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Sweden is modifying the tracking of virus variants in circulation. The coronavirus genome of one-tenth of all newly infected Swedes will now be mapped in detail.
Sofia Gruvberger Saal, section chief of the Molecular Diagnostic Center on the sequencing machine where the coronavirus genome can be mapped in detail.
The staff at the Lund Center for Molecular Diagnostics have been working intensively in recent weeks to develop analytical capabilities.
Sequencing machines already exist, but it is usually not genetic material from viruses, but from bacteria and human cells, which is usually mapped here. A first challenge has been to obtain the necessary material.
– There has been a great rush for all types of reagents and plastic materials, because everyone has to sequence, says section director Sofia Gruvberger Saal.
When he started talking about the British mutation in December, he felt the mission to start looking for it and all other variants of the virus would land here.
– Now we have succeeded, but we had to push a bit. We already have contacts in these companies.
Microbiologist Jonas Björkman compares the virus genome to a very long word with 30,000 letters. The word consists of only the letters C, G, T and A, but the question is in what order they come. The answer is given in the sequencing machine.
In a mutated variant of the coronavirus, the letters are swapped or slightly reversed in some places.
– Usually there are only a handful of changes when we look at a variant. It’s only a few per thousand of the “letters” that distinguish the different known mutational variants, says Björkman.
But even small investments in sequencing can have major consequences for the properties of the virus – for example, how contagious it is or whether it is resistant to vaccines, hence the large investment in sequencing.
In the Lund laboratory, which belongs to the Skåne Region, virus samples from the entire southern health region can be analyzed. Since the goal is to map the viruses from one-tenth of those that tested positive, the infection situation will be decisive for the number.
– If a third wave comes, ten percent will be much more in number per week than it is now, says Gruvberger Saal.
The goal is to map a representative sample of those who get COVID-19 to get an idea of which variants of the virus are in circulation. But special attention will be maintained on some groups, such as returning travelers who have tested positive for COVID-19.
If people do get sick from covid-19 despite vaccination, this will of course also be a high priority group to map, as well as those who are infected in local outbreaks.
– We look for known and new mutations, says Björkman.
This is how virus variants are tested
The laboratory receives a selection of viruses from the Department of Clinical Microbiology. It comes in the form of viral RNA, which has been extracted and purified. The virus is inactive and therefore cannot be transmitted. It is contained in a liquid in small virus-spaced plates of 96 patients each.
First, the virus converts from RNA to DNA.
Because there is such a small amount of virus in each patient, that it has been acquired by nasal and pharyngeal insufficiency, copies of the virus are made to increase the amount.
The sample is purified in a machine using magnets.
Each virus is provided with a label, which allows you to keep track of which virus came from which human. At this stage, the virus also receives a sequence that allows it to bind to the instrument on the sequencing machine.
Viruses from 380 different people can be placed in approximately one milliliter of liquid, which is fed into the sequencing machine.
The machine reads the virus samples and with the help of different reagents the structure of the genome is mapped.
The data from the sequencing machine is then processed on a computing computer.
