Widera Marek, Mühlemann Barbara, Corman Victor M, Toptan Tuna, Beheim-Schwarzbach Jörn, Kohmer Niko, Schneider Julia, Berger Annemarie, Veith Talitha, Pallas Christiane, Bleicker Tobias, Goetsch Udo, Tesch Julia, Gottschalk Rene, Jones Terry C, Ciesek Sandra, Drosten Christian
Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, 60596 Frankfurt am Main, Germany.
German Centre for Infection Research (DZIF), Institute of Virology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany.
Microorganisms. 2021 Apr 2;9(4):748. doi: 10.3390/microorganisms9040748.
International travel is a major driver of the introduction and spread of SARS-CoV-2.
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.
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.
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.
国际旅行是严重急性呼吸综合征冠状病毒2（SARS-CoV-2）传入和传播的主要驱动因素。
为了调查德国一个主要交通枢纽地区的SARS-CoV-2基因多样性，我们对2020年10月底至12月底在德国最大机场所在城市美因河畔法兰克福流行的SARS-CoV-2变体的病毒序列多样性进行了表征。
我们总共从鼻咽拭子样本中获得了136个SARS-CoV-2基因组。我们分离出104株在细胞培养中生长的毒株，并从回收的病毒中提取RNA，对其进行全基因组序列分析。此外，对32份鼻咽拭子样本进行了直接测序。
我们发现在研究期间有28种不同的SARS-CoV-2谱系在传播，包括值得关注的变体B.1.1.7（Δ69/70，N501Y）。其中6个谱系此前在德国未曾被观察到。我们在所有序列的15%中检测到刺突蛋白（S）缺失Δ69/Δ70，在开放阅读框3a（ORF3a）中有一个四碱基对（bp）缺失（在2.9%的序列中）和一个单碱基对缺失（在0.7%的序列中），导致ORF3a截短。在4个序列（2.9%）中，鉴定出S蛋白第210位氨基酸缺失。在单个样本（0.7%）中，同时鉴定出ORF1ab中的9 bp缺失和ORF7a中的7 bp缺失。B.1.1.70谱系中的一个序列有N501Y替换，而S蛋白中没有Δ69/70缺失。在美因河畔法兰克福两个月内观察到的序列高度多样性凸显了持续使用全基因组测序进行SARS-CoV-2监测的持续必要性，特别是在有国际机场连接的城市。
