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The new genomic weapons against the omicron variant (that's technology too)

On Sunday, a passenger arrived in Madrid infected by a virus under surveillance. The case was detected by an antigen screening at the same airport, and in just 24 hours a genomic analysis confirmed that it was the omicron variant, which had no name three days earlier. The scene sounds almost routine, but it hides technologies that were impossible a decade ago.

During the pandemic we were grateful to have doctors and scientists, but we forgot to celebrate certain technical advances. Imagine what these two years would have been like without PCR, without RNA vaccines, or without the machines that decipher genomes. These days we see countries taking precautions because a worrisome mutation has been detected. It seems normal to us, but this is new: although viruses have mutated since life (or no life) exists on Earth, humans have only been able to see it for two decades.

“The first bacterium was sequenced in 1996,” Iñaki Comas, a biologist at the Valencia Institute of Biomedicine (CSIC), told me. “The new technologies that allow massive analysis began in 2005. But their use in pathogen epidemiology began to take off ten years ago and definitely five years ago.”

A virus like now has never been followed. There are dozens of countries taking millions of samples and analyzing their entire genome (the set of letters that defines it, with all its mutations). That information is then shared in open databases, such as Nextstrain or Covariants, to scrutinize their changes and follow their spatial and temporal spread. In Denmark, which is one of the benchmark countries, 80% of all known COVID cases are being sequenced, up to 10,000 sequences per week.

The omicron variant has been detected like this. Scientists in South Africa saw cases rise and sequencing the virus found a constellation of disturbing mutations. The omicron has alterations that can make it, perhaps, more contagious and elusive to the immune system. This data was collected and circulated in a matter of days, which is another innovation, as Comas explains: “We can do the sequencing in almost real time. It does not tell you what happened, but what is happening. It has a direct impact on epidemiological control: the early identification of variants such as alpha, delta or omicron are a clear example. It is a potential that we were aware of in the research, but that has needed a pandemic to materialize. ”

Comparison of the omicron variant (B11529) with alpha, beta, gamma and delta. The omicron has the highest number of mutations in the spicule. nference

To these merits of genomics must be added another: the sequencing of the virus brought the first mRNA vaccines.

In January 2020, Chinese scientists took a sample from a patient with the mysterious disease, to sequence everything there: “It took us less than 40 hours. It was very, very fast, ”Professor Zhang Yongzhen explained later. They found a new coronavirus and got its genetic code, which an Australian colleague shared in a database, with this historic tweet from January 11, 2020. That same day, thousands of miles away, the Moderna and Pfizer – BioNTech teams began to work to bring the fastest vaccines in history.

The expectation is that in the coming years the applications will multiply.

For example, sequencing will once again be a lifesaver if the virus manages to mutate to escape current vaccines. Marta Tortajada, a researcher at the ADM Biopolis company reminded me: “Sequencing will be the basis for updating them. Knowing the changes of the virus is what allows us to modify its design so that they maintain all the effectiveness “.

There are portable sequencers that can be used in epidemiological surveillance where it is necessary to respond quickly, even if they are places without laboratories nearby. We can fantasize about a futuristic trace, which traces the chains of infection knowing with certainty who infected whom. The technology is practically here: the first omicron case in Spain, the one confirmed by the Gregorio Marañón hospital on Monday, seems to have been detected with a minION device, which is a device not much larger than a USB.

When I ask Comas to do futurism, he talks about using genomics to tackle antibiotic resistance from superbugs, which is a serious and growing problem. Reading DNA and RNA can end up being as routine as PCR. And if so, won't we end up attacking each infection in a doubly individualized way? We will have the genetic code of the pathogen and that of its host, which will be you or me.

The paradox with these advances is that they are less visible than a scrubbing robot or a social network. The word technology brings to mind televisions and telephones; or what Apple, Google and Amazon do. But technology is also a safer baby carrier, a solar panel ten times more efficient, or these machines that read genomes, which helped bring the first vaccines and now monitor the tricks of the virus.

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