One of the positive experiences during two years of pandemic gloom has been the speed of scientific progress in understanding and treating Covid. Many effective vaccines were launched in less than a year and rapid large-scale trials found a cheap and effective drug, dexamethasone, that saved thousands of lives.
The global scientific community has also carried out “genomic surveillance” – sequencing the genome of the virus to track how it evolves and spreads at an unprecedented level: the public genome database has more than 5.5m genomes. The great value of that genomic surveillance, underpinned by a commitment to rapid and open sharing of the data by all countries in near-real time, has been seen in the last few days as we’ve learned of the Covid variant called Omicron.
The surveillance requires a remarkable amount of cooperation between scientists to build compatible laboratory protocols, software systems and databases. Many of these scientists are not directly paid for this work and do it in addition to their existing jobs. They are motivated by a belief that sharing data relevant to public health, especially in a pandemic, can help speed up scientific understanding, aid in decision-making and contribute to the next generation of medicines.
This commitment to rapid data sharing has deep roots in genomics. At a 1996 summit in Bermuda, the leaders of the Human Genome Project established a set of principles to release a new DNA sequence to public databases within 24 hours. This approach departed from the established convention that experimental data only needed to be released when a study was published, months or years later. Sir John Sulston, founding director of the Wellcome Sanger Institute, said: “All of this [genome data] should be in the public domain… I think we need a public social welfare attitude to the use of this information.”
That attitude now prevails around the world, as evidenced by the rapid sharing of more than 1m Sars-CoV-2 sequences by the Sanger Institute since March 2020.
On 23 November, scientists in Botswana uploaded 99 Sars-CoV-2 genome sequences to this database. Like most submissions that day, nearly all the sequences were the dominant Delta variant. But three of them looked different from anything seen before.
Later the same day, an independent team in South Africa uploaded seven nearly identical genomes. These teams noticed that the new variant contained an eye-watering number of mutations in the part of the virus’s genome that encodes the spike protein, which it uses to infect human cells. Most concerningly, nearly half of these mutations had previously been seen in the earlier variants of concern (Alpha, Beta, Gamma, Delta) or predicted in laboratory experiments to increase the virus’s ability to latch on to human cells. They notified health authorities of their concerns and began an immediate investigation into how widespread this new variant might be.
While these scientists worked around the clock, the fact that they had shared the sequences with the world as part of their routine process, before they even knew what they were, meant that other scientists, thousands of miles away, could study them as well. Within just a few hours of the sequences being shared, a post was made on the pango designation forum, a corner of the internet where virus genome experts discuss new sequences and assign name that makes it easier to refer to specific parts of the Sars-CoV-2 family trees.
The mutations in the new variant also alarmed the international scientists. It was quickly dubbed B.1.1.529 and prioritised for further study. Once additional evidence gathered by the local teams in South Africa had been presented, the World Health Organization (WHO) made it the fifth variant of concern, Omicron. Just 72 hours had passed since the original discovery.
The scientists who sounded the alarm because they are committed to the moral imperative of rapid data sharing knew that in the midst of the pandemic it would have consequences. Tulio de Oliveira, one of the leaders of the South African genomics team, announcing the variant, tweeted: “The world should provide support to South Africa and Africa and not discriminate or isolate it! By protecting and supporting it, we will protect the world!”
By the next day, dozens of countries, including the UK, had announced new travel restrictions on countries in southern Africa. Some restrictions may have been unavoidable to buy time to understand this new threat, but travel bans come with serious consequences for people and economies in affected countries. Previously, they have delayed, but not prevented, the spread of new variants. There is some chance in this situation that they may be more effective, precisely because of the excellent work done to share information so rapidly.
Genomic surveillance in India when Delta appeared was less comprehensive and the seriousness of that new variant did not become apparent until weeks after it had been circulating widely, and exported around the world.
While scientists around the world are scrambling to understand Omicron, and national governments are making response plans, we must also find ways to reward the critical early warning provided by South Africa. Less than 25% of South Africans are fully vaccinated, and while that may be due to complicated reasons involving both supply and demand, it is not for us in the rest of the world to determine what would be most helpful. Countries with an abundance of vaccine doses and other resources should offer whatever is asked for by countries now at the front edge of the confrontation with Omicron.
The pandemic has emphasised that we are a single global community and our policy responses must reflect that reality. It would be a disaster if the global response to this heroically open science sent the message that the reward for such bravery is isolation.