4.6 Article

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

期刊

MICROORGANISMS
卷 9, 期 4, 页码 -

出版社

MDPI
DOI: 10.3390/microorganisms9040748

关键词

SARS-CoV-2; genetic diversity; molecular surveillance; B; 1; 1; 7; natural selection; spike mutation; N501Y

资金

  1. European Union's Horizon 2020 research and innovation program through RECOVER [GA101003589]
  2. German Ministry of Research through project RAPID [01KI1723A]
  3. German Ministry of Health (Konsiliarlabor fur Coronaviren)
  4. Deutsche Forschungsgemeinschaft (DFG) [WI 5086/1-1]
  5. NIAID-NIH CEIRS [HHSN272201400008C]
  6. Goethe-Corona-Fond of the Goethe University
  7. German Ministry of Research through project DZIF [301-4-7-01.703]
  8. German Ministry of Health (SeCoV)
  9. University Hospital Frankfurt

向作者/读者索取更多资源

The research discovered 28 different lineages of SARS-CoV-2 circulating in Frankfurt during the study period, including six that had not been observed in Germany previously. Various mutations were found in the viral sequences, emphasizing the need for continuous SARS-CoV-2 surveillance using full-genome sequencing.
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 (Delta 69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion Delta 69/Delta 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 Delta 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.

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