Fig. 1: Characteristics of chronic-like clades compared to control clades and bona fide chronic infections.

a The number of chronic-like clades stratified by background variant. Pre-VOC refers to any variant that was dominant before the emergence of Alpha. b Distribution of age and percentage of male/female shown for control clades (n = 15,163), chronic-like clades (n = 271) and bona fide chronic infections (n = 32). The central line of box defines the median value. The box itself encompasses the interquartile range (IQR), with the lower and upper edges indicating the 25th and 75th percentiles, respectively. On average chronic-like clades were characterized by older age (p < 0.001, two-tailed t-test), and a higher proportion of males (p < 10⁻⁴, permutation test). c The distribution of average Sackin index values over 10,000 repeated stratified sampling of n = 271 control clades, with the orange circle representing the average Sackin index of the chronic-like clades. d Distributions of substitutions along the SARS-CoV-2 genome observed across all bona fide chronic infections, chronic-like clades, and control clades. Substitutions are counted in bins of 500 nucleotides. Of note, for clarity the y-axis is not shared among the groups shown. Asterisks mark bins significantly enriched for more substitutions using a one-tailed binominal test, after correction for multiple testing (p < 0.0001, following false discovery rate (FDR) correction).