Widera, M.M.WideraMühlemann, B.B.MühlemannCorman, V.M.V.M.CormanToptan, T.T.ToptanBeheim-Schwarzbach, J.J.Beheim-SchwarzbachKohmer, N.N.KohmerSchneider, J.J.SchneiderBerger, A.A.BergerVeith, T.T.VeithPallas, C.C.PallasBleicker, T.T.BleickerGoetsch, U.U.GoetschTesch, J.J.TeschGottschalk, R.R.GottschalkJones, T.C.T.C.JonesCiesek, S.S.CiesekDrosten, C.C.Drosten2022-03-062022-03-062021https://publica.fraunhofer.de/handle/publica/26864110.3390/microorganisms9040748Background: 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 (D69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion D69/D70 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 D69/70 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.en540571572journal article