Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike.

Soon after the emergence and global spread of the SARS-CoV-2 Omicron lineage BA.1, another Omicron lineage, BA.2, began outcompeting BA.1. The results of statistical analysis showed that the effective reproduction number of BA.2 is 1.4-fold higher than that of BA.1. Neutralization experiments revealed that immunity induced by COVID vaccines widely administered to human populations is not effective against BA.2, similar to BA.1, and that the antigenicity of BA.2 is notably different from that of BA.1. Cell culture experiments showed that the BA.2 spike confers higher replication efficacy in human nasal epithelial cells and is more efficient in mediating syncytia formation than the BA.1 spike. Furthermore, infection experiments using hamsters indicated that the BA.2 spike-bearing virus is more pathogenic than the BA.1 spike-bearing virus. Altogether, the results of our multiscale investigations suggest that the risk of BA.2 to global health is potentially higher than that of BA.1.

Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5.

After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. We further provided the structure of the BA.4/5 spike receptor-binding domain that binds to human ACE2 and considered how the substitutions in the BA.4/5 spike play roles in ACE2 binding and immune evasion. Moreover, experiments using hamsters suggested that BA.4/5 is more pathogenic than BA.2. Our multiscale investigations suggest that the risk of BA.2 subvariants, particularly BA.4/5, to global health is greater than that of original BA.2.

Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.

The SARS-CoV-2 Omicron BA.1 variant emerged in 20211 and has multiple mutations in its spike protein2. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways3 demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.

Coronavirus Disease 19 (COVID-19) Vaccine Effectiveness Against Symptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Delta-Dominant and Omicron-Dominant Periods in Japan: A Multicenter Prospective Case-control Study (Factors Associated with SARS-CoV-2 Infection and the Effectiveness of COVID-19 Vaccines Study).

BACKGROUND: Although several coronavirus disease 2019 (COVID-19) vaccines initially showed high efficacy, there have been concerns because of waning immunity and the emergence of variants with immune escape capacity. METHODS: A test-negative design case-control study was conducted in 16 healthcare facilities in Japan during the Delta-dominant period (August-September 2021) and the Omicron-dominant period (January-March 2022). Vaccine effectiveness (VE) against symptomatic severe acute respiratory syndrome coronavirus 2 infection was calculated for 2 doses for the Delta-dominant period and 2 or 3 doses for the Omicron-dominant period compared with unvaccinated individuals. RESULTS: The analysis included 5795 individuals with 2595 (44.8%) cases. Among vaccinees, 2242 (55.8%) received BNT162b2 and 1624 (40.4%) received messenger RNA (mRNA)-1273 at manufacturer-recommended intervals. During the Delta-dominant period, VE was 88% (95% confidence interval [CI], 82-93) 14 days to 3 months after dose 2 and 87% (95% CI, 38-97) 3 to 6 months after dose 2. During the Omicron-dominant period, VE was 56% (95% CI, 37-70) 14 days to 3 months since dose 2, 52% (95% CI, 40-62) 3 to 6 months after dose 2, 49% (95% CI, 34-61) 6+ months after dose 2, and 74% (95% CI, 62-83) 14+ days after dose 3. Restricting to individuals at high risk of severe COVID-19 and additional adjustment for preventive measures (ie, mask wearing/high-risk behaviors) yielded similar estimates, respectively. CONCLUSIONS: In Japan, where most are infection-naïve, and strict prevention measures are maintained regardless of vaccination status, 2-dose mRNA vaccines provided high protection against symptomatic infection during the Delta-dominant period and moderate protection during the Omicron-dominant period. Among individuals who received an mRNA booster dose, VE recovered to a high level.

Interplay between social isolation and loneliness and chronic systemic inflammation during the COVID-19 pandemic in Japan: Results from U-CORONA study.

In the face of the global coronavirus disease 2019 (COVID-19) pandemic, billions of people were forced to stay at home due to the implementation of social distancing and lockdown policies. As a result, individuals lost their social relationships, leading to social isolation and loneliness. Both social isolation and loneliness are major risk factors for poor physical and mental health status through enhanced chronic inflammation; however, there might be an interplay between social isolation and loneliness on the association with chronic inflammation. We aimed to clarify the link between social relationships and inflammation in the context of the COVID-19 pandemic by distinguishing whether social isolation only, loneliness only, or both were associated with chronic inflammation markers among community-dwelling adults. The data of 624 people (aged 18-92 years, mean 51.4) from the Utsunomiya COVID-19 seROprevalence Neighborhood Association (U-CORONA) study, which targeted randomly sampled households in Utsunomiya city, Japan, were analyzed. Social isolation was assessed as a structural social network by asking the number of social roles they have on a daily basis. Loneliness was measured with the UCLA loneliness scale. As chronic inflammation biomarkers, neutrophil-to-lymphocyte ratio (NLR) and the concentration of high-sensitivity C-reactive protein (CRP) were measured. Generalized estimating equations method was employed to take into account the correlations within households. Isolated-Lonely condition (i.e., being both socially isolated and feeling lonely) was associated with higher NLR among men (B = 0.141, 95%CI = -0.01 to 0.29). Interestingly, Nonisolated-Lonely condition (i.e., not socially isolated but feeling lonely) was associated with lower CRP among women (B = -0.462, 95%CI = -0.82 to -0.10) and among the working-age population (B = -0.495, 95%CI = -0.76 to -0.23). In conclusion, being both socially isolated and feeling lonely was associated with chronic inflammation. Assessing both social isolation and loneliness is critical for proper interventions to mitigate the impact of poor social relationships on health, especially in the context of the COVID-19 pandemic.

Specific sequelae symptoms of COVID-19 of Omicron variant in comparison with non-COVID-19 patients: a retrospective cohort study in Japan.

Background: The specific long-term sequela of coronavirus disease 2019 (COVID-19), also known as long COVID of the Omicron variant remain unclear, due to a lack of cohort studies that include non-COVID patients with cold-like symptoms. The study was conducted to examine specific sequelae symptoms after severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, which is considered the Omicron variant, compared with patients who were never-infected. Methods: In this retrospective cohort study, we sent questionnaires in November 2022, targeting those who visited our fever outpatient unit of a single institution from July to September 2022. SARS-CoV-2 infection status was determined by SARS-CoV-2 polymerase chain reaction (PCR) test results during the study period collected in electronic medical records. Clinical characteristics at 30 days or more since the date of SARS-CoV-2 PCR test were assessed by the questionnaires. Multiple logistic regression was performed to investigate the independent association between SARS-CoV-2 infection and possible sequelae symptoms. Results: In total, valid responses were received from 4,779 patients (mean age: 41.4 years, standard deviation: 19.8 years old). Among them, 3,326 (69.6%) and 1,453 (30.4%) were SARS-CoV-2 PCR test positive and never-infected, respectively. We found that patients with SARS-CoV-2 infection were more likely to have a loss of taste or smell [odds ratio (OR) 4.55, 95% confidence interval (CI): 1.93, 10.71], hair loss (OR 3.19, 95% CI: 1.67, 6.09), neurocognitive symptoms (OR 1.95, 95% CI: 1.43, 2.65), and respiratory symptoms (OR 1.23, 95% CI: 1.03, 1.47) than never-infected patients. SARS-CoV-2 infection was not associated with common cold symptoms, chronic physical distress, or diarrhea as sequelae symptoms. Further, SARS-CoV-2 vaccination showed protective effects on sequelae of loss of taste or smell and hair loss. Conclusions: Loss of taste or smell, hair loss, neurocognitive symptoms, and respiratory symptoms were found to be specific sequelae of the SARS-CoV-2 Omicron variant. It is important not to miss these symptoms that follow SARS-CoV-2 infection and to recognize and manage the long COVID.

Association of lifestyle and flourishing during the COVID-19 pandemic in Japan.

Introduction: COVID-19 have changed our lifestyle and little is known how our lifestyle associated with flourishing during COVID-19. This study examined the association between lifestyle, including sleep time, drinking, and smoking, and flourishing during the COVID-19 pandemic in Japan. Methods: We used the population-based study, Utsunomiya COVID-19 seROprevalence Neighborhood Association (U-CORONA) survey conducted in November 2021 to examine the association between lifestyle such as sleeping time, drinking and smoking, and flourishing (n = 473). Flourishing was assessed with the flourishing index, a 10-item multidimensional scale with five domains. Multivariate linear regression analysis was performed adjusted for sex, age, income, and education. Results: We found that the flourishing index was significantly lower in the group that slept less than 6 h than in the group that slept 6-8 h (coef = -0.49, SE = 0.17, p < 0.01). We also found that drinking once to several times/week showed higher flourishing than those who almost never drink (coef = 0.57, SE = 0.19, p < 0.01). Smoking was not associated with flourishing. Discussion: Sleep duration and drinking habit, but not smoking, may be important for flourishing during the COVID-19 pandemic.

Applying negative ions and an electric field to countermeasure droplets/aerosol transmission without hindering communication.

In the COVID-19 pandemic, lockdown and acryl partitions were adopted as countermeasures against droplets/aerosol infections; however, these countermeasures restrict communication. In this study, a blocking device was developed using negative ions and an electric field. The device blocks mists simulating droplets/aerosol by a maximum of 89% but transmits light and sound, which is important for communication. The device demonstrated effective blocking performance for aerosol, including the COVID-19 virus spread from patients in a clinic. Our device can help prevent infections without disrupting communication.

Effectiveness of BA.1- and BA.4/BA. 5-Containing Bivalent COVID-19 mRNA Vaccines Against Symptomatic SARS-CoV-2 Infection During the BA.5-Dominant Period in Japan.

In this multicenter, prospective, test-negative, case-control study in Japan, the effectiveness of both BA.1-containing and BA.4/BA.5-containing bivalent coronavirus disease 2019 mRNA vaccines against symptomatic infection during the BA.5-dominant period was high compared with no vaccination (65% and 76%) and moderate compared with monovalent vaccines administered over half a year earlier (46% combined).

Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.

In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.

Immune escape and waning immunity of COVID-19 monovalent mRNA vaccines against symptomatic infection with BA.1/BA.2 and BA.5 in Japan.

BACKGROUND: Repeated emergence of variants with immune escape capacity and waning immunity from vaccination are major concerns for COVID-19. We examined whether the surge in Omicron subvariant BA.5 cases was due to immune escape or waning immunity through vaccine effectiveness (VE) evaluation. METHODS: A test-negative case-control study was conducted in 16 clinics/hospitals during the BA.1/BA.2-dominant and BA.5-dominant periods. VE against symptomatic infection was estimated after adjusting for age, sex, comorbidity, occupation, testing frequency, prior infection, close contact history, clinic/hospital, week, and preventive measures. Absolute VE (aVE) was calculated for 2/3/4 doses, compared to the unvaccinated. Relative VE (rVE) was calculated, comparing 3 vs 2 and 4 vs 3 doses. RESULTS: 13,025 individuals were tested during the BA.1/BA.2-dominant and BA.5-dominant periods with similar baseline characteristics. For BA.1/BA.2, aVE was 52 % (95 %CI:34-66) 14 days-3 months post-dose 2, 42 % (29-52) > 6 months post-dose 2, 71 % (64-77) 14 days-3 months post-dose 3, and 68 % (52-79) 3-6 months post-dose 3. rVE was 49 % (38-57) 14 days-3 months post-dose 3 and 45 % (18-63) 3-6 months post-dose 3. For BA.5, aVE was 56 % (27-73) 3-6 months post-dose 2, 32 % (12-47) > 6 months post-dose 2, 70 % (61-78) 14 days-3 months post-dose 3, 59 % (48-68) 3-6 months post-dose 3, 50 % (29-64) > 6 months post-dose 3, and 74 % (61-83) ≥ 14 days post-dose 4. rVE was 56 % (45-65) 14 days-3 months post-dose 3, 39 % (27-48) 3-6 months post-dose 3, 25 % (-2-45) > 6 months post-dose 3, and 30 % (-6-54) ≥ 14 days post-dose 4. CONCLUSIONS: Booster doses initially provided high protection against BA.5 at a level similar to that against BA.1/BA.2. However, the protection seemed shorter-lasting against BA.5, which likely contributed to the surge. Furthermore, rVE post-dose 4 was low even among recent vaccinees. These results support the introduction of variant-containing vaccines and emphasize the need for vaccines with longer duration of protection.

Association between Social Engagements and Stigmatization of COVID-19 Infection among Community Population in Japan.

In the face of unknown risks, including the coronavirus disease 2019 (COVID-19) pandemic, we tend to have stigmatized perceptions. The current study aimed to examine the association of social engagements with the level of stigmatization of COVID-19 infection among the general population. The data of 429 participants of the Utsunomiya COVID-19 seroprevalence neighborhood association (U-CORONA) study, a population-based cohort study conducted in Utsunomiya City, Japan, were analyzed. Their stigmatized perception of people with COVID-19 infection was evaluated via a questionnaire for the situation if they or others in their community were to get infected. The association between social engagements (community social capital, social network diversity, and social network size) and stigmatization were analyzed by a multiple linear regression model with generalized estimating equations. Overall, females reported a higher stigmatized perception of people with COVID-19 than males. Lower education and depressive symptoms were also positively associated with higher stigmatization, while age, household income, and comorbidities were not. People with higher community social capital reported lower stigmatization (B = -0.69, 95% CI = -1.23 to -0.16), while social network diversity and social network size did not show an association with stigmatization. We found an association between community social capital and stigmatization, suggesting that enhancing their community social capital, but not social network diversity and size, has the potential to mitigate the levels of stigmatization.

Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant.

The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2.75 has a greater effective reproduction number and different immunogenicity profile than BA.5. We determined the sensitivity of BA.2.75 to vaccinee and convalescent sera as well as a panel of clinically available antiviral drugs and antibodies. Antiviral drugs largely retained potency, but antibody sensitivity varied depending on several key BA.2.75-specific substitutions. The BA.2.75 spike exhibited a profoundly higher affinity for its human receptor, ACE2. Additionally, the fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were greater than those of BA.2. Our multilevel investigations suggest that BA.2.75 acquired virological properties independent of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.

Clinical features of the 2009 swine-origin influenza A (H1N1) outbreak in Japan.

To clarify the clinical symptoms of the influenza A virus during the 2009 pandemic influenza outbreak, we describe the clinical features of outpatients diagnosed with type A influenza by use of the rapid influenza diagnostic test (RIDT) from September to December 2009. Questionnaires were used to collect prospective data on 1,122 cases with influenza-like illness at our medical institutions. The independent predictors of influenza A virus were identified on the basis of demographic features and the clinical symptoms of the patients who tested positive for influenza A virus in the RIDT test. Of the 1,122 cases tested, 389 (34.7%) were positive for the influenza A virus. The median age of the influenza-positive patients was 14, and 58.9% of the patients were male. The symptoms fever, cough, rhinorrhea, and headache were statistically dominant. A history of recent contact with persons suffering from influenza or influenza-like illness at home, school, or in the workplace was significantly more common in the positive group than in the negative group. Pneumonia was observed in 2 (0.5%) of the positive patients, but the symptoms were only severe enough to require hospitalization in 1 of the 2. No deaths were observed among the 389 RIDT-positive patients. Although the spread of influenza A virus was both rapid and extensive, mainly among children under the age of 18, it seemed to be mild. Appropriate interpretation of the RIDT on the basis of recent clinical information, and early treatment with antiviral drugs might help to prevent severe illness from influenza pandemics in the future.

Validity of Clinical Symptoms Score to Discriminate Patients with COVID-19 from Common Cold Out-Patients in General Practitioner Clinics in Japan.

OBJECTIVE: Coronavirus disease 2019 (COVID-19) has spread worldwide, including Japan. However, little is known about the clinical symptoms which discriminate between COVID-19 and non-COVID-19 among outpatients in general practitioner clinics, which is important for efficient case detection. The aim of this study was to investigate the clinical symptoms to discriminate between COVID-19 and non-COVID-19 cases among outpatients in general practitioner clinics during the second wave of the COVID-19 pandemic in Japan in August 2020. METHODS: The records of 360 patients who visited a clinic with suspicion of infectious disease and underwent COVID-19 PCR test between 1 and 14 August 2020 were used. The patients filled out a questionnaire on possible clinical symptoms and transmission routes. Multivariate logistic regression was used to investigate the association between clinical symptoms and COVID-19 status. RESULTS: COVID-19-positive patients were 17 (4.7%). Multiple logistic regression analyses showed that anosmia (odds ratio (OR), 25.94 95% confidence interval (CI), 7.15-94.14; p < 0.001), headache (OR, 3.31 95% confidence interval (CI), 0.98-11.20; p = 0.054), sputum production (OR, 3.32 CI, 1.01-10.90; p = 0.048) and history of visiting an izakaya or bar (OR, 4.23 CI, 0.99-18.03; p = 0.051) were marginally significantly associated withbeing COVID-19 positive. This model showed moderate predictive power (area under receiver operating characteristic curve = 0.870 CI, 0.761 to 0.971). CONCLUSIONS: We found that anosmia, headache, sputum production, history of visiting an izakaya or bar were associated with COVID-19, which can be used to detect patients with COVID-19 in out-patient clinics in Japan. The findings of this study need to be verified in other clinics and hospitals in Japan and other countries with universal healthcare coverages.

Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan.

The clinical characteristics of patients with N501Y mutation in SARS-CoV-2 variants (N501YV) is not fully understood, especially in the setting of general practice. In this retrospective cohort study, COVID-19 patients admitted to one general practitioner clinic between 26 March and 26 May 2021 were retrospectively analyzed. The characteristics, clinical symptoms and radiological findings before treatment were compared between N501YV and wild-type 501N. Twenty-eight patients were classified as wild-type 501N and 24 as N501YV. The mean (±standard deviation) age was 37.4 (±16.1) years, with no significant difference between groups. Among clinical symptoms, prevalence of fever of 38 degrees Celsius (°C) or higher was significantly higher in the N501YV group than in the wild-type 501N group (p = 0.001). Multivariate analysis showed that fever of 38 °C or higher remained significantly associated with N501YV (adjust odds ratio [aOR]: 6.07, 95% confidence interval [CI]: 1.68 to 21.94). For radiological findings, the lung involvement area was significantly larger in patients infected with N501YV (p = 0.013). In conclusion, in the N501YV group, fever of 38 °C or higher and extensive pneumonia were more frequently observed compared to the wild-type 501N group. There was no significant difference in terms of other demographics and clinical symptoms.

Seroprevalence of SARS-CoV-2 in Utsunomiya City, Greater Tokyo, after the first pandemic in 2020.

BACKGROUND: A seroepidemiological study was conducted on a random sample of households in Utsunomiya City, Tochigi Prefecture, Greater Tokyo, Japan, to assess the seroprevalence of SARS-CoV-2. METHODS: The level of IgG antibodies in the blood of the recruited subjects was assessed using chemiluminescence immunoassay analysis. In addition, the population-based prevalence of SARS-CoV-2 was estimated. RESULTS: Three positive afebrile cases were confirmed. The estimated unweighted prevalence and weighted prevalence of SARS-CoV-2 infection were 0.40% and 1.23%, respectively. CONCLUSIONS: This study suggests that the prevalence of SARS-CoV-2 may have been underestimated. Wider testing strategies may lead to revealing more SARS-CoV-2 cases.

Association between Social Integration and Face Mask Use Behavior during the SARS-CoV-2 Pandemic in Japan: Results from U-CORONA Study.

Face mask use is a critical behavior to prevent the spread of SARS-CoV-2. We aimed to evaluate the association between social integration and face mask use during the COVID-19 pandemic in a random sample of households in Utsunomiya City, Greater Tokyo, Japan. Data included 645 adults in the Utsunomiya COVID-19 seROprevalence Neighborhood Association (U-CORONA) study, which was conducted after the first wave of the pandemic, between 14 June 2020 and 5 July 2020, in Utsunomiya City. Social integration before the pandemic was assessed by counting the number of social roles, based on the Cohen's social network index. Face mask use before and during the pandemic was assessed by questionnaire, and participants were categorized into consistent mask users, new users, and current non-users. Multinomial logistic regression analysis was used to examine the association between lower social integration score and face mask use. To account for possible differential non-response bias, non-response weights were used. Of the 645 participants, 172 (26.7%) were consistent mask users and 460 (71.3%) were new users, while 13 (2.0%) were current non-users. Lower social integration level was positively associated with non-users (RRR: 1.76, 95% CI: 1.10, 2.82). Social integration may be important to promote face mask use.