We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container. Data set 04 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (negative control). The recorded area shows the profiles of four keratinocytes which are surrounded by heterogenous material (e.g. membrane lamella, needle-like crystals, round profiles with a fine-fibrous matrix). Virus partricles are not visible. Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.