Easy to use and quick, antigen tests are increasingly used for mass investigations with the aim of decreasing the transmission of the virus in large communities. But it seems they can’t detect genetic variants. To say it is a study, conducted by researchers from the Department of Molecular Medicine of Padua, which demonstrates how the genetic variants of the N gene can compromise the ability to use antigenic tests both for diagnosis and for mass tests aimed at controlling transmission. of the virus. The study is being reviewed by a prestigious British journal, but has already been published in these days in «medRxiv».
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Genetic variants of the SARS-Cov-2 virus pose a major threat to the vaccination campaign around the world because they can increase the rate of transmission of the virus or confer the ability of the virus to escape vaccine-induced immunity, with knock-on effects. both on the threshold of herd immunity and on the efficacy of the vaccine. These variants concern the Spike protein encoded by the S gene involved in virus entry into host cells and the main target of vaccines.
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But in reality, the presence of variants does not only affect the Spike protein but rather the entire genome of the virus. In particular, one of the genes that has numerous variants, even slightly more than the others according to the latest estimates, is the one that codes for the ‘N’ protein of the virus which is responsible for the packaging of the genetic material of the virus and which is called, in fact, nucleoprotein.
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The study ‘Emergence of genetic variants of the N Sars-CoV-2 antigen that elude the detection of antigen tests’ demonstrates how genetic variants of the N gene can impair the ability to use antigen tests for both diagnosis and testing of mass aimed at controlling the transmission of the virus. Since June last year, some regions in Italy have extended the mass use of the antigen test with the aim of progressively replacing the molecular swabs.
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While conducting a diagnostic investigation it was found that some swab samples that were not positive in the antigen tests showed a high viral load in the Rt-Pcr tests. Sequencing analysis of viruses showing discordant results in Rt-PCR and antigenic tests revealed the presence of multiple destructive mutations in the structure of the N protein (the viral protein used to detect the presence of the virus in antigenic tests) clustered by the positions 229 to 374, a region known to contain the key regions that allow identification of the virus in these tests. A relevant fraction of the undetectable variants in the antigen test contained A376T mutations coupled to M241I.
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What does this mean in practice? “Further laboratory tests – he replies Andrea Crisanti, director of the Department of Molecular Medicine at the University of Padua – have also shown that this problem is common to antigenic tests developed by various manufacturers. Virus sequences with these mutations are much more frequent in samples negative for antigen tests but with Pcr positive and have progressively increased in frequency over time in Veneto, an Italian region that has significantly increased the use of antigen tests reaching almost 68% of all swab tests for Sars-Cov-2. For this reason, it is hypothesized that the mass use of rapid antigenic tests may unintentionally favor the spread of viral variants that are not detectable by these tests, thus contributing to their free circulation and the ineffectiveness of their containment “.
The plasticity of the virus
“These results – he adds Stefano Toppo, another author of the study and also from the Department of Molecular Medicine of the University of Padua – provide a first evidence that the mass use of antigenic tests to block the transmission of the virus favors the spread of undetectable variants of the virus as a consequence of pressure selection exercised by the test itself. This knowledge, while expanding our understanding of virus plasticity, will provide the foundation for implementing better and more informed approaches in using antigen testing for both diagnosis and control approaches. “
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