Estimates of new positive patients for Omicron variant(Tokyo) #3

・We compared the number of new positive cases against both infectivity of the Omicron variant and the start of the 3rd vaccination in Tokyo.

・If the infectivity of the Omicron variant is assumed to be equivalent to the average of January 11 to 16, and if the 3rd vaccination is administered within 210 days to those who vaccinated, the number of new positive cases could reach about 47,500 persons per day in early March.

・If the population remaining at night in downtown areas is controlled to 70%, the number of new positive cases could be reduced to 25,000/day, and to 15,000 if the 3rd vaccination for the elderly is administered within 180 days.

・The number of seriously ill patients was estimated to range from 600 to 160 per day at a Delta variant ratio of 0.1, and from 310 to 80 per day at the ratio of 0.05. However, these values are for reference due to lack of data.

・Effective control measures are as below.
　・Decrease the population remaining out at night to 70%
　・Booster vaccination for the elderly after 180 days

From the report on January 7, 2022, a rapid rise in the number of positive patients in early January was produced by: (1) changing the onset interval of the Omicron variant from 5.6 days to 2.9 days and (2) changing the inflow of Omicron variant-affected patients to Tokyo from once (5 patients) to twice (5 patients each).

Comparison of the Delta and Omicron variants with 3rd vaccination

If human flow is not controlled, the number of new positives during the peak period is 47,000.
By controlling the population remaining downtown at 21:00 to 70%, the number of positive cases during the peak period is 25,000.
As a short-term measure, it was suggested that human flow control is highly effective.

Booster vaccination period: 7 months after vaccination for ages 60 and over, 7 months after vaccination for ages under 60.
Efficacy of 2nd vaccination for preventing infection: 33%
Efficacy of 3rd vaccination for preventing infection: 75%
Rate of 3rd vaccination: 90% (rate among people with 2nd vaccination)
Remaining Population: Downtown at 21:00 average of November 25 to December 24, 2021

If the 3rd vaccination for the elderly could be given 6 months after the 2nd vaccination instead of 7 months after the 2nd vaccination, it would be very effective in controlling the number of new positive cases.

Booster vaccination period: 6 months after vaccination for ages 60 and over, 7 months after vaccination for ages under 60
Efficacy of 2nd vaccination for preventing infection: 33%
Efficacy of 3rd vaccination for preventing infection: 75%
Rate of 3rd vaccination: 90% (rate among people with 2nd vaccination)
Remaining Population: Downtown at 21:00 average of November 25 to December 24, 2021

The number of serious cases is estimated to be about 600 in the most pessimistic scenario (no human flow control and the severity rate of the Omicron variant is 0.1 times that of the Delta variant).
If the severity rate of the Omicron variant is 0.05 times that of the Delta variant, the number of seriously ill patients during the peak period is about 300, which is on par with the peak in the summer of 2021.
There is a possibility of further reducing the number of serious cases by controlling human flow.
*However, these values are for reference due to the lack of data.

Booster vaccination period: 7 months after vaccination for ages 60 and over, 7 months after vaccination for ages under 60
Efficacy of 3rd vaccination for preventing infection: 75%
Rate of 3rd vaccination: 90% (rate among people with 2nd vaccination)
Remaining Population: Downtown at 21:00 average of November 25 to December 24, 2021
Number of seriously ill patients: 0.1 times that of Delta variant (hospitalization rate 0.3, decline rate 0.5, oral medication 0.7)
　　　　: 0.05 times that of Delta variant (hospitalization rate: 0.2; decline rate: 0.35; oral medication: 0.7)

If the 3rd vaccination of the elderly can be administered 6 months after the 2nd vaccination, even in the most pessimistic scenario (no human flow suppression and the severity rate of the Omicron variant is 0.1 times that of the Delta variant), the number of serious cases will be about 270, which is on par with the peak in the summer of 2021.
If the severity rate of the Omicron variant is 0.05, the number of seriously ill people is about 140 at peak period.
There is a possibility of further reducing the number of serious cases by controlling human flow.
*However, these values are for reference due to the lack of data.

Booster vaccination period: 6 months after vaccination for ages 60 and over, 7 months after vaccination for ages under 60
Efficacy of 3rd vaccination for preventing infection: 75%
Rate of 3rd vaccination: 90% (rate among people with 2nd vaccination)
Remaining Population: Downtown at 21:00 average of November 25 to December 24, 2021
Number of seriously ill patients: 0.1 times that of Delta variant (hospitalization rate 0.3, decline rate 0.5, oral medication 0.7)
　　　　: 0.05 times that of Delta variant (hospitalization rate: 0.2; decline rate: 0.35; oral medication: 0.7)

1.Infection model by SEIR mathematical model and AI optimization method
The SEIR model, which takes into account population flow and AI technology (evolutionary optimization + quasi-Newton method), were used to optimize infection model estimation within and between three age groups (0-39 years, 40-59 years, and 60 years or older). The number of positive patient inflows from outside the prefecture was estimated from mobile spatial statistics data (NTT Docomo) and LocationMind xPop*1 and incorporated into the model, and the model was trained from data from March 1 to October 30, 2021.

2.Effects of vaccine and behavior change
Vaccine efficacy was 33% for the 2nd and 75% for the 3rd dose against the Omicron variant. The Omicron variant was assumed to have started to infect 5 people via community spread on December 10 and December 20, respectively. The onset interval for the Omicron variant was 2.9 days.
Measured values are used for changes in the effective reproduction number and the number of populations flows from March 1 to December 18. The effective reproductions number and risk of inflow of infected persons were estimated assuming that the population remaining in downtown areas (13:00, 19:00, and 21:00) and the population coming from outside Tokyo were at the same levels as in November after December 19.
Diminishing vaccine efficacy was assumed to diminish to 50% in 180 days. Booster vaccinations were to begin on December 1 for medical personnel 180 days after the 2nd vaccination, from January 5 for the elderly, and from February 1 for those under 60 years of age.

https://www.gov.il/en/departments/news/05072021-03,https://www.gov.il/en/departments/news/06072021-04
Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce, DOI: 10.1056/NEJMc2112981, The new England journal of medicine
COVID vaccines protect against Delta, but their effectiveness wanes, doi: https://doi.org/10.1038/d41586-021-02261-8, Nature
Comparative Effectiveness of Moderna, Pfizer-BioNTech, and Janssen (Johnson & Johnson) Vaccines in Preventing COVID-19 Hospitalizations Among Adults Without Immunocompromising Conditions — United States, March–August 2021, CDC vol.70, 17, Sep. 2021
National Institute of Infectious Diseases, Mutated variant B.1.1.529 (the Omicron variant) of SARS-CoV-2 (5th report), 2021

Tokyo suburbs agent base model
We constructed a model represented by 1,348 agents in 2 cities based on the household structure of a Tokyo suburb, and restricted workplaces, restaurants, and event venues by vaccination proof, and measured the rate of change in Rt from 500 trials each. Companions to eat and drink together were assumed to be chosen randomly from a network of friends (the number of friends was a power-law distributed Galton-Watson network).

*1 "LocationMind xPop" data is data that NTT DOCOMO collectively and statistically processes from mobile phone location information sent with permission from users of applications* provided by NTT DOCOMO. Location information is GPS data (latitude and longitude information) that is measured at a minimum of every five minutes, and does not contain information that identifies an individual. DOCOMO Map Navi Service (map application, local guide) and some other applications

The time series of the effectiveness of vaccination in preventing the onset of illness is expressed as the amount of antibodies possessed (the number of people who have vaccine effectiveness).
Since vaccine effectiveness is expected to decline, the overall preventive effect of the vaccine is shown by the bold lines in the figures.