{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T18:54:09Z","timestamp":1773687249831,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013990","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T00:00:00Z","timestamp":1773619200000}}],"reference-count":72,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T00:00:00Z","timestamp":1772755200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004298","name":"Secom Science and Technology Foundation","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/501100004298","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Health and Labour Sciences Research Grants","award":["20CA2024, 21HB1002, 21HA2016, and 23HA2005"],"award-info":[{"award-number":["20CA2024, 21HB1002, 21HA2016, and 23HA2005"]}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP23fk0108612 and JP23fk0108685"],"award-info":[{"award-number":["JP23fk0108612 and JP23fk0108685"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"name":"JSPS KAKENHI","award":["21H03198 and 22K19670"],"award-info":[{"award-number":["21H03198 and 22K19670"]}]},{"name":"Environment Research and Technology Development Fund","award":["JPMEERF20S11804"],"award-info":[{"award-number":["JPMEERF20S11804"]}]},{"name":"Environmental Restoration and Conservation Agency of Japan, the Daikin GAP Fund of Kyoto University"},{"name":"HU-RIZONT international research excellence program","award":["Rapid-GRIP project: 2024-1.2.3-HU-RIZONT-2024-00034"],"award-info":[{"award-number":["Rapid-GRIP project: 2024-1.2.3-HU-RIZONT-2024-00034"]}]},{"name":"WHO"},{"name":"Japan Science and Technology Agency SICORP program","award":["JPMJSC20U3 and JPMJSC2105"],"award-info":[{"award-number":["JPMJSC20U3 and JPMJSC2105"]}]},{"name":"CREST program","award":["JPMJCR24Q3"],"award-info":[{"award-number":["JPMJCR24Q3"]}]},{"name":"RISTEX program for Science, Technology, and Innovation Policy","award":["JPMJRS22B4"],"award-info":[{"award-number":["JPMJRS22B4"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>While the global health burden of COVID-19 continues, multifaceted epidemiological surveillance is required to monitor the epidemic\u2019s dynamics and its population-wide risk. By collecting information that is used in conventional vaccine effectiveness studies through questionnaire surveys, 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 diagnosed infection was substantially higher in younger adults and risk was heterogenous across prefectures. Diabetes mellitus (relative hazard ratio 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 1.4, 3.3), and cardiovascular disease (2.3; 95% CrI 1.3, 3.9) were risk factors for diagnosed 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\u2009+\u2009Omicron BA.1\/5 vaccine was substantially lower than other vaccines (28.7; 95% CrI 17.3, 40.6). By statistically 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\u201329 years and 60\u201369 years, respectively. The force of infection measured by diagnosed 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 diagnosed 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.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013990","type":"journal-article","created":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T18:39:51Z","timestamp":1772822391000},"page":"e1013990","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Reconstructing the incidence rate and immune fraction of the population via a single snapshot survey: A case study of COVID-19 in Japan"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2607-3606","authenticated-orcid":true,"given":"Yuta","family":"Okada","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0941-8537","authenticated-orcid":true,"given":"Hiroshi","family":"Nishiura","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,3,6]]},"reference":[{"issue":"7942","key":"pcbi.1013990.ref001","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/s41586-022-05522-2","article-title":"The WHO estimates of excess mortality associated with the COVID-19 pandemic","volume":"613","author":"W Msemburi","year":"2023","journal-title":"Nature"},{"key":"pcbi.1013990.ref002","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1016\/S0140-6736(24)00476-8","article-title":"Global age-sex-specific mortality, life expectancy, and population estimates in 204 countries and territories and 811 subnational locations, 1950-2021, and the impact of the COVID-19 pandemic: a comprehensive demographic analysis for the Global Burden of Disease Study 2021","volume":"403","year":"2024","journal-title":"Lancet"},{"key":"pcbi.1013990.ref003","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1016\/S0140-6736(21)02796-3","article-title":"Estimating excess mortality due to the COVID-19 pandemic: a systematic analysis of COVID-19-related mortality, 2020-21","volume":"399","year":"2022","journal-title":"Lancet"},{"issue":"12","key":"pcbi.1013990.ref004","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1161\/CIRCULATIONAHA.122.060785","article-title":"Association of COVID-19 With Major Arterial and Venous Thrombotic Diseases: A Population-Wide Cohort Study of 48 Million Adults in England and Wales","volume":"146","author":"R Knight","year":"2022","journal-title":"Circulation"},{"issue":"1","key":"pcbi.1013990.ref005","doi-asserted-by":"crossref","first-page":"1904","DOI":"10.1038\/s41467-021-22214-z","article-title":"Hospital load and increased COVID-19 related mortality in Israel","volume":"12","author":"H Rossman","year":"2021","journal-title":"Nat Commun"},{"issue":"46","key":"pcbi.1013990.ref006","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.15585\/mmwr.mm7046a5","article-title":"Impact of Hospital Strain on Excess Deaths During the COVID-19 Pandemic - United States, July 2020-July 2021","volume":"70","author":"G French","year":"2021","journal-title":"MMWR Morb Mortal Wkly Rep"},{"issue":"2","key":"pcbi.1013990.ref007","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1136\/heartjnl-2022-321492","article-title":"Cardiovascular disease and mortality sequelae of COVID-19 in the UK Biobank","volume":"109","author":"Z Raisi-Estabragh","year":"2022","journal-title":"Heart"},{"issue":"7862","key":"pcbi.1013990.ref008","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/s41586-021-03553-9","article-title":"High-dimensional characterization of post-acute sequelae of COVID-19","volume":"594","author":"Z Al-Aly","year":"2021","journal-title":"Nature"},{"key":"pcbi.1013990.ref009","doi-asserted-by":"crossref","first-page":"102000","DOI":"10.1016\/j.eclinm.2023.102000","article-title":"Long-term post-acute sequelae of COVID-19 infection: a retrospective, multi-database cohort study in Hong Kong and the UK","volume":"60","author":"ICH Lam","year":"2023","journal-title":"eClinicalMedicine"},{"key":"pcbi.1013990.ref010","doi-asserted-by":"crossref","first-page":"107223","DOI":"10.1016\/j.ijid.2024.107223","article-title":"Reconstructing the age-structured case count of COVID-19 from sentinel surveillance data in Japan: A modeling study","volume":"148","author":"Y Okada","year":"2024","journal-title":"Int J Infect Dis"},{"issue":"3","key":"pcbi.1013990.ref011","first-page":"645","article-title":"Estimating the effective reproduction number of COVID-19 from population-wide wastewater data: An application in Kagawa, Japan","volume":"9","author":"Y Okada","year":"2024","journal-title":"Infect Dis Model"},{"key":"pcbi.1013990.ref012","unstructured":"Office for National Statistics. 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