Large-scale genomic surveillance reveals immunosuppression drives mutation dynamics in persistent SARS-CoV-2 infections.

Authors

Mark P Khurana, Alexandros Katsiferis, Neil Scheidwasser, Mathilde Marie Brünnich Sloth, Jacob Curran-Sebastian, Christian Morgenstern, Man-Hung Eric Tang, Jannik Fonager, Morten Rasmussen, Marc Stegger, Sune Lehmann, Charles Whittaker, Laust H Mortensen, Pikka Jokelainen, Moritz U G Kraemer, Neil M Ferguson, Mahan Ghafari, Tyra G Krause, David A Duchêne, Samir Bhatt

Published in

Nature communications. Jun 19, 2026. Epub Jun 19, 2026.

Abstract

Persistent SARS-CoV-2 infections have been hypothesized to play a key role in the emergence of variants of concern. However, the factors determining which individuals are at risk and their viral molecular signatures during infection remain poorly understood. Using Denmark's extensive COVID-19 surveillance, comprising over 700,000 genomes, we identify 303 persistent infections and, critically, link them to health and sociodemographic data. Our analysis confirms the hypothesis that immunocompromised individuals are at the highest risk of experiencing persistent infections. Other disease groups associated with mortality, such as diabetes, show no such associations. Among these persistent infections, the viral sequences exhibit signs of positive selection, with recurrent mutations linked to treatment resistance. Our findings suggest that immunosuppression plays a key role in the emergence of novelty in persistent infections.

PMID:
42321162
Bibliographic data and abstract were imported from PubMed on 20 Jun 2026.

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