Looking back at 15 years of sharing viral genomes to forge ahead

Anniversaries represent an opportunity for revisiting the past to make a leap forward. I’m using a 15-year anniversary of an act of scientific rebellion that changed my life — and affected the lives of many others — to look beyond Covid-19.

In March 2006, Europe and other parts of the world were threatened by H5N1, the so-called bird flu virus. As a virologist working in Italy on viruses of pandemic potential, I ignited an animated international debate by refusing to send the sequence of the H5N1 viral genome to a password-protected database, but made it publicly available instead. And I urged my colleagues the world over to do the same.

I believed then, as I do now, that sharing the sequences of viral genomes will accelerate research about these highly prevalent and adaptable organisms, and help us fight them if necessary.

My call to action was endorsed by international organizations such as OIE (now called the World Organisation for Animal Health), the United Nations’ Food and Agriculture Organization, and the World Health Organization, though it took a very dark turn. Sharing the sequences of viral genomes has since become standard practice.

Why is this relevant today? Because on Jan. 10, 2020, just days after the outside world began learning of a mysterious pneumonia outbreak in China, the sequence of the novel coronavirus causing the disease was made available to the scientific community worldwide. Since then, hundreds of thousands of sequences of SARS-CoV-2 have been, and continue to be, hosted in publicly available databases. This open sharing has made it possible for scientists to respond rapidly to the diagnostic and immunization challenges that a pandemic requires.

It was clear to me years ago that the globalized socioeconomic structure the citizens of the world inhabit would present only weak barriers to viral spread — and may even encourage it. If new viruses and viral variants emerging in different countries were monitored and compared efficiently, this knowledge could be used to update vaccines and diagnostics in an ongoing manner to try and get ahead of any pandemic wave.

The concept is even more true today as scientists have developed the mindset and infrastructure to share what will soon become millions of genetic sequences of interest. But this is not enough. Because viral surveillance and sequencing capacity are insufficient in some geographical areas, the sequences are not representative of the worldwide distribution of viruses.

Given that this is a globally relevant problem, it is essential to ensure that proper surveillance and sequencing capacities exist in most, if not all, countries, including low-income countries. My call to action 15 years ago was, “Genetic sequences should be shared.” Today it is, “All countries need the capability for viral surveillance and sequencing — now.”

As we look ahead to post-pandemic scientific life, I believe that information sharing must go beyond viral genomes and take full advantage of the ever-expanding availability of open data to exploit one of the hidden truths of the SARS-CoV-2 pandemic: This is the most measured event in human history.

This multidomain approach would be totally unrealistic had Covid-19 occurred a decade earlier, when our abilities to capture, store, and process data were not as advanced as they are today. Virtually every variable of the pandemic actively and passively generated by the billions of personal or institutional devices we use every day to manage our lives is now being measured in some form or other. For example, weather data, pollen and allergen concentration, pollution levels, and other variables such as mobility and the features of everyday life that favor viral spread and perpetuation of infection can be explored as drivers of hospitalizations and excess deaths.

Covid-19 could become the perfect justification to maximize the potential of the data we are generating to discover novel interactions that can support real-time decision-making. These discoveries can also serve as springboards to the future.

The SARS-CoV-2 pandemic has once again shown us that human disease can be linked to the spillover of an animal virus, but its course and ramifications are linked to multiple other drivers. We have watched this pandemic act as a multisystem stress test for interconnected and interdependent domains. We have seen its tragic effect on millions of individuals around the world, and upon health and health care systems. It has also altered the management of personal and social interactions and mobility patterns, causing us to rethink our social behaviors.

We marvel at the mind-blowing efforts of pandemic response to create, test, and deliver vaccines within one year of discovering a virus. But the pandemic has also exposed a huge strategic failure in thinking about vaccines: requiring a cold chain to store and deliver them. This has affected the rollout of vaccination in developed countries and is a huge unresolved problem in middle- and low-income countries. Now is the time to invest in thermostable vaccines, that are resistant to damage cause by heat or freezing, starting today with Covid-19 and extending the technology for other vaccine-preventable diseases tomorrow.

We are being forced to rethink — or reinvent — entire systems that have been disrupted by the pandemic. During this process, we should be motivated to explore novel solutions that build on the ever-expanding knowledge about the interplay between human, animal, plant, and environmental health, ideally dovetailing into actions towards the United Nation’s Sustainable Development Goals.

I like to imagine this vision as Circular Health.

Ilaria Capua is a virologist and director of the One Health Center of Excellence at the University of Florida in Gainesville.