DTU discovers Brazilian variant of coronavirus

In January 2021, the Center for Diagnostics DTU entered an agreement with the Crisis Management Department of Danish Regions about examining all positive samples in DTU laboratories for all known coronavirus variants. The agreement covers sequencing of all positive samples from DTU’s own pipeline (samples from Slagelse Hospital and the Capital Region of Denmark), and from the Capital Region of Denmark’s own laboratories. One variant that has caused a lot of concern around the world is the Brazilian variant P.1, which has now been found in one of these samples.

Recently, there has been a large focus on the British and South African variants of coronavirus in Denmark. The reason for this being that they are both flourishing in society, although to varying extents. At the time of writing, the British variant accounts for about 70% of the Danish epidemic, while the South African variant is yet to become widespread. The Brazilian variant especially causes a lot of concern because, as with some of the other variants, it is potentially more contagious and can possibly infect individuals, who have been infected before. Also, it is not known for certain how effective current vaccines will be against it.

In contrast to the so-called Delta-2 PCR-test, where it is not possible to distinguish between the South African and the Brazilian variant, it can be easily done with a procedure called Sanger sequencing. A method that has been developed by Tue Sparholt Jørgensen, Postdoc at DTU Biosustain.

Sanger sequencing

There exists a large number of methods for DNA sequencing. The Sanger method is the oldest, and in larger sequencing tasks, it has, to a large extent, been replaced with newer methods. Nevertheless, it does have more advantages in the current scenario, explains Helene Larsen, Head of Development at Center for Diagnostics DTU:

“Sanger sequencing is a well-known method in the majority of the world, and it does not demand as much preparation of the samples as other methods do. Also, it has continued to be one of the methods that newer methods are being measured against. Finally, and this is particularly relevant in the current Danish context, Sanger sequencing is capable of both confirming that the specific Brazilian P.1 mutations are present, and that the specific South African ones are not present.”

With Sanger sequencing, you also gain a quality assessment of the reliability of the result. There was therefore no doubt about the result that Center for Diagnostics got handed back on Monday, March 1 from its subcontractor Eurofin Genomics in Cologne, Germany. A positive sample, from one of the Capital Region of Denmark’s laboratories, had shown clear signs of originating from the Brazilian variant. After the mutations had been discovered, raw data was being thoroughly checked several times. There were noticeably clear signs, and the rate of errors is in the range of one in a million.

Three mutations

Three mutations were discovered in the sample, which are characteristic for P.1: E484K, N501Y and H655Y. Simultaneously, the sample had none of the distinctive mutations related to B.1.1.7 (the British variant) nor B1.351 (the South African variant). Even though the mutated virus bears a striking resemblance to the Brazilian variant, and none of the other known variants, a sequencing of the entire genome is still necessary to conclusively prove the presence of the Brazilian coronavirus variant. This sequencing will be performed by Statens Serum Institut (SSI).

“It is of course immediately concerning for us that we are now able to see the Brazilian variant in a Danish COVID-19 sample, even though we do not know the specific circumstances behind the test. However, seen from our perspective, it is at the same time comforting that we, with the sequencing method we have chosen, have succeeded with proving its presence within such a short timeframe,” says Helene Larsen.