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
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Preparation and RT-qPCR-Testing
2.2. Cell Culture and Viral Outgrowth Assay
2.3. RNA Isolation and Confirmatory RT-qPCR
2.4. NGS Sequencing of SARS-CoV-2 Genomes
2.5. Bioinformatics
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Deletion/Mutation | Number of Sequences | PANGO Lineage | Sequence ID |
---|---|---|---|
9 bp deletion in ORF1ab (amino acid position 141–143), 7 bp deletion in ORF7a which truncates ORF7a at amino acid position 108 | 1 | B.1.160 | ChVir21561 |
Deletion of amino acid position 69/70 in S | 17 | B.1.1.70, B.1.258 | ChVir21551, ChVir21580, ChVir21582, ChVir21585, ChVir21586, ChVir21588, ChVir21589, ChVir21591, ChVir21596, ChVir21597, ChVir21598, ChVir21606, ChVir21609, ChVir21618, ChVir21619, ChVir21621, ChVir21626 |
Deletion of amino acid positions 141-144 in S | 1 | B.1.1.153 | ChVir22027 |
Deletion of amino acid position 210 in S | 4 | B.1.36 | ChVir21555, ChVir21563, ChVir21571, ChVir21603 |
N501Y substitution in S | 1 | B.1.1.70 | ChVir21997 |
4 bp deletion in ORF3a, which truncates ORF3a at amino acid position 259 | 3 | B.1.160, B.1.1.67 | ChVir21565, ChVir21625, ChVir21632, ChVir22011 |
1 bp deletion in ORF3a, which truncates ORF3a at amino acid position 259 | 1 | B.1.160 | ChVir21550 |
Deletion of amino acid position 58 in ORF8 | 1 | B.1.258 | ChVir21586 |
12 bp deletion in 3p UTR | 1 | B.1.258 | ChVir21502 |
41 bp deletion in the 3’ UTR | 4 | B.1.221 | ChVir21994, ChVir21995, ChVir21996, ChVir22006 |
Substitutions typical of B.1.1.7, including a deletion of amino acid position 69/70 and N501Y in S | 1 | B.1.1.7 | ChVir22031 |
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Widera, M.; Mühlemann, B.; Corman, V.M.; Toptan, T.; Beheim-Schwarzbach, J.; Kohmer, N.; Schneider, J.; Berger, A.; Veith, T.; Pallas, C.; et al. 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. Microorganisms 2021, 9, 748. https://doi.org/10.3390/microorganisms9040748
Widera M, Mühlemann B, Corman VM, Toptan T, Beheim-Schwarzbach J, Kohmer N, Schneider J, Berger A, Veith T, Pallas C, et al. 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. Microorganisms. 2021; 9(4):748. https://doi.org/10.3390/microorganisms9040748
Chicago/Turabian StyleWidera, Marek, Barbara Mühlemann, Victor M. Corman, Tuna Toptan, Jörn Beheim-Schwarzbach, Niko Kohmer, Julia Schneider, Annemarie Berger, Talitha Veith, Christiane Pallas, and et al. 2021. "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" Microorganisms 9, no. 4: 748. https://doi.org/10.3390/microorganisms9040748
APA StyleWidera, M., Mühlemann, B., Corman, V. M., Toptan, T., Beheim-Schwarzbach, J., Kohmer, N., Schneider, J., Berger, A., Veith, T., Pallas, C., Bleicker, T., Goetsch, U., Tesch, J., Gottschalk, R., Jones, T. C., Ciesek, S., & Drosten, C. (2021). 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. Microorganisms, 9(4), 748. https://doi.org/10.3390/microorganisms9040748