Few studies have assessed incubation periods of the severe acute respiratory syndrome coronavirus 2 Delta variant. This study aimed to elucidate the transmission dynamics, especially the incubation period, for the Delta variant compared with non-Delta strains. We studied unvaccinated coronavirus disease 2019 patients with definite single exposure date from August 2020 to September 2021 in Japan. The incubation periods were calculated and compared by Mann–Whitney U test for Delta (with L452R mutation) and non-Delta cases. We estimated mean and percentiles of incubation period by fitting parametric distribution to data in the Bayesian statistical framework. We enrolled 214 patients (121 Delta and 103 non-Delta cases) with one specific date of exposure to the virus. The mean incubation period was 3.7 days and 4.9 days for Delta and non-Delta cases, respectively (p-value = 0.000). When lognormal distributions were fitted, the estimated mean incubation periods were 3.7 (95% credible interval (CI) 3.4–4.0) and 5.0 (95% CI 4.5–5.6) days for Delta and non-Delta cases, respectively. The estimated 97.5th percentile of incubation period was 6.9 (95% CI 5.9–8.0) days and 10.4 (95% CI 8.6–12.7) days for Delta and non–Delta cases, respectively. Unvaccinated Delta variant cases had shorter incubation periods than non–Delta variant cases.

Household secondary attack rate (HSAR) by risk factor might have a higher transmission rate between spouses. We investigated risk factors for the HSAR among non-spousal household contacts of patients with coronavirus disease 2019 (COVID-19). We studied household contacts of index cases of COVID-19 in Tsuchiura, Japan, from August 2020 through February 2021. The HSARs of the whole household contacts and non-spousal household contacts were calculated and compared across risk factors. We used a generalized linear mixed regression model for multivariate analysis. We enrolled 496 household contacts of 236 index COVID-19 cases. The HSAR was higher for spousal household contacts (37.8%) than for other contacts (21.2%). The HSAR was lower for non-spousal household contacts with a household size (number of household members) of two (18.2%), compared to the HSAR for contacts with a household size ≥4. The HSAR was higher for non-spousal household contacts of index patients with ≥3 days of diagnostic delay (period between onset and diagnosis) (26.0%) compared to those with ≤2 days’ delay (12.5%) (p = 0.033). Among non-spousal household contacts, the HSAR was low for those with a household size of two and was high for contacts of index patients with a long diagnostic delay.

To assess temporal changes to the risk of death in COVID-19 cases caused by the Omicron variant, we calculated age-standardized case fatality rates (CFR) in patients aged ≥40 years over nine diagnostic periods (3 January to 28 August 2022) in ten Japanese prefectures (14.8 million residents). Among 552,581 study subjects, we found that there were 1836 fatalities during the isolation period (up to 28 days from date of onset). The highest age-standardized CFR (0.85%, 95% confidence interval (CI):0.78–0.92) was observed in cases diagnosed in the second 4-week period (January 31 to February 27), after which it declined significantly up to the 6th 4-week period (0.23%, 95% CI: 0.13–0.33, May 23 to June 19). The CFR then increased again but remained at 0.39% in the eighth period (July 18 to August 28). The CFR in cases with the BA.2 or BA.5 sublineages in the age range 60–80 years was significantly lower than that with BA.1 infections (60 years: 0.19%, 0.02%, 0.053%, respectively; 70 years: 0.91%, 0.33%, 0.39%; ≥80 years: 3.78%, 1.96%, 1.81%, respectively). We conclude that the risk of death in Japanese COVID-19 patients infected with Omicron variants declined through February to mid-June 2022.

Background: Residents of facilities for older people are vulnerable to COVID-19 outbreaks. Nevertheless, timely recognition of outbreaks at facilities for older people at public health centers has been impossible in Japan since May 8, 2023, when the Japanese government discontinued aggressive countermeasures against COVID-19 because of the waning severity of the dominant Omicron strain. The Facility for Elderly Surveillance System (FESSy) has been developed to improve information collection. Objective: This study examined FESSy experiences and effectiveness in two public health center jurisdictions in Japan. Methods: This study assessed the use by public health centers of the detection mode of an automated AI detection system (ie, FESSy AI), as well as manual detection by the public health centers’ staff (ie, FESSy staff) and direct reporting by facilities to the public health centers. We considered the following aspects: (1) diagnoses or symptoms, (2) numbers of patients as of their detection date, and (3) ultimate numbers of patients involved in incidents. Subsequently, effectiveness was assessed and compared based on detection modes. The study lasted from June 1, 2023, through January 2024. Results: In both areas, this study examined 31 facilities at which 87 incidents were detected. FESSy (AI or staff) detected significantly fewer patients than non-FESSy methods, that is, direct reporting to the public health center of the detection date and ultimate number of patients. Conclusions: FESSy was superior to direct reporting from facilities for the number of patients as of the detection date and for the ultimate outbreak size.

Introduction and Aims: Change in estimated GFR (eGFR) is frequently used to track CKD progression in clinical practice, trials and cohort studies but its association with mortality has not been studied extensively.