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Article ; Online: Public holidays increased the transmission of COVID-19 in Japan, 2020-2021: a mathematical modelling study.

Qiao, Jiaying / Nishiura, Hiroshi

2024 , Page(s) e2024025

Abstract: Objectives: Although the role of specific holidays in modifying transmission dynamics of infectious diseases has received some research attention, the epidemiological impact of public holidays on the transmission of coronavirus disease 2019 (COVID-19) ... ...

Abstract	Objectives: Although the role of specific holidays in modifying transmission dynamics of infectious diseases has received some research attention, the epidemiological impact of public holidays on the transmission of coronavirus disease 2019 (COVID-19) remains unclear. Methods: To assess the extent of increased transmission frequency during public holidays, we collected COVID-19 incidence and mobility data in Hokkaido, Tokyo, Aichi, and Osaka from 15 February 2020 to 30 September 2021. Models linking the estimated effective reproduction number (Rt) with raw or adjusted mobility, public holidays, and the state of emergency declaration were developed. The best-fit model included public holidays as an essential input variable, and was used to calculate counterfactuals of Rt in the absence of holidays. Results: During public holidays, on average, Rt increased by 5.71%, 3.19%, 4.84%, and 24.82% in Hokkaido, Tokyo, Aichi, and Osaka, respectively, resulting in a total increase of 580 (95% confidence interval [CI], 213-954), 2,209 (95% CI, 1,230-3,201), 1,086 (95% CI, 478-1,686), and 5,211 (95% CI, 4,554-5,867) cases that were attributable to the impact of public holidays. Conclusion: Public holidays intensified the transmission of COVID-19, highlighting the importance of considering public holidays in designing appropriate public health and social measures in the future.
Language	English
Publishing date	2024-01-22
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2590698-7
ISSN	2092-7193 ; 2092-7193
ISSN (online)	2092-7193
ISSN	2092-7193
DOI	10.4178/epih.e2024025
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Estimating the effective reproduction number of COVID-19 from population-wide wastewater data: An application in Kagawa, Japan.

Okada, Yuta / Nishiura, Hiroshi

Infectious Disease Modelling

2024 Volume 9, Issue 3, Page(s) 645–656

Abstract: Although epidemiological surveillance of COVID-19 has been gradually downgraded globally, the transmission of COVID-19 continues. It is critical to quantify the transmission dynamics of COVID-19 using multiple datasets including wastewater virus ... ...

Abstract	Although epidemiological surveillance of COVID-19 has been gradually downgraded globally, the transmission of COVID-19 continues. It is critical to quantify the transmission dynamics of COVID-19 using multiple datasets including wastewater virus concentration data. Herein, we propose a comprehensive method for estimating the effective reproduction number using wastewater data. The wastewater virus concentration data, which were collected twice a week, were analyzed using daily COVID-19 incidence data obtained from Takamatsu, Japan between January 2022 and September 2022. We estimated the shedding load distribution (SLD) as a function of time since the date of infection, using a model employing the delay distribution, which is assumed to follow a gamma distribution, multiplied by a scaling factor. We also examined models that accounted for the temporal smoothness of viral load measurement data. The model that smoothed temporal patterns of viral load was the best fit model (WAIC = 2795.8), which yielded a mean estimated distribution of SLD of 3.46 days (95% CrI: 3.01-3.95 days). Using this SLD, we reconstructed the daily incidence, which enabled computation of the effective reproduction number. Using the best fit posterior draws of parameters directly, or as a prior distribution for subsequent analyses, we first used a model that assumed temporal smoothness of viral load concentrations in wastewater, as well as infection counts by date of infection. In the subsequent approach, we examined models that also incorporated weekly reported case counts as a proxy for weekly incidence reporting. Both approaches enabled estimations of the epidemic curve as well as the effective reproduction number from twice-weekly wastewater viral load data. Adding weekly case count data reduced the uncertainty of the effective reproduction number. We conclude that wastewater data are still a valuable source of information for inferring the transmission dynamics of COVID-19, and that inferential performance is enhanced when those data are combined with weekly incidence data.
Language	English
Publishing date	2024-04-03
Publishing country	China
Document type	Journal Article
ZDB-ID	3015225-2
ISSN	2468-0427 ; 2468-2152
ISSN (online)	2468-0427
ISSN	2468-2152
DOI	10.1016/j.idm.2024.03.006
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Article ; Online: Bayesian Modeling Method for an Observational Data Analysis.

Nishiura, Hiroshi

Internal medicine (Tokyo, Japan)

2020 Volume 59, Issue 21, Page(s) 2641–2642

MeSH term(s)	Bayes Theorem ; Data Analysis ; Humans ; Isoniazid ; Japan ; Latent Tuberculosis ; Markov Chains ; Monte Carlo Method ; Rifampin
Chemical Substances	Isoniazid (V83O1VOZ8L) ; Rifampin (VJT6J7R4TR)
Language	English
Publishing date	2020-07-14
Publishing country	Japan
Document type	Editorial ; Comment
ZDB-ID	32371-8
ISSN	1349-7235 ; 0021-5120 ; 0918-2918
ISSN (online)	1349-7235
ISSN	0021-5120 ; 0918-2918
DOI	10.2169/internalmedicine.4670-20
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Zs.A 240: Show issues

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Article: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess.

Nishiura, Hiroshi

Journal of clinical medicine

2020 Volume 9, Issue 3

Abstract: To understand the time-dependent risk of infection on a cruise ship, the Diamond Princess, I estimated the incidence of infection with novel coronavirus (COVID-19). The epidemic curve of a total of 199 confirmed cases was drawn, classifying individuals ... ...

Abstract	To understand the time-dependent risk of infection on a cruise ship, the Diamond Princess, I estimated the incidence of infection with novel coronavirus (COVID-19). The epidemic curve of a total of 199 confirmed cases was drawn, classifying individuals into passengers with and without close contact and crew members. A backcalculation method was employed to estimate the incidence of infection. The peak time of infection was seen for the time period from 2 to 4 February 2020, and the incidence has abruptly declined afterwards. The estimated number of new infections among passengers without close contact was very small from 5 February on which a movement restriction policy was imposed. Without the intervention from 5 February, it was predicted that the cumulative incidence with and without close contact would have been as large as 1373 (95% CI: 570, 2176) and 766 (95% CI: 587, 946) cases, respectively, while these were kept to be 102 and 47 cases, respectively. Based on an analysis of illness onset data on board, the risk of infection among passengers without close contact was considered to be very limited. Movement restriction greatly reduced the number of infections from 5 February onwards.
Keywords	covid19
Language	English
Publishing date	2020-02-29
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm9030657
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Article: [Grasping COVID-19 immune landscape in Japan].

Sasanami, Misaki / Nishiura, Hiroshi

Uirusu

2023 Volume 72, Issue 1, Page(s) 31–38

Abstract: COVID-19 vaccination commenced globally in December 2020. Japan launched its vaccination rollout on February 17, 2021 and commenced booster vaccination campaign on December 1, 2021. It has been crucial to grasp the immune landscape in the country in ... ...

Abstract	COVID-19 vaccination commenced globally in December 2020. Japan launched its vaccination rollout on February 17, 2021 and commenced booster vaccination campaign on December 1, 2021. It has been crucial to grasp the immune landscape in the country in order to aid in decision-making and evaluation of vaccination campaigns as well as understating the transmission dynamics of various variants of SARS-CoV-2. The present article shows a framework that enables us to predict the immune landscape, specifically, the proportion of immune population, using a mathematical modeling approach. This involved: prediction of vaccine coverage; estimation of vaccine effectiveness against the dominant SARS-CoV-2 variant in circulation; the quantification of increasing vaccine effectiveness (immune-build up) since receiving the first dose; the estimation of waning rate of vaccine effectiveness since receiving the second and third doses; and the consideration on the infection-induced immunity.
Language	Japanese
Publishing date	2023-10-27
Publishing country	Japan
Document type	English Abstract ; Journal Article
ZDB-ID	603272-2
ISSN	0042-6857
ISSN	0042-6857
DOI	10.2222/jsv.72.31
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Zs.A 266: Show issues

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Article ; Online: Estimating infection fatality risk and ascertainment bias of COVID-19 in Osaka, Japan from February 2020 to January 2022.

Zhang, Tong / Nishiura, Hiroshi

Scientific reports

2023 Volume 13, Issue 1, Page(s) 5540

Abstract: The present study aimed to estimate the infection fatality risk (IFR) and ascertainment bias of SARS-CoV-2 for six epidemic waves in Japan from February 2020 to January 2022. We used two types of datasets: (i) surveillance-based datasets containing the ... ...

Abstract	The present study aimed to estimate the infection fatality risk (IFR) and ascertainment bias of SARS-CoV-2 for six epidemic waves in Japan from February 2020 to January 2022. We used two types of datasets: (i) surveillance-based datasets containing the cumulative numbers of confirmed cases and deaths in each epidemic wave and (ii) seroepidemiological datasets conducted in a serial cross-sectional manner. Smoothing spline function was employed to reconstruct the age-specific cumulative incidence of infection. We found that IFR was highest during the first wave, and the second highest during the fourth wave, caused by the Alpha variant. Once vaccination became widespread, IFR decreased considerably among adults aged 40 years plus during the fifth wave caused by the Delta variant, although the epidemic size of fifth wave was the largest before the Omicron variant emerged. We also found that ascertainment bias was relatively high during the first and second waves and, notably, RT-PCR testing capacity during these early periods was limited. Improvements in the ascertainment were seen during the third and fourth waves. Once the Omicron variant began spreading, IFR diminished while ascertainment bias was considerably elevated.
MeSH term(s)	Adult ; Humans ; COVID-19/epidemiology ; Japan/epidemiology ; Cross-Sectional Studies ; SARS-CoV-2
Language	English
Publishing date	2023-04-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-32639-9
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Article ; Online: Combined effect of early diagnosis and treatment on the case fatality risk of COVID-19 in Japan, 2020.

Amemiya, Yuri / Nishiura, Hiroshi

Scientific reports

2023 Volume 13, Issue 1, Page(s) 6679

Abstract: Japanese government initially enforced restrictions on outpatient attendances among febrile individuals suspected of having COVID-19, asking everyone to remain at home for at least 4 days from the onset of fever. This restriction was cancelled on 8 May ... ...

Abstract	Japanese government initially enforced restrictions on outpatient attendances among febrile individuals suspected of having COVID-19, asking everyone to remain at home for at least 4 days from the onset of fever. This restriction was cancelled on 8 May 2020, and a new antiviral, remdesivir, was approved from 7 May 2020. To investigate how this policy change influenced the prognosis of people with COVID-19, we estimated the case fatality risk as a function of the date of illness onset from April to June 2020. We used an interrupted time-series analysis model with an intervention date of 8 May 2020, and estimated time-dependent case fatality risk by age group. The case fatality risk showed a decreasing trend in all groups, and models were favored accounting for an abrupt causal effect, i.e., immediate decline in fatality risk. The trend was estimated at - 1.1% (95% CI [confidence interval]: - 3.9, 3.0) among people aged 60-69 years, - 7.2% (95% CI - 11.2, - 2.4) among those aged 70-79 years, - 7.4% (95% CI - 14.2, 0.2) among those aged 80-89 years, and - 10.3% (95% CI - 21.1, 2.7) among those aged 90 and over. Early diagnosis and treatment greatly contributed to reducing the case fatality risk.
MeSH term(s)	Humans ; COVID-19 ; Japan ; Prognosis ; Early Diagnosis ; Interrupted Time Series Analysis ; COVID-19 Testing
Language	English
Publishing date	2023-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-33929-y
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Article ; Online: Assessing the COVID-19 vaccination program during the Omicron variant (B.1.1.529) epidemic in early 2022, Tokyo.

Kayano, Taishi / Nishiura, Hiroshi

BMC infectious diseases

2023 Volume 23, Issue 1, Page(s) 748

Abstract: Background: Many countries, including high-income nations, struggled to control epidemic waves caused by the Omicron variant (B.1.1.529), which had an antigenically distinct evolution. Evaluating the direct and indirect effects of vaccination during the ...

Abstract	Background: Many countries, including high-income nations, struggled to control epidemic waves caused by the Omicron variant (B.1.1.529), which had an antigenically distinct evolution. Evaluating the direct and indirect effects of vaccination during the Omicron waves is essential to assess virus control policies. The present study assessed the population impacts of a vaccination program during the sixth wave caused by BA.1 and BA.2 from January to May 2022, in Tokyo. Methods: We analyzed the primary series and booster vaccination coverages and the confirmed cases stratified by vaccination history. We estimated the number of COVID-19 cases that were directly and indirectly prevented by vaccination. To estimate the direct impact, we used a statistical model that compared risks between unvaccinated and vaccinated individuals. A transmission model employing the renewal process was devised to quantify the total effect, given as the sum of the direct and indirect effects. Results: Assuming that the reporting coverage of cases was 25%, mass vaccination programs, including primary and booster immunizations, directly averted 640,000 COVID-19 cases (95% confidence interval: 624-655). Furthermore, these programs directly and indirectly prevented 8.5 million infections (95% confidence interval: 8.4-8.6). Hypothetical scenarios indicated that we could have expected a 19% or 7% relative reduction in the number of infections, respectively, compared with the observed number of infections, if the booster coverage had been equivalent to that of the second dose or if coverage among people aged 10-49 years had been 10% higher. If the third dose coverage was smaller and comparable to that of the fourth dose, the total number of infections would have increased by 52% compared with the observed number of infections. Conclusions: The population benefit of vaccination via direct and indirect effects was substantial, with an estimated 65% reduction in the number of SARS-CoV-2 infections compared with counterfactual (without vaccination) in Tokyo during the sixth wave caused by BA.1 and BA.2.
MeSH term(s)	Humans ; Tokyo/epidemiology ; COVID-19 Vaccines ; COVID-19/epidemiology ; COVID-19/prevention & control ; SARS-CoV-2 ; Vaccination ; Mass Vaccination
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2023-10-31
Publishing country	England
Document type	Journal Article
ZDB-ID	2041550-3
ISSN	1471-2334 ; 1471-2334
ISSN (online)	1471-2334
ISSN	1471-2334
DOI	10.1186/s12879-023-08748-1
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Article ; Online: Decomposing mechanisms of COVID-19 mortality in empirical datasets: A modeling study.

Zhang, Tong / Qiao, Jiaying / Hayashi, Katsuma / Nishiura, Hiroshi

Journal of theoretical biology

2024 Volume 584, Page(s) 111771

Abstract: Our objective was to decompose mortality mechanisms during the coronavirus disease 2019 (COVID-19) pandemic to estimate direct, indirect, and associated deaths from COVID-19. Given the confirmatory diagnosis of COVID-19, a death event that was not ... ...

Abstract	Our objective was to decompose mortality mechanisms during the coronavirus disease 2019 (COVID-19) pandemic to estimate direct, indirect, and associated deaths from COVID-19. Given the confirmatory diagnosis of COVID-19, a death event that was not necessarily caused by respiratory complications but stemmed from other complications was categorized as an indirect death from COVID-19. Associated deaths occurred in patients who did not have COVID-19 but died during the surge in COVID-19 cases when overwhelming pressure was exerted on the healthcare system. Analyzing the sixth wave (i.e., the first epidemic wave of the Omicron B.1.1.529 variant from January to May 2022), decomposition was achieved using the binomial and Poisson sampling process models fitted to two pieces of data (i.e., COVID-19 death certificate and excess data by major cause of death). The total numbers of direct, indirect, and associated deaths during the sixth wave in Osaka were estimated at 1,071; 948; and 2,157; respectively. The number of associated deaths was greater than the sum of direct and indirect deaths. We further observed that the composition of indirect and associated deaths differed by major cause of death, and deaths caused by circulatory disease included a greater proportion of indirect deaths compared with deaths by other causes. The goals of healthcare services for endemic COVID-19 include the sustainable provision of services to avoid preventable deaths. Therefore, gaining an in-depth understanding of mechanisms that lead to excess death is vital for improving future pandemic response efforts.
MeSH term(s)	Humans ; COVID-19 ; Pandemics ; Seizures ; Mortality
Language	English
Publishing date	2024-03-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2972-5
ISSN	1095-8541 ; 0022-5193
ISSN (online)	1095-8541
ISSN	0022-5193
DOI	10.1016/j.jtbi.2024.111771
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Zs.A 923: Show issues

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Article ; Online: Identifying the population susceptible to rubella in Japan, 2020: Fine-scale risk mapping.

Kinoshita, Ryo / Arai, Satoru / Suzuki, Motoi / Nishiura, Hiroshi

Journal of infection and public health

2024 Volume 17, Issue 6, Page(s) 947–955

Abstract: Background: Rubella remains a public health challenge in Japan, impeding the attainment of herd immunity. Despite vaccination efforts since 1976, persistent outbreaks reveal a susceptibility gap in male adults born before 1995. Seroepidemiological ... ...

Abstract	Background: Rubella remains a public health challenge in Japan, impeding the attainment of herd immunity. Despite vaccination efforts since 1976, persistent outbreaks reveal a susceptibility gap in male adults born before 1995. Seroepidemiological surveys are pivotal in evaluating population immunity and identifying at-risk groups. Methods: This study aims to pinpoint high-risk areas for potential rubella outbreaks in Japan by merging seroepidemiological data from 2020 with population census information. Various data sources, including spatial demographic data, reported rubella and congenital rubella syndrome (CRS) cases, and traveler lodging statistics, were employed. Geospatial information for Japan's 230,300 small geographic areas was analyzed, and HI (hemagglutination inhibition) titers were examined by age and sex. Seroconversion was defined as an HI titer ≥ 1:32 or 1:16, indicating protective immunity. Geospatial maps illustrated the distribution of susceptible individuals per square kilometer, emphasizing high-risk urban areas like Tokyo and Osaka. Demographic shifts in the working-age population were assessed. Results: Susceptible individuals cluster in densely populated urban centers, persisting despite demographic changes. The study highlights areas at risk of increased susceptibility, particularly with an HI titer cut-off of 1:16. Foreign travelers pose potential rubella importation risks as travel volume to Japan rises. To prevent epidemics and congenital rubella syndrome burden, achieving and sustaining herd immunity in high-risk areas is crucial. Conclusions: This study offers a comprehensive assessment of vulnerability in densely populated Japanese regions. Integrating population statistics with seroepidemiological data enhances our understanding of population immunity, guiding resource allocation for supplementary vaccination planning. To avert rubella epidemics, high-risk locations must bolster indirect protection through herd immunity, ultimately preventing congenital rubella syndrome.
Language	English
Publishing date	2024-03-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2467587-8
ISSN	1876-035X ; 1876-0341
ISSN (online)	1876-035X
ISSN	1876-0341
DOI	10.1016/j.jiph.2024.03.029
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