Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization

Figure 1.. HRV evolution in upper and lower respiratory tract samples in immunocompromised individuals. Allele frequency (in percentage) of each iSNV across the HRV genome in individuals S01 (A), S03 (B), S04 (C) and S05 (D) is depicted. iSNV causing synonymous mutation are shown in blue, while non-synonymous mutations are shown in red and include the amino acid change description. Upper (NW, nasal wash) and lower (BAL, bronchioalveolar lavage) respiratory tract samples are detailed in the upper right of each plot. In addition, the day when the sample was collected relative to the first HRV positive and the maximum sequencing depth of coverage for each sample is shown. HRV mature peptides are annotated at the bottom of each panel. The grey background plot illustrates the sequencing coverage profile for each sample. Regions with low sequencing coverage (<30X) are shown in pink.

Figure 2.. Long-term HRV infection dynamics in immunocompromised individuals. Minor allele frequency (in percentage) of each iSNV across the HRV genome in individuals S07 (A), S10 (B) and S11 (C) is represented by dots. Blue dots indicate iSNV causing synonymous mutation and red dots indicate non-synonymous mutation which also includes the amino acid change description. Upper (NW, nasal wash) and lower (BAL, bronchioalveolar lavage) respiratory tract samples are detailed in the upper right of each plot. In addition, the day when the sample was collected relative to the first HRV positive and the maximum sequencing depth of coverage for each sample is shown. HRV mature peptides are annotated at the bottom of each panel. The grey background plot illustrates the sequencing coverage profile for each sample. Regions with low sequencing coverage (<30X) are shown in pink.

Figure 3.. HRV-A capsid evolution dynamics during prolonged within-host infection. iSNVs modeled in the 3D crystal structure of the HRV-A16 capsid (PDB accession number 1AYM). Proteins VP1, VP2 and VP3 are differentiated in the 3D model with different gray degrees. iSNV allele frequency is depicted on a scale from yellow to red (from 10% to 100%). iSNV detection was categorized in day zero (first sample positive detected), after 12 to 30 days from the first HRV positive and after more than 68 days from the first HRV positive.