Covid-19, a new quick test arrives to identify variants too

Rapid antigen tests are blunt weapons to fight the circulation of the variants of Sars-CoV-2: some are in fact designed to recognize (also) the antigens of the spike protein, that is the glycoprotein with which the virus binds to the Ace2 receptor of our cells to penetrate them and in which it concentrates there most mutations which so far have given rise to variants. They can therefore provide a high rate of false negatives, because the available procedure may not recognize the modified protein S.

For this reason, the circulation phase of the virus we are experiencing is particularly insidious: in addition to the intrinsic characteristics of the variants identified in England, South Africa and Brazil, the point is that to identify and trace them it is necessary to start from molecular tests and carry out the genetic sequencing. In some ways, it is as if we have gone back a year or so, given that for months now we have begun to rely heavily on rapid antigenic and that we do few sequencing.

In fact, most of the antigen tests in circulation identify another protein of the virus, the N. However, mutations are also emerging on that, as on the spike. In short, the picture is complex and it is no coincidence that a few days ago the Ministry of Health has asked hospitals, institutes and laboratories to “monitor the effectiveness of antigen tests, the so-called rapid swabs now very widely used, in detecting Covid infection with the new viral variants “.

Soon, however, we may have a (fairly) quick test capable of detecting coronavirus variants that have dangerous mutations. A group of researchers from the Novozymes, a Danish biotech company, coordinated by Stephanie Oerum. It would give us a big hand in terms of surveillance, allowing us – as we continue to vaccinate, hopefully at ever faster rates – to contain the outbreaks marked by the new variants before they spread further.

Apparently, the new test would require only a small modification to the PCR tests, the golden molecular standards carried out with the polymerase chain reaction technique which consists in the amplification of nucleic acid fragments identified in the buffers. The traditional procedure searches for short sequences, of about 20 letters, specific to the Sars-CoV-2 genome, on the basis of a “primer”, that is a target fragment of artificial DNA that acts as a trigger for replication and amplification. But mutations are often like this minimal which may escape this comparison: Novozymes’ proposal is to perform an additional PCR test on a sample in the context of which additional artificial DNA is added to a mutant target sequence, comparing it with a non-mutant “primer”.

The test, therefore, cannot really be superimposed on a rapid antigenic but an evolution of PCRs, could soon be made available non-profit, according to the New Scientist and, in fact, should be able not only to assign a positivity with a high margin of certainty but determine if that genetic material has one or more fundamental mutations that characterize the variants, such as the N501Y, in position 501 of the spike that characterizes the English variant, or the more formidable E484K which would seem to be able to partially circumvent the efficacy of vaccines or of the immunity naturally acquired by overcoming the infection.

“When you have the result, you could tell a person that they are positive for coronavirus and carry a problematic variant,” he explained. Astrid Iversen of the University of Oxford, which is collaborating with Novozymes. It would really be an essential step: “As soon as you know that a person is positive, you need to know if he carries a problematic variant, to prevent that variant from spreading in the community.” Overcoming the expensive and slow process of sequencing, which at that point could be optimized and reserved only to confirm any positivity to variants. Perhaps giving the opportunity for some people to choose a more effective vaccine.

Compared to normal molecular PCR tests the new test requires 30 more minutes of work. An aggravation balanced precisely by the fact of discharging the need to sequence all the samples, being able to concentrate the surveillance work on those that have already reported a positivity to variants. While initial studies suggest the method is extremely accurate, the Danish team is now trying to confirm the results by testing already sequenced samples. Within a few weeks we could have the complete protocol available to the laboratories to process them.