"Given that therapeutics (vaccines and antibody-based therapies) target mainly the SARS-CoV-2 spike protein, the selection pressures that favour the emergence of new variants carrying immune escape mutations generated in chronic infections24,25,26 will be similar to those selecting for mutations that allow reinfections within the wider population27,28,29. Therefore, sequencing of viruses associated with prolonged infections will provide useful information on mutations that could contribute to increased transmissibility or escape from vaccine-mediated immunity."