The story: Scientists want to keep an eye on how a single pathogen navigates, mutation by mutation, through a worldwide landscape of adaptation. Just
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Tracking the viruses of the world
- The story: Scientists want to keep an eye on how a single pathogen navigates, mutation by mutation, through a worldwide landscape of adaptation. Just a decade ago, this would have been science fiction, but not any more. The novel coronavirus pandemic made this possible.
- Why not track all: Today, there are at least 264 virus species known to infect humans. Why not track them all, and why not focus on the nearly 8,00,000 which could, in the right circumstances, jump from their habitual hosts into humans and start spreading?
- Is it possible to identify all such viruses, and create mechanism to identify their jumping from natural to the human world?
- Such ideas, till 2020, would be laughed away, but not any more.
- Realism: As the pandemic progressed, the cost of tracking pathogens has proven to be the lesser problem to the real world biological limitations. RNA vaccination seemed like a wild idea less than a decade ago, and impractical to implement but now it's happening.
- GIO: The Global Immunological Observatory (GIO) aims to use modern lab techniques to spot incipient health crises before they take off, by providing near-real-time insight into what infections are where. How would it do so? By looking at hundreds of thousands of blood samples every day.
- The blood stores a history of the immune system written in antibodies. Seeing what antibodies someone’s blood contains can show, for instance, whether they had measles as a child, which flu virus laid them low last winter or which cold virus they sniffed their way through with mild irritation three weeks ago. Even if a pathogen never made them sick, the memory of its attempt to do so may still circulate.
- The GIO will ideally test every tiny sample of blood for hundreds of thousands of distinct antibodies. Considering how hard large-scale testing for just SARS-COV-2 has proved, this might seem too ambitious. But there are tools like VirScan that may be able to do it.
- VirScan - It is a platform developed by scientists at Harvard Medical School which looks for antibodies to more than 1,000 strains of 206 different viruses in a single tiny sample of blood using a canny combination of DNA synthesis and DNA sequencing,
- The process: The VirScan team synthesised genes describing the proteins found on the surfaces of all those viral strains—the sort of proteins which, like SARS-COV-2’s spike, are most likely to elicit antibodies. It then used those genes to create thousands of slightly different “phages”—simple and easily mass-produced viruses that infect bacteria. Each phage in this library expresses one of those tell-tale proteins on its surface and the relevant gene in its DNA. Expose a copy of this library, containing billions of phage particles, to someone’s blood and the antibodies which recognise a particular viral protein will bind to the appropriate bacteriophage. Rinse away the phages that are not attached to antibodies—those which have gone unrecognised—then amplify the DNA from all the others and sequence it. The sequencing data reveal what the antibodies recognised.
- A viable idea: Since blood and plasma banks already exist in every city in the world, and blood samples that are collected by doctors and nurses for any number of medical reasons, it can be done. Anonymising the samples and providing them to the GIO could be a simple additional task for any laboratory.
- One of the advantages would be that it would detect the true prevalence of pathogens, rather than just seeing them when they cause symptoms.
- It could also reveal the presence of a new virus not represented in the phage library.
- Some of the antibodies which recognise a given virus will also recognise others to which that virus bears a family resemblance, though not as well. Thus some SARS-CoV-2 antibodies recognise the viruses behind SARS, MERS and some forms of the common cold.
- Imagine if: If GIO had been operating in late 2019 and early 2020, it would have seen antibodies to a range of coronaviruses starting to turn up in various places, a molecular shadow alerting it to a new pathogen it could not yet see directly, but which, after a little sequencing, it would understand intimately. Such anonymised antibody surveillance could be supplemented by sequencing not just of blood. Scientists have shown that the SARS-CoV-2 virus can be detected in waste water and sewage. Using such systems to see where a virus is, neighbourhood by neighbourhood, would give public-health officials useful almost-real-time insights into pockets of infection.
- Summary: Pathogens have crossed between species and people for as long as humans and animals have been in close contact. Measles emerged in people during the domestication of livestock. HIV originated in chimpanzees, influenza in birds and pigs, ebola in bats, which also teem with coronaviruses. Around 1,500 viral species which belong to families known to infect both humans and non-human animals have been discovered to date. The rate of their discovery suggests that mammals and birds together may harbour 1.67m more. Up to 8,27,000 of them could cross over into humans.
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