Reconstructing the force of infection and immune fraction of the population via a single snapshot survey: a case study of COVID-19 in Japan

While the global health burden of COVID-19 continues, multifaceted epidemiological surveillance is required to monitor the epidemic’s dynamics and its population-wide risk. We proposed a simple framework using a population-wide snapshot questionnaire survey to estimate the incidence and protective effect of immunity by natural infection or vaccination against the SARS-CoV-2 JN.1 variant.

Our results revealed that in Japan in February 2024, the personal risk of infection was substantially higher in younger adults and risk was heterogenous across prefectures. Diabetes mellitus (relative risk 1.8; 95% credible interval [CrI] 1.1, 2.9), neoplastic disorders (5.2; 95% CrI 3.1, 8.6), immunological suppression (2.6; 95% CrI 1.3, 4.6), respiratory diseases (2.2; 95% CrI 1.46, 3.3), and cardiovascular disease (2.3; 95% CrI 1.3, 3.9) were risk factors for infection.

The highest peak protection after infection was after exposure to pre-XBB.1.5 Omicron variants (52.0%; 95% CrI 33.2, 68.7), whereas the XBB.1.5 monovalent vaccine provided the highest protection (45.1%; 95% CrI 37.8, 52.7) among three vaccine types. Notably, the peak protection of the bivalent Wuhan + Omicron BA.1/5 vaccine was substantially lower than other vaccines (28.7; 95% CrI 17.3, 40.6). By statistical matching the respondent cohort to the 2020 population census, we revealed that the national COVID-19 incidence rate in February 2024 by age group was highest (4.73%; 95% CrI 4.17, 5.38) and lowest (1.19%; 95% CrI 0.94, 1.47) among those aged 20–29 years and 60–69 years, respectively. The force of infection was high and more heterogeneous in younger groups, whereas younger populations were more concentrated than older populations in low-protection regions.

Our framework revealed biological and epidemiological insights into protection and risk of infection from past immunizing events and personal attributes during the JN.1-dominant period. Moreover, we proposed a framework for the rapid evaluation of epidemiological dynamics whose application is not limited to COVID-19.

Author Summary

The questionnaire survey is a powerful tool for generating population-wide data in fields including public health, but its application in tracking the immunological characteristics and incidence rate of COVID-19 is limited. We proposed a new framework to leverage the advantages of this tool by combining an Internet-based questionnaire survey with statistical models. Two findings emerged from our study, which focused on COVID-19 infection in February 2024, when the JN.1 variants of severe acute respiratory syndrome coronavirus 2 were dominant in Japan. First, the overall reduction in the relative risk of infection from vaccinations or natural infection was at most roughly 60% and had substantial time decay. Second, compared with older age groups, a higher incidence rate and lower protection from acquired immunity were observed in young age groups, with substantial heterogeneity within each age-stratified population. This study revealed important immune profiles against the emerging JN.1 variant and identified an effective framework that can be added to the array of epidemiological programs that complement routine public health surveillance.