COVID-19 in Japan, January-March 2020: insights from the first three months of the epidemic

Treatment Behaviors of Patients With Odontogenic Infections During the COVID-19 Pandemic

OBJECTIVE

Using a severity scale, this study aimed to investigate the treatment behavior of patients with odontogenic infections during the COVID-19 pandemic.

MATERIALS AND METHODS

This study included patients admitted for odontogenic deep neck infection (DNI) treatment at a single center in Japan between 2017 and 2022. Participants were divided into two groups: a pre-COVID group before 2019 and a COVID group after 2020. Patient characteristics, clinical data, and DNI severity were compared.

RESULTS

During the pandemic, the number of patients with mild DNIs decreased significantly, whereas the number of patients with severe DNIs did not change significantly, resulting in a significant increase in the latter proportion (42/101 (41.6%) vs. 26/43 (60.5%); p=0.045). In addition, the patients in the COVID group were significantly older than those in the pre-COVID group (median 66.0 years vs. 56.0 years; p=0.018).

CONCLUSIONS

Our results suggest that patients with odontogenic infections, especially the elderly, may have avoided hospitals until their symptoms became severe during the COVID-19 pandemic.

Greater impact of COVID-19 on peer-supported addiction services than government-owned services for addiction in Japan: A nationwide 3-year longitudinal cohort study

Aim

This study aims to investigate how the coronavirus disease (COVID-19) pandemic impacted service provision of peer-supported addiction services, such as self-help groups or recovery houses and government-owned addiction healthcare services, in Japan, as well as the quality of their interaction.

Methods

An online survey was distributed to all 69 public regional healthcare facilities (Mental Health and Welfare Centers [MHWCs]) across the 47 prefectures of Japan annually from 2021 to 2023, totaling three surveys. The survey asked about: (1) the current status of addiction healthcare services at each center, (2) the current status of peer-supported addiction services within each center's area, and (3) changes in connectivity between centers and peer-supported addiction services.

Results

All 69 centers participated in the survey each year. Following the second year of the pandemic, both MHWCs and peer-supported services experienced service closures and restrictions; however, peer-supported services were notably more affected nationwide, such as downsizing of services, decreased number of users, shortage of operation funds, and inability to connect with other services being widely reported (p < 0.0001). Despite the easing of most restrictions by the fourth year, MHWCs in 18 out of 47 prefectures reported at least one sustained negative impact on their service provision, while peer-supported services struggled to recover, with 40 out of 47 prefectures still observing difficulties.

Conclusion

The COVID-19 pandemic significantly affected both types of service, with peer-supported services facing greater challenges in recovery. Additional support is essential to restore these services to normal operation.

Human Papillomavirus Self-Sampling for Unscreened Women Aged 24 Years During the COVID-19 Pandemic

BACKGROUND

The increasing trend of cervical cancer in women in their 20s in Japan is largely attributable to the low rate of cervical cancer screening. This study aimed to assess the usefulness of human papillomavirus (HPV) self-sampling among 24-year-old Japanese women who had never previously been screened for cervical cancer during the coronavirus disease (COVID-19) pandemic.

METHODS

In August 2021, consenting eligible women received HPV self-sampling kits. An Evalyn brush was used for self-sampling, and a Cobas 4800 PCR-based HPV DNA test was used to detect high-risk HPV genotypes. We analyzed the return rates of self-sampling kits and conducted a survey on the acceptability of the self-sampling method.

RESULTS

Of the total 1997 eligible women, 13.4% (268/1997) agreed to participate. The return rate of the kits was 72.4% (194/268), corresponding to 9.7% of the eligible population. Among the participants who returned the kits, 14.9% (29/194) tested positive for HPV, and 41.4% (12/29) of these underwent subsequent cytological testing. The questionnaire results indicated that 57.8% of participants reported no pain during self-sampling, and 72.9% expressed a willingness to continue using the self-sampling method in the future.

CONCLUSION

This study demonstrated that opt-in HPV self-sampling among 24-year-old women who had never been screened for cervical cancer had a favorable kit return rate and was well accepted by the participants, especially during the COVID-19 pandemic. However, the follow-up cytology test rates were low, highlighting the need for improved post-screening management.

In-depth analysis of ambient air pollution changes due to the COVID-19 pandemic in the Asian Monsoon region

The COVID-19 pandemic has given a chance for researchers and policymakers all over the world to study the impact of lockdowns on air quality in each country. This review aims to investigate the impact of the restriction of activities during the lockdowns in the Asian Monsoon region on the main criteria air pollutants. The various types of lockdowns implemented in each country were based on the severity of the COVID-19 pandemic. The concentrations of major air pollutants, especially particulate matter (PM) and nitrogen dioxide (NO2), reduced significantly in all countries, especially in South Asia (India and Bangladesh), during periods of full lockdown. There were also indications of a significant reduction of sulfur dioxide (SO2) and carbon monoxide (CO). At the same time, there were indications of increasing trends in surface ozone (O3), presumably due to nonlinear chemistry associated with the reduction of oxides of nitrogens (NOX). The reduction in the concentration of air pollutants can also be seen in satellite images. The results of aerosol optical depth (AOD) values followed the PM concentrations in many cities. A significant reduction of NO2 was recorded by satellite images in almost all cities in the Asian Monsoon region. The major reductions in air pollutants were associated with reductions in mobility. Pakistan, Bangladesh, Myanmar, Vietnam, and Taiwan had comparatively positive gross domestic product growth indices in comparison to other Asian Monsoon nations during the COVID-19 pandemic. A positive outcome suggests that the economy of these nations, particularly in terms of industrial activity, persisted during the COVID-19 pandemic. Overall, the lockdowns implemented during COVID-19 suggest that air quality in the Asian Monsoon region can be improved by the reduction of emissions, especially those due to mobility as an indicator of traffic in major cities.

Effect of Long-Distance Domestic Travel Ban Policies in Japan on COVID-19 Outbreak Dynamics During Dominance of the Ancestral Strain: Ex Post Facto Retrospective Observation Study

BACKGROUND

In Japan, long-distance domestic travel was banned while the ancestral SARS-CoV-2 strain was dominant under the first declared state of emergency from March 2020 until the end of May 2020. Subsequently, the "Go To Travel" campaign travel subsidy policy was activated, allowing long-distance domestic travel, until the second state of emergency as of January 7, 2021. The effects of this long-distance domestic travel ban on SARS-CoV-2 infectivity have not been adequately evaluated.

OBJECTIVE

We evaluated the effects of the long-distance domestic travel ban in Japan on SARS-CoV-2 infectivity, considering climate conditions, mobility, and countermeasures such as the "Go To Travel" campaign and emergency status.

METHODS

We calculated the effective reproduction number R(t), representing infectivity, using the epidemic curve in Kagoshima prefecture based on the empirical distribution of the incubation period and procedurally delayed reporting from an earlier study. Kagoshima prefecture, in southern Japan, has several resorts, with an airport commonly used for transportation to Tokyo or Osaka. We regressed R(t) on the number of long-distance domestic travelers (based on the number of airport limousine bus users provided by the operating company), temperature, humidity, mobility, and countermeasures such as state of emergency declarations and the "Go To Travel" campaign in Kagoshima. The study period was June 20, 2020, through February 2021, before variant strains became dominant. A second state of emergency was not declared in Kagoshima prefecture but was declared in major cities such as Tokyo and Osaka.

RESULTS

Estimation results indicated a pattern of declining infectivity with reduced long-distance domestic travel volumes as measured by the number of airport limousine bus users. Moreover, infectivity was lower during the "Go To Travel" campaign and the second state of emergency. Regarding mobility, going to restaurants, shopping malls, and amusement venues was associated with increased infectivity. However, going to grocery stores and pharmacies was associated with decreased infectivity. Climate conditions showed no significant association with infectivity patterns.

CONCLUSIONS

The results of this retrospective analysis suggest that the volume of long-distance domestic travel might reduce SARS-CoV-2 infectivity. Infectivity was lower during the "Go To Travel" campaign period, during which long-distance domestic travel was promoted, compared to that outside this campaign period. These findings suggest that policies banning long-distance domestic travel had little legitimacy or rationale. Long-distance domestic travel with appropriate infection control measures might not increase SARS-CoV-2 infectivity in tourist areas. Even though this analysis was performed much later than the study period, if we had performed this study focusing on the period of April or May 2021, it would likely yield the same results. These findings might be helpful for government decision-making in considering restarting a "Go To Travel" campaign in light of evidence-based policy.

Fukuchi-Manabe Score for Infection Control Measures During the Very Early COVID-19 Pandemic Period When Access to Reverse Transcription-Polymerase Chain Reaction Testing Was Poor in Japan: A Single-Center Observational Prospective Cohort Study

BACKGROUND

During the early stages of the COVID-19 pandemic in Japan, access to reverse transcription-polymerase chain reaction (RT-PCR) testing was limited. All patients with COVID-19 required hospitalization, and isolation of suspected COVID-19 patients had not yet been implemented. With the recently acquired evidence on COVID-19, it is important to develop a risk stratification system for isolation rooms in the context of limited resources for better resource management.

OBJECTIVE

This study aimed to develop and validate a COVID-19 risk-scoring strategy, the Fukuchi-Manabe score, to safely stratify and manage isolation rooms, personal protective equipment (PPE), and RT-PCR testing in the context of limited RT-PCR testing and a short supply of PPE.

METHODS

This single-center prospective study consecutively enrolled suspected COVID-19 adult inpatients between March 1 and August 31, 2020. The primary and secondary outcomes were a positive RT-PCR test and the occurrence of nosocomial infections during the study period, respectively. Factors related to patient history, symptoms, chest computed tomography findings, and laboratory data suggestive of COVID-19 were scored, totaled, and divided into four categories ("probable," "possible," "less likely," and "non-suspicious") based on the likelihood of COVID-19. Sensitivity, specificity, and positive and negative predictive values were evaluated for each probability category.

FINDINGS

Twenty of 224 inpatients were positive on the RT-PCR test, including 18 "probable" patients (90.0%), one "possible" patient, and one "less likely" patient. The area under the curve (AUC) (95% confidence interval: 0.841-0.977), sensitivity, and specificity were 0.909, 90.0%, and 80.4%, respectively. The positive and negative predictive values and accuracy for the "probable" category were 0.90, 0.80, and 0.82, respectively. The mean and standard deviation of AUCs, validated by bootstrap analysis, were 0.910±0.034. No nosocomial infections were observed.

CONCLUSION

The Fukuchi-Manabe score will be helpful when other novel pathogens emerge in the future before the availability of genetic testing methods.

The Emergence and Widespread Circulation of Enteric Viruses Throughout the COVID-19 Pandemic: A Wastewater-Based Evidence

Growing evidence shed light on the importance of wastewater-based epidemiology (WBE) during the pandemic, when the patients rarely visited the clinics despite the fact that the infections were still prevalent in the community as before. The abundance of infections in the community poses a constant threat of the emergence of new epidemic strains. Herein, we investigated enteric viruses in raw sewage water (SW) from Japan's Tohoku region and compared them to those from the Kansai region to better understand the circulating strains and their distribution across communities during the COVID-19 pandemic. Raw SW was collected between 2019 and 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major AGE viruses by RT-PCR. Sequence-based analyses were used to assess genotypes and evolutionary relationships. The most commonly detected enteric virus was rotavirus A (RVA) at 63.8%, followed by astrovirus (AstV) at 61.1%, norovirus (NoV) GII and adenovirus (AdV) at 33.3%, sapovirus (SV) at 25.0%, enterovirus (EV) at 19.4%, and NoV GI at 13.9%. The highest prevalence (46.0%) was found in the spring. Importantly, enteric viruses did not decline during the pandemic. Rather, several strains like NoV GII.2, DS-1-like human G3 (equine) RVA, MLB1 AstV, and different F41 HAdV emerged throughout the pandemic and spread widely over the Tohoku and Kansai regions. Tohoku's detection rate remained lower than that of the Kansai area (36 vs 58%). This study provides evidence for the emergence and spread of enteric viruses during the pandemic.

Evolution of the viral genomes of SARS-CoV-2 in association with the changes in local condition: a genomic epidemiological study of a suburban city of Japan

Understanding the factors driving the spread and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the local, regional, national, and international levels is important in protecting against future pandemics. By exploring their viral genomes, we attempted to analyse the spread of SARS-CoV-2 and its evolutionary convergence in Kashiwa City, as an example of a representative commuter town in Japan. From September 2020 to January 2023, a total of 47,134 nasopharyngeal swab and saliva specimens were collected from patients in 47 local clinics and hospitals, covering the vast majority of healthcare facilities. All SARS-CoV-2-positive samples were subjected to whole genome sequencing. Based on the analysis of 5,536 identified genomes, all major strains were represented. Unique regional mutations were occasionally identified in each strain. Inspection of these mutations revealed that the overall base substitution rate increased with progressive waves of the pandemic, at an overall rate of 2.56 bases/year. Interestingly, the spread and evolutionary patterns appeared to be distinct between regions and between individual clinics. Further analysis of the synonymous base substitution rate showed that the speed of viral evolution accelerated coincident with the beginning of public vaccination. Comprehensive genomic epidemiological studies, as presented here, should be useful in precisely understanding the pandemic and preparing for possible future pandemics.

Genetic diversity and declining norovirus prevalence in infants and children during Japan's COVID-19 pandemic: a three-year molecular surveillance

Noroviruses (NoVs) are a global concern, causing widespread outbreaks and sporadic acute gastroenteritis (AGE) cases across all age groups. Recent research has shed light on the emergence of novel recombinant strains of NoV in various countries. To delve deeper into this phenomenon, we extensively analyzed 1,175 stool samples collected from Japanese infants and children with AGE from six different prefectures in Japan over three years, from July 2018 to June 2021. Our investigation aimed to determine the prevalence and genetic characteristics of NoV associated with sporadic AGE while exploring the possibility of detecting NoV recombination events. Among the analyzed samples, we identified 355 cases positive for NoV, 11 cases attributed to GI genotypes, and 344 associated with GII genotypes. Notably, we discovered four distinct GI genotypes (GI.2, GI.3, GI.4, and GI.6) and seven diverse GII genotypes (GII.2, GII.3, GII.4, GII.6, GII.7, GII.14, and GII.17). The predominant genotypes were GII.4 (56.4%; 194 out of 344), followed by GII.2 and GII.3. Through dual genotyping based on sequencing of the ORF1/ORF2 junction region, we identified a total of 14 different RdRp/capsid genotypes. Of particular interest were the prevalent recombinant genotypes GII.4[P31] and GII.2[P16]. Notably, our study revealed a decrease in the number of children infected with NoV during and after the COVID-19 pandemic. These findings underscore the importance of continuous NoV surveillance efforts.

Validity of prognostic models of critical COVID-19 is variable. A systematic review with external validation

OBJECTIVES

To identify prognostic models which estimate the risk of critical COVID-19 in hospitalized patients and to assess their validation properties.

STUDY DESIGN AND SETTING

We conducted a systematic review in Medline (up to January 2021) of studies developing or updating a model that estimated the risk of critical COVID-19, defined as death, admission to intensive care unit, and/or use of mechanical ventilation during admission. Models were validated in two datasets with different backgrounds (HM [private Spanish hospital network], n = 1,753, and ICS [public Catalan health system], n = 1,104), by assessing discrimination (area under the curve [AUC]) and calibration (plots).

RESULTS

We validated 18 prognostic models. Discrimination was good in nine of them (AUCs ≥ 80%) and higher in those predicting mortality (AUCs 65%-87%) than those predicting intensive care unit admission or a composite outcome (AUCs 53%-78%). Calibration was poor in all models providing outcome's probabilities and good in four models providing a point-based score. These four models used mortality as outcome and included age, oxygen saturation, and C-reactive protein among their predictors.

CONCLUSION

The validity of models predicting critical COVID-19 by using only routinely collected predictors is variable. Four models showed good discrimination and calibration when externally validated and are recommended for their use.

Genotype Diversity of Enteric Viruses in Wastewater Amid the COVID-19 Pandemic

Viruses remain the leading cause of acute gastroenteritis (AGE) worldwide. Recently, we reported the abundance of AGE viruses in raw sewage water (SW) during the COVID-19 pandemic, when viral AGE patients decreased dramatically in clinics. Since clinical samples were not reflecting the actual state, it remained important to determine the circulating strains in the SW for preparedness against impending outbreaks. Raw SW was collected from a sewage treatment plant in Japan from August 2018 to March 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major gastroenteritis viruses by RT-PCR. Genotypes and evolutionary relationships were evaluated through sequence-based analyses. Major AGE viruses like rotavirus A (RVA), norovirus (NoV) GI and GII, and astrovirus (AstV) increased sharply (10-20%) in SW during the COVID-19 pandemic, though some AGE viruses like sapovirus (SV), adenovirus (AdV), and enterovirus (EV) decreased slightly (3-10%). The prevalence remained top in the winter. Importantly, several strains, including G1 and G3 of RVA, GI.1 and GII.2 of NoV, GI.1 of SV, MLB1 of AstV, and F41 of AdV, either emerged or increased amid the pandemic, suggesting that the normal phenomenon of genotype changing remained active over this time. This study crucially presents the molecular characteristics of circulating AGE viruses, explaining the importance of SW investigation during the pandemic when a clinical investigation may not produce the complete scenario.