Clusters of Coronavirus Disease in Communities, Japan, January-April 2020

A COVID-19 cluster analysis in an office: Assessing the long-range aerosol and fomite transmissions with infection control measures

Simulated exposure to severe acute respiratory syndrome coronavirus 2 in the environment was demonstrated based on the actual coronavirus disease 2019 cluster occurrence in an office, with a projected risk considering the likely transmission pathways via aerosols and fomites. A total of 35/85 occupants were infected, with the attack rate in the first stage as 0.30. It was inferred that the aerosol transmission at long-range produced the cluster at virus concentration in the saliva of the infected cases on the basis of the simulation, more than 108 PFU mL-1. Additionally, all wearing masks effectiveness was estimated to be 61%-81% and 88%-95% reduction in risk for long-range aerosol transmission in the normal and fit state of the masks, respectively, and a 99.8% or above decline in risk of fomite transmission. The ventilation effectiveness for long-range aerosol transmission was also calculated to be 12%-29% and 36%-66% reductions with increases from one air change per hour (ACH) to two ACH and six ACH, respectively. Furthermore, the virus concentration reduction in the saliva to 1/3 corresponded to the risk reduction for long-range aerosol transmission by 60%-64% and 40%-51% with and without masks, respectively.

COVID-19 cluster surveillance using exposure data collected from routine contact tracing: The genomic validation of a novel informatics-based approach to outbreak detection in England

Contact tracing was used globally to prevent onwards transmission of COVID-19. Tracing contacts alone is unlikely to be sufficient in controlling community transmission, due to the pre-symptomatic, overdispersed and airborne nature of COVID-19 transmission. We describe and demonstrate the validity of a national enhanced contact tracing programme for COVID-19 cluster surveillance in England. Data on cases occurring between October 2020 and September 2021 were extracted from the national contact tracing system. Exposure clusters were identified algorithmically by matching ≥2 cases attending the same event, identified by matching postcode and event category within a 7-day rolling window. Genetic validity was defined as exposure clusters with ≥2 cases from different households with identical viral sequences. Exposure clusters were fuzzy matched to the national incident management system (HPZone) by postcode and setting description. Multivariable logistic regression modelling was used to determine cluster characteristics associated with genetic validity. Over a quarter of a million (269,470) exposure clusters were identified. Of the eligible clusters, 25% (3,306/13,008) were genetically valid. 81% (2684/3306) of these were not recorded on HPZone and were identified on average of one day earlier than incidents recorded on HPZone. Multivariable analysis demonstrated that exposure clusters occurring in workplaces (aOR = 5·10, 95% CI 4·23-6·17) and education (aOR = 3·72, 95% CI 3·08-4·49) settings were those most strongly associated with genetic validity. Cluster surveillance using enhanced contact tracing in England was a timely, comprehensive and systematic approach to the detection of transmission events occurring in community settings. Cluster surveillance can provide intelligence to stakeholders to support the assessment and management of clusters of COVID-19 at a local, regional, and national level. Future systems should include predictive modelling and network analysis to support risk assessment of exposure clusters to improve the effectiveness of enhanced contract tracing for outbreak detection.

Impact of COVID-19 and Closed Transmission of SARS-CoV-2 during the First Wave in Toyama Prefecture, Japan, March 30 to May 18, 2020

We studied 226 patients in Toyama Prefecture who were notified of COVID-19 during the first wave between March 30 and May 18, 2020. Of the 226 patients, 22 (9.7%) died, most (95%) of whom were aged ≥65 years. A large cluster comprising 59 patients (41 residents and 18 staff members) was identified in a nursing home on April 17. No deaths occurred among staff members; however, 12 of the 41 residents (29%) died. Although the threshold cycle (Ct) values were significantly lower in the 20-64 and ≥65 years age groups than in the <20 years age group, no correlation was found between the Ct values and severity, fatal outcome, or secondary infection. The haplotype network of 145 SARS-CoV-2 isolates (64%) from 226 patients was analyzed. The viral genomes of the case groups differed by less than five nucleotide bases. These data suggest that the SARS-CoV-2 strains, which were initially introduced into Toyama Prefecture in late March and early April 2020, and their closely related strains, identified as lineage B.1.1, circulated during the first wave. The reduced inter-prefectural mobility of local residents may support the lack of strain diversity in SARS-CoV-2 during the first wave of the state of emergency.

Association of Ambient Temperature and Absolute Humidity with the Effective Reproduction Number of COVID-19 in Japan

This study aimed to quantify the exposure-lag-response relationship between short-term changes in ambient temperature and absolute humidity and the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Japan. The prefecture-specific daily time-series of newly confirmed cases, meteorological variables, retail and recreation mobility, and Government Stringency Index were collected for all 47 prefectures of Japan for the study period from 15 February 2020 to 15 October 2022. Generalized conditional Gamma regression models were formulated with distributed lag nonlinear models by adopting the case-time-series design to assess the independent and interactive effects of ambient temperature and absolute humidity on the relative risk (RR) of the time-varying effective reproductive number (Rt). With reference to 17.8 °C, the corresponding cumulative RRs (95% confidence interval) at a mean ambient temperatures of 5.1 °C and 27.9 °C were 1.027 (1.016-1.038) and 0.982 (0.974-0.989), respectively, whereas those at an absolute humidity of 4.2 m/g3 and 20.6 m/g3 were 1.026 (1.017-1.036) and 0.995 (0.985-1.006), respectively, with reference to 10.6 m/g3. Both extremely hot and humid conditions synergistically and slightly reduced the Rt. Our findings provide a better understanding of how meteorological drivers shape the complex heterogeneous dynamics of SARS-CoV-2 in Japan.

Modeling homophily in dynamic networks with application to HIV molecular surveillance

BACKGROUND

Efforts to control the HIV epidemic can benefit from knowledge of the relationships between the characteristics of people who have transmitted HIV and those who became infected by them. Investigation of this relationship is facilitated by the use of HIV genetic linkage analyses, which allows inference about possible transmission events among people with HIV infection. Two persons with HIV (PWH) are considered linked if the genetic distance between their HIV sequences is less than a given threshold, which implies proximity in a transmission network. The tendency of pairs of nodes (in our case PWH) that share (or differ in) certain attributes to be linked is denoted homophily. Below, we describe a novel approach to modeling homophily with application to analyses of HIV viral genetic sequences from clinical series of participants followed in San Diego. Over the 22-year period of follow-up, increases in cluster size results from HIV transmissions to new people from those already in the cluster-either directly or through intermediaries.

METHODS

Our analytical approach makes use of a logistic model to describe homophily with regard to demographic, clinical, and behavioral characteristics-that is we investigate whether similarities (or differences) between PWH in these characteristics are associated with their sequences being linked. To investigate the performance of our methods, we conducted on a simulation study for which data sets were generated in a way that reproduced the structure of the observed database.

RESULTS

Our results demonstrated strong positive homophily associated with hispanic ethnicity, and strong negative homophily, with birth year difference. The second result implies that the larger the difference between the age of a newly-infected PWH and the average age for an available cluster, the lower the odds of a newly infected person joining that cluster. We did not observe homophily associated with prior diagnosis of sexually transmitted diseases. Our simulation studies demonstrated the validity of our approach for modeling homophily, by showing that the estimates it produced matched the specified values of the statistical network generating model.

CONCLUSIONS

Our novel methods provide a simple and flexible statistical network-based approach for modeling the growth of viral (or other microbial) genetic clusters from linkage to new infections based on genetic distance.

Containment of COVID-19 outbreaks with lower incidence and case fatality rates in long-term care facilities by early intervention of emergency response teams

OBJECTIVE

To examine whether post-outbreak early-phase interventions by emergency response teams (ERTs) in long-term care facilities (LTCFs) contribute to containment with lower incidence and case-fatality rate of COVID-19 and analyse the required assistance.

METHODS

Records from 59 LTCFs (28 hospitals, 15 nursing homes, and 16 homes) assisted by ERTs after the COVID-19 outbreak, between May 2020 and January 2021, were used for the analysis. Incidence and case-fatality rates among 6,432 residents and 8,586 care workers were calculated. The daily reports of ERTs were reviewed, and content analysis was performed.

RESULTS

Incidence rates among residents and care workers with early phase (<7 days from onset) interventions (30·3%, 10·8%) were lower than those with late phase (≥7 days from onset) interventions (36·6%, 12·6%) (p<0·001, p = 0·011, respectively). The case-fatality rate among residents with early-phase and late-phase interventions were 14·8% and 16·9%, respectively. ERT assistance in LTCFs was not limited to infection control but extended to command and coordination assistance in all studied facilities.

CONCLUSION

Assistance in the facility's operational governance from the early phase of an outbreak in LTCFs contributed to a significant decline in incidence rate and case fatality rate among LTCF residents and care workers in facilities.

Community-Based Outbreak Investigation And Response: Enhancing Preparedness, Public Health Capacity, And Equity

Throughout the COVID-19 pandemic, the US has struggled with many aspects of the public health response, from determining where transmission is occurring to building trust with communities and implementing interventions. Three factors have contributed to these challenges: insufficient local public health capacity, siloed interventions, and underuse of a cluster-based approach to outbreak response. In this article we introduce Community-based Outbreak Investigation and Response (COIR), a local public health strategy developed during the COVID-19 pandemic that addresses these shortcomings. COIR can help local public health entities conduct disease surveillance more effectively, take a more proactive and efficient approach to mitigating transmission, coordinate response efforts, build community trust, and advance equity. We offer a practitioner's lens, informed through on-the-ground experience and engagement with policy makers, to highlight the financing, workforce, data system, and information-sharing policy changes needed to scale up COIR throughout the country. COIR can enable the US public health system to develop effective solutions to many of today's public health challenges and improve the nation's preparedness for public health crises in the years to come.

COVID-19 Incidence and Vaccine Effectiveness in University Staff, 1 March 2020-2 April 2022

Background: University workers undergo intense social interactions due to frequent contact with students and colleagues and lectures in crowdy conditions. The aim of our study was to assess the incidence of COVID-19 infection and vaccine effectiveness in a cohort of workers of the University of Trieste from 1 March 2020 (start of the pandemic) through 2 April 2022. Methods: The University of Trieste implemented a number of public health policies to contain the spread of SARS-CoV-2 on the campus, including prompt contact tracing, enhanced ventilation of all premises, fomites disinfection and mandatory use of face masks indoors. In compliance with the surveillance protocol of the local public health department, university personnel were tested for SARS-CoV-2 by polymerase chain reaction (PCR) on a nasopharyngeal swab on demand, in the event of symptoms consistent with COVID-19 or for contact tracing, following close contact with a confirmed COVID-19 case. The incidence rates of SARS-CoV-2 infections were estimated as number of cases by number of person-days (p-d) at risk. Multivariable Cox proportional hazard regression model was employed to investigate the risk of primary COVID-19 infection, controlling for a number of potential confounders and expressing the risk as the adjusted hazard ratio (aHR) with a 95% confidence interval (95% CI). Results: The incidence of SARS-CoV-2 infection among university staff was lower than that of healthcare workers (HCWs) of the same area. Compared to unvaccinated colleagues (6.55 × 10,000 p-d), the raw incidence of SARS-CoV-2 infection was higher among university workers immunized with one (7.22 × 10,000 p-d) or two (7.48 × 10,000 p-d) doses of COVID-19 vaccines, decreasing in those receiving the booster (1.98 × 1000 p-d). The risk of infection increased only in postgraduate medical trainees (aHR = 2.16; 95% CI: 1.04; 4.48), though this was limited to the Omicron transmission period. After the implementation of the national vaccination campaign against COVID-19, workers immunized with the booster were less likely than unvaccinated workers to be infected by SARS-CoV-2 both before (aHR = 0.10; 95% CI: 0.06; 0.16) and after (aHR = 0.37; 95% CI: 0.27; 0.52) the Omicron transmission period. Vaccine effectiveness of the booster was 90% (=(1-0.10) × 100) before versus 63% (=(1-0.37) × 100) during the Omicron wave, without a significant difference between homologous (three doses of m-RNA vaccines) and heterologous immunization (first two doses of Vaxzevria followed by a third dose of m-RNA vaccine). Conclusions: The incidence of SARS-CoV-2 infection in university staff was lower than that of HCWs of ASUGI, likely because the testing-on-demand schedule inevitably missed the vast majority of asymptomatic infections. Therefore, the observed significantly protective effect of the booster dose in university personnel referred to symptomatic SARS-CoV-2 infections. The infection prevention and control policies implemented by the University of Trieste managed to equalize the biological risk between administrative and teaching staff.

Identifying High-Risk Events for COVID-19 Transmission: Estimating the Risk of Clustering Using Nationwide Data

The transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to be overdispersed, meaning that only a fraction of infected cases contributes to super-spreading. While cluster interventions are an effective measure for controlling pandemics due to the viruses' overdispersed nature, a quantitative assessment of the risk of clustering has yet to be sufficiently presented. Using systematically collected cluster surveillance data for coronavirus disease 2019 (COVID-19) from June 2020 to June 2021 in Japan, we estimated the activity-dependent risk of clustering in 23 establishment types. The analysis indicated that elderly care facilities, welfare facilities for people with disabilities, and hospitals had the highest risk of clustering, with 4.65 (95% confidence interval [CI]: 4.43-4.87), 2.99 (2.59-3.46), and 2.00 (1.88-2.12) cluster reports per million event users, respectively. Risks in educational settings were higher overall among older age groups, potentially being affected by activities with close and uncontrollable contact during extracurricular hours. In dining settings, drinking and singing increased the risk by 10- to 70-fold compared with regular eating settings. The comprehensive analysis of the COVID-19 cluster records provides an additional scientific basis for the design of customized interventions.

The impact of mass gatherings on the local transmission of COVID-19 and the implications for social distancing policies: Evidence from Hong Kong

Mass gatherings provide conditions for the transmission of infectious diseases and pose complex challenges to public health. Faced with the COVID-19 pandemic, governments and health experts called for suspension of gatherings in order to reduce social contact via which virus is transmitted. However, few studies have investigated the contribution of mass gatherings to COVID-19 transmission in local communities. In Hong Kong, the coincidence of the relaxation of group gathering restrictions with demonstrations against the National Security Law in mid-2020 raised concerns about the safety of mass gatherings under the pandemic. Therefore, this study examines the impacts of mass gatherings on the local transmission of COVID-19 and evaluates the importance of social distancing policies. With an aggregated dataset of epidemiological, city-level meteorological and socioeconomic data, a Synthetic Control Method (SCM) is used for constructing a 'synthetic Hong Kong' from over 200 Chinese cities. This counterfactual control unit is used to simulate COVID-19 infection patterns (i.e., the number of total cases and daily new cases) in the absence of mass gatherings. Comparing the hypothetical trends and the actual ones, our results indicate that the infection rate observed in Hong Kong is substantially higher than that in the counterfactual control unit (2.63% vs. 0.07%). As estimated, mass gatherings increased the number of new infections by 62 cases (or 87.58% of total new cases) over the 10-day period and by 737 cases (or 97.23%) over the 30-day period. These findings suggest the necessity of tightening social distancing policies, especially the prohibition on group gathering regulation (POGGR), to prevent and control COVID-19 outbreaks.

Transmission Analysis of COVID-19 Outbreaks Associated with Places of Worship, Arkansas, May 2020-December 2020

The purpose of this study was to describe a statewide COVID-19 transmission involving places of worship (POWs) during the early phase of the pandemic. During the period of May 2020-December 2020, this analysis evaluated COVID-19 cases in Arkansas reported in REDCap for overall cases associated with POWs, cluster detection, and network analysis of one POW utilizing Microbetrace. A total of 9904 COVID-19 cases reported attending an in-person POW service during the early phase of the pandemic with 353 probable POW-associated clusters identified. Network analysis for 'POW A' showed at least 60 COVID-19 cases were traced to at least 4 different settings. The pandemic gave an opportunity to observe and stress the importance of public health and POWs working closely together with a shared goal of facilitating worship in a manner that optimizes congregational and community safety during a public health emergency.

Trend changes in age-related body mass index gain after coronavirus disease 2019 pandemic in Japan: a multicenter retrospective cohort study

BACKGROUND

Accumulating studies suggest that strict lockdown with enforcement including segregation to control the coronavirus disease 2019 (COVID-19) pandemic is associated with excess weight gain, but the such lockdown was not practiced in Japan. We aimed to compare the age-related weight gain before and after the COVID-19 pandemic in Japan where achieved epidemic control based on individual voluntary action.

METHODS

This multicenter retrospective cohort study used electronic data from annual health checkups for workers from January 2015 to December 2021 at four facilities belonging to the Central Clinic Group, Aichi, Japan. We defined pre-pandemic and post-pandemic periods as January 2015-December 2019 and January 2020-December 2021, respectively. Participants were grouped by sex, age, and body mass index (BMI) stratus as of 2015, and the pre-pandemic and post-pandemic age-related BMI changes in overall individuals and each specific group were compared using a paired t-test.

RESULTS

The total number of eligible participants was 19,290. During the pre-pandemic period, the mean BMI increased linearly in every group. The mean age-related BMI changes in females' pre-pandemic and post-pandemic periods were + 0.11 and + 0.02 kg/m²/year, respectively. This significant decrease was also shown in males, + 0.11 in the pre-pandemic and - 0.02 kg/m²/year in the post-pandemic periods. The reduction was consistently observed in all age strata. Furthermore, a significant reduction was also observed in the normal-weight females of reproductive ages aged 15-44 years.

CONCLUSIONS

This is the first report showing that age-related weight gain was reduced after the COVID-19 pandemic in Japan, which could affect the reproductive age of females.

Diminishing returns: Nudging Covid-19 prevention among Colombian young adults

Nonpharmaceutical interventions (NPIs) like social distancing, face masks, and handwashing will continue to be a frontline defense against Covid-19 for some time. But their effectiveness depends critically on compliance by young adults, who are most likely both to become infected and to infect others. We conducted a randomized controlled trial in Bogotá, Colombia, to assess the effectiveness of informational nudges emphasizing the private and public benefits of compliance on university students' concern about Covid-19, recent compliance with NPI recommendations, and intended future compliance. Although nudges boosted concern, they had limited effects on either recent or intended future compliance. We attribute these null results to high baseline levels of information about and compliance with NPIs, an informational diminishing returns scenario that is likely to be increasingly common globally.

Association between Cooperative Attitude and High-Risk Behaviors on the Spread of COVID-19 Infection among Medical Students in Japan

The impact of high-risk behaviors on the spread of COVID-19 infection among young people is an important problem to address. This study analyzed the association between cooperativeness and high-risk behaviors. We conducted a cross-sectional study among fourth-year medical students at Tokyo Medical and Dental University. The students were asked about cooperative attitude in a hypothetical situation of performing a task together with an unfamiliar classmate, who did not cooperate to complete the task previously. The response items were as follows: "cooperate", "don't want to cooperate and do it alone (non-cooperative)", and "don't want to cooperate and let the partner do it alone (punishment)". Eating out and vaccine hesitancy were also treated as high-risk behaviors. Poisson regression was used to investigate the association between cooperative attitude and each high-risk behavior, adjusted for demographics. Of the 98 students, 23 (23.5%), 44 (44.9%), and 31 (31.6%) students chose "noncooperative", "cooperative", and "punishment", respectively. Cooperative-type students exhibited 2.77-fold (PR: 2.77, 95% CI: 1.03-7.46), and punishment-type students exhibited 3.16-fold greater risk of eating or drinking out (PR: 3.16, 95% CI: 1.14-8.75) compared with those of the noncooperative type. Among medical students, the "cooperative" type and "punishment" type comprised the high-risk group for eating out during the pandemic.

Use of surveillance data to elucidate household clustering of SARS-CoV-2 in Fulton County, Georgia a major metropolitan area

BACKGROUND

Households are important for SARS-CoV-2 transmission due to high intensity exposure in enclosed spaces over prolonged durations. We quantified and characterized household clustering of COVID-19 cases in Fulton County, Georgia.

METHODS

We used surveillance data to identify all confirmed COVID-19 cases in Fulton County. Household clustered cases were defined as cases with matching residential address. We described the proportion of COVID-19 cases that were clustered, stratified by age over time and explore trends in age of first diagnosed case within households and subsequent household cases.

RESULTS

Between June 1, 2020 and October 31, 2021, 31,449(37%) of 106,233 cases were clustered in households. Children were the most likely to be in household clusters than any other age group. Initially, children were rarely (∼ 10%) the first cases diagnosed in the household but increased to almost 1 of 3 in later periods.

DISCUSSION

One-third of COVID-19 cases in Fulton County were part of a household cluster. Increasingly children were the first diagnosed case, coinciding with temporal trends in vaccine roll-out among the elderly and the return to in-person schooling in Fall 2021. Limitations include restrictions to cases with a valid address and unit number and that the first diagnosed case may not be the infection source for the household.

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications

Clusters of genetically similar infections suggest rapid transmission and may indicate priorities for public health action or reveal underlying epidemiological processes. However, clusters often require user-defined thresholds and are sensitive to non-epidemiological factors, such as non-random sampling. Consequently the ideal threshold for public health applications varies substantially across settings. Here, we show a method which selects optimal thresholds for phylogenetic (subset tree) clustering based on population. We evaluated this method on HIV-1 pol datasets (n = 14, 221 sequences) from four sites in USA (Tennessee, Washington), Canada (Northern Alberta) and China (Beijing). Clusters were defined by tips descending from an ancestral node (with a minimum bootstrap support of 95%) through a series of branches, each with a length below a given threshold. Next, we used pplacer to graft new cases to the fixed tree by maximum likelihood. We evaluated the effect of varying branch-length thresholds on cluster growth as a count outcome by fitting two Poisson regression models: a null model that predicts growth from cluster size, and an alternative model that includes mean collection date as an additional covariate. The alternative model was favoured by AIC across most thresholds, with optimal (greatest difference in AIC) thresholds ranging 0.007-0.013 across sites. The range of optimal thresholds was more variable when re-sampling 80% of the data by location (IQR 0.008 - 0.016, n = 100 replicates). Our results use prospective phylogenetic cluster growth and suggest that there is more variation in effective thresholds for public health than those typically used in clustering studies.

Assessing the Pre-Vaccination Anti-SARS-CoV-2 IgG Seroprevalence among Residents and Staff in Nursing Home in Niigata, Japan, November 2020

An outbreak of coronavirus disease 2019 (COVID-19) occurred in a nursing home in Niigata, Japan, November 2020, with an attack rate of 32.0% (63/197). The present study was aimed at assessing the pre-vaccination seroprevalence almost half a year after the COVID-19 outbreak in residents and staff in the facility, along with an assessment of the performance of the enzyme-linked immunosorbent assay (ELISA) and the chemiluminescent immunoassay (CLIA), regarding test seropositivity and seronegativity in detecting immunoglobulin G (IgG) anti-severe acute respiratory syndrome 2 (SARS-CoV-2) antibodies (anti-nucleocapsid (N) and spike (S) proteins). A total of 101 people (30 reverse transcription PCR (RT-PCR)-positive and 71 RT-PCR-negative at the time of the outbreak in November 2020) were tested for anti-IgG antibody titers in April 2021, and the seroprevalence was approximately 40.0-60.0% for residents and 10.0-20.0% for staff, which was almost consistent with the RT-PCR test results that were implemented during the outbreak. The seropositivity for anti-S antibodies showed 90.0% and was almost identical to the RT-PCR positives even after approximately six months of infections, suggesting that the anti-S antibody titer test is reliable for a close assessment of the infection history. Meanwhile, seropositivity for anti-N antibodies was relatively low, at 66.7%. There was one staff member and one resident that were RT-PCR-negative but seropositive for both anti-S and anti-N antibody, indicating overlooked infections despite periodical RT-PCR testing at the time of the outbreak. Our study indicated the impact of transmission of SARS-CoV-2 in a vulnerable elderly nursing home in the pre-vaccination period and the value of a serological study to supplement RT-PCR results retrospectively.

Age-Stratified Seroprevalence of SARS-CoV-2 Antibodies before and during the Vaccination Era, Japan, February 2020–March 2022

Japan has reported a relatively small number of COVID-19 cases. Because not all infected persons receive diagnostic tests for COVID-19, the reported number must be lower than the actual number of infections. We assessed SARS-CoV-2 seroprevalence by analyzing >60,000 samples collected in Japan (Tokyo Metropolitan Area and Hokkaido Prefecture) during February 2020–March 2022. The results showed that ≈3.8% of the population had become seropositive by January 2021. The seroprevalence increased with the administration of vaccinations; however, among the elderly, seroprevalence was not as high as the vaccination rate. Among children, who were not eligible for vaccination, infection was spread during the epidemic waves caused by the SARS-CoV-2 Delta and Omicron variants. Nevertheless, seroprevalence for unvaccinated children <5 years of age was as low as 10% as of March 2022. Our study underscores the low incidence of SARS-CoV-2 infection in Japan and the effects of vaccination on immunity at the population level.

Actual conditions of person-to-object contact and a proposal for prevention measures during the COVID-19 pandemic

This study focused on human contact behavior with objects and discussed countermeasures during the COVID-19 pandemic across 15 location types. Reducing contact with objects and disinfecting items can be implemented at a relatively low cost. We created a protocol for organizing the objects, and 1260 subjects who went outside during a day between December 3-7, 2020 in Tokyo and Kanagawa, Japan were surveyed. The participants touched 7317 objects in total; the most common objects were doors, chairs, baskets, elevator equipment, and cash. One-way analysis of variance and Scheffé's multiple comparison test showed that supermarkets had the lowest mean and median values despite having the highest number of users, contact objects, and object types. Conversely, the values for hotels were the highest, significantly higher than that for other places, excluding amusement parks, workplaces, and schools and universities. Furthermore, the long-tailed frequency distribution of the number of objects suggests that the objects touched by many individuals are limited; thus, it is important to determine the objects to be prioritized for disinfection at each location. The data and protocol could inform infection countermeasures that properly address the contact realities as they pertain to people's behavior and objects.

SARS-COV-2/COVID-19: scenario, epidemiology, adaptive mutations, and environmental factors

The coronavirus pandemic of 2019 has already exerted an enormous impact. For over a year, the worldwide pandemic has ravaged the whole globe, with approximately 250 million verified human infection cases and a mortality rate surpassing 4 million. While the genetic makeup of the related pathogen (SARS-CoV-2) was identified, many unknown facets remain a mystery, comprising the virus's origin and evolutionary trend. There were many rumors that SARS-CoV-2 was human-borne and its evolution was predicted many years ago, but scientific investigation proved them wrong and concluded that bats might be the origin of SARS-CoV-2 and pangolins act as intermediary species to transmit the virus from bats to humans. Airborne droplets were found to be the leading cause of human-to-human transmission of this virus, but later studies showed that contaminated surfaces and other environmental factors are also involved in its transmission. The evolution of different SARS-CoV-2 variants worsens the condition and has become a challenge to overcome this pandemic. The emergence of COVID-19 is still a mystery, and scientists are unable to explain the exact origin of SARS-CoV-2. This review sheds light on the possible origin of SARS-CoV-2, its transmission, and the key factors that worsen the situation.

Ceiling impact on air disinfection performance of Upper-Room Germicidal Ultraviolet (UR-GUV)

This study used Computational Fluid Dynamics (CFD) to investigate air disinfection for SARS-CoV-2 by the Upper-Room Germicidal Ultraviolet (UR-GUV), with focus on ceiling impact. The study includes three indoor settings, i.e., low (airport bus), medium (classroom) and high (rehearsal room) ceilings, which were ventilated with 100% clean air (CA case), 80% air-recirculation with a low filtration (LF case), and 80% air-recirculation with a high filtration (HF case). According to the results, using UR-GUV can offset the increased infection risk caused by air recirculation, with viral concentrations in near field (NF) and far field (FF) in the LF case similar to those in the CA case. In the CA case, fraction remaining (FR) was 0.48-0.73 with 25% occupancy rate (OR) and 0.49-0.91 with 45% OR in the bus, 0.41 in NF and 0.11 in FF in the classroom, and 0.18 in NF and 0.09 in FF in the rehearsal room. Obviously, UR-GUV performance in NF can be improved in a room with a high ceiling where FR has a power relationship with UV zone height. As using UR-GUV can only extend the exposure time to get infection risk of 1% (T _1% ) to 8 min in NF in the classroom, and 47 min in NF in the rehearsal room, it is necessary to abide by social distancing in the two rooms. In addition, T _1% in FF was calculated to be 18.3 min with 25% OR and 21.4% with 45% OR in the airport bus, showing the necessity to further wear a mask.

A survey of COVID-19 in public transportation: Transmission risk, mitigation and prevention

The COVID-19 pandemic is posing significant challenges to public transport operators by drastically reducing demand while also requiring them to implement measures that minimize risks to the health of the passengers. While the collective scientific understanding of the SARS-CoV-2 virus and COVID-19 pandemic are rapidly increasing, currently there is a lack of understanding of how the COVID-19 relates to public transport operations. This article presents a comprehensive survey of the current research on COVID-19 transmission mechanisms and how they relate to public transport. We critically assess literature through a lens of disaster management and survey the main transmission mechanisms, forecasting, risks, mitigation, and prevention mechanisms. Social distancing and control on passenger density are found to be the most effective mechanisms. Computing and digital technology can support risk control. Based on our survey, we draw guidelines for public transport operators and highlight open research challenges to establish a research roadmap for the path forward.

The global response: How cities and provinces around the globe tackled Covid-19 outbreaks in 2021

Background

Tackling the spread of COVID-19 remains a crucial part of ending the pandemic. Its highly contagious nature and constant evolution coupled with a relative lack of immunity make the virus difficult to control. For this, various strategies have been proposed and adopted including limiting contact, social isolation, vaccination, contact tracing, etc. However, given the heterogeneity in the enforcement of these strategies and constant fluctuations in the strictness levels of these strategies, it becomes challenging to assess the true impact of these strategies in controlling the spread of COVID-19.

Methods

In the present study, we evaluated various transmission control measures that were imposed in 10 global urban cities and provinces in 2021- Bangkok, Gauteng, Ho Chi Minh City, Jakarta, London, Manila City, New Delhi, New York City, Singapore, and Tokyo.

Findings

Based on our analysis, we herein propose the population-level Swiss cheese model for the failures and pitfalls in various strategies that each of these cities and provinces had. Furthermore, whilst all the evaluated cities and provinces took a different personalized approach to managing the pandemic, what remained common was dynamic enforcement and monitoring of breaches of each barrier of protection. The measures taken to reinforce the barriers were adjusted continuously based on the evolving epidemiological situation.

Interpretation

How an individual city or province handled the pandemic profoundly affected and determined how the entire country handled the pandemic since the chain of transmission needs to be broken at the very grassroot level to achieve nationwide control.

Funding

The present study did not receive any external funding.

Characterizing respiratory aerosol emissions during sustained phonation

OBJECTIVE

To elucidate the role of phonation frequency (i.e., pitch) and intensity of speech on respiratory aerosol emissions during sustained phonations.

METHODS

Respiratory aerosol emissions are measured in 40 (24 males and 16 females) healthy, non-trained singers phonating the phoneme /a/ at seven specific frequencies at varying vocal intensity levels.

RESULTS

Increasing frequency of phonation was positively correlated with particle production (r = 0.28, p < 0.001). Particle production rate was also positively correlated (r = 0.37, p < 0.001) with the vocal intensity of phonation, confirming previously reported findings. The primary mode (particle diameter ~0.6 μm) and width of the particle number size distribution were independent of frequency and vocal intensity. Regression models of the particle production rate using frequency, vocal intensity, and the individual subject as predictor variables only produced goodness of fit of adjusted R² = 40% (p < 0.001). Finally, it is proposed that superemitters be defined as statistical outliers, which resulted in the identification of one superemitter in the sample of 40 participants.

SIGNIFICANCE

The results suggest there remain unexplored effects (e.g., biomechanical, environmental, behavioral, etc.) that contribute to the high variability in respiratory particle production rates, which ranged from 0.2 particles/s to 142 particles/s across all trials. This is evidenced as well by changes in the distribution of participant particle production that transitions to a more bimodal distribution (second mode at particle diameter ~2 μm) at higher frequencies and vocal intensity levels.

Relationship between COVID-19-specific occupational stressors and mental distress in frontline and non-frontline staff

This study investigated the difference in the severity of mental distress and factors contributing to mental distress in frontline and non-frontline healthcare professionals during the coronavirus disease (COVID-19) pandemic. A cross-sectional web-based survey of medical staff collected by snow-ball sampling was performed in Japan in October 2020 using the Kessler Psychological Distress Scale (K6) as an outcome measure for mental distress. Originally developed items asking about the degree of change in psychological and physical burdens, COVID-19-related fear, and experience of discrimination were obtained. The median score of the K6 was 7 in the frontline staff group (n = 86) and 6 in the non-frontline staff group (n = 504), without a statistically significant difference. Multiple regression analyses showed that among the participants, an increase in psychological burden and COVID-19-related fear was significantly associated with mental distress in both groups. Experience of discrimination was significantly associated with mental distress only in the frontline staff group. However, an increase in physical burden was significantly associated with mental distress only in the non-frontline staff group. The results indicate that the factors contributing to mental distress between frontline and non-frontline staff can be different, although the severity of mental distress is comparable between them.

Transmissibility of SARS-CoV-2 B.1.1.214 and Alpha Variants during 4 COVID-19 Waves, Kyoto, Japan, January 2020-June 2021

Household transmission is a primary source of SARS-CoV-2 spread. We used COVID-19 epidemiologic investigation data and viral genome analysis data collected in the city of Kyoto, Japan, during January 2020–June 2021 to evaluate the effects of different settings and viral strains on SARS-CoV-2 transmission. Epidemiologic investigations of 5,061 COVID-19 cases found that the most common category for close contact was within households (35.3%); this category also had the highest reverse transcription PCR positivity. The prevalent viral lineage shifted from B.1.1.214 in the third wave to the Alpha variant in the fourth wave. The proportion of secondary cases associated with households also increased from the third to fourth waves (27% vs. 29%). Among 564 contacts from 206 households, Alpha variant was significantly associated with household transmission (odds ratio 1.52, 95% CI 1.06–2.18) compared with B.1.1.214. Public health interventions targeting household contacts and specific variants could help control SARS-CoV-2 transmission.

Exposure and respiratory infection risk via the short-range airborne route

Leading health authorities have suggested short-range airborne transmission as a major route of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, there is no simple method to assess the short-range airborne infection risk or identify its governing parameters. We proposed a short-range airborne infection risk assessment model based on the continuum model and two-stage jet model. The effects of ventilation, physical distance and activity intensity on the short-range airborne exposure were studied systematically. The results suggested that increasing physical distance and ventilation reduced short-range airborne exposure and infection risk. However, a diminishing return phenomenon was observed when the ventilation rate or physical distance was beyond a certain threshold. When the infectious quantum concentration was less than 1 quantum/L at the mouth, our newly defined threshold distance and threshold ventilation rate were independent of quantum concentration. We estimated threshold distances of 0.59, 1.1, 1.7 and 2.6 m for sedentary/passive, light, moderate and intense activities, respectively. At these distances, the threshold ventilation was estimated to be 8, 20, 43, and 83 L/s per person, respectively. The findings show that both physical distancing and adequate ventilation are essential for minimising infection risk, especially in high-intensity activity or densely populated spaces.

Did the Tokyo Olympic Games enhance the transmission of COVID-19? An interpretation with machine learning

BACKGROUND

In the summer of 2021, the Olympic Games were held in Tokyo during the state of emergency due to the spread of COVID-19 pandemic. New daily positive cases (DPC) increased before the Olympic Games, and then decreased a few weeks after the Games. However, several cofactors influencing DPC exist; consequently, careful consideration is needed for future international events during an epidemic.

METHODS

The impact of the Olympic Games on new DPC were evaluated in the Tokyo, Osaka, and Aichi Prefectures using a well-trained and -evaluated long short-term memory (LSTM) network. In addition, we proposed a compensation method based on effective reproduction number (ERN) to assess the effect of the national holidays on the DPC.

RESULTS

During the spread phase, the estimated DPC with LSTM was 30%-60% lower than that of the observed value, but was consistent with the compensated value of the ERN for the three prefectures. During the decay phase, the estimated DPC was consistent with the observed values. The timing of the decay coincided with achievement of a fully-vaccinated rate of 10%-15% of people aged <65 years.

CONCLUSIONS

The up- and downsurge of the pandemic wave observed in July and September are likely attributable to high ERN during national holiday periods and to the vaccination effect, especially for people aged <65 years. The effect of national holidays in Tokyo was rather notable in Aichi and Osaka, which are distant from Tokyo. The effect of the Olympic Games on the spread and decay of the pandemic wave is neither dominant nor negligible due to the shifting of the national holiday dates to coincide with the Olympic Games.

Was the Reduction in Seasonal Influenza Transmission during 2020 Attributable to Non-Pharmaceutical Interventions to Contain Coronavirus Disease 2019 (COVID-19) in Japan?

We quantified the effects of adherence to various non-pharmaceutical interventions (NPIs) on the seasonal influenza epidemic dynamics in Japan during 2020. The total monthly number of seasonal influenza cases per sentinel site (seasonal influenza activity) reported to the National Epidemiological Surveillance of Infectious Diseases and alternative NPI indicators (retail sales of hand hygiene products and number of airline passenger arrivals) from 2014−2020 were collected. The average number of monthly seasonal influenza cases in 2020 had decreased by approximately 66.0% (p < 0.001) compared to those in the preceding six years. An increase in retail sales of hand hygiene products of ¥1 billion over a 3-month period led to a 15.5% (95% confidence interval [CI]: 10.9−20.0%; p < 0.001) reduction in seasonal influenza activity. An increase in the average of one million domestic and international airline passenger arrivals had a significant association with seasonal influenza activity by 11.6% at lag 0−2 months (95% CI: 6.70−16.5%; p < 0.001) and 30.9% at lag 0−2 months (95% CI: 20.9−40.9%; p < 0.001). NPI adherence was associated with decreased seasonal influenza activity during the COVID-19 pandemic in Japan, which has crucial implications for planning public health interventions to minimize the health consequences of adverse seasonal influenza epidemics.

Problem drinkers and high risk-taking behaviors under the stay-at-home policy of the COVID-19 emergency declaration

Background

To the best of the authors’ knowledge, this is the first study to examine whether problem drinkers have had high risk-taking behaviors during the stay-at-home policy (e.g., dining out at a bar) under the COVID-19 emergency declaration.

Methods

We investigated data from Japan COVID-19 and Society Internet Survey(JACSIS)study—a web-based nationwide survey, conducted from August to September 2020. From a total of 12,076 current drinkers, problem drinkers were detected by Cut, Annoyed, Guilty, and Eye-opener (CAGE) questions. A CAGE score of 4 showed potential alcohol use disorder and scores of 2 to3 showed potential alcohol abuse; individuals with these scores were regarded as problem drinkers compared to light-or-no-risk drinkers, with a CAGE score of 0 to 1. The outcome assessed the presence of 18 behaviors against the stay-at-home policy, such as dining out at a bar, meeting people, or going to crowded places. All these behaviors were limited in Japan during the first declaration of emergency between April and May 2020.

Results

Based on the multivariable logistic regression, the participants with potential alcohol use disorder demonstrated 16 out of the 18 risk-taking behaviors, such as dining out at a bar (adjusted odds ratio (aOR): 2.08; 95% confidence interval (CI): 1.56–2.79), dining out at a restaurant (aOR: 1.79; 95% CI:1.37–2.35), visiting friends (aOR: 1.81; 95% CI: 1.34–2.44), going to karaoke (1.97; 95% CI: 1.26–3.10), and riding on a crowded train (aOR: 1.46; 95% CI: 1.07–1.99), compared to light-or-no risk drinkers with a CAGE score of 0 to 1. Additionally, participants with potential alcohol abuse (CAGE score of 2 to 3) had 10 out of 18 behaviors against the stay-at-home policy: the corresponding aORs for the aforementioned behaviors were 1.45 (95% CI: 1.25–1.67), 1.27 (95% CI: 1.12–1.44), 1.17 (95% CI: 1.01–1.36), 1.49 (95% CI: 1.17–1.90), and 1.19 (95% CI: 1.03–1.38), respectively. Problem drinkers had a significant association with being men, a higher income and job position, smoking, sleep deprivation, depression, and other mental diseases.

Conclusions

Overall, problem drinkers were more likely to have higher risk-taking behaviors against the stay-at-home policy, compared to light-or-no-risk drinkers.

Behavioral factors associated with SARS-CoV-2 infection

OBJECTIVE

To study the association between behavioural factors and incidence rates of SARS-CoV-2 infection.

DESIGN

Case-control web-based questionnaire study.

SETTING

Questionnaire data were collected in the Capital Region of Denmark in December 2020 when limited restrictions were in place, while the number of daily SARS-CoV-2 cases increased rapidly.

PARTICIPANTS

8913 cases of laboratory-confirmed SARS-CoV-2 infection were compared with two groups of controls: (1) 34 063 individuals with a negative SARS-CoV-2 test from the same date (negative controls, NCs) and 2) 25 989 individuals who had never been tested for a SARS-CoV-2 infection (untested controls, UC). Controls were matched on sex, age, test date and municipality.

EXPOSURE

Activities during the 14 days prior to being tested positive for SARS-CoV-2 or during the same period for matched controls and precautions taken during the entire pandemic.

MAIN OUTCOMES AND MEASURES

SARS-CoV-2 infection incidence rate ratios (IRR).

RESULTS

Response rate was 41.4% (n=93 121). Using public transportation, grocery shopping (IRR: NC: 0.52; UC: 0.63) and outdoor sports activities (NC: 0.75; UC: 0.96) were not associated with increased rate of SARS-CoV-2 infection. Most precautions, for example, using hand sanitizer (NC: 0.79; UC: 0.98), physical distancing (NC: 0.79; UC: 0.82) and avoiding handshakes (NC: 0.74; UC: 0.77), were associated with a lower rate of infection. Activities associated with many close contacts, especially indoors, increased rate of infection. Except for working from home, all types of occupation were linked to increased rate of infection.

CONCLUSIONS

In a community setting with moderate restrictions, activities such as using public transportation and grocery shopping with the relevant precautions were not associated with an increased rate of SARS-CoV-2 infection. Exposures and activities where safety measures are difficult to maintain might be important risk factors for infection. These findings may help public health authorities tailor their strategies for limiting the spread of SARS-CoV-2.

SARS-CoV-2 Transmission and Prevention in the Era of the Delta Variant

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant transmits much more rapidly than prior SARS-CoV-2 viruses. The primary mode of transmission is via short range aerosols that are emitted from the respiratory tract of an index case. There is marked heterogeneity in the spread of this virus, with 10% to 20% of index cases contributing to 80% of secondary cases, while most index cases have no subsequent transmissions. Vaccination, ventilation, masking, eye protection, and rapid case identification with contact tracing and isolation can all decrease the transmission of this virus.

Characterization of aerosol plumes from singing and playing wind instruments associated with the risk of airborne virus transmission

The exhalation of aerosols during musical performances or rehearsals posed a risk of airborne virus transmission in the COVID-19 pandemic. Previous research studied aerosol plumes by only focusing on one risk factor, either the source strength or convective transport capability. Furthermore, the source strength was characterized by the aerosol concentration and ignored the airflow rate needed for risk analysis in actual musical performances. This study characterizes aerosol plumes that account for both the source strength and convective transport capability by conducting experiments with 18 human subjects. The source strength was characterized by the source aerosol emission rate, defined as the source aerosol concentration multiplied by the source airflow rate (brass 383 particle/s, singing 408 particle/s, and woodwind 480 particle/s). The convective transport capability was characterized by the plume influence distance, defined as the sum of the horizontal jet length and horizontal instrument length (brass 0.6 m, singing 0.6 m and woodwind 0.8 m). Results indicate that woodwind instruments produced the highest risk with approximately 20% higher source aerosol emission rates and 30% higher plume influence distances compared with the average of the same risk indicators for singing and brass instruments. Interestingly, the clarinet performance produced moderate source aerosol concentrations at the instrument's bell, but had the highest source aerosol emission rates due to high source airflow rates. Flute performance generated plumes with the lowest source aerosol emission rates but the highest plume influence distances due to the highest source airflow rate. Notably, these comprehensive results show that the source airflow is a critical component of the risk of airborne disease transmission. The effectiveness of masking and bell covering in reducing aerosol transmission is due to the mitigation of both source aerosol concentrations and plume influence distances. This study also found a musician who generated approximately five times more source aerosol concentrations than those of the other musicians who played the same instrument. Despite voice and brass instruments producing measurably lower average risk, it is possible to have an individual musician produce aerosol plumes with high source strength, resulting in enhanced transmission risk; however, our sample size was too small to make generalizable conclusions regarding the broad musician population.

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

BACKGROUND

Understanding the characteristics and natural history of novel pathogens is crucial to inform successful control measures. Japan was one of the first affected countries in the COVID-19 pandemic reporting their first case on 14 January 2020. Interventions including airport screening, contact tracing, and cluster investigations were quickly implemented. Here we present insights from the first 3 months of the epidemic in Japan based on detailed case data.

METHODS

We conducted descriptive analyses based on information systematically extracted from individual case reports from 13 January to 31 March 2020 including patient demographics, date of report and symptom onset, symptom progression, travel history, and contact type. We analysed symptom progression and estimated the time-varying reproduction number, Rt, correcting for epidemic growth using an established Bayesian framework. Key delays and the age-specific probability of transmission were estimated using data on exposures and transmission pairs.

RESULTS

The corrected fitted mean onset-to-reporting delay after the peak was 4 days (standard deviation: ± 2 days). Early transmission was driven primarily by returning travellers with Rt peaking at 2.4 (95% CrI: 1.6, 3.3) nationally. In the final week of the trusted period (16-23 March 2020), Rt accounting for importations diverged from overall Rt at 1.1 (95% CrI: 1.0, 1.2) compared to 1.5 (95% CrI: 1.3, 1.6), respectively. Household (39.0%) and workplace (11.6%) exposures were the most frequently reported potential source of infection. The estimated probability of transmission was assortative by age with individuals more likely to infect, and be infected by, contacts in a similar age group to them. Across all age groups, cases most frequently onset with cough, fever, and fatigue. There were no reported cases of patients < 20 years old developing pneumonia or severe respiratory symptoms.

CONCLUSIONS

Information collected in the early phases of an outbreak are important in characterising any novel pathogen. The availability of timely and detailed data and appropriate analyses is critical to estimate and understand a pathogen's transmissibility, high-risk settings for transmission, and key symptoms. These insights can help to inform urgent response strategies.

Efficacy of Combining an Extraoral High-Volume Evacuator with Preprocedural Mouth Rinsing in Reducing Aerosol Contamination Produced by Ultrasonic Scaling

The coronavirus disease pandemic has afforded dental professionals an opportunity to reconsider infection control during treatment. We investigated the efficacy of combining extraoral high-volume evacuators (eHVEs) with preprocedural mouth rinsing in reducing aerosol contamination by ultrasonic scalers. A double-masked, two-group, crossover randomized clinical trial was conducted over eight weeks. A total of 10 healthy subjects were divided into two groups; they received 0.5% povidone-iodine (PI), essential oil (EO), or water as preprocedural rinse. Aerosols produced during ultrasonic scaling were collected from the chest area (PC), dentist's mask, dentist's chest area (DC), bracket table, and assistant's area. Bacterial contamination was assessed using colony counting and adenosine triphosphate assays. With the eHVE 10 cm away from the mouth, bacterial contamination by aerosols was negligible. With the eHVE 20 cm away, more dental aerosols containing bacteria were detected at the DC and PC. Mouth rinsing decreased viable bacterial count by 31-38% (PI) and 22-33% (EO), compared with no rinsing. The eHVE prevents bacterial contamination when close to the patient's mouth. Preprocedural mouth rinsing can reduce bacterial contamination where the eHVE is positioned away from the mouth, depending on the procedure. Combining an eHVE with preprocedural mouth rinsing can reduce bacterial contamination in dental offices.

Workplace exposures associated with COVID-19: evidence from a case-control study with multiple sampling periods in England, August-October 2020

We investigated risk factors associated with COVID-19 by conducting a retrospective, frequency-matched case-control study, with three sampling periods (August-October 2020). We compared cases completing routine contact tracing to asymptomatic population controls. Multivariable analyses estimated adjusted odds ratios (aORs) for non-household community settings. Meta-analyses using random effects provided pooled odds ratios (pORs). Working in healthcare (pOR 2.87; aORs 2.72, 2.81, 3.08, for study periods 1-3 respectively), social care (pOR 4.15; aORs 2.46, 5.06, 5.41, for study periods 1-3 respectively) or hospitality (pOR 2.36; aORs 2.01, 2.54, 2.63, for study periods 1-3 respectively) were associated with increased odds of being a COVID-19 case. Additionally, working in bars, pubs and restaurants, warehouse settings, construction, educational settings were significantly associated. While definitively determining where transmission occurs is impossible, we provide evidence that in certain sectors, the impact of mitigation measures may only be partial and reinforcement of measures should be considered in these settings.

SARS-CoV-2 Droplet and Airborne Transmission Heterogeneity

The spread dynamics of the SARS-CoV-2 virus have not yet been fully understood after two years of the pandemic. The virus's global spread represented a unique scenario for advancing infectious disease research. Consequently, mechanistic epidemiological theories were quickly dismissed, and more attention was paid to other approaches that considered heterogeneity in the spread. One of the most critical advances in aerial pathogens transmission was the global acceptance of the airborne model, where the airway is presented as the epicenter of the spread of the disease. Although the aerodynamics and persistence of the SARS-CoV-2 virus in the air have been extensively studied, the actual probability of contagion is still unknown. In this work, the individual heterogeneity in the transmission of 22 patients infected with COVID-19 was analyzed by close contact (cough samples) and air (environmental samples). Viral RNA was detected in 2/19 cough samples from patient subgroups, with a mean Ct (Cycle Threshold in Quantitative Polymerase Chain Reaction analysis) of 25.7 ± 7.0. Nevertheless, viral RNA was only detected in air samples from 1/8 patients, with an average Ct of 25.0 ± 4.0. Viral load in cough samples ranged from 7.3 × 105 to 8.7 × 108 copies/mL among patients, while concentrations between 1.1-4.8 copies/m3 were found in air, consistent with other reports in the literature. In patients undergoing follow-up, no viral load was found (neither in coughs nor in the air) after the third day of symptoms, which could help define quarantine periods in infected individuals. In addition, it was found that the patient's Ct should not be considered an indicator of infectiousness, since it could not be correlated with the viral load disseminated. The results of this work are in line with proposed hypotheses of superspreaders, which can attribute part of the heterogeneity of the spread to the oversized emission of a small percentage of infected people.

Behavioral factors associated with SARS-CoV-2 infection in Japan

Background

The relative burden of COVID‐19 has been less severe in Japan. One reason for this may be the uniquely strict restrictions imposed upon bars/restaurants. To assess if this approach was appropriately targeting high‐risk individuals, we examined behavioral factors associated with SARS‐CoV‐2 infection in the community.

Methods

This multicenter case–control study involved individuals receiving SARS‐CoV‐2 testing in June–August 2021. Behavioral exposures in the past 2 weeks were collected via questionnaire. SARS‐CoV‐2 PCR‐positive individuals were cases, while PCR‐negative individuals were controls.

Results

The analysis included 778 individuals (266 [34.2%] positives; median age [interquartile range] 33 [27–43] years). Attending three or more social gatherings was associated with SARS‐CoV‐2 infection (adjusted odds ratio [aOR] 2.00 [95% CI 1.31–3.05]). Attending gatherings with alcohol (aOR 2.29 [1.53–3.42]), at bars/restaurants (aOR 1.55 [1.04–2.30]), outdoors/at parks (aOR 2.87 [1.01–8.13]), at night (aOR 2.07 [1.40–3.04]), five or more people (aOR 1.81 [1.00–3.30]), 2 hours or longer (aOR 1.76 [1.14–2.71]), not wearing a mask during gatherings (aOR 4.18 [2.29–7.64]), and cloth mask use (aOR 1.77 [1.11–2.83]) were associated with infection. Going to karaoke (aOR 2.53 [1.25–5.09]) and to a gym (aOR 1.87 [1.11–3.16]) were also associated with infection. Factors not associated with infection included visiting a cafe with others, ordering takeout, using food delivery services, eating out by oneself, and work/school/travel‐related exposures including teleworking.

Conclusions

We identified multiple behavioral factors associated with SARS‐CoV‐2 infection, many of which were in line with the policy/risk communication implemented in Japan. Rapid assessment of risk factors can inform decision making.

Beta-negative binomial nonlinear spatio-temporal random effects modeling of COVID-19 case counts in Japan

Coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 virus has spread seriously throughout the world. Predicting the spread, or the number of cases, in the future can facilitate preparation for, and prevention of, a worst-case scenario. To achieve these purposes, statistical modeling using past data is one feasible approach. This paper describes spatio-temporal modeling of COVID-19 case counts in 47 prefectures of Japan using a nonlinear random effects model, where random effects are introduced to capture the heterogeneity of a number of model parameters associated with the prefectures. The negative binomial distribution is frequently used with the Paul-Held random effects model to account for overdispersion in count data; however, the negative binomial distribution is known to be incapable of accommodating extreme observations such as those found in the COVID-19 case count data. We therefore propose use of the beta-negative binomial distribution with the Paul-Held model. This distribution is a generalization of the negative binomial distribution that has attracted much attention in recent years because it can model extreme observations with analytical tractability. The proposed beta-negative binomial model was applied to multivariate count time series data of COVID-19 cases in the 47 prefectures of Japan. Evaluation by one-step-ahead prediction showed that the proposed model can accommodate extreme observations without sacrificing predictive performance.

Properties of the Omicron Variant of SARS-CoV-2 Affect Public Health Measure Effectiveness in the COVID-19 Epidemic

Nonpharmaceutical and pharmaceutical public health interventions are important to mitigate the coronavirus disease 2019 (COVID-19) epidemic. However, it is still unclear how the effectiveness of these interventions changes with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) novel variants. This simulation study utilized data from Japan and investigated how the characteristic properties of the Omicron variant, which emerged in late 2021, influence the effectiveness of public health interventions, including vaccination, the reduction of interpersonal contact, and the early isolation of infectious people. Although the short generation time of the Omicron variant increases the effectiveness of vaccination and the reduction of interpersonal contact, it decreases the effectiveness of early isolation. The latter feature may make the containment of case clusters difficult. The increase of infected children during the Omicron-dominant epidemic diminishes the effects of previously adult-targeted interventions. These findings underscore the importance of monitoring viral evolution and consequent changes in epidemiological characteristics. An assessment and adaptation of public health measures against COVID-19 are required as SARS-CoV-2 novel variants continue to emerge.

The Analysis of Patterns of Two COVID-19 Outbreak Clusters in China

Since the emergence of COVID-19, there have been many local outbreaks with foci at shopping malls in China. We compared and analyzed the epidemiological and spatiotemporal characteristics of local COVID-19 outbreaks in two commercial locations, a department store building (DSB) in Baodi District, Tianjin, and the Xinfadi wholesale market (XFD) in Fengtai District, Beijing. The spread of the infection at different times was analyzed by the standard deviation elliptical method. The spatial transfer mode demonstrated that outbreaks started at the center of each commercial location and spread to the periphery. The number of cases and the distance from the central outbreak showed an inverse proportional logarithmic function shape. Most cases were distributed within a 10 km radius; infected individuals who lived far from the outbreak center were mainly infected by close-contact transmission at home or in the workplace. There was no efficient and rapid detection method at the time of the DSB outbreak; the main preventative measure was the timing of COVID-19 precautions. Emergency interventions (closing shopping malls and home isolation) were initiated five days before confirmation of the first case from the shopping center. In contrast, XFD closed after the first confirmed cases appeared, but those infected during this outbreak benefitted from efficient nucleic acid testing. Quick results and isolation of infected individuals were the main methods of epidemic control in this area. The difference in the COVID-19 epidemic patterns between the two shopping malls reflects the progress of Chinese technology in the prevention and control of COVID-19.

Epidemiology of coronavirus disease 2019 (COVID-19) in Japan during the first and second waves

Following the emergence and worldwide spread of coronavirus disease 2019 (COVID-19), each country has attempted to control the disease in different ways. The first patient with COVID-19 in Japan was diagnosed on 15 January 2020, and until 31 October 2020, the epidemic was characterized by two large waves. To prevent the first wave, the Japanese government imposed several control measures such as advising the public to avoid the 3Cs (closed spaces with poor ventilation, crowded places with many people nearby, and close-contact settings such as close-range conversations) and implementation of "cluster buster" strategies. After a major epidemic occurred in April 2020 (the first wave), Japan asked its citizens to limit their numbers of physical contacts and announced a non-legally binding state of emergency. Following a drop in the number of diagnosed cases, the state of emergency was gradually relaxed and then lifted in all prefectures of Japan by 25 May 2020. However, the development of another major epidemic (the second wave) could not be prevented because of continued chains of transmission, especially in urban locations. The present study aimed to descriptively examine propagation of the COVID-19 epidemic in Japan with respect to time, age, space, and interventions implemented during the first and second waves. Using publicly available data, we calculated the effective reproduction number and its associations with the timing of measures imposed to suppress transmission. Finally, we crudely calculated the proportions of severe and fatal COVID-19 cases during the first and second waves. Our analysis identified key characteristics of COVID-19, including density dependence and also the age dependence in the risk of severe outcomes. We also identified that the effective reproduction number during the state of emergency was maintained below the value of 1 during the first wave.

Rapid response to a coronavirus disease 2019 (COVID-19) outbreak in a psychiatry hospital-Kanazawa City, Japan, March to April 2020

A coronavirus disease 2019 (COVID-19) outbreak in a psychiatry hospital revealed specific challenges in its response such as difficulty in isolation, transfer, and identification of close contacts, suboptimal infection control practices, and shortage of personal protective equipment, which were overcome by support from the public health center and a neighboring university hospital.

The Environment Encouraging COVID-19 Response at Public Health Centers and Future Challenges in Japan

The coronavirus disease 2019 (COVID-19) pandemic has triggered the implementation of public health measures globally. The health department of local governments has played a critical role in confronting COVID-19. In Japan, public health centers (PHCs) are focal points for COVID-19 response. Understanding the response to COVID-19 in local areas is critical to ensure adequate preparation for future emergencies. Therefore, the purpose of this study is to clarify how the COVID-19 operations by PHCs in Japan were managed and facilitated at the beginning of the infection spread, and their future challenges. We designed a case study that included two PHCs with a population of approximately 400,000 in Japan. Semi-structured focus group interviews with public health nurses from these two PHCs were conducted in September and October 2020. The data were analyzed using chronological time-series analysis. The switch to crisis response was encouraged by the business continuity plan. Their operations for the prevention of COVID-19 in the community were facilitated by the existing network. Further, strengthening the knowledge and skill regarding infectious disease control and management skills during infectious disease-related health emergencies were recommended. It is important to ensure that the environment facilitates emergency response and that people-and-community-centered health promotion activities are conducted, during an emergency situation, with more innovative action and leadership.

Transmission in home environment associated with the second wave of COVID-19 pandemic in India

India has suffered from the second wave of COVID-19 pandemic since March 2021. This wave of the outbreak has been more serious than the first wave pandemic in 2020, which suggests that some new transmission characteristics may exist. COVID-19 is transmitted through droplets, aerosols, and contact with infected surfaces. Air pollutants are also considered to be associated with COVID-19 transmission. However, the roles of indoor transmission in the COVID-19 pandemic and the effects of these factors in indoor environments are still poorly understood. Our study focused on reveal the role of indoor transmission in the second wave of COVID-19 pandemic in India. Our results indicated that human mobility in the home environment had the highest relative influence on COVID-19 daily growth rate in the country. The COVID-19 daily growth rate was significantly positively correlated with the residential percent rate in most state-level areas in India. A significant positive nonlinear relationship was found when the residential percent ratio ranged from 100 to 120%. Further, epidemic dynamics modelling indicated that a higher proportion of indoor transmission in the home environment was able to intensify the severity of the second wave of COVID-19 pandemic in India. Our findings suggested that more attention should be paid to the indoor transmission in home environment. The public health strategies to reduce indoor transmission such as ventilation and centralized isolation will be beneficial to the prevention and control of COVID-19.

Predictors of life-threatening complications in relatively lower-risk patients hospitalized with COVID-19

Older individuals with chronic health conditions are at highest risk of adverse clinical outcomes from COVID-19, but there is widespread belief that risk to younger, relatively lower-risk individuals is negligible. We assessed the rate and predictors of life-threatening complications among relatively lower-risk adults hospitalized with COVID-19. Of 3766 adults hospitalized with COVID-19 to three hospitals in New York City from March to May 2020, 963 were relatively lower-risk based on absence of preexisting health conditions. Multivariable logistic regression models examined in-hospital development of life-threatening complications (major medical events, intubation, or death). Covariates included age, sex, race/ethnicity, hypertension, weight, insurance type, and area-level sociodemographic factors (poverty, crowdedness, and limited English proficiency). In individuals ≥55 years old (n = 522), 33.3% experienced a life-threatening complication, 17.4% were intubated, and 22.6% died. Among those <55 years (n = 441), 15.0% experienced a life-threatening complication, 11.1% were intubated, and 5.9% died. In multivariable analyses among those ≥55 years, age (OR 1.03 [95%CI 1.01–1.06]), male sex (OR 1.72 [95%CI 1.14–2.64]), being publicly insured (versus commercial insurance: Medicare, OR 2.02 [95%CI 1.22–3.38], Medicaid, OR 1.87 [95%CI 1.10–3.20]) and living in areas with relatively high limited English proficiency (highest versus lowest quartile: OR 3.50 [95%CI 1.74–7.13]) predicted life-threatening complications. In those <55 years, no sociodemographic factors significantly predicted life-threatening complications. A substantial proportion of relatively lower-risk patients hospitalized with COVID-19 experienced life-threatening complications and more than 1 in 20 died. Public messaging needs to effectively convey that relatively lower-risk individuals are still at risk of serious complications.

Influenza Outbreak and a Group Meal in a Geriatric Long-term Care Facility in Japan

Influenza outbreaks at geriatric long-term care facilities (g-LTCFs) can be deadly and their prevention is important. However, the factors influencing disease transmission in g-LTCFs remain controversial. In this descriptive study, we tried to identify the potential risk factors influencing influenza outbreaks that occurred in different influenza seasons within a single g-LTCF with 100 residents in Gunma Prefecture. We reviewed the detailed facility records for all influenza cases in both residents and staff between January 2012 and June 2020. Facility preventive measures were also reviewed. We found that community meals may have been a potential source of transmission leading to the outbreaks. When influenza infection is noted, implementation of strict preventive measures and restriction of meal provision to resident rooms may help to prevent disease transmission and the development of an outbreak. Such measures may also be useful to prevent the transmission of other serious droplet-borne diseases within g-LTCFs.

The number of COVID-19 clusters in healthcare and elderly care facilities averted by vaccination of healthcare workers in Japan, February-June 2021

In Japan, a prioritized COVID-19 vaccination program using Pfizer/BioNTech messenger RNA (mRNA) vaccine among healthcare workers commenced on February 17, 2021. As vaccination coverage increases, clusters in healthcare and elderly care facilities including hospitals and nursing homes are expected to be reduced. The present study aimed to explicitly estimate the protective effect of vaccination in reducing cluster incidence in those facilities. A mathematical model was formulated using three pieces of information: (1) the incidence of clusters in facilities from October 26, 2020 to June 27, 2021; (2) the incidence of confirmed COVID-19 cases during the same period; and (3) vaccine doses among healthcare workers from February 17 to June 27, 2021, extracted from the national Vaccination System database. We found that the estimated proportion at risk in healthcare and elderly care facilities declined substantially as the vaccination coverage among healthcare workers increased; the greater risk reduction was observed in healthcare facilities, at 0.10 (95% confidence interval (CI): 0.04-0.16) times that in the pre-vaccination period, while that in elderly care facilities was 0.34 (95% CI: 0.24-0.43) times that in the earlier period. The averted numbers of clusters in healthcare facilities and elderly care facilities were estimated to be 247 (95% CI: 210-301) and 279 (95% CI: 218-354), respectively. Prioritized vaccination among healthcare workers had a marked impact on preventing the incidence of clusters in facilities.