There is a recently published book that has quickly risen to the top of the best-seller lists, telling many unknown stories about the public health environment that led to the COVID-19 pandemic. Well named, The P.remonition highlights key figures in research and policy who set the stage for our global and national response. Through these personal stories, author Michael Lewis provides readers with insight into the many early warnings, the premonitions, that a major viral outbreak was about to change our lives for a long time. One of those stories highlights a tool that will invariably help us detect the next outbreak. In today’s post, we will learn about that technology and the steps being taken to make bioinformatics an early warning system.
The story of the box that could identify the next pandemic begins, in many ways, in the year 2000, when researcher Joe DeRisi and his colleague David Wang reasoned that DNA microarrays could also be used to identify and discover viruses. They created ViroChip, a small glass slide that contains more than 22,000 tiny fragments or sequences of all the viruses ever discovered. When exposed to samples taken from patients, the slide fragments adhere to those of the sample and reveal which viruses are present. That’s ID part. If the patient sample activates strange combinations of viruses or incomplete fragments, then the result could be the discovery of a new, or novel, virus. The ViroChip played a key role in identifying SARS-CoV-1, known as SARS, in 2003. It was also used to confirm the identity of its deadliest cousin, SARS-CoV-2, the virus that causes COVID- 19. All that was needed to get an early warning of more new viruses were tons and tons and tons of samples. Dr. DeRisi and his team did not patent the technology, so it was available to anyone who wanted, or rather could access, that level of biological and computational infrastructure.
The story continues in 2016 when the Chan Zuckerberg Initiative funded BioHub, an independent, non-profit research center, with Dr. DeRisi at the helm. Co-Chair DeRisi, not just a biologist but also a self-proclaimed “computer nerd,” realized that the next step in getting ViroChip to give us the information researchers needed to anticipate potential new pathogens was more data. Obtaining more samples, and millions more, would reveal patterns, expose the early emergence of new pathogens, and give us time to sequence the entire virus and prepare for a possible outbreak, including treatments and even vaccines. How would they manage to analyze the millions of samples in progress in near real time from all over the world, even countries with less technological infrastructure? Analyzing the ViroChip data requires massive computational power, requiring everything from expensive equipment to a reliable power grid, two things that developing countries don’t have.
Pay in IDSeq, the box (and the cloud) that can predict the world’s next pandemic. IDSeq is a free, open, and accessible cloud-based dashboard that allows researchers to upload their ViroChip data and retrieve analysis through a process called metagenomic sequencing. Their data joins the growing database of samples needed for global viral surveillance, and they get a powerful analytical tool they might never otherwise be able to access. All they need to have is a basic genome sequencing lab (which has become much more affordable and accessible in the last five years) and an internet connection (even a spotty one).
How important is it to have a “real-time pathogen detection” tool? It is the difference between finding patient zero (or even patient 15) instead of patient 100 or 1000. It means discovering The actual cause behind an outbreak of flu-like symptoms in one area is the same as the cause of an outbreak 100 miles away, and the realization that there is a connection. It means detector, monitoring and reviewing outbreaks as they occur to better understand transmission speed and geographic distribution. Finally, it means deciphering new viruses (or organisms, as you are not restricted to viruses) and sequence them so that treatments and vaccines can have an advantage if an outbreak occurs.
It is exciting and also encouraging to know that such an accessible tool is available around the world to better prepare for the next pandemic. While the COVID-19 pandemic still continues, it is worth noting that Dr. DeRisi and his colleagues are not always attended. When SARS-CoV-2 first began to be detected in the US, they did not believe that the federal response was fast enough, so they converted their lab to a diagnostic lab within 8 days so they could start processing. COVID testing. It takes this kind of trained intuition to inform our nation on how to prepare, if we listen.