Fig. 2: SARS-CoV-2 whole genome sequencing and phylogenetic analysis.
Phylogenetic analysis of the viral sequences obtained from patient swabs between day 0 to day 140, after the first positive RT-qPCR result in March 2020. The sequences were aligned to a set of representative SARS-CoV-2 genome sequences from the Freiburg area (a) and from Germany (b) between February and April 2020 which have been deposited in the GISAID data bank (Supplementary table 2 and 3). The circularized maximum-likelihood phylogenetic tree was constructed with IQ-Tree (GTR + F + I) and rooted on the Wuhan-Hu-1 reference sequence (NC_045512). The sequences obtained from the immunosuppressed patient are indicated as red dots and lineage-defining mutations are indicated at the respective branches. The scale represents nucleotide substitutions per site. c Schematic overview of the viral genome variations from patient swab samples (day 0-140) in comparison to the Wuhan-Hu-1 reference sequence. The heatmap summarizes the positions in the viral genome and the variant frequencies in the different samples (cut off values of 25 and 10% for the S gene, respectively). The days of sampling are indicated at the right and the heatmap color intensity indicates variant frequencies. Stars denote non-synonymous mutations leading to amino acid substitutions in the spike protein (> 50 % of reads). d Schematic overview of the SARS-CoV-2 spike protein including the S1 and S2 cleavage products and functional domains such as the N-terminal domain (NTD), receptor-binding domain (RBD), receptor binding motif (RBM), S1/S2 proteolytic furin cleavage site, fusion peptide (FP), heptad repeat regions (HR1/HR2), transmembrane domain (TM) and C-terminal domain (CT). Selected non-synonymous changes in the spike (S) gene from panel c are indicated. e Summary of mutations found in the spike protein of the patient sequences obtained on d14, d105, and d140 (>50 % of reads) in comparison to circulating new variants of concern: alpha, B.1.1.73, beta, B.1.3514, and gamma, P.15.
