Ethical statement
Samples included in this study have been collected as part of Danish COVID-19 surveillance and according to the Danish law, ethical approval is not required for this type of study. The research is approved by the legal advisory board at SSI, a public research institute under the auspices of the Danish Ministry of Health. The study contains aggregated results without identifiable personal data and therefore complies with the European General Data Protection Regulations (GDPR).
Data availability
The raw reads of all samples have been deposited into GISAID’s EpiCoV database, under the EPI_SET identifiers: EPI_SET_230103mu (Alpha), EPI_SET_230103zt (Delta), EPI_SET_230103ek (Late Delta), EPI_SET_230103ky (BA.1), EPI_SET_230103ar (BA.2), EPI_SET_230103te (BA.5). All EPI ISL accession identifiers, sample group labels and collection dates are available in Supplementary Table 1.
Code availability
All scripts used to perform the subgenomic RNAs detection, statistical analyses and generation of the figures are available in the Git repository https://github.com/ssi-dk/project-covid19_subgenomic.
Acknowledgements
The authors would like to thank the Danish Covid-19 Genome Consortium for providing the whole genome sequencing data of SARS-CoV-2 positive samples, the Division of Infectious Disease Preparedness at Statens Serum Institut for providing the patient data and Henrik Ullum for his comments on the manuscript.
Consortia
The Danish COVID-19 Genome Consortium
Anders Fomsgaard, Morten Rasmussen, Søren M. Karst, Jannik Fonager, Vithiagaran Gunalan, Marc Bennedbæk, Aleksander Ring, Marc Stegger, Raphael Sieber, Kirsten Ellegaard, Anna C. Ingham, Thor B. Johannesen, Gitte Nygaard Aasbjerg, Berit Lilje,
Kim L. Ng, Sofie M. Edslev, Sharmin Baig, Povilas Matusevicius, Lars Bustamante Christoffersen, Man-Hung Eric Tang, Leandro Andrés Escobar-Herrera, Casper Westergaard, Christina Wiid Svarrer, Nour Saad Al-Tamimi, Marie Bækvad-Hansen, Jonas Byberg-Grauholm, Mette Theilgaard Christiansen, Karen Marie Jørgensen, Tobias Nikolaj Gress Hansen, Esben Mørk Hartmann, Nicolai Balle Larsen, Arieh Cohen, Kasper Holtz Uhre, Christian Nielsen, Anders Jensen, Jakob Matias Melbye, Bartlomiej Wilkowski, Karina Meden Sørensen, Mads Albertsen, Thomas Y. Michaelsen, Vang Le-Quy, Mantas Sereika, Rasmus H. Kirkegaard, Kasper S. Andersen, Martin H. Andersen, Karsten K. Hansen, Mads Boye, Mads P. Bach, Peter Dissing, Anton Drastrup-Fjordbak, Michael Collin, Finn Büttner, Jakob Brandt, Simon Knuttson, Emil A. Sørensen Thomas B. N. Jensen, Trine Sørensen, Celine Petersen, Clarisse Chiche-Lapierre, Frederik T. Hansen, Emilio F. Collados, Amalie Berg, Susanne R. Bielidt, Sebastian M. Dall, Erika Dvarionaite, Susan H. Hansen, Vibeke R., Jørgensen, Trine B. Nicolajsen, Wagma Saei, Stine K. Østergaard, Martin Bøgsted, Rasmus Brøndu, Katja Hose, Tomer Sagi, Miroslav Pakanec, Henrik Krarup, David Fuglsang-Damgaard, Mette Mølvadgaard, Marc T. K. Nielsen, Kristian Schønning, Martin S. Pedersen, Rasmus L. Marvig, Nikolai Kirkby, Uffe V. Schneider, Jose A. S. Castruita, Nana G. Jacobsen, Christian Ø. Andersen, Mette Christiansen, Ole H. Larsen, Kristian A. Skipper, Søren Vang, Kurt J. Handberg, Carl M. Kobel, Camilla Andersen, Irene H. Tarpgaard, Svend Ellermann-Eriksen, Marianne Skov, Thomas V. Sydenham, Lene Nielsen, Line L. Nilsson, Martin B. Friis ,Thomas Sundelin, Thomas A. Hansen, Dorte T. Andersen, John E. Coia, Anders Jensen, Ea S. Marmolin, Xiaohui C. Nielsen, Christian H. Schouw
Author contributions
S.A. conceptualized the study, M-H.E.T. and K.N. performed the analyses, S.M.E. assembled the patient metadata, K.E. provided the WGS QC data. M-H.E.T. drafted the initial manuscript with inputs of S.A., M.S., K.N. All authors contributed to the final submitted version. All authors have read and agreed to the final version of the manuscript.
Competing interests
The authors declare no competing or conflict of interest. The funders had no role in the design of the study, in the collection, analyses or interpretation of data, in the writing of the manuscript or in the decision to publish the results.