SARS-CoV-2 Genome Sequencing and Analysis

NGS was used to verify the sequence of isolates and isogenic clones prior to experimentation. RNA was extracted using the RNAdvance Tissue kit (Beckman Coulter) and the KingFisher Flex System (Thermo Fisher Scientific). Subsequently, RNA was transcribed into cDNA and sequencing libraries were generated as described^{27 (link)} and were sequenced using the Ion Torrent S5XL Instrument (ThermoFisher). Samples with C_t values >20 for SARS-CoV-2 were additionally treated with RNA baits (myBaits, Arbor Biosciences) for SARS-CoV-2 enrichment before sequencing^{28 (link)}. Sequence datasets were analysed by reference mapping with the Genome Sequencer Software Suite (version 2.6, Roche), default software settings for quality filtering and mapping using EPI_ISL_414019 (Alpha), EPI_ISL_2131446 (Alpha) and EPI_ISL_981782 (Beta) as references. To identify potential single nucleotide polymorphisms in the read data, the variant analysis tool integrated in Geneious Prime (2019.2.3) was applied (default settings).

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Ulrich L., Halwe N.J., Taddeo A., Ebert N., Schön J., Devisme C., Trüeb B.S., Hoffmann B., Wider M., Fan X., Bekliz M., Essaidi-Laziosi M., Schmidt M.L., Niemeyer D., Corman V.M., Kraft A., Godel A., Laloli L., Kelly J.N., Calderon B.M., Breithaupt A., Wylezich C., Berenguer Veiga I., Gultom M., Osman S., Zhou B., Adea K., Meyer B., Eberhardt C.S., Thomann L., Gsell M., Labroussaa F., Jores J., Summerfield A., Drosten C., Eckerle I.A., Wentworth D.E., Dijkman R., Hoffmann D., Thiel V., Beer M, & Benarafa C. (2021). Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Nature, 602(7896), 307-313.

Publication 2021

RNAdvance Tissue kit KingFisher Flex System Ion Torrent S5XL Instrument Genome Sequencer Software Suite

Cdna Clones Genome Sars cov 2 Settings Single nucleotide polymorphisms Tissue

Corresponding Organization : University of Bern

Other organizations : Centers for Disease Control and Prevention, University of Geneva, Charité - Universitätsmedizin Berlin, German Center for Infection Research, University Hospital of Geneva

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Variable analysis

independent variables

NGS was used to verify the sequence of isolates and isogenic clones prior to experimentation.

dependent variables

Sequence datasets were analysed by reference mapping with the Genome Sequencer Software Suite (version 2.6, Roche), default software settings for quality filtering and mapping using EPI_ISL_414019 (Alpha), EPI_ISL_2131446 (Alpha) and EPI_ISL_981782 (Beta) as references.
To identify potential single nucleotide polymorphisms in the read data, the variant analysis tool integrated in Geneious Prime (2019.2.3) was applied (default settings).

control variables

RNA was extracted using the RNAdvance Tissue kit (Beckman Coulter) and the KingFisher Flex System (Thermo Fisher Scientific).
Samples with Ct values >20 for SARS-CoV-2 were additionally treated with RNA baits (myBaits, Arbor Biosciences) for SARS-CoV-2 enrichment before sequencing.

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