The most detailed database of COVID-19 variants available has been launched and will likely play a critical role in the coming months, as the focus shifts from just vaccinating as many people as possible to making certain they are protected against all the most common variants of the disease. Launching at about the same time as a multi-billion dollar rise in the US’s investment in variant tracking, including sequencing, this could mark a turning point in the fight against COVID-19.
The Global.health database already contains extensive information on more than five million anonymized cases from more than 100 countries. It aims to answer questions such as how rapidly are variants spreading, do current vaccines protect against them, and how long does immunity last?
The platform was created by researchers from around the world, including at Oxford, Harvard, Northeastern, Boston Children’s Hospital, Georgetown, University of Washington, and Johns Hopkins Center for Health Security. It contains an unparalleled amount of information, including up to 40 associated variables, such as the date when the patient first had COVID-19 symptoms, the date they received a positive test, and their travel history.
The project evolved as the pandemic grew. “There were a group of us hand-entering COVID-19 case records, and we hit a limit to what a Google spreadsheet could accommodate,” said Samuel V. Scarpino, Ph.D., assistant professor at Northeastern University. Now, Google is the main funder of the project.
The most common variants being tracked are: B.1.1.7 (originating in the UK), B.1.351 (originating in South Africa), and P.1, (originating from Brazil). Big questions about these variants, and others, regard how transmissible they are, how many people get serious disease from them, whether current vaccines can prevent them, and how quickly they are spreading worldwide. The researchers behind it hope the database will help answer such questions.
However, this Global.health project is not just about the COVID-19 pandemic. “This has been an issue with pandemic response for a long time. Every few years we have a different pandemic,” said Scarpino, referring back to the H1N1 pandemic of 2009. “They are sporadic, but they are regular and we need a coordinated way to collect and share the data.”
The database arrives at a critical time for the current pandemic. Once the first vaccine (from Pfizer-BioNTech) was approved by the FDA in December 2020, the world started to breath a collective sigh of relief. People could finally see some way out of this strained existence of isolation, constant hand-washing, and wearing masks whenever in the company of people you don’t live with. A second vaccine (from Moderna) followed quickly, leading to even greater confidence that the pandemic was finally being controlled.
And then, the variants came. At first, they were just blips on the screen. But It quickly become clear that they could form another surge, and one that would require new vaccines or at least boosters to keep up the momentum against the virus. Global.health has already “led to a number of important scientific findings,” Scarpino said. Those relate particularly to the main variants now being tracked and how they are spreading. That tracking ability will be crucial going forward.
For example, the Bristol, U.K., variant contains the E484K mutation that is also found in the South African and Brazilian variants. The U.K.’s New and Emerging Respiratory Virus Threats Advisory Group (Nervtag) has identified this as the Kent variant with the E484K mutation.
Laboratory studies have shown that this mutation is better at evading natural and vaccine-triggered immunity. It’s possible that infection with virus containning the E484K mutation will require a booster shot at least. “Our work suggests the [Pfizer BioNTech] vaccine is likely to be less effective when dealing with this mutation,” said Ravi Gupta, of the Cambridge Institute of Therapeutic Immunology & Infectious Disease, in a press release.
Further, P.1 appears to be highly transmissible. It has already been found in at least 20 countries and it appears it can re-infect people who previously recovered from the disease. According to a Reuters report, scientists said the variant has a “unique constellation of mutations” and had very rapidly become the dominant variant circulating there [Brazil].” Out of 100 people in Manaus who had previously recovered from infection with the coronavirus, “somewhere between 25 and 61 of them are susceptible to re-infection with P.1,” said Nuno Faria, a virus expert at Imperial College London, according to Reuters.
This also comes at a time when the U.S. is boosting its variant tracing efforts. Currently, the country is only conducting sequence-based surveillance of approximately 0.3 percent of coronavirus cases, which leaves it lagging far behind other developed nations. But the CDC has recently boosted its funding for “testing, tracing, surveillance, containment, and mitigation to monitor and suppress spread of COVID-19” by more than $19 billion, according to a recent release.
Clearly, the U.S. is running to catch up. Britain’s world-leading COVD-19 effort runs on little funding to provide a big payback. “It is supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute.”
Even the U.K., which is ahead of the world in term of sequencing of COVID-19 samples admits it is an uphill battle. Prof Peacock, director of the Covid-19 Genomics UK consortium, said recently: “What’s really affected us at the moment is transmissibility.” She added: “Once we get on top of [the virus] or it mutates itself out of being virulent – causing disease. We’re still going to be doing this 10 years down the line, in my view.”
Further moving this trend towards variant identificartion forward, the Tracking COVID-19 Variants Act aims to add another $2 billion to the now muti-billion US effort. “Variants represent a growing threat to the health and security of our nation, and right now the US is lagging behind other countries in tracking new and emerging variants of this deadly virus,” said Senator Tammy Baldwin (D-WI), who sponsored the bill.
She added that, “The U.S. should be a world leader in this effort, and that means we must invest more funding and resources to allow the CDC to ramp up national sequence-based surveillance and support our public health infrastructure so we can better identify, survey and understand these variants, and better protect all Americans from this public health crisis.”
Perhaps the best advice comes from Sharon Peacock, director of the COVID-19 Genonics Consortium, who helped the U.K. build the variant-testing system that is now the gold standard for the rest of the world.
In a blog post Peacock writes: “Detecting mutations (increasingly in different combinations) that are worrying enough to study them in detail—and make decisions around matters such as lockdown and travel—depend on routinely sequencing viruses that are infecting us. Mutations in the virus genome are happening all around the world—this is an unstoppable force of nature.”