Michael Sahli (text) and Siggi Bucher (photos)
It is quite possible that this question will decide the further course of the pandemic: Which variants does the corona virus still have in stock? Omikron managed to outwit the vaccination in places. And up to Omega there are still many free letters in the Greek alphabet. Scientists around the world are therefore feverishly looking for the unknown in corona samples. In search of new variants, Chaoran Chen (27) and Timothy Sykes (37) sequence smears from Swiss Covid-infected people in Zurich. They open the doors of the ETH and university laboratories on the Irchel campus for Blick.
Doctoral student Chen, who originally comes from computer science, says: “We are constantly looking for mutations, but we hope not to find anything new.” From this perspective, his mission has been successful so far: there has never been a “Swiss variant”. It would also be statistically quite unlikely.
The search for the needle in the haystack
The Functional Genomics Center of the Zurich virus hunters also fulfills another function. It’s a radar to get an overview of what’s happening in Switzerland. “In the past few weeks, we have systematically searched the samples for omicrons,” says Chen. The finding allows conclusions to be drawn as to how dominant the variant is at the moment. “We are at around 90 percent omicron, which currently still coexists with delta,” summarizes the scientist.
Special safety precautions are not necessary in the laboratory. “What we get is the RNA, just the genetic information of the virus,” explains Timothy Sykes. That means the samples are no longer contagious.
At its heart is a sequencing machine that looks almost like an oversized (and very expensive) copier. Here, genome specialist Sykes converts around 1,200 samples a week into digital data, which bioinformatician Chen can then analyze on the computer. The latter does the actual detective work at the ETH Department of Biosystems in Basel. And looks for recurring patterns in the apparent chaos of thousands of virus genome sequences, all of which differ slightly from one another. “Most samples look different, which in itself is nothing unusual,” he says. “But if we see the same mutation in many samples, or if that mutation keeps spreading, then we would see that. This variant could be dangerous.”
Despite high-tech: A lot of manual work is required in the sequencing laboratory after the samples have been delivered cooled with dry ice. Each sample has to be transferred and prepared in a complicated process so that the sequencing device can read the corona genetic information.
Canton doctors deliver suspicious swabs
The researchers who work together here come from very different countries: Chen has his roots in China, Sykes is Australian. Common language is English. They constantly exchange their data with colleagues abroad. “We get a lot of data from the UK, for example, where a lot more is being sequenced. And then look specifically for deviations that have appeared there, »says Chen.
When it comes to deciding which samples to sequence, chance is often the most representative: “Sometimes I would stand in front of a large refrigerator and take out random samples.” But not always: “When the first worrying variant Alpha came at the end of 2020, with many reports from Great Britain, we specifically sequenced samples from cantons where there are many British tourists.” And sometimes cantonal doctors report suspicious samples directly.
The question of how the deviations found work – whether they make the virus more dangerous or maybe even less dangerous – is no longer part of Chen’s area of expertise. “That would be questions for the virologists,” he dismisses. Nevertheless, he appeals: “The fewer infections there are, the less chance the virus has of mutating.” Therefore, protective measures and vaccination are still the only mutation prevention. The virus hunters shouldn’t run out of work any time soon.