Impact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants

Claudia Del Vecchio, Bethan Cracknell Daniels, Giuseppina Brancaccio, Alessandra Rosalba Brazzale, Enrico Lavezzo, Constanze Ciavarella, Francesco Onelia, Elisa Franchin, Laura Manuto, Federico Bianca, Vito Cianci, Anna Maria Cattelan, Ilaria Dorigatti (), Stefano Toppo () and Andrea Crisanti ()
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Claudia Del Vecchio: University of Padua
Bethan Cracknell Daniels: School of Public Health, Imperial College London
Giuseppina Brancaccio: University of Padua
Alessandra Rosalba Brazzale: University of Padua
Enrico Lavezzo: University of Padua
Constanze Ciavarella: School of Public Health, Imperial College London
Francesco Onelia: Padua University Hospital
Elisa Franchin: Padua University Hospital
Laura Manuto: University of Padua
Federico Bianca: University of Padua
Vito Cianci: Padua University Hospital
Anna Maria Cattelan: Padua University Hospital
Ilaria Dorigatti: School of Public Health, Imperial College London
Stefano Toppo: University of Padua
Andrea Crisanti: University of Padua

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract Population testing remains central to COVID-19 control and surveillance, with countries increasingly using antigen tests rather than molecular tests. Here we describe a SARS-CoV-2 variant that escapes N antigen tests due to multiple disruptive amino-acid substitutions in the N protein. By fitting a multistrain compartmental model to genomic and epidemiological data, we show that widespread antigen testing in the Italian region of Veneto favored the undetected spread of the antigen-escape variant compared to the rest of Italy. We highlight novel limitations of widespread antigen testing in the absence of molecular testing for diagnostic or confirmatory purposes. Notably, we find that genomic surveillance systems which rely on antigen population testing to identify samples for sequencing will bias detection of escape antigen test variants. Together, these findings highlight the importance of retaining molecular testing for surveillance purposes, including in contexts where the use of antigen tests is widespread.

Date: 2022
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DOI: 10.1038/s41467-022-33460-0

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