Fig. 6
Complementation of incomplete genomes occurs efficiently at high MOI and during secondary spread from low MOI. a The model shown in Fig. 3 was used to calculate the probability that a given infected cell contained an IVG. The percentage of infected cells that contain fewer than eight segments is shown at a range of MOIs for PP = 0.58. b An infection in which multi-cycle replication occurs with the spatial structure was simulated as in Fig. 4. The maximum number of cells that contain IVGs in each simulation is shown for a range of diffusion coefficients. Shading represents 95% CI of local regression (mean ± 1.96 * SE). c Visualization of spatially structured and unstructured infections. Cells were inoculated with Pan/99-NP_TC virus and incubated under single-cycle conditions for 12 h (top), multi-cycle conditions for 12 h followed by single-cycle conditions for 12 h (middle), or sham-inoculated and incubated under single-cycle conditions for 12 h (bottom), then visualized by FlaSH staining (left) or phase-contrast imaging (right). Scale bar represents 200 µm. d The extent to which the presence of Pan/99-Helper virus increased WT HA positivity (% enrichment) was evaluated at the outset of infection (open blue circles) and following secondary spread (filled green circles). To gauge potential for complementation at the outset of infection, cells were simultaneously inoculated with Pan/99-WT virus and Pan/99-Helper, then incubated under single-cycle conditions for 12 h (N = 3 replicates per MOI, four MOIs per experiment, and three independent experiments). To test the impact of secondary spread on potential for complementation, cells were inoculated with Pan/99-WT virus at low MOI and incubated under multi-cycle conditions for 12 h, then inoculated with Pan/99-Helper virus and incubated under single-cycle conditions for 12 h (N = 3 replicates per MOI, two MOIs per experiment, and three independent experiments). Curves represent estimates of a fixed effects model with the formula \(\% {\mathrm{Enrichment}} = \beta _1\frac{{{\mathrm{Multi-cycle}}}}{{\% {\mathrm{WT}}\,{\mathrm{HA}}^ + }} + \beta _2\frac{1}{{\% {\mathrm{WT}}\,{\mathrm{HA}}^ + }} + \beta _3^\ast {\mathrm{Multi-cycle}}\), with shading representing 95% CI (mean ± 1.96 * SE) of model estimate. IVGs = incomplete viral genomes. Source data are provided as a Source Data file
