After implementing the “zero-COVID” strategy for more than two years, China has recently begun to adjust its COVID-19 response strategies, notably by announcing the “20 measures” on November 11 and further the “10 measures” on December 7, 2022 1,2. Since then, Omicron infections spread rapidly in major cities of China, including Beijing, where the Omicron subvariant BF.7 epidemic has been putting great pressure on the healthcare system since early December 3,4.
Regular mass testing and intensive contact tracing were suspended in late November and nucleic acid testing is conducted on a voluntary basis 5. As such, the daily number of confirmed cases reported by Beijing Municipal Health Commission (BMHC, http://wjw.beijing.gov.cn/) thereafter was no longer an accurate reflection of the epidemic curve, making it difficult to assess the transmission dynamics. Here we tracked the effective reproduction number of Omicron BF.7 in Beijing in November – December 2022 using our previous epidemic nowcast framework which comprised disease transmission models parameterised with real-time mobility data 6
The Effective Reproduction Number \({R}_{t}\) Of Omicron In Beijing
We categorized the COVID-19 response adjustments in Beijing in three stages:
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Stage 1 (November 1–11): Zero-COVID strategy was strictly implemented with regular mass testing, intensive contact tracing and lockdown of residential buildings or communities once PCR-positive infections and their close contacts were traced.
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Stage 2 (November 12–25): Although mass testing and contact tracing were maintained after the announcement of “20 measures” on November 11, lockdown was limited to the residential buildings or only the floors or units where PCR-positive infections lived.
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Stage 3 (after November 25): The requirement of regular mass testing, intensive contact tracing and lockdown were gradually relaxed and finally suspended on November 30. The nucleic acid testing is conducted only on a voluntary basis after the announcement of “10 measures” on December 7.
We parameterised the disease transmission model with daily number of passengers from Beijing MTR, which manage 5 of 25 subway lines in Beijing (Fig. 1). We fitted the model to two data streams to estimate effective reproduction number \({R}_{t}\): i) the daily number of symptomatic cases reported to BMHC between November 1 and 11 when the testing and reporting behaviour were relatively stable; and ii) the proportion of participants who reported to be ever positive by polymerase chain reaction (PCR) or rapid antigen test (RAT) since November 1, by convenience sampling in Weibo online polls conducted between December 10 and 14 (Fig. 1). See Methods for details.
Within one week after the announcement of “20 measures”, \({R}_{t}\) increased from 1.02 (95% CrI: 0.75–1.29) on November 11 to 3.42 (95% CrI: 2.79–4.17) on November 18 (Fig. 2). With the increasing number of cases, public health and social measures (PHSMs) were implemented: residents were urged to stay home over the weekend of November 19–20; 95% of staff were suggested to work from home in the week of November 21–25; kindergartens, primary and secondary schools were closed on November 21. Mobility and hence \({R}_{t}\) dropped substantially below 1 to 0.87 (95% CrI: 0.71–1.01) on November 27.
However, the surge of infections saturated the capacity of PCR testing and quarantine facility in late November. The requirement of regular mass testing, intensive contact tracing and lockdown were gradually relaxed and finally suspended with the announcement of “10 measures”. PHSMs were relaxed and consequently \({R}_{t}\) increased to 2.71 (95% CrI: 2.04–2.89) on December 7 (Fig. 2), which was substantially higher than \({R}_{t}\) of 1.9 under similar PHSMs in the early stage of Hong Kong’s Omicron wave in February – March 2022 7.
Omicron infections grew rapidly again starting from early December, and many symptomatic infected individuals and their close contacts were self-isolated. At the time of writing, Beijing MTR’s mobility dropped to low levels, and we estimated that \({R}_{t}\) dropped below 1 on December 12 and \({R}_{t}\) was 0.81 (95% CrI: 0.29–1.13) on December 14.
The Daily Incidence And Cumulative Infection Attack Rate
We estimated the daily incidence and cumulative infection attack rate from the fitted model accordingly (Fig. 2). On November 30, when regular mass testing was suspended, we estimated the daily number of infections was 62,531 (95% CrI: 26,292–142,613). The daily incidence increased rapidly since then and peaked on December 10, with an estimated daily number of infections of 1.19 million (95% CrI: 0.55–1.93), i.e. 5.5% of the population.
At the time of writing, we estimated that the cumulative infection attack rate (IAR) was 42.5% (95% CrI: 20.3–63.9) on December 14. The daily incidence started to decrease after December 10, and we estimated the cumulative IAR would reach 58.3% (95% CrI: 36.4–73.6) in one week on December 21.
In the base case scenario above, we assumed each participant of the online polls underwent multiple RATs and the ascertainment probability of previous infection was 1 after November 11 (Fig. 2). As a sensitivity analysis, we assumed that the ascertainment probability was 0.8 in the inference (Supplementary Fig. 1). The corresponding estimated\({ R}_{t}\) was slightly higher, e.g. 3.53 (95% CrI: 2.89–4.29) vs. 3.42 (95% CrI: 2.79–4.17) on November 18, and 2.73 (95% CrI: 2.07–2.89) vs. 2.71 (95% CrI: 2.04–2.89) on December 7. The estimated cumulative IAR was higher accordingly, reaching 50.8% (95% CrI: 26.8–71.4) on December 14 and 64.7% (95% CrI: 44.0–78.2) on December 21.