Figure 1
Selection within individuals with COVID-19 leads to selection of more fit viral variants. (A) Schematic of viral replication model used to simulate SARS-CoV-2 evolutionary dynamics. Colors denote the descendants created in generation Ni+1 by the replication burst of each individual ancestor in generation Ni. (B) Sputum viral load curve for a typical COVID-19 infection. The x-axis represents the time starting from the initial transmission event that caused the infection. (C) Mean frequency of variants with point mutations within individuals with COVID-19 for different mutation fitness effects (colors). (D) Probability of a specific single mutation to be present in at least one virion transmitted if transmission occurs within the first 3–7 days of infection (lighter red curves) or anytime during infection (darker red). For (C) and (D), shaded areas represent ± SEM, n = 1000 simulations per condition. (E) Number of total new single mutant infections generated per day that establish a surviving variant lineage, assuming all infections are of standard length with viral load profile given in (B) and that transmission occurs within the first 7 days of infection. Unless otherwise specified, simulation parameter values are those given in Table 1.
