Large-scale serosurveillance of COVID-19 in Japan: Acquisition of neutralizing antibodies for Delta but not for Omicron and requirement of booster vaccination to overcome the Omicron's outbreak

Determinants and dynamics of the seroprevalence of anti-SARS-CoV-2 antibodies in Poland

PURPOSE

In the present study, we aimed to assess the anti-SARS-CoV-2 antibodies in population and in convalescents 6 months after infection with COVID-19.

PATIENTS AND METHODS

The study population consisted of 2 groups, i.e. group I: 232 post-COVID-19 patients, and group II: 544 patients from a population cohort. Detection of anti-N antibodies was performed with Elecsys Anti-SARS-CoV-2 and anti-S antibodies with LIAISON SARS-CoV-2 S1/S2 IgG tests.

RESULTS

After the Omicron wave, gradual increase in the prevalence of the analyzed antibodies was observed in the general population - up to 92.5 ​% of anti-S and 69.7 ​% of anti-N antibodies. In the COVID-19 convalescents, 6 months after infection, 4.3 ​% and 3.7 ​% did not generate significant titers of anti-S and anti-N antibodies, respectively. Among patients, who were vaccinated, 1 ​% did not generate anti-S antibodies. The median age of non-responders was higher than that of responders. Sex did not influence the results. Comparison of anti-N and anti-S antibodies 6 months after infection in the whole group showed higher anti-N titer in patients who suffered from the disease than in the general population. In the general population, 17.4 ​% of participants had anti-N antibodies, and 9 ​% had anti-S antibodies, despite no prior vaccination or history of COVID-19.

CONCLUSIONS

High prevalence of anti-N antibodies in patients reporting no history of COVID-19 during last wave, even after official end of the pandemic suggests high prevalence of SARS-CoV-2 in the environment and frequent asymptomatic or unspecific COVID-19, what is of high importance from the public health perspective.

Sustained applicability of SARS-CoV-2 variants identification by Sanger Sequencing Strategy on emerging various SARS-CoV-2 Omicron variants in Hiroshima, Japan

BACKGROUND

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) persists, giving rise to new variants characterized by mutations in the spike protein. However, public data regarding the virus's evolutionary trend is not widely available after the downgrade of coronavirus disease 2019(COVID-19). Therefore, this study aimed to investigate the applicability of an in-house Sanger-based method for identifying SARS-CoV-2 variants, particularly focusing on newly emerged Omicron variants, and updating the epidemiology of COVID-19 during the 8th wave in Hiroshima Prefecture.

RESULTS

A total of 639 saliva samples of individuals who had tested positive for COVID-19, received from Hiroshima City Medical Association Clinical Laboratory Center between February 01, 2023, and March 12, 2024, were included in the study. SARS-CoV-2 variants were identified in 69.3% (443/639) with the mean viral titer 2 × 106 copies/mL, and high viral titer in Omicron variant XBC.1.6* (5 × 108 copies/mL) using RT-qPCR. By partial Spike gene-based sequencing using the Sanger Sequencing strategy, Omicron sub-lineages XXB.1, BA.5, and EG.1 were identified during different periods. A comprehensive phylogenetic analysis of 7383 SARS-CoV-2 strains retrieved from GISAID, collected in Hiroshima from the onset of the COVID-19 pandemic in early 2020 until July 2024, revealed the dynamic evolution of SARS-CoV-2 variants over time. The study found a similar pattern of variant distribution between the full genomes from GISAID, and the partial genomes obtained from our screening strategy during the same period.

CONCLUSIONS

Our study revealed that all SARS-CoV-2 viruses circulated in Hiroshima were Omicron variants and their sub-lineages during the 8th wave outbreak in Hiroshima. Persistent molecular surveillance of SARS-CoV-2 is needed for the decision-making and strategic planning of the public promptly. Our study added evidence for the usefulness of SARS-CoV-2 spike gene partial sequencing-based SARS-CoV-2 variant identification strategy for mass screening and molecular surveillance even though the evolution of newly emerged various SARS-CoV-2 Omicron variants.

Unravelling habituation for COVID-19-related information: A panel data study in Japan

This study examines people's habituation to COVID-19-related information over almost three years. Using publicly available data from 47 Japanese prefectures, I analyse how human mobility responded to COVID-19-related information, such as the number of COVID-19-infected cases, the declaration of a state of emergency (DSE), and several doses of vaccine using an interactive effects model, which is a type of panel data regression. The results show that Japanese citizens were generally fearful and cautious during the first wave of the unknown infection. As such, a 1% week-on-week increase in the number of infected cases results in a decrease in human mobility by 1.09-percentage-point (pp) week-on-week. However, they gradually became habituated to similar infection information during the subsequent waves, which is reflected in 0.71 pp and 0.29 pp decreases in human mobility in the second and third waves. Nevertheless, the level of habituation decreased in response to the different types of the infection, such as new variants in the fourth wave, with 0.50 pp decrease. By contrast, regarding the DSE, it is more plausible to consider that human mobility responds to varying requests rather than habituate them. Whereas a rapid vaccination program could alleviate people's concerns. I also find spatial spillovers of infection information on human mobility using a spatial weight matrix included in the regression model. However, there is no evidence of DSE or vaccination spatial spillovers, likely because both are valid only in one's own prefecture. The implementation of flexible human mobility control policies by closely monitoring human mobility can prevent excessive or insufficient mobility control requests. Such a flexible policy can efficiently suppress infection spread and prevent economic activity reduction more than necessary. These implications are useful for evidence-based policymaking during future pandemics.

Epitopes of an antibody that neutralizes a wide range of SARS-CoV-2 variants in a conserved subdomain 1 of the spike protein

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued, enabling the virus to escape from host immunity by changing its spike antigen, while biased toward the receptor-binding domain and N-terminal domain. Here, we isolated a novel pan-SARS-CoV-2 neutralizing antibody (which we named MO11) for even the recent dominators XBB.1.16 and EG.5.1, from a convalescent patient who had received three doses of an original mRNA COVID-19 vaccination. A cryo-electron microscopy analysis of the spike-MO11 complex at 2.3 Å atomic resolution revealed that it recognizes a conserved epitope hidden behind a glycan shield at N331 on subdomain 1 (SD1), holding both the N- and C-terminal segments comprising SD1. Our identification of MO11 unveiled the functional importance of SD1 for the spike's function, and we discuss the potential availability of a novel common epitope among the SARS-CoV-2 variants.IMPORTANCENovel severe acute respiratory syndrome coronavirus 2 variants with immune evasion ability are still repeatedly emerging, nonetheless, a part of immunity developed in responding to the antigen of earlier variants retains efficacy against recent variants irrespective of the numerous mutations. In exploration for the broadly effective antibodies, we identified a cross-neutralizing antibody, named MO11, from the B cells of the convalescent patient. MO11 targets a novel epitope in subdomain 1 (SD1) and was effective against all emerging variants including XBB.1.16 and EG.5.1. The neutralizing activity covering from D614G to EG.5.1 variants was explained by the conservation of the epitope, and it revealed the importance of the subdomain on regulating the function of the antigen for viral infection. Demonstrated identification of the neutralizing antibody that recognizes a conserved epitope implies basal contribution of such group of antibodies for prophylaxis against COVID-19.

Real-world clinical outcomes of treatment with molnupiravir for patients with mild-to-moderate coronavirus disease 2019 during the Omicron variant pandemic

It is unclear whether molnupiravir has a beneficial effect on vaccinated patients infected with the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We here evaluated the efficacy of molnupiravir in patients with mild-to-moderate coronavirus disease 2019 (COVID-19) during the Omicron variant surge in Fukushima Prefecture, Japan. We enrolled patients with mild-to-moderate COVID-19 who were admitted to hospitals between January and April, 2022. Clinical deterioration after admission was compared between molnupiravir users (n = 230) and non-users (n  = 690) after 1:3 propensity score matching. Additionally, we performed forward stepwise multivariate logistic regression analysis to evaluate the association between clinical deterioration after admission and molnupiravir treatment in the 1:3 propensity score-matched subjects. The characteristics of participants in both groups were balanced as indicated by covariates with a standardized mean difference of < 0.1. Regarding comorbidities, there was no imbalance between the two groups, except for the presence of hypertension, dyslipidemia, diabetes mellitus, and cardiac disease. The clinical deterioration rate was significantly lower in the molnupiravir users compared to the non-users (3.90% vs 8.40%; P = 0.034). Multivariate logistic regression analysis demonstrated that receiving molnupiravir was a factor for preventing deterioration (odds ratio 0.448; 95% confidence interval 0.206-0.973; P = 0.042), independent of other covariates. This real-world study demonstrates that molnupiravir contributes to the prevention of deterioration in COVID-19 patients after hospitalization during the Omicron variant phase.

Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants

We identified neutralizing monoclonal antibodies against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants (including Omicron variants BA.5 and BA.2.75) from individuals who received two doses of mRNA vaccination after they had been infected with the D614G virus. We named them MO1, MO2, and MO3. Among them, MO1 showed particularly high neutralizing activity against authentic variants: D614G, Delta, BA.1, BA.1.1, BA.2, BA.2.75, and BA.5. Furthermore, MO1 suppressed BA.5 infection in hamsters. A structural analysis revealed that MO1 binds to the conserved epitope of seven variants, including Omicron variants BA.5 and BA.2.75, in the receptor-binding domain of the spike protein. MO1 targets an epitope conserved among Omicron variants BA.1, BA.2, and BA.5 in a unique binding mode. Our findings confirm that D614G-derived vaccination can induce neutralizing antibodies that recognize the epitopes conserved among the SARS-CoV-2 variants. IMPORTANCE Omicron variants of SARS-CoV-2 acquired escape ability from host immunity and authorized antibody therapeutics and thereby have been spreading worldwide. We reported that patients infected with an early SARS-CoV-2 variant, D614G, and who received subsequent two-dose mRNA vaccination have high neutralizing antibody titer against Omicron lineages. It was speculated that the patients have neutralizing antibodies broadly effective against SARS-CoV-2 variants by targeting common epitopes. Here, we explored human monoclonal antibodies from B cells of the patients. One of the monoclonal antibodies, named MO1, showed high potency against broad SARS-CoV-2 variants including BA.2.75 and BA.5 variants. The results prove that monoclonal antibodies that have common neutralizing epitopes among several Omicrons were produced in patients infected with D614G and who received mRNA vaccination.

Using Serological Markers for the Surveillance of Plasmodium vivax Malaria: A Scoping Review

The utilisation of serological surveillance methods for malaria has the potential to identify individuals exposed to Plasmodium vivax, including asymptomatic carriers. However, the application of serosurveillance varies globally, including variations in methodology and transmission context. No systematic review exists describing the advantages and disadvantages of utilising serosurveillance in various settings. Collation and comparison of these results is a necessary first step to standardise and validate the use of serology for the surveillance of P. vivax in specific transmission contexts. A scoping review was performed of P. vivax serosurveillance applications globally. Ninety-four studies were found that met predefined inclusion and exclusion criteria. These studies were examined to determine the advantages and disadvantages of serosurveillance experienced in each study. If studies reported seroprevalence results, this information was also captured. Measurement of antibodies serves as a proxy by which individuals exposed to P. vivax may be indirectly identified, including those with asymptomatic infections, which may be missed by other technologies. Other thematic advantages identified included the ease and simplicity of serological assays compared to both microscopy and molecular diagnostics. Seroprevalence rates varied widely from 0-93%. Methodologies must be validated across various transmission contexts to ensure the applicability and comparability of results. Other thematic disadvantages identified included challenges with species cross-reactivity and determining changes in transmission patterns in both the short- and long-term. Serosurveillance requires further refinement to be fully realised as an actionable tool. Some work has begun in this area, but more is required.

Fourth mRNA vaccination increases cross-neutralizing antibody titers against SARS-CoV-2 variants, including BQ.1.1 and XBB, in a very elderly population

BACKGROUND

Omicron variants with immune evasion have emerged, and they continue to mutate rapidly, raising concerns about the weakening of vaccine efficacy, and the very elderly populations are vulnerable to Coronavirus Disease 2019 (COVID-19). Therefore, to investigate the effect of multiple doses of mRNA vaccine for the newly emerged variants on these populations, cross-neutralizing antibody titers were examined against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants, including BQ.1.1 and XBB.

METHODS

Blood samples were taken from residents at four long-term care facilities in Hyogo prefecture, Japan (median age, 91 years), after 3rd (n = 67) and 4th (n = 48) mRNA vaccinations, from April to October 2022. A live virus microneutralization assay was performed to determine the neutralizing antibody titers in participants' sera.

RESULTS

After 3rd vaccination, cross-neutralizing antibody prevalence against conventional (D614G) virus, Delta, Omicron BA.2, BA.5, BA.2.75, BQ.1.1, and XBB were 100%, 97%, 81%, 51%, 67%, 4%, and 21%, respectively. After 4th vaccination, the antibody positivity rates increased to 100%, 100%, 98%, 79%, 92%, 31%, and 52%, respectively. The 4th vaccination significantly increased cross-neutralizing antibody titers against all tested variants.

CONCLUSION

The positivity rates for BQ.1.1 and XBB increased after 4th vaccination, although the titer value was lower than those of BA.5 and BA.2.75. Considering the rapid mutation of viruses and the efficacy of vaccines, it may be necessary to create a system that can develop vaccines suitable for each epidemic in consideration of the epidemic of the virus.

Distinguish the Severity of Illness Associated with Novel Coronavirus (COVID-19) Infection via Sustained Vowel Speech Features

The authors are currently conducting research on methods to estimate psychiatric and neurological disorders from a voice by focusing on the features of speech. It is empirically known that numerous psychosomatic symptoms appear in voice biomarkers; in this study, we examined the effectiveness of distinguishing changes in the symptoms associated with novel coronavirus infection using speech features. Multiple speech features were extracted from the voice recordings, and, as a countermeasure against overfitting, we selected features using statistical analysis and feature selection methods utilizing pseudo data and built and verified machine learning algorithm models using LightGBM. Applying 5-fold cross-validation, and using three types of sustained vowel sounds of /Ah/, /Eh/, and /Uh/, we achieved a high performance (accuracy and AUC) of over 88% in distinguishing "asymptomatic or mild illness (symptoms)" and "moderate illness 1 (symptoms)". Accordingly, the results suggest that the proposed index using voice (speech features) can likely be used in distinguishing the symptoms associated with novel coronavirus infection.

Global SARS-CoV-2 seroprevalence from January 2020 to April 2022: A systematic review and meta-analysis of standardized population-based studies

BACKGROUND

Our understanding of the global scale of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection remains incomplete: Routine surveillance data underestimate infection and cannot infer on population immunity; there is a predominance of asymptomatic infections, and uneven access to diagnostics. We meta-analyzed SARS-CoV-2 seroprevalence studies, standardized to those described in the World Health Organization's Unity protocol (WHO Unity) for general population seroepidemiological studies, to estimate the extent of population infection and seropositivity to the virus 2 years into the pandemic.

METHODS AND FINDINGS

We conducted a systematic review and meta-analysis, searching MEDLINE, Embase, Web of Science, preprints, and grey literature for SARS-CoV-2 seroprevalence published between January 1, 2020 and May 20, 2022. The review protocol is registered with PROSPERO (CRD42020183634). We included general population cross-sectional and cohort studies meeting an assay quality threshold (90% sensitivity, 97% specificity; exceptions for humanitarian settings). We excluded studies with an unclear or closed population sample frame. Eligible studies-those aligned with the WHO Unity protocol-were extracted and critically appraised in duplicate, with risk of bias evaluated using a modified Joanna Briggs Institute checklist. We meta-analyzed seroprevalence by country and month, pooling to estimate regional and global seroprevalence over time; compared seroprevalence from infection to confirmed cases to estimate underascertainment; meta-analyzed differences in seroprevalence between demographic subgroups such as age and sex; and identified national factors associated with seroprevalence using meta-regression. We identified 513 full texts reporting 965 distinct seroprevalence studies (41% low- and middle-income countries [LMICs]) sampling 5,346,069 participants between January 2020 and April 2022, including 459 low/moderate risk of bias studies with national/subnational scope in further analysis. By September 2021, global SARS-CoV-2 seroprevalence from infection or vaccination was 59.2%, 95% CI [56.1% to 62.2%]. Overall seroprevalence rose steeply in 2021 due to infection in some regions (e.g., 26.6% [24.6 to 28.8] to 86.7% [84.6% to 88.5%] in Africa in December 2021) and vaccination and infection in others (e.g., 9.6% [8.3% to 11.0%] in June 2020 to 95.9% [92.6% to 97.8%] in December 2021, in European high-income countries [HICs]). After the emergence of Omicron in March 2022, infection-induced seroprevalence rose to 47.9% [41.0% to 54.9%] in Europe HIC and 33.7% [31.6% to 36.0%] in Americas HIC. In 2021 Quarter Three (July to September), median seroprevalence to cumulative incidence ratios ranged from around 2:1 in the Americas and Europe HICs to over 100:1 in Africa (LMICs). Children 0 to 9 years and adults 60+ were at lower risk of seropositivity than adults 20 to 29 (p < 0.001 and p = 0.005, respectively). In a multivariable model using prevaccination data, stringent public health and social measures were associated with lower seroprevalence (p = 0.02). The main limitations of our methodology include that some estimates were driven by certain countries or populations being overrepresented.

CONCLUSIONS

In this study, we observed that global seroprevalence has risen considerably over time and with regional variation; however, over one-third of the global population are seronegative to the SARS-CoV-2 virus. Our estimates of infections based on seroprevalence far exceed reported Coronavirus Disease 2019 (COVID-19) cases. Quality and standardized seroprevalence studies are essential to inform COVID-19 response, particularly in resource-limited regions.

Real-World Effectiveness of a Booster Dose of the COVID-19 Vaccines among Japanese University Students

With the spread of the Coronavirus disease 2019 (COVID-19), missing learning opportunities due to COVID-19 has been raised as a major concern for university education. We aimed to examine the effectiveness of a booster dose of COVID-19 vaccines among Japanese university students during the spread of the Omicron variant. We enrolled 249 students who became a close contact and 294 COVID-19-infected students though the Hiroshima University COVID-19 registration system. Infection rates of people in close contact with sick individuals and symptoms of infected students were examined. Close contacts who had received a booster dose showed a significantly lower infection rate (31%) compared with those with two doses (50%, p = 0.02) and the unvaccinated (71%, p = 0.002). Age- and sex-adjusted odds ratios of receipt of a booster dose vs. two doses and unvaccinated were 0.40 (95% confidence interval [CI], 0.23−0.70, p = 0.001) and 0.44 (95% CI, 0.25−0.77, p = 0.004), respectively. The incidence of severe fever (38.5°C or higher) was significantly less prevalent in those with a booster dose (16%) compared with two doses (40%, p = 0.002) and those who were unvaccinated (75%, p < 0.0001). Booster doses reduced infection rates among close-contact students and can help students to avoid missing learning opportunities.