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. 2022 May 31:eabo7081. doi: 10.1126/scitranslmed.abo7081

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Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works

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Fig. 4. — (A) Phase diagram of estimated reproduction number ratio between Omicron and Delta ( $R_{0}^{O m i c r o n} / R_{0}^{D e l t a}$ ) as a function of immune escape parameters ( $σ_{O m}^{i}$ =escape on infection) and $σ_{O m}^{t | i}$ (escape on transmission reduction conditional on infection). Parameters shown are those that matched the observed growth advantage of Omicron over Delta and the timing of the Omicron peak in the urban district of the PHIRST-C study. (B-E) Phase diagram of the infection rate of the Omicron wave (B), epidemic duration (C), the fraction of reinfections (D), and the infection case ratio (ICR) (E) of the Omicron wave as a function of $σ_{O m}^{i}$ and $σ_{O m}^{t | i}$ and the corresponding $R_{0}^{O m i c r o n} / R_{0}^{D e l t a}$ in (A). In (A)-(E), white dots marks three specific scenarios including a reference scenario (RS) with $σ_{O m}^{i} = 0.7$ and $σ_{O m}^{t | i} = 0.2$ , a low immune escape scenario (LE) with $σ_{O m}^{i} = 0.1$ and $σ_{O m}^{t | i} = 0.1$ , and a high immune escape scenario (HE) with $σ_{O m}^{i} = 0.9$ and $σ_{O m}^{t | i} = 0.9$ . (F) For the reference scenario (dot in the middle), reconstruction of infection time series and exposure histories by variant are shown. Top panel y axis upwards: Weekly incidence per 10,000 individuals of SARS-CoV-2 cases reported to the District till January 2022, in the period before Omicron (dark blue bars) and during Omicron (dark red bars). Top panel y axis downwards: Weekly incidence per 100 individuals of SARS-CoV-2 infections reconstructed based on PHRIST-C data (prior to September 2021) and estimated using Delta/Omicron-specific transmission models from September 2021 to the end of the Omicron wave at the end of January 2022. Pre-Omicron infections are in light blue and Omicron infections are in light red. For the top panel, the y axis upwards and downwards have different scales (by a factor of 100). Insert panel: the prevalence of the population with specific SARS-CoV-2 antigen exposure histories. Legend abbreviations: D614G: individuals who only experienced one D614G infection; Beta: individuals who only experienced one Beta infection; Delta: individuals who only experienced one Delta infection; Omicron: individuals who only experienced one Omicron infection; Others: individuals who only experienced one SARS-CoV-2 infection with genotype other than the D614G, Beta, Delta and Omicron variants; Vacc: individuals who had received at least one dose of vaccines but had not yet been infected by SARS-CoV-2; Vacc-Omicron: individuals who were vaccinated first then infected by Omicron; D614G-Omicron: individuals who were first infected by D614G then infected by Omicron; Beta-Omicron: individuals who were infected by Beta first then infected by Omicron; Delta-Omicron: individuals who were infected by Delta first then infected by Omicron; Others-Omicron: individuals who were infected by a variant other than D614G, Beta, Delta and Omicron first then infected by Omicron; Repeat exposures: individuals who were exposed to SARS-CoV-2 antigens more than once (through vaccination or infection) without Omicron infection; Repeat exposures-Omicron: individuals who were exposed to SARS-CoV-2 antigens more than twice (through vaccination or infection) then infected by Omicron.