Further deep whole-genome sequencing of SARS-CoV-2 patient samples from Austria

This is a collection of previously unpublished amplicon-based whole genome-sequencing data of SARS-CoV2 sampled from patients in Austria between March 2020 and Sept 2022. The sequencing was performed by the Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM) for the Austrian Agency for Health and Food Safety (AGES) for national surveillance. If available, the GISAID EPI and sample CT value are given in the sample description. Most individuals sampled have a specific host subject id, which allows to identify longitudinal sampling of the same case over multiple times. Potential human reads were removed from the raw reads using the NCBI Human Reads Removal Tools (HRRT, https://github.com/ncbi/sra-human-scrubber/, rel. vers. 2.2.0, db: human_filter.db.20230410v2) 747 samples from 2020-21 have been published under projects PRJEB42987 and PRJEB39849, most consensus sequences are published in GISAID (see IDs in sample description).