2023-09-02 21:08:13
They called them citizen-scientists, hunters of Covid variants. They are figures who grew up in the shadow of the pandemic, research outsiders. For weeks that turned into years, they spent hours upon hours sifting through viral sequences, making sense of infinite alphanumeric codes. An apparently chaotic cascade in which their trained gaze, with the help of some tools, is able to grasp the film of the evolution of the virus. For some, like Federico Gueli, 47, a Milanese based in Como, in the end “it became a real job”. Among his intuitions, having “found when it was still at 6 sequences the famous variant called Cerberus (BQ.1), which last year spread by feeding the winter wave”.
Dog educator in life before Covid, sifter of sequences out of curiosity in the lockdown phase, Gueli acquired great familiarity with the Sars-CoV-2 coronavirus and in September 2021 in response to the ‘call’ of a scientist, “the bioinformatician Cornelius Roemer “, with an original group of about ten people scattered in different countries and united by social networks, ended up dedicating energy and time to tracking variants with the idea of ”making a contribution to research and the protection of public health”, he explains to time.news Salute. Until, in June, he was recruited by an American company that produces monoclonal antibodies. And now from the accumulated experience, “one of a kind”, he also draws a salary. A source of income with which he contributes to the budget of his family, made up of his wife and two children. And 2 dogs of course (“two greyhounds”).
“When the pandemic broke out in 2020 – says Gueli – I immediately became interested in genomics, in the aspect of the evolution of the virus. We all had a lot of time. I started reading, then following it up with a group of people. All “At the beginning, the lineages of Sars-CoV-2 were few and with few differences. But already the virus that caused the disaster in Bergamo was not the same as that of Wuhan. It was among the first significant differentiations”. After this, “the first lineages were assigned manually by a group of British researchers who developed a system of nomenclature” called ‘Pango’ (the committee includes Andrew Rambaut, Aine O Toole, Oliver Pybus), thanks to which “it was possible tracing lineages”.
Initially, Gueli continues, “they did it manually, but as the virus evolved they realized that it was a titanic operation on their own and they had a brilliant and innovative idea: to create an open Pango page on GitHub, in which anyone could have proposed lineages. It was probably designed for scientists and laboratories. But that was how we too began to trace. The first identification of the Delta variant – she goes back – was made through that page, by a researcher in India who noticed some sequences and proposed them. Then it was understood that it was a variant with significant severity “, cataloged by the WHO as a variant of concern. The qualities to become a good variant hunter? “Excellent memory and passion”, lists Gueli. And master the tools developed by the experts for this mission.
“The main one is Covspectrum, created by Eth Zurich in Basel (Tanya Stadler and Chaoran Chen), a site that makes the genomes loaded into the Gisaid database readable and consultable – which is instead a closed space – with ‘queries’ (requests With this and other tools we started counting the sequences, consulting them, monitoring the mutations, where they emerged, in what percentage compared to previous periods”. Eventually Gueli also had access to Gisaid. And she found Cerberus “thanks to a sample from Africa sequenced in a Japanese airport-remember-He turned on a light bulb. We went to check and found 5 sequences originating in Nigeria, we understood that it was spreading”.
Browsing among genomes, using predictive tools and information from tests performed in laboratories, “we monitor the most significant evolutions of Sars-CoV-2, already knowing which mutation can be beneficial (if it gives the ability to escape antibodies, for example) or detriment of the virus”. The original group of experts – including the Italian Gianluca Codagnone, from the finance sector, but also scientists such as Thomas Peacock of Imperial College London – gradually expanded. “After the wave in China – explains Gueli – a contribution was made by scientists, for example, but also by Chinese citizens who sift through the sequences with a special eye on the Asian giant but they really do a great job, very organized”.
“The nice thing – he reflects – is that everything was born with a self-organization and horizontal collaboration between scientists and citizens, but also expert researchers in other fields (among the Italians the hematologist Daniele Focosi and the physicist Manlio Di Domenico) , who started doing a job in the shadows, even in an altruistic way. Some top-level scientists, like Roemer, believed in our effort and let us enter this world. And now we have a paper about to be published”. In the original group of ‘variant seekers’ is Ryan Hisner, a teacher at a school in Indiana in the USA, “who then obtained a scholarship at a top South African university on viral genomics. He really understood how the virus works, it managed to find conformations, mutations, use of secondary proteins that no one had seen”.
Gueli also had an intuition with the Acrux variant (XBB.2.3). On the latest new entry, BA.2.86 alias Pirola, at the moment he doesn’t say too much. The meaning is “being able to understand from just a few sequences (less than 100) if there is any change that makes sense to monitor, a competitive advantage, and anticipate the alert by 1 or 2 months. Timeliness matters. XBB.1.5, the Kraken variant on which the new updated vaccines are based, was discovered by Roemer with 3 sequences. We who contributed to the long daily analysis activity are now trained citizens who work side by side with experts. Even if we are rarely mentioned or receive awards, we have acquired unique skills” that can be useful “for public health” and “for companies that work on treatments and vaccines, to understand where the virus is going and move quickly”.
What Gueli is most passionate about is “going to the origin of a variant, the work of reconstruction. There are areas that are great hubs of variants, from Africa to South America. I don’t know if it’s a question of overpopulation or if it weighs a situation of social injustice. It should be explored”. Why give nicknames to new versions of Sars-CoV-2? “It’s not an aspect that interests me so much – he points out – The idea came from a user who invented Centaurus for BA.2.75 and it worked. At first we were lukewarm, then the evolutionary biologist Ryan Gregory tried to structure a system. It can be improved, but it is an easy way to make interested people follow the path of the virus. Now we have moved on to the constellations and we are looking for names that are as harmless as possible. Pirola was also chosen so that if the WHO decides to give him a new letter greek, it could be ‘pi’ or ‘ro’ and that nickname contains both. Nobody says that a new variant is scary or bad. Only that in the Omicron family there are many protagonists, and the virus will continue to evolve because it is too good at We will continue to collaborate with scientists – he comments – A comparison can be made with amateur astronomers and astronomers: the former contribute to the discoveries of the latter, dedicating time and passion”.
The Pirola variant (BA.2.86)? “Too soon to say what future it will have” – Gueli does not say too much about the latest new entry among the versions of Sars-CoV-2, BA.2.86, alias Pirola as it was baptized by experts on social media. “It’s changed a lot”, there are over 30 variations at the level of the Spike protein, which is used by the virus to hook human cells, “and it’s circulating”, she explains. “We follow these sequences, but I couldn’t say now what future it will have.”
Meanwhile, the virus continues to mutate. “If Pirola does not catch on – concludes Gueli – there are lineages, such as those with the so-called ‘Flip’ mutations, which are already going fast”.
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