Fig. 3: Acquired deletion in the spike protein sequence. | npj Genomic Medicine

Fig. 3: Acquired deletion in the spike protein sequence.

From: Adaptive evolution of SARS-CoV-2 during a persistent infection for 521 days in an immunocompromised patient

Fig. 3

The upper part shows the genome region from position 21,589–21,644 for the five samples plus the reference sequence Wuhan-Hu-1 in a MEGA-X alignment. Samples are sorted by sampling date. The prominent, large deletion to the left (12, respectively 27 bp) was acquired in the patient’s virus population in a two-step process: the sequence coding for four amino acids (S:S13, S:Q14, S:C15, and S:V16) was deleted between October 2022 and March 2023, and the coding sequence for another five amino acids (S:V11, S:S12, S:N17, S:L18, and S:T19) was deleted between June 2023 and October 2023. No frameshift or amino acid substitution resulted from the deletions. The corresponding section from the sequence read mapping analysis of one representative sample for both states (short and long deletion) is shown in the IGV screenshot below. The smaller deletion to the right (9 bp) was present in the patient’s virus population from the beginning and resulted in the deletion of three amino acids (S:L24, S:P25, and S:P26) and an amino acid substitution (S:A27S) at the cleavage site.

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