Dynamics of SARS-CoV-2 variants and mutations in Central Sweden between 2023 and 2024 and their potential implications on monoclonal antibodies pemivibart and sipavibart as PrEP in the region
Jonathan Haars, Frans Wallin, Karin Elfving, Anna-Karin Jonsson, Patrik Ellström, Paula Mölling, Johan Lindh, Hong Yin, Martin Sundqvist, René Kaden, Navaneethan Palanisamy, Johan Lennerstrand
Infectious Diseases, doi:10.1080/23744235.2025.2509011
Background: Monoclonal antibodies (mAbs) are an important option against SARS-CoV-2, especially as pre-exposure prophylaxis (PrEP) for patients with immune system impairment. PrEP mAbs like sipavibart and pemivibart have been approved for limited use in several countries. Certain SARS-CoV-2 variants carry mutations in the spike (S) protein, conferring resistance to these mAbs. Objectives: We aimed to examine the relative abundance of different circulating SARS-CoV-2 variants/ mutations in central Sweden between 2023 and 2024, and to predict the effectiveness of sipavibart and pemivibart. Methods: An amplicon-based Nanopore sequencing method was used for sequencing SARS-CoV-2 samples. Coronapp was used to identify mutations in these sequences. Using the published in vitro resistance data for sipavibart and pemivibart, the effectiveness of these mAbs was inferred.
Results: We have observed that the relative abundance of the KP.3.1.1 variant and the Q493E mutation started to increase in the later part of 2024 in the region. Also, since April 2024, the relative abundance of the F456L mutation reached 100% during many weeks until the end of the study period. The KP.3.1.1 variant is significantly resistant to pemivibart. Further, the presence of the F456L mutation in the Omicron subvariants confers high fold resistance towards sipavibart.
Conclusion: The use of sipavibart or pemivibart as PrEP for COVID-19 in the region may currently not be effective unless new SARS-CoV-2 variants appear not containing these resistance mutations. Further, new mAbs under development as PrEP for COVID-19 can be effectively used by routinely sequencing SARS-CoV-2 in patients to identify variants and resistance mutations.
Author contributions Conceptualisation, J.H., N.P. and J.Le.; methodology, J.H. and J.Le.; software, J.H. and R.K.; formal analysis, J.H.; investigation, J.H., F.W., K.E., P.M., P.E., R.K. and J.Le.; resources, J.Li., H.Y., M.S. and R.K.; data curation, J.H. and F.W.; writing-original draft preparation, J.H.; writing-review and editing, J.H., N.P., K.E., F.W., P.M., P.E., J.Li., M.S., R.K. and J.Le.; visualisation, J.H.; supervision, R.K. and J.Le.; funding acquisition, J.Le. All authors have read and agreed to the published version of the manuscript.
Disclosure statement Johan Lennerstrand received an unrestricted research grant from AstraZeneca AB, Sweden, but this company was not involved in any part of this study. All other authors declare no conflict of interest.
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