Surveillance of SARS-CoV-2 in Frankfurt am Main from october to december 2020 reveals high viral diversity including spike mutation N501Y in B.1.1.70 and B.1.1.7

  • Background: International travel is a major driver of the introduction and spread of SARS- CoV-2. Aim: To investigate SARS-CoV-2 genetic diversity in the region of a major transport hub in Germany, we characterized the viral sequence diversity of the SARS-CoV-2 variants circulating in Frankfurt am Main, the city with the largest airport in Germany, from the end of October to the end of December 2020. Methods: In total, we recovered 136 SARS-CoV-2 genomes from nasopharyngeal swab samples. We isolated 104 isolates that were grown in cell culture and RNA from the recovered viruses and subjected them to full-genome sequence analysis. In addition, 32 nasopharyngeal swab samples were directly sequenced. Results and conclusion: We found 28 different lineages of SARS- CoV-2 circulating during the study period, including the variant of concern B.1.1.7 (∆69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion ∆69/∆70 in 15% of all sequences, a four base pair (bp) deletion (in 2.9% of sequences) and a single bp deletion (in 0.7% of sequences) in ORF3a, leading to ORF3a truncations. In four sequences (2.9%), an amino acid deletion at position 210 in S was identified. In a single sample (0.7%), both a 9 bp deletion in ORF1ab and a 7 bp deletion in ORF7a were identified. One sequence in lineage B.1.1.70 had an N501Y substitution while lacking the ∆69/70 in S. The high diversity of sequences observed over two months in Frankfurt am Main highlights the persisting need for continuous SARS-CoV-2 surveillance using full-genome sequencing, particularly in cities with international airport connections.
Author:Marek WideraORCiDGND, Barbara Mühlemann, Victor Max CormanORCiDGND, Tuna ToptanORCiDGND, Jörn Beheim-Schwarzbach, Niko KohmerORCiDGND, Julia SchneiderORCiD, Annemarie BergerGND, Talitha Veith, Christiane Pallas, Tobias Bleicker, Udo GötschGND, Julia Tesch, René GottschalkGND, Terry C. JonesORCiD, Sandra CiesekORCiDGND, Christian DrostenORCiDGND
Parent Title (English):Microorganisms
Place of publication:Basel
Document Type:Article
Date of Publication (online):2021/04/02
Date of first Publication:2021/04/02
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2021/06/09
Tag:B.1.1.7; N501Y; SARS-CoV-2; genetic diversity; molecular surveillance; natural selection; spike mutation
Issue:4, art. 748
Page Number:10
First Page:1
Last Page:10
Parts of this work was funded by European Union’s Horizon 2020 research and innovation program through RECOVER (GA101003589) to CD, the German Ministry of Research through projects RAPID (01KI1723A) and DZIF (301-4-7-01.703) to CD, and by the German Ministry of Health (Konsiliarlabor für Coronaviren and SeCoV) to C.D. and V.M.C. M.W. was supported by the Deutsche Forschungsgemeinschaft (DFG, WI 5086/1–1). T.C.J was in part funded through NIAID-NIH CEIRS contract HHSN272201400008C. M.W. and S.C. were supported by the Goethe-Corona-Fond of the Goethe University & University Hospital Frankfurt.
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Licence (German):License LogoCreative Commons - Namensnennung 4.0