Additional file 1 of Twice evasions of Omicron variants explain the temporal patterns in six Asian and Oceanic countries
Creators: name: Chen, Boqiang
name: Zhao, Yanji
name: Jin, Zhen
name: He, Daihai
name: Li, Huaichen
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Computational Biology

description: Additional file 1: Table S1. The population, Log likelihood value and Log likelihood value standard derivation. Table S2. The parameters in the model simulation. Table S3. The cubic spline nodes number and nodes value of the transmission rate β(t) (log.βi, i = 1, . . . , 16). Table S4. The ratio of excess death vs report deaths and its 95% CI. Table S5. Literature statistics under different keywords and search settings. Figure S1. Model simulated death vs. reported death with the assumption of only one Omicron invasion and the rate of loss of immunity protection ψ = 1/2 in India(a), Indonesia(b), Malaysia(c), Bangladesh(d), Nepal(e) and Myanmar(f). The brown curve, green curve and blue curve at the top of each panel show the currently immunized people per capita, the number of persons who received a second dose per capita and the number of persons who received a booster dose per capita, respectively. The sudden drop in the brown curve shows the immune evasion caused by one Omicron variant invasion. The red circles, black curve and blue cure with the plus sign at the bottom of each panel show the reported cases, the simulation median and the transmission rate (in the unit of R0(t) = β(t)/γ), respectively. The grey region denotes the 95% CI of 1000 model simulations. The green circles that overlap the black curve are the reported deaths for testing part. The extra green circles are the reported deaths to show the COVID-19 pandemic trends. The percent on the top of each panel is the estimated maximum log likelihood pre-Omicron IFR. Figure S2. Model simulated death vs. reported death with the assumption of only one Omicron invasion and the rate of loss of immunity protection ψ = 1/3 in India(a), Indonesia(b), Malaysia(c), Bangladesh(d), Nepal(e) and Myanmar(f). The brown curve, green curve and blue curve at the top of each panel show the currently immunized people per capita, the number of persons who received a second dose per capita and the number of persons who received a booster dose per capita, respectively. The sudden drop in the brown curve shows the immune evasion caused by one Omicron variant invasion. The red circles, black curve and blue cure with the plus sign at the bottom of each panel show the reported cases, the simulation median and the transmission rate (in the unit of R0(t) = β(t)/γ), respectively. The grey region denotes the 95% CI of 1000 model simulations. The green circles that overlap the black curve are the reported deaths for testing part. The extra green circles are the reported deaths to show the COVID-19 pandemic trends. The percent on the top of each panel is the estimated maximum log likelihood pre-Omicron IFR. Figure S3. Model simulated death vs. reported death with the assumption of two Omicron invasions and the rate of loss of immunity protection ψ = 1/2 in India(a), Indonesia(b), Malaysia(c), Bangladesh(d), Nepal(e) and Myanmar(f). The brown curve, green curve and blue curve at the top of each panel show the currently immunized people per capita, the number of persons who received a second dose per capita and the number of persons who received a booster dose per capita, respectively. The sudden drops in the brown curve demonstrate the immune evasion caused by two Omicron variant invasions. The red circles, black curve and blue curve with the plus sign at the bottom of each panel show the reported cases, the simulation median and the transmission rate (in the unit of R0(t) = β(t)/γ), respectively. The grey region denotes the 95% CI of 1000 model simulations. The green circles that overlap the black curve are the reported deaths for testing part. The extra green circles are the reported deaths to show the COVID-19 pandemic trends. The percent on the top of each panel is the estimated maximum log likelihood pre-Omicron IFR. Figure S4. Model simulated death vs. reported death with the assumption of twice Omicron invasions and the rate of loss of immunity protection ψ = 1/3 in India(a), Indonesia(b), Malaysia(c), Bangladesh(d), Nepal(e) and Myanmar(f). The brown curve, green curve and blue curve at the top of each panel show the currently immunized people per capita, the number of persons who received a second dose per capita and the number of persons who received a booster dose per capita, respectively. The sudden drops in the brown curve demonstrate the immune evasion caused by two Omicron variant invasions. The red circles, black curve and blue curve with the plus sign at the bottom of each panel show the reported cases, the simulation median and the transmission rate (in the unit of R0(t) = β(t)/γ), respectively. The grey region denotes the 95% CI of 1000 model simulations. The green circles that overlap the black curve are the reported deaths for testing part. The extra green circles are the reported deaths to show the COVID-19 pandemic trends. The percent on the top of each panel is the estimated maximum log likelihood pre-Omicron IFR.