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1.
J Med Virol ; 2021 Dec 30.
Article in English | MEDLINE | ID: covidwho-1589015

ABSTRACT

The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become widespread across the world in a flashing manner. As of December 7, 2021, a total of 758 Omicron cases were confirmed in Denmark. Using the nucleotide sequences of the Delta and Omicron variants registered from Denmark in the GISAID database, we found that the effective (instantaneous) reproduction number of Omicron is 3.19 (95% confidence interval [CI]: 2.82-3.61) times greater than that of Delta under the same epidemiological conditions. The proportion of Omicron infections among all SARS-CoV-2 infections in Denmark was expected to exceed 95% on December 28, 2021, with a 95% CI from December 25 to December 31, 2021. Given that the Delta variant or variants less transmissible than Delta are dominant in most countries, the rapid increase in Omicron in the virus population may be observed as soon as the Omicron is introduced. Preparing proactive control measures is vital, assuming the substantial advantage of the transmission by Omicron.

2.
J Clin Med ; 11(1)2021 Dec 23.
Article in English | MEDLINE | ID: covidwho-1580657

ABSTRACT

The world identified the rapidly increasing incidence of the causative variant of SARS-CoV-2 Pangolin B [...].

3.
Int J Infect Dis ; 115: 109-115, 2021 Dec 10.
Article in English | MEDLINE | ID: covidwho-1560960

ABSTRACT

BACKGROUND: Following an outbreak of coronavirus disease 2019 (COVID-19) on the cruise ship Diamond Princess, passengers and crew were followed-up to determine prognosis. This study examined the epidemiological determinants of COVID-19 natural history using these follow-up data. METHODS: Infection status, diagnosis, clinical symptoms and prognosis were analysed for all passengers and crew members on the Diamond Princess. In addition, the risk of infection associated with exposure within cabin rooms, as well as the risks of various clinical manifestations of disease, along with their epidemiological determinants, were analysed. RESULTS: The adjusted odds ratio (aOR) of infection for individuals tested by polymerase chain reaction on or after 12 February 2020 compared with individuals tested before this date was 0.53 [95% confidence interval (CI) 0.39-0.72], reflecting decreased transmission during onboard quarantine. Among infected individuals, older age was associated with elevated odds of symptomatic illness (aOR 1.01, 95% CI 1.00-1.02), severe disease (aOR 1.08, 95% CI 1.05-1.12) and death (aOR 1.12, 95% CI 1.05-1.21). CONCLUSIONS: Severe COVID-19 disease, death and symptomatic illness were more frequent among older individuals on the Diamond Princess. Older elderly cases (age ≥80 years) had the highest risks of severe disease and death. Inter-room transmission was prevented successfully by the onboard quarantine.

4.
Preprint in English | Other preprints | ID: ppcovidwho-295724

ABSTRACT

The B.1.1.7 strain, also referred to as Alpha variant, is a variant strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Alpha variant is considered to possess higher transmissibility compared to the strains previously circulating in England. This paper proposes a new method to estimate the selective advantage of a mutant strain over another strain using the time course of strain frequencies and the distribution of the serial interval of infections. This method allows the instantaneous reproduction numbers of infections to vary over calendar time. The proposed method also assumes that the selective advantage of a mutant strain over previously circulating strains is constant. Applying the method to SARS-CoV-2 sequence data from England, the instantaneous reproduction number of the B.1.1.7 strain was estimated to be 26.6-45.9% higher than previously circulating strains in England. This result indicates that control measures should be strengthened by 26.6-45.9% when the B.1.1.7 strain is newly introduced to a country where viruses with similar transmissibility to the preexisting strain in England are predominant.

5.
Math Biosci Eng ; 18(6): 9685-9696, 2021 11 04.
Article in English | MEDLINE | ID: covidwho-1526882

ABSTRACT

The Tokyo 2020 Olympic and Paralympic Games represent the most diverse international mass gathering event held since the start of the coronavirus disease 2019 (COVID-19) pandemic. Postponed to summer 2021, the rescheduled Games were set to be held amidst what would become the highest-ever levels of COVID-19 transmission in the host city of Tokyo. At the same time, the Delta variant of concern was gaining traction as the dominant viral strain and Japan had yet to exceed fifteen percent of its population fully vaccinated against COVID-19. To quantify the potential number of secondary cases that might arise during the Olympic Games, we performed a scenario analysis using a multitype branching process model. We considered the different contributions to transmission of Games accredited individuals, the general Tokyo population, and domestic spectators. In doing so, we demonstrate how transmission might evolve in these different groups over time, cautioning against any loosening of infection prevention protocols and supporting the decision to ban all spectators. If prevention measures were well observed, we estimated that the number of new cases among Games accredited individuals would approach zero by the end of the Games. However, if transmission was not controlled our model indicated hundreds of Games accredited individuals would become infected and daily incidence in Tokyo would reach upwards of 4,000 cases. Had domestic spectators been allowed (at 50% venue capacity), we estimated that over 250 spectators might have arrived infected to Tokyo venues, potentially generating more than 300 additional secondary infections while in Tokyo/at the Games. We also found the number of cases with infection directly attributable to hypothetical exposure during the Games was highly sensitive to the local epidemic dynamics. Therefore, reducing and maintaining transmission levels below epidemic levels using public health measures would be necessary to prevent cross-group transmission.

6.
Emerg Infect Dis ; 27(10): 1-9, 2021 10.
Article in English | MEDLINE | ID: covidwho-1486730

ABSTRACT

To deal with the risk of emerging diseases with many unknowns, close and timely collaboration and communication between science experts and policymakers are crucial to developing and implementing an effective science-based intervention strategy. The Expert Meeting, an ad hoc medical advisory body, was established in February 2020 to advise Japan's COVID-19 Response Headquarters. The group played an important role in the policymaking process, promoting timely situation awareness and developing science-based proposals on interventions that were promptly reflected in government actions. However, this expert group may have been overly proactive in taking on the government's role in crisis management. For the next stage of managing the coronavirus disease pandemic and future pandemics, the respective roles of the government and its advisory bodies need to be clearly defined. Leadership and strategic risk communication by the government are key.


Subject(s)
COVID-19 , Government , Humans , Japan/epidemiology , Pandemics , SARS-CoV-2
7.
Int J Infect Dis ; 113: 47-54, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1458656

ABSTRACT

OBJECTIVES: The effective reproduction number (Rt) has been critical for assessing the effectiveness of countermeasures during the coronavirus disease 2019 (COVID-19) pandemic. Conventional methods using reported incidences are unable to provide timely Rt data due to the delay from infection to reporting. Our study aimed to develop a framework for predicting Rt in real time, using timely accessible data - i.e. human mobility, temperature, and risk awareness. METHODS: A linear regression model to predict Rt was designed and embedded in the renewal process. Four prefectures of Japan with high incidences in the first wave were selected for model fitting and validation. Predictive performance was assessed by comparing the observed and predicted incidences using cross-validation, and by testing on a separate dataset in two other prefectures with distinct geographical settings from the four studied prefectures. RESULTS: The predicted mean values of Rt and 95% uncertainty intervals followed the overall trends for incidence, while predictive performance was diminished when Rt changed abruptly, potentially due to superspreading events or when stringent countermeasures were implemented. CONCLUSIONS: The described model can potentially be used for monitoring the transmission dynamics of COVID-19 ahead of the formal estimates, subject to delay, providing essential information for timely planning and assessment of countermeasures.

8.
Theor Biol Med Model ; 18(1): 13, 2021 07 17.
Article in English | MEDLINE | ID: covidwho-1403242

ABSTRACT

BACKGROUND: In Japan, a part of confirmed patients' samples have been screened for the variant of concern (VOC), including the variant alpha with N501Y mutation. The present study aimed to estimate the actual number of cases with variant alpha and reconstruct the epidemiological dynamics. METHODS: The number of cases with variant alpha out of all PCR confirmed cases was estimated, employing a hypergeometric distribution. An exponential growth model was fitted to the growth data of variant alpha cases over fourteen weeks in Tokyo. RESULTS: The weekly incidence with variant alpha from 18-24 January 2021 was estimated at 4.2 (95% confidence interval (CI): 0.7, 44.0) cases. The expected incidence in early May ranged from 420-1120 cases per week, and the reproduction number of variant alpha was on the order of 1.5 even under the restriction of contact from January-March, 2021, Tokyo. CONCLUSIONS: The variant alpha was predicted to swiftly dominate COVID-19 cases in Tokyo, and this has actually occurred by May 2021. Devising the proposed method, any country or location can interpret the virological sampling data.


Subject(s)
COVID-19 , Humans , Japan/epidemiology , SARS-CoV-2 , Tokyo/epidemiology
9.
Theor Biol Med Model ; 18(1): 12, 2021 07 16.
Article in English | MEDLINE | ID: covidwho-1314267

ABSTRACT

BACKGROUND: Individuals with asymptomatic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can propagate the virus unknowingly and thus have been a focus of public health attentions since the early stages of the pandemic. Understanding viral transmissibility among asymptomatic individuals is critical for successful control of coronavirus disease 2019 (COVID-19). The present study aimed to understand SARS-CoV-2 transmissibility among young asymptomatic individuals and to assess whether symptomatology was associated with transmission of symptomatic vs. asymptomatic infections. METHODS: We analyzed one of the first-identified clusters of SARS-CoV-2 infections with multiple chains of transmission that occurred among university students in March 2020 in Kyoto prefecture, Japan, using discrete and two-type branching process models. Assuming that the number of secondary cases resulting from either primary symptomatic or asymptomatic cases independently followed negative binomial distributions, we estimated the relative reproduction numbers of an asymptomatic case compared with a symptomatic case. To explore the potential association between symptomatology and transmission of symptomatic vs. asymptomatic incident infections, we also estimated the proportion of secondary symptomatic cases produced by primary symptomatic and asymptomatic cases. RESULTS: The reproduction number for a symptomatic primary case was estimated at 1.14 (95% confidence interval [CI]: 0.61-2.09). The relative reproduction number for asymptomatic cases was estimated at 0.19 (95% CI: 0.03-0.66), indicating that asymptomatic primary cases did not result in sufficient numbers of secondary infections to maintain chains of transmission. There was no apparent tendency for symptomatic primary cases to preferentially produce symptomatic secondary cases. CONCLUSIONS: Using data from a transmission network during the early epidemic in Japan, we successfully estimated the relative transmissibility of asymptomatic cases of SARS-CoV-2 infection at 0.22. These results suggest that contract tracing focusing on symptomatic index cases may be justified given limited testing capacity.


Subject(s)
COVID-19 , Contact Tracing , Humans , Japan/epidemiology , Pandemics , SARS-CoV-2
10.
Euro Surveill ; 26(27)2021 07.
Article in English | MEDLINE | ID: covidwho-1304571

ABSTRACT

Using numbers of SARS-CoV-2 variants detected in Japan as at 13 June 2021, relative instantaneous reproduction numbers (RRI) of the R.1, Alpha, and Delta variants with respect to other strains circulating in Japan were estimated at 1.25, 1.44, and 1.95. Depending on the assumed serial interval distributions, RRI varies from 1.20-1.32 for R.1, 1.34-1.58 for Alpha, and 1.70-2.30 for Delta. The frequency of Delta is expected to take over Alpha in Japan before 23 July 2021.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Japan/epidemiology , Tokyo
11.
Lancet Reg Health West Pac ; 3: 100016, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-1281486

ABSTRACT

Background: On April 7, 2020, the Japanese government declared a state of emergency regarding the novel coronavirus (COVID-19). Given the nation-wide spread of the coronavirus in major Japanese cities and the rapid increase in the number of cases with untraceable infection routes, large-scale monitoring for capturing the current epidemiological situation of COVID-19 in Japan is urgently required. Methods: A chatbot-based healthcare system named COOPERA (COvid-19: Operation for Personalized Empowerment to Render smart prevention And AN care seeking) was developed to surveil the Japanese epidemiological situation in real-time. COOPERA asked questions regarding personal information, location, preventive actions, COVID-19 related symptoms and their residence. Empirical Bayes estimates of the age-sex-standardized incidence rate and disease mapping approach using scan statistics were utilized to identify the geographical distribution of the symptoms in Tokyo and their spatial correlation r with the identified COVID-19 cases. Findings: We analyzed 353,010 participants from Tokyo recruited from 27th March to 6th April 2020. The mean (SD) age of participants was 42.7 (12.3), and 63.4%, 36.4% or 0.2% were female, male, or others, respectively. 95.6% of participants had no subjective symptoms. We identified several geographical clusters with high spatial correlation (r = 0.9), especially in downtown areas in central Tokyo such as Shibuya and Shinjuku. Interpretation: With the global spread of COVID-19, medical resources are being depleted. A new system to monitor the epidemiological situation, COOPERA, can provide insights to assist political decision to tackle the epidemic. In addition, given that Japan has not had a strong lockdown policy to weaken the spread of the infection, our result would be useful for preparing for the second wave in other countries during the next flu season without a strong lockdown. Funding: The present work was supported in part by a grant from the Ministry of Health, Labour and Welfare of Japan (H29-Gantaisaku-ippan-009).

12.
J Clin Med ; 10(11)2021 May 28.
Article in English | MEDLINE | ID: covidwho-1256586

ABSTRACT

Following the first report of the coronavirus disease 2019 (COVID-19) in Sapporo city, Hokkaido Prefecture, Japan, on 14 February 2020, a surge of cases was observed in Hokkaido during February and March. As of 6 March, 90 cases were diagnosed in Hokkaido. Unfortunately, many infected persons may not have been recognized due to having mild or no symptoms during the initial months of the outbreak. We therefore aimed to predict the actual number of COVID-19 cases in (i) Hokkaido Prefecture and (ii) Sapporo city using data on cases diagnosed outside these areas. Two statistical frameworks involving a balance equation and an extrapolated linear regression model with a negative binomial link were used for deriving both estimates, respectively. The estimated cumulative incidence in Hokkaido as of 27 February was 2,297 cases (95% confidence interval (CI): 382-7091) based on data on travelers outbound from Hokkaido. The cumulative incidence in Sapporo city as of 28 February was estimated at 2233 cases (95% CI: 0-4893) based on the count of confirmed cases within Hokkaido. Both approaches resulted in similar estimates, indicating a higher incidence of infections in Hokkaido than were detected by the surveillance system. This quantification of the gap between detected and estimated cases helped to inform the public health response at the beginning of the pandemic and provided insight into the possible scope of undetected transmission for future assessments.

13.
JMIR Mhealth Uhealth ; 9(5): e27342, 2021 05 11.
Article in English | MEDLINE | ID: covidwho-1223830

ABSTRACT

BACKGROUND: During the second wave of COVID-19 in August 2020, the Tokyo Metropolitan Government implemented public health and social measures to reduce on-site dining. Assessing the associations between human behavior, infection, and social measures is essential to understand achievable reductions in cases and identify the factors driving changes in social dynamics. OBJECTIVE: The aim of this study was to investigate the association between nighttime population volumes, the COVID-19 epidemic, and the implementation of public health and social measures in Tokyo. METHODS: We used mobile phone location data to estimate populations between 10 PM and midnight in seven Tokyo metropolitan areas. Mobile phone trajectories were used to distinguish and extract on-site dining from stay-at-work and stay-at-home behaviors. Numbers of new cases and symptom onsets were obtained. Weekly mobility and infection data from March 1 to November 14, 2020, were analyzed using a vector autoregression model. RESULTS: An increase in the number of symptom onsets was observed 1 week after the nighttime population volume increased (coefficient=0.60, 95% CI 0.28 to 0.92). The effective reproduction number significantly increased 3 weeks after the nighttime population volume increased (coefficient=1.30, 95% CI 0.72 to 1.89). The nighttime population volume increased significantly following reports of decreasing numbers of confirmed cases (coefficient=-0.44, 95% CI -0.73 to -0.15). Implementation of social measures to restaurants and bars was not significantly associated with nighttime population volume (coefficient=0.004, 95% CI -0.07 to 0.08). CONCLUSIONS: The nighttime population started to increase after decreasing incidence of COVID-19 was announced. Considering time lags between infection and behavior changes, social measures should be planned in advance of the surge of an epidemic, sufficiently informed by mobility data.


Subject(s)
COVID-19 , Cell Phone , Humans , Pandemics , SARS-CoV-2 , Tokyo/epidemiology
14.
R Soc Open Sci ; 8(3): 202169, 2021 Mar 31.
Article in English | MEDLINE | ID: covidwho-1199604

ABSTRACT

An initial set of interventions, including the closure of host and hostess clubs and voluntary limitation of non-household contact, probably greatly contributed to reducing the disease incidence of coronavirus disease (COVID-19) in Japan, but this approach must eventually be replaced by a more sustainable strategy. To characterize such a possible exit strategy from the restrictive guidelines, we quantified the next-generation matrix, accounting for high- and low-risk transmission settings. This matrix was used to project the future incidence in Tokyo and Osaka after the state of emergency is lifted, presenting multiple 'post-emergency' scenarios with different levels of restriction. The effective reproduction numbers (R) for the increasing phase, the transition phase and the state-of-emergency phase in the first wave of the disease were estimated as 1.78 (95% credible interval (CrI): 1.73-1.82), 0.74 (95% CrI: 0.71-0.78) and 0.63 (95% CrI: 0.61-0.65), respectively, in Tokyo and as 1.58 (95% CrI: 1.51-1.64), 1.20 (95% CrI: 1.15-1.25) and 0.48 (95% CrI: 0.44-0.51), respectively, in Osaka. Projections showed that a 50% decrease in the high-risk transmission is required to keep R less than 1 in both locations-a level necessary to maintain control of the epidemic and minimize the risk of resurgence.

15.
J Epidemiol ; 31(6): 387-391, 2021 06 05.
Article in English | MEDLINE | ID: covidwho-1170044

ABSTRACT

BACKGROUND: As the COVID-19 pandemic spread, the Japanese government declared a state of emergency on April 7, 2020 for seven prefectures, and on April 16, 2020 for all prefectures. The Japanese Prime Minister and governors requested people to adopt self-restraint behaviors, including working from home and refraining from visiting nightlife spots. However, the effectiveness of the mobility change due to such requests in reducing the spread of COVID-19 has been little investigated. The present study examined the association of the mobility change in working, nightlife, and residential places and the COVID-19 outbreaks in Tokyo, Osaka, and Nagoya metropolitan areas in Japan. METHODS: First, we calculated the daily mobility change in working, nightlife, and residential places compared to the mobility before the outbreak using mobile device data. Second, we estimated the sensitivity of mobility changes to the reproduction number by generalized least squares. RESULTS: Mobility change had already started in March, 2020. However, mobility reduction in nightlife places was particularly significant due to the state of emergency declaration. Although the mobility in each place type was associated with the COVID-19 outbreak, the mobility changes in nightlife places were more significantly associated with the outbreak than those in the other place types. There were regional differences in intensity of sensitivity among each metropolitan area. CONCLUSIONS: Our findings indicated the effectiveness of the mobility changes, particularly in nightlife places, in reducing the outbreak of COVID-19.


Subject(s)
COVID-19/prevention & control , Cell Phone , Communicable Disease Control , Travel/statistics & numerical data , COVID-19/epidemiology , Disease Outbreaks/statistics & numerical data , Geographic Information Systems , Humans , Japan/epidemiology , Pandemics/prevention & control , Physical Distancing , SARS-CoV-2 , Travel/trends
16.
J Clin Med ; 10(6)2021 Mar 18.
Article in English | MEDLINE | ID: covidwho-1158379

ABSTRACT

Estimation of the effective reproduction number, R(t), of coronavirus disease (COVID-19) in real-time is a continuing challenge. R(t) reflects the epidemic dynamics based on readily available illness onset data, and is useful for the planning and implementation of public health and social measures. In the present study, we proposed a method for computing the R(t) of COVID-19, and applied this method to the epidemic in Osaka prefecture from February to September 2020. We estimated R(t) as a function of the time of infection using the date of illness onset. The epidemic in Osaka came under control around 2 April during the first wave, and 26 July during the second wave. R(t) did not decline drastically following any single intervention. However, when multiple interventions were combined, the relative reductions in R(t) during the first and second waves were 70% and 51%, respectively. Although the second wave was brought under control without declaring a state of emergency, our model comparison indicated that relying on a single intervention would not be sufficient to reduce R(t) < 1. The outcome of the COVID-19 pandemic continues to rely on political leadership to swiftly design and implement combined interventions capable of broadly and appropriately reducing contacts.

17.
Epidemics ; 35: 100454, 2021 06.
Article in English | MEDLINE | ID: covidwho-1135321

ABSTRACT

The incubation period, or the time from infection to symptom onset, of COVID-19 has usually been estimated by using data collected through interviews with cases and their contacts. However, this estimation is influenced by uncertainty in the cases' recall of exposure time. We propose a novel method that uses viral load data collected over time since hospitalization, hindcasting the timing of infection with a mathematical model for viral dynamics. As an example, we used reported data on viral load for 30 hospitalized patients from multiple countries (Singapore, China, Germany, and Korea) and estimated the incubation period. The median, 2.5, and 97.5 percentiles of the incubation period were 5.85 days (95 % CI: 5.05, 6.77), 2.65 days (2.04, 3.41), and 12.99 days (9.98, 16.79), respectively, which are comparable to the values estimated in previous studies. Using viral load to estimate the incubation period might be a useful approach, especially when it is impractical to directly observe the infection event.


Subject(s)
COVID-19/transmission , Infectious Disease Incubation Period , Viral Load/statistics & numerical data , Adult , COVID-19/virology , China , Hospitalization , Humans , Male , Models, Theoretical , SARS-CoV-2
18.
Journal of Clinical and Experimental Medicine ; 276(1):20-24, 2021.
Article in Japanese | WHO COVID | ID: covidwho-1124080
19.
Int J Infect Dis ; 105: 286-292, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1116858

ABSTRACT

OBJECTIVES: End-of-outbreak declarations are an important component of outbreak response because they indicate that public health and social interventions may be relaxed or lapsed. Our study aimed to assess end-of-outbreak probabilities for clusters of coronavirus disease 2019 (COVID-19) cases detected during the first wave of the COVID-19 pandemic in Japan. METHODS: A statistical model for end-of-outbreak determination, which accounted for reporting delays for new cases, was computed. Four clusters, representing different social contexts and time points during the first wave of the epidemic, were selected and their end-of-outbreak probabilities were evaluated. RESULTS: The speed of end-of-outbreak determination was most closely tied to outbreak size. Notably, accounting underascertainment of cases led to later end-of-outbreak determinations. In addition, end-of-outbreak determination was closely related to estimates of case dispersionk and the effective reproduction number Re. Increasing local transmission (Re>1) leads to greater uncertainty in the probability estimates. CONCLUSIONS: When public health measures are effective, lowerRe (less transmission on average) and larger k (lower risk of superspreading) will be in effect, and end-of-outbreak determinations can be declared with greater confidence. The application of end-of-outbreak probabilities can help distinguish between local extinction and low levels of transmission, and communicating these end-of-outbreak probabilities can help inform public health decision making with regard to the appropriate use of resources.


Subject(s)
COVID-19/epidemiology , Disease Hotspot , Models, Statistical , Probability , Basic Reproduction Number , Humans , Japan/epidemiology , Public Health , SARS-CoV-2
20.
Emerg Infect Dis ; 27(3): 915-918, 2021 03.
Article in English | MEDLINE | ID: covidwho-1100023

ABSTRACT

The overall coronavirus disease secondary attack rate (SAR) in family members was 19.0% in 10 prefectures of Japan during February 22-May 31, 2020. The SAR was lower for primary cases diagnosed early, within 2 days after symptom onset. The SAR of asymptomatic primary cases was 11.8%.


Subject(s)
COVID-19/epidemiology , Family , Asymptomatic Infections/epidemiology , COVID-19/diagnosis , COVID-19/transmission , Contact Tracing/statistics & numerical data , Female , Humans , Incidence , Japan/epidemiology , Male , SARS-CoV-2/isolation & purification , Time Factors
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