something more affordable and easily transportable to medically under-served communities. The result was a prototype for an “echo-stethoscope”—a medical imaging device that allows healthcare professionals to read diagnosis via a smartphone.

In the same way open-science methodologies were employed by EchOpen, communities of researchers have created global, open-sourced initiatives to respond to the current crisis. In particular, institutional shortcomings have delayed accessible and affordable coronavirus testing for all who have needed it.

In the US, many healthcare workers and people showing symptoms have been unable to access tests to get a diagnosis. Combined with inaccurate reporting of the virus’s spread, this has crippled the country’s containment and mitigation efforts.

Testing in the US typically involves a healthcare professional swabbing the back of a patient’s nasal passage and sending the sample to a lab, where specialized equipment is used to detect genetic material from the virus. But the lack of available tests has partly been due to an initial requirement that they could only be processed at the Centers for Disease Control and Prevention (CDC).

By the end of February, the US Food and Drug Administration announced a new policy that would allow elite academic and commercial laboratories to test patient samples. While publicly traded companies and healthcare startups have accelerated efforts to bring at-home testing kits to the market, these sample collection kits could cost well over US$100 each.

The OpenCovid19 initiative, launched by Just One Giant Lab (JOGL), a distributed research laboratory based in Paris, is aiming to produce a low-cost and open-source coronavirus test kit. Zach Mueller, a co-leader of the initiative, explained in an interview with Crosscut at the beginning of March that its primary goal is not necessarily to equip people with the ability to safely test themselves at home, but to develop “an open-source protocol that people in appropriately certified labs around the world can use to easily produce test kits for their communities.”

Thomas Landrain, a biologist and the other leader of OpenCovid19, told Crosscut that they were prioritizing the need for an accessible, alternative test that could be easily shared in a “nonoptimal environment.” Landrain pointed out that since countries with modern healthcare systems such as France were experiencing difficulties providing accessibility to testing, then the situation in remote communities with rudimentary healthcare systems was likely to be much worse.

OpenCovid19 currently has more than 300 members from around the world who are scientists, engineers, healthcare professionals, students, and citizens. Its project framework is broken into sub-objectives, with assigned teams that maintain iterative workflows and open research notebooks that can be accessed by members. Participation is open to the public.

However, due to safety issues, public-health officials in the US have raised concerns regarding the participation of well-intended yet nonspecialized participants in initiatives such as virus testing. During OpenCovid19’s second conference call in early March, a participant identified as Ellen talked of her experience of how citizen involvement in combating coronavirus was being received. “We were told that the only thing we were good for was to spread information,” Ellen said. “There’s a fear that amateurs will get involved and hurt themselves and others.”

Also during the call, OpenCovid19’s members discussed the pressing need to create a biosecurity board that could review their subprojects for safety. Chris Monaco, another conference participant and an Atlanta-based microbiologist at the CDC, responded with his interest in the biosafety aspect of the initiative. He mentioned his initial hesitation to join OpenCovid19 because of biosafety concerns, but offered to reach out to his colleagues at the CDC to see who would be interested in providing expertise and reviewing protocols.

As the scientific community collaborates to understand the novel coronavirus, and communities organize to provide resources for frontline healthcare workers, individuals from all over the world are applying open-science methodologies to do what they can to respond to the global health emergency. “In times of crisis, most people want to help,” Jaqua says. “Open source has brought obscure medicine down to the people.”

This article is part of Behind the Code, the media for developers, by developers. Discover more articles and videos by visiting Behind the Code!

Want to contribute? Get published!

Follow us on Twitter to stay tuned!

Illustration by Blok

Las temáticas de este artículo