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.
【저자키워드】 SARS-CoV-2, B.1.1.7, spike mutation, N501Y, natural selection, genetic diversity, molecular surveillance, 【초록키워드】 Sequencing, variant, virus, RNA, Spread, Nasopharyngeal swab, ORF3a, Germany, SARS-CoV-2 genome, Cell culture, International, Sequence analysis, Travel, Lineage, ORF7a, Amino acid, ORF1ab, SARS-CoV-2 surveillance, Transport, study period, sequence, circulating, nasopharyngeal swab sample, isolate, highlight, Frankfurt, Result, sequenced, addition, characterized, the spike protein, the SARS-CoV-2, 【제목키워드】 spike, Diversity, mutation N501Y, Frankfurt, Including,