Fig. 1: History of the infection and resulting amino acid substitutions and deletions.

The graph at the bottom shows the course of the SARS-CoV-2 Ct values of the patient. Note the reversed y-axis. Negative tests are displayed as 45 (maximum of the applied test). Additional negative test results at the beginning and end of the shown time slot are documented but not shown. The blue bar behind the curve indicates the period during which the patient was administered tixagevimab and cilgavimab (10/24/2022) as well as molnupiravir (10/24–10/29/2022) as prescribed. The green bar behind the curve indicates the period during which the patient was administered remdesivir as prescribed (05/10–05/19/2023). Dashed vertical lines indicate the time points at which the patient’s virus population was whole-genome-sequenced, with the respective dates on the x-axis. The colored lines above this plot show the time windows (between two sequencing events) in which substitutions and deletions have become established in the virus population, each line representing one substitution/deletion. Light blue lines indicate amino acid substitutions (N = 34), and dark pink lines indicate deletions (N = 8). Deletions are given with genomic nucleotide coordinates. Hash signs after deletions indicate frameshift mutations, resulting in a presumably dysfunctional protein. Lines spanning two or more time intervals show the fixation process of the mutation in the virus population. Substitutions/deletions in the spike protein are highlighted in red, asterisks mark mutations in the receptor binding domain of the spike protein. S spike protein, N nucleocapsid protein, NSP nonstructural protein, ORF open reading frame, Ct value threshold cycle value in q-RT-PCR.