Centre for Diagnostics DTU finds Brazilian variant of coronavirus

In January 2021, the Centre for Diagnostics DTU agreed with the Danish Regions' Crisis Management to examine all positive samples in DTU's test facility for all known coronavirus variants. These are samples from Slagelse Hospital, the Capital Region, and samples from Rigshospitalet and Bispebjerg Hospital laboratories. One variant that has caused great concern elsewhere in the world is the Brazilian P.1, which has now been found in one of these samples.

There has been a particular focus on the British and South African variants in Denmark in recent times. This is because they are both found in society, albeit to varying degrees. At the time of writing, the British variant accounts for about 70 per cent of the Danish epidemic, while the South African is not widespread. The Brazilian variant is of particular concern because it may be more contagious and may infect previously infected individuals like some of the other variants. It is not yet known for sure how effective the vaccines will be against it.

In contrast to the so-called Delta-2 PCR test, where it is impossible to distinguish between the South African and the Brazilian variant, it can be achieved with a protocol for so-called Sanger sequencing, developed by Tue Sparholt Jørgensen, a postdoc at DTU Biosustain.

Sanger sequencing

There are a variety of methods for DNA sequencing. The Sanger method is the oldest, and for large sequencing tasks, it has mainly been replaced by newer methods. However, it has several advantages in the current scenario, says Helene Larsen, Head of Development at the Centre for Diagnostics DTU:

"Sanger sequencing is a well-known method in large parts of the world and will not require as much preparation of the samples as other methods. And it is still one of the methods against which newer methods are measured. Finally, and this is particularly relevant in a Danish context right now, Sanger sequencing can both confirm that the specific Brazilian P.1 mutations are there and that the specifically South African ones are not there."

With Sanger sequencing, you also get a quality determination of how reliable the result is. Therefore, there was no doubt about the outcome when the Centre for Diagnostic DTU on Monday 1 March got it back from its subcontractor, Eurofin Genomics in Cologne: : A sample, which had been found positive at one of the Capital Region's laboratories, showed clear signs of originating from the Brazilian variant. After the mutations were found, the raw data was thoroughly checked several times. The signal was apparent, and the error rate is in the neighbourhood of one in a million.

Three mutations

In the sample, three mutations characteristic of P.1 were found: E484K, N501Y and H655Y. Simultaneously, the sample has none of the characteristic mutations specific for B.1.1.7 (British) or B.1.351 (South African). Although the mutated virus in the sample was very similar to the Brazilian variant and none of the other known variants, whole-genome sequencing was required before it could be definitively detected. Statens Serum Institut performed this sequencing, and confirmed DTU's finding.

"It is, of course, worrying that we now see the Brazilian variant in a Danish covid-19 test, even though we do not know the details behind the test. From our perspective, however, it is at the same time reassuring that the sequencing method we have developed has succeeded in locating it within a short time," says Helene Larsen.