ABSTRACT
Background: Starting in January 2021 we established fast genetic sequencing of the SARS-CoV2 virus genome using the Nanopore sequencing technology. Up to now we analyzed more than 400 virus samples including all of the so called different Variants of Concern (VOC) emerging in Germany. Method(s): We established a method to sequence the whole SARS-CoV-2 genome by Nanopore sequencing using previously taken nasopharyngeal swabs (already used for SARS-CoV-2 PCR testing) as viral RNA source. The whole analysis pipeline from RNA-isolation to virus variant classification and result report can be conducted within 2-3 working days. The method is highly scalable. Result(s): We analyzed more than 400 SARS-CoV2 viral isolates from 2021 to the present day. We observed, that most Variants of Concern (VOC) (Alpha, Delta, or Omicron) locally take over all infection events within only one week. While 50-70% of the Alpha and Delta variant isolates show besides the variant defining mutations additional mutations in the S gene, additional mutations in the S gene in Omicron were seen rarely. Also we could see that the Omicron variants nearly had no mutations in the ORF3, and ORF6-8 genes, while mutations in Alpha and Delta were frequent. Conclusion(s): We are able to accurately identify different SARS-CoV-2 variants and detect potential new ones in a cost-efficient and fast way even for low sample numbers. Mutational analysis of the different virus isolates show differences in mutation frequency and localization maybe indicating correlations between mutation localization and disease process.