Marek Widera1, Barbara Mühlemann2, Victor M Corman2, Tuna Toptan1, Jörn Beheim-Schwarzbach2, Niko Kohmer1, Julia Schneider2, Annemarie Berger1, Talitha Veith2, Christiane Pallas1, Tobias Bleicker2, Udo Goetsch3, Julia Tesch2, Rene Gottschalk3, Terry C Jones2,4, Sandra Ciesek1,5,6, Christian Drosten2,5. 1. Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, 60596 Frankfurt am Main, Germany. 2. German Centre for Infection Research (DZIF), Institute of Virology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany. 3. Public Health Department of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany. 4. Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing St., Cambridge CB2 3EJ, UK. 5. German Center for Infection Research, DZIF, 60596 Braunschweig, Germany. 6. Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, 60596 Frankfurt am Main, Germany.
Abstract
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 (Δ69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion Δ69/Δ70 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 Δ69/70 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.
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 (Δ69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion Δ69/Δ70 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 Δ69/70 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.
Authors: Andrei Veleanu; Maximilian A Kelch; Chengjin Ye; Melanie Flohr; Alexander Wilhelm; Marek Widera; Luis Martinez-Sobrido; Sandra Ciesek; Tuna Toptan Journal: Viruses Date: 2022-09-12 Impact factor: 5.818
Authors: Terry C Jones; Guido Biele; Barbara Mühlemann; Talitha Veith; Julia Schneider; Jörn Beheim-Schwarzbach; Tobias Bleicker; Julia Tesch; Marie Luisa Schmidt; Leif Erik Sander; Florian Kurth; Peter Menzel; Rolf Schwarzer; Marta Zuchowski; Jörg Hofmann; Andi Krumbholz; Angela Stein; Anke Edelmann; Victor Max Corman; Christian Drosten Journal: Science Date: 2021-05-25 Impact factor: 63.714