Fig. 1
The daily number of COVID-19 cases (panel A), the reconstructed reproduction number (Rt, panel B), proportion of the G on the 614-th codon of the S protein (panel C), and estimated transmission advantage of G on the real-time basis (η, panel D). Panel A shows the daily number of COVID-19 time series in California state, USA. Panel B shows the estimated Rts of G (in orange) and D (in green). Panel C shows the observed (dots) and fitted (curve) proportion of the Glycine (G) on the 614-th codon of the S protein. Panel D shows the real-time estimates of the transmission advantage of G (η). In panels B and D, the dots are the estimates, and bars are the 95%CIs. In panel C, the curve indicates the mean fitting results, the shading area indicates the 95%CIs, and horizontal dashed grey line represents proportion level at 0.5. In panels C and D, the vertical bold purple line represents the date, March 12, 2020 when the η estimates yields an ‘early warning signal’, i.e., η > 0 significantly, detecting the transmission advantage of G (against D)