Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients
Cristina Andrés, Damir García‐Cehic, Josep Gregori, María Piñana, Francisco Rodríguez‐Frias, Mercedes Guerrero-Murillo, Juliana Esperalba, Ariadna Rando‐Segura, Lidia Goterris, María Gema Codina, Susanna Quer, Maria Carmen Martín, Magda Campins, Ricard Ferrer, Benito Almirante, Juan Ignacio Esteban, Tomàs Pumarola, Andrés Antón, Josep Quer
Abstract
gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site (PRRAR/S), generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We suggest that natural selection has favoured a "Don't burn down the house" strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.