SARS-CoV-2 genetic variants are emerging as a major threat to vaccination efforts worldwide as they may increase virus transmission rate and/or confer the ability to escape vaccine induced immunity with knock on effects on the level of herd immunity and vaccine efficacy respectively . These variants concern the Spike protein, which is encoded by the S gene, involved in virus entry into host cells and the major target of vaccine development . We report here that genetic variants of the N gene can impair our ability to utilize antigenic tests for both diagnosis and mass testing efforts aimed at controlling virus transmission . While conducting a large validation study on the Abbott Panbio COVID-19 Ag test, we noticed that some swab samples failed to generate a positive result in spite of a high viral load in Rt-PCR assays . Sequencing analysis of viruses showing discordant results in the Rt-PCR and antigen assays revealed the presence of multiple disruptive amino-acid substitutions in the N antigen (the viral protein detected in the antigen test) clustered from position 229 to 374 a region known to contain an immunodominant epitope . A relevant fraction of the variants, undetected by the antigen test, contained the mutations A376T coupled to M241I . Intriguingly we found that virus sequences with this mutation were over-represented in the antigen-test-negative and PCR-positive samples and progressively increased in frequency over time in Veneto, a region of Italy that has aggressively scaled up the utilization of antigen tests, which reached nearly 68% of all the SARS-CoV-2 swab assays performed there . We speculate that mass utilization of antigen assays could create a selection pressure on the target that may favor the spread of undetectable virus variants.