Epidemiology of Coronavirus Disease 2019 in Japan: Descriptive Findings and Lessons Learned through Surveillance during the First Three Waves

Usefulness of a Pluralistic Approach in Sentinel Surveillance: Seasonal Influenza Activity Based on Case Counts per Sentinel Site in the National Epidemiological Surveillance of Infectious Diseases Program and Test Counts, Case Counts, and Test Positivity from the National Hospital Organization

In Japan, based on the National Epidemiological Surveillance of Infectious Diseases (NESID) Program, influenza cases from approximately 5,000 sentinel sites are monitored weekly as part of influenza surveillance (as the number of influenza cases per sentinel site). One limitation is that the number of influenza tests conducted is not reported. However, the National Hospital Organization (NHO), with approximately 140 hospitals, routinely publishes three indicators: the number of influenza tests, the number of influenza-positive cases, and test positivity. We used the NESID and NHO data from April 2011 to June 2022 to assess the usefulness of multiple indicators for monitoring influenza activity. The temporal trends of the NHO and NESID indicator were similar, and the NHO indicator levels correlated well with those of the NESID indicators. However, influenza positivity in the NHO data showed an earlier rise and peak time than that in the NESID indicator. Importantly, during the non-epidemic summer periods and the coronavirus disease 2019 pandemic, a sizable number of influenza tests were still performed at NHO hospitals, with results showing considerably low case counts and test positivity. These data show that a relatively small number of sentinel sites is sufficient to monitor influenza activity nationally and that utilizing multiple indicators can increase our confidence in situational awareness and data interpretations.

SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan

Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.

Effectiveness of feedback control and the trade-off between death by COVID-19 and costs of countermeasures

We provided a framework of a mathematical epidemic modeling and a countermeasure against the novel coronavirus disease (COVID-19) under no vaccines and specific medicines. The fact that even asymptomatic cases are infectious plays an important role for disease transmission and control. Some patients recover without developing the disease; therefore, the actual number of infected persons is expected to be greater than the number of confirmed cases of infection. Our study distinguished between cases of confirmed infection and infected persons in public places to investigate the effect of isolation. An epidemic model was established by utilizing a modified extended Susceptible-Exposed-Infectious-Recovered model incorporating three types of infectious and isolated compartments, abbreviated as SEIIIHHHR. Assuming that the intensity of behavioral restrictions can be controlled and be divided into multiple levels, we proposed the feedback controller approach to implement behavioral restrictions based on the active number of hospitalized persons. Numerical simulations were conducted using different detection rates and symptomatic ratios of infected persons. We investigated the appropriate timing for changing the degree of behavioral restrictions and confirmed that early initiating behavioral restrictions is a reasonable measure to reduce the burden on the health care system. We also examined the trade-off between reducing the cumulative number of deaths by the COVID-19 and saving the cost to prevent the spread of the virus. We concluded that a bang-bang control of the behavioral restriction can reduce the socio-economic cost, while a control of the restrictions with multiple levels can reduce the cumulative number of deaths by infection.

Transmission of COVID-19 in Nightlife, Household, and Health Care Settings in Tokyo, Japan, in 2020

IMPORTANCE

There have been few studies on the heterogeneous interconnection of COVID-19 outbreaks occurring in different social settings using robust, surveillance epidemiological data.

OBJECTIVES

To describe the characteristics of COVID-19 transmission within different social settings and to evaluate settings associated with onward transmission to other settings.

DESIGN, SETTING, AND PARTICIPANTS

This is a case series study of laboratory-confirmed COVID-19 cases in Tokyo between January 23 and December 5, 2020, when vaccination was not yet implemented. Using epidemiological investigation data collected by public health centers, epidemiological links were identified and classified into 7 transmission settings: imported, nightlife, dining, workplace, household, health care, and other.

MAIN OUTCOMES AND MEASURES

The number of cases per setting and the likelihood of generating onward transmissions were compared between different transmission settings.

RESULTS

Of the 44 054 confirmed COVID-19 cases in this study, 25 241 (57.3%) were among male patients, and the median (IQR) age of patients was 36 (26-52) years. Transmission settings were identified in 13 122 cases, including 6768 household, 2733 health care, and 1174 nightlife cases. More than 6600 transmission settings were detected, and nightlife (72 of 380 [18.9%]; P < .001) and health care (119 [36.2%]; P < .001) settings were more likely to involve 5 or more cases than dining, workplace, household, and other settings. Nightlife cases appeared in the earlier phase of the epidemic, while household and health care cases appeared later. After adjustment for transmission setting, sex, age group, presence of symptoms, and wave, household and health care cases were less likely to generate onward transmission compared with nightlife cases (household: adjusted odds ratio, 0.03; 95% CI, 0.02-0.05; health care: adjusted odds ratio, 0.57; 95% CI, 0.41-0.79). Household settings were associated with intergenerational transmission, while nonhousehold settings mainly comprised transmission between the same age group. Among 30 932 cases without identified transmission settings, cases with a history of visiting nightlife establishments were more likely to generate onward transmission to nonhousehold settings (adjusted odds ratio, 5.30 [95% CI, 4.64-6.05]; P < .001) than those without such history.

CONCLUSIONS AND RELEVANCE

In this case series study, COVID-19 cases identified in nightlife settings were associated with a higher likelihood of spreading COVID-19 than household and health care cases. Surveillance and interventions targeting nightlife settings should be prioritized to disrupt COVID-19 transmission, especially in the early stage of an epidemic.

Public-private partnership to rapidly strengthen and scale COVID-19 response in Western Kenya

Introduction

In Africa almost half of healthcare services are delivered through private sector providers. These are often underused in national public health responses. To support and accelerate the public sector's COVID-19 response, we facilitated recruitment of additional private sector capacity by initiating a public-private partnership (PPP) in Kisumu County, Kenya. In this manuscript we demonstrate this PPP's performance.

Methods

COVID-19 diagnostic testing formed the basis for a PPP between Kenyan Medical Research Institute (KEMRI), Department of Health Kisumu County, PharmAccess Foundation, and local faith-based and private healthcare facilities: COVID-Dx. First phase COVID-Dx was implemented from June 01, 2020, to March 31, 2021 in Kisumu County, Kenya. Trained laboratory technologists in participating healthcare facilities collected nasopharyngeal and oropharyngeal samples from patients meeting the Kenyan MoH COVID-19 case definition. Healthcare workers in participating facilities collected patient clinical data using a digitized MoH COVID-19 Case Identification Form. We shared aggregated results from these data via (semi-) live dashboards with all relevant stakeholders through their mobile phones and tablets. Statistical analyses were performed using Stata 16 to inform project processes.

Results

Nine private facilities participated in the project. A patient trajectory was developed from case identification to result reporting, all steps supported by a semi-real time digital dashboard. A total of 4,324 PCR tests for SARS-CoV-2 were added to the public response, identifying 425 positives, accounting for 16% of all COVID-19 tests performed in the County over the given time-period. Geo-mapped and time-tagged information on incident cases was depicted on Google maps through PowerBI-dashboards and fed back to policymakers for informed rapid decision making. Preferential COVID-19 testing was performed on health workers at risk, with 1,009 tests performed (up to 43% of all County health workforce).

Conclusion

We demonstrate feasibility of rapidly increasing the public health sector COVID-19 response through coordinated private sector efforts in an African setting. Our PPP intervention in Kisumu, Kenya was based on a joint testing strategy and demonstrated that semi-real time digitalization of patient trajectories can gain significant efficiencies, linking public and private healthcare efforts, increasing transparency, support better quality health services and informing policy makers to target interventions.

Internet search data with spatiotemporal analysis in infectious disease surveillance: Challenges and perspectives

With the rapid development of the internet, the application of internet search data has been seen as a novel data source to offer timely infectious disease surveillance intelligence. Moreover, the advancements in internet search data, which include rich information at both space and time scales, enable investigators to sufficiently consider the spatiotemporal uncertainty, which can benefit researchers to better monitor infectious diseases and epidemics. In the present study, we present the necessary groundwork and critical appraisal of the use of internet search data and spatiotemporal analysis approaches in infectious disease surveillance by updating the current stage of knowledge on them. The study also provides future directions for researchers to investigate the combination of internet search data with the spatiotemporal analysis in infectious disease surveillance. Internet search data demonstrate a promising potential to offer timely epidemic intelligence, which can be seen as the prerequisite for improving infectious disease surveillance.

Young Healthy Patient With Severe COVID-19 and Fulminant Community-Acquired Pseudomonas aeruginosa Pneumonia: A Case Report

Community-acquired pneumonia (CAP) caused by Pseudomonas aeruginosa in healthy adults can rapidly lead to severe outcomes. We treated a case of P. aeruginosa-induced CAP and concurrent severe coronavirus disease (COVID-19) in a healthy 39-year-old man without other serious risk factors for severe illness except smoking. Immediately after admission, the patient developed sepsis and received intensive broad-spectrum antibacterial therapy with meropenem and vancomycin, veno-arterial extracorporeal membrane oxygenation (VAECMO), and catecholamine supplementation. Despite receiving multidisciplinary treatment, the patient died within 24 hours. P. aeruginosa with normal antimicrobial susceptibility was identified in blood and sputum cultures of samples taken at admission. Gram staining of the bacteria detected in blood cultures was suspicious for non-glucose-fermenting Gram-negative rods, including P. aeruginosa, and the antimicrobial regimen that was initiated following admission was considered effective. The patient was a plumber and a smoker, which are risk factors for P. aeruginosa-induced CAP, and the clinical course matched those in previous reports of P. aeruginosa-induced CAP, including necrotizing pneumonia with cavities and rapid progression of sepsis. Although COVID-19 can be the sole cause of septic shock, the combination of P. aeruginosa bacteremia and COVID-19 was possibly the cause of septic shock in this case. Even during an infectious disease pandemic, reviewing the patient's occupational history and comorbidities and performing blood and sputum culture tests, including Gram staining, are important for the provision of appropriate treatment.

A narrative review on drug development for the management of antimicrobial- resistant infection crisis in Japan: the past, present, and future

INTRODUCTION

Antimicrobial resistance (AMR) is a major threat to global health requiring continuous development of new antimicrobial agents. Antimicrobial research and development (R&D) should be promoted in the pharmaceutical industry and academia to ensure sustainable patient access to new treatment options and reduce the global AMR burden.

AREAS COVERED

This review describes the historical challenges in novel antimicrobial drug development in Japan, current national efforts to promote the development, and proposals to effectively manage future AMR pandemics. Literature searches were performed in the PubMed database (from inception to January 2022).

EXPERT OPINION

R&D activities in the antimicrobial space in Japan have been insufficient due to multiple factors, including unfavorable cost-profit balance and differences in regulatory requirements between Japan and Western countries. However, the situation is improving with the implementation of the Japanese AMR action plan, drug R&D programs led by the Japan Agency for Medical Research and Development, and efforts of regulatory agencies in the United States, Europe, and Japan in aligning and expediting the clinical development process. Further actions during the interpandemic period will strengthen antimicrobial R&D, including international and interdisciplinary collaboration, continued funding and investment with the national government's leadership, and fostering of new-generation academic research leaders.PLAINLANGUAGE SUMMARYEvery year, many people suffer and die of antimicrobial-resistant infections worldwide. New treatment options are required to tackle antimicrobial-resistant infections; however, pharmaceutical companies have not been very active in developing antimicrobial agents in the last two decades. This was mainly due to the difficulty in discovering new and effective compounds and insufficient funds being spent on drug discovery. In addition, differences in drug development requirements between the United States (US), Europe, and Japan have made it difficult for Japanese pharmaceutical companies to develop antimicrobial agents that can be used in all regions in a timely manner. In the last decade, several measures have been taken to re-activate antimicrobial research and development in the pharmaceutical industry, as well as in academia, in Japan. These measures include a national action plan to combat antimicrobial-resistant infections and research support programs led by the Japan Agency for Medical Research and Development. Regulatory authorities in the US, Europe, and Japan have initiated efforts to expedite the development of drugs to treat infections. Moreover, pathways for accelerated regulatory review have been established to reduce the time taken for new drugs to be approved, and this has already been applied to several new anti-infective drugs. To combat the coronavirus disease 2019 (COVID-19) pandemic, the development of novel vaccines and antiviral drugs has been accelerated with unprecedented speed. Additional actions, such as international research collaboration programs and investment in new antimicrobial development, may help promote antimicrobial research and development activities in Japan.

Adverse events after administration of the first and second doses of messenger RNA-based COVID-19 vaccines in Japanese subjects aged 12-18 years

OBJECTIVE

Using a prospective observational design, we assessed adverse events (AEs) after COVID-19 vaccination in Japanese patients.

METHODS

Two doses of the mRNA-1273 (SPIKEVAX®) or BNT162b2 (COMIRNATY®) vaccine were administered to participants aged 12 to 18 years, and AEs after each dose were recorded for 14 days. Data on the duration and nature (local vs. systemic) of AEs were collected using a questionnaire. Sex-based differences in AE frequency were also analyzed.

RESULTS

After the first and second doses, 152 and 135 vaccinees were enrolled, respectively. After the first dose, fever (>37.1°C) occurred in 38.9% of males and 50.0% of females, whereas local pain occurred in 89.8% and 97.7% of males and females, respectively (only SPIKEVAX® was used as the first dose). After the second dose, fever (>37.1°C) occurred in 77.8% and 82.6% of males vaccinated with COMIRNATY® and SPIKEVAX®, respectively, and 82.6% of females (all received SPIKEVAX®). The local pain rates in these groups were 80.6%, 76.3%, and 100%, respectively. After the second dose, local pain, fever (>38.1°C) and headache were significantly more common in female participants, and the median symptom duration was 3 days.

CONCLUSIONS

AEs were more frequent after the second dose and in females.

Impact of the COVID-19 pandemic on changes in temperature-sensitive cardiovascular and respiratory disease mortality in Japan

Some cardiovascular and respiratory diseases are triggered by changes in ambient temperature or extremes of temperature. This study aimed to clarify the changes in mortality associated with temperature-sensitive diseases in Japan during the COVID-19 pandemic. We used data from three major cities (Sapporo City, Tokyo 23 wards, and Osaka City) from 2010 to 2019 to determine disease mortality rates and monthly mean temperatures from April to December. If the pandemic had not occurred in 2020, the results showed that temperature-sensitive disease death counts would have increased from 324 to 980, based on a 95% confidence interval estimated from the past 10 years in Sapporo (19-56% increase in actual deaths from 2020), from 651 to 2,653 in Tokyo (10-39% increase), and from 235 to 1,343 in Osaka (8-48% increase). Analyses of meshed population data during the COVID-19 pandemic indicated that inhibiting people's behaviour and outdoor mobility, especially in older men, caused a decrease in mortality.

Application of the advanced lung cancer inflammation index for patients with coronavirus disease 2019 pneumonia: Combined risk prediction model with lung cancer inflammation index, computed tomography and chest radiograph

The purpose of the present study was to evaluate the feasibility of applying the advanced lung cancer inflammation index (ALI) in patients with coronavirus disease 2019 (COVID-19) and to establish a combined ALI and radiologic risk prediction model for disease exacerbation. The present study included patients diagnosed with COVID-19 infection in our single institution from March to October 2020. Patients without clinical information and/or chest computed tomography (CT) upon admission were excluded. A radiologist assessed the CT severity score and abnormality on chest radiograph. The combined ALI and radiologic risk prediction model was developed via random forest classification. Among 79 patients (age, 43±19 years; male/female, 45:34), 72 experienced improvement and seven patients experienced exacerbation after admission. Significant differences were observed between the improved and exacerbated groups in the ALI (median, 47.6 vs. 13.2; P=0.011), frequency of chest radiograph abnormality (24.7 vs. 83.3%; P<0.001), and chest CT score (CCTS; median, 1 vs. 9; P<0.001). For the accuracy of predicting exacerbation, the receiver-operating characteristic curve analysis demonstrated an area under the curve of 0.79 and 0.92 for the ALI and CCTS, respectively. The combined ALI and radiologic risk prediction model had a sensitivity of 1.00 and a specificity of 0.81. Overall, ALI alone and CCTS alone modestly predicted the exacerbation of COVID-19, and the combined ALI and radiologic risk prediction model exhibited decent sensitivity and specificity.

Clinical Effectiveness of REGN-COV2 in Patients with COVID-19 in Japan: A Retrospective Cohort Study with a Bayesian Inference

Background

Neutralizing antibody cocktail therapy, REGN-COV2, is promising in preventing a severe form of coronavirus disease 2019 (COVID-19), but its effectiveness in Japan has not been fully investigated.

Materials and Methods

To evaluate the effectiveness of REGN-COV2, clinical data of 20 patients with COVID-19 who received REGN-COV2 was compared with the control by matching age and sex. The primary outcome was the time from the onset to defervescence, the duration of hospitalization, and oxygen requirement. A sensitivity analysis using Bayesian analysis was also conducted.

Results

The time to defervescence was significantly shorter in the treatment group (5.25 vs. 7.95 days, P = 0.02), and so was the duration of hospitalization (7.115 vs. 11.45, P = 0.0009). However, the oxygen therapy requirement did not differ between the two groups (15% vs. 35%, P = 0.27). For Bayesian analysis, the median posterior probability of the time to defervescence since the symptom onset on the REGN-COV2 group was 5.28 days [95% credible interval (CrI): 4.28 - 6.31 days], compared with the control of 7.99 days (95% CrI: 6.81 - 9.24 days). The posterior probability of the duration of the hospitalization on the REGN-COV2 group was 7.17 days (95% CrI: 5.99 - 8.24 days), compared with the control of 11.54 days (95% CrI: 10.28 - 13.14 days). The posterior probability of the oxygen requirement on the REGN-COV2 group was 18% (95% CrI: 3 - 33%), compared with the control of 36% (95% CrI: 16 - 54%).

Conclusion

REGN-COV2 may be effective in early defervescence and shorter hospitalization. Its effectiveness for preventing a severe form of infection needs to be evaluated by further studies.