How to record probing tests

This is how corona mutations are tracked down in Bremen

Sequencing is considered the silver bullet to identify virus mutations. However, Bremen is now opting for an inexpensive alternative - for every positive PCR test.

The mutated corona virus has been spreading in Germany for weeks. The recent outbreaks in Bremerhaven could be a consequence of this. At least this was what the head of the Bremerhaven Corona crisis team, Ronny Möckel, suspected days ago. "We are now experiencing transmissions in situations that we would not have expected earlier and a dynamic in the outbreak that leaves us almost speechless," said the head of the Bremerhaven health department, referring to the high viral load of the samples. This could indicate a mutation.

Mutations in five percent of all Corona cases in Bremen

The fact that mutants are already circulating in the state of Bremen has long been proven beyond the known individual cases. Because, contrary to what many had previously assumed, lengthy and expensive sequencing of samples is not even necessary in order to detect at least the known mutations. A network of 36 laboratories that have tested tens of thousands of samples for mutations wants to publish the first nationwide data this week. "Here in Bremen and around we found variants in exactly five percent of all evaluable PCR-positive samples, most of them the English variant B117," says the managing director of the Bremen Medical Laboratory, Andreas Gerritzen.

Probing only targets known mutations

In addition to the Bremen Medical Laboratory, two other laboratories in Bremen and Bremerhaven now also offer mutation analysis using a so-called probing test, which does not require expensive sequencing.

The cost advantage of the probing test arises because it specifically only tests those genetic components in the long chain of the virus RNA strand that may have been changed by the mutation. "A specially coordinated, separate PCR test is sufficient," says Laboratory Director Gerritzen.

Sequencing decodes almost 40,000 RNA building blocks

In sequencing, on the other hand, all of the almost 40,000 RNA building blocks of the virus genome are broken down with the help of special machines, so-called next-generation sequencing devices. In this way, a complete image of the genetic information of the corona virus is provided. And so it is also possible to identify rare or previously unknown mutations beyond the previously common mutations from Great Britain, South Africa and Brazil. However, sequencing is also more expensive and takes longer.

For a probing test for a certain mutation, laboratories receive 50.50 euros, which is paid by the federal government. It takes no longer than other PCR tests. The federal government pays 220 euros for sequencing. The fully automated decoding of the genome alone takes around 30 hours. Added to this are the shipping times of the samples and the analysis by bioinformaticians.

Doing this for every rehearsal would be shooting at sparrows with cannons.

Andreas Gerritzen, managing director of the Bremen Medical Laboratory

In some cases, for example for some samples from the Elisabeth-Haus nursing home in Bremerhaven, in which none of the known mutations from Great Britain, South Africa or Brazil could be detected, sequencing is still unavoidable. Because only in this way can other mutations be recognized. In addition, it can be traced whether an infection was caused by a single virus strain. The latter would suggest a common source of contagion. If there are several strains, however, the health department would have to find the other sources of infection.

"Whole genome sequencing is done, for example, in outbreaks that could not be controlled for no apparent reason," says health department spokesman Lukas Fuhrmann. Cases, for example, in which the infected actually wore protective equipment. "So far there have been very few in Bremen," said Fuhrmann.

Bremen samples end up in the Charité

If the health authorities in Bremen or Bremerhaven arrange for appropriate sequencing, the samples are sent to Berlin, where they are examined in the Charité laboratories. The workload there is likely to increase. Because the Federal Ministry of Health has decreed that up to 5 percent of positive PCR tests across Germany should generally be sequenced.

And the laboratories in Bremen that carry out probing tests will probably not run out of work either. Because the Senate decided last week to also probe all positive PCR tests for the three known and most widespread mutations of the virus from this week.

Soon no more quarantine shortening?

And should the number of mutations found continue to rise, this would probably also have concrete consequences for contact persons. "So far it has been possible to test yourself out of quarantine in individual cases and in consultation with the health department with a negative rapid test after five days," says health department spokesman Fuhrmann. If mutations occur, the situation changes. "Anyone who has come from Great Britain, for example, where the mutation is very common, is already no longer able to shorten this."

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