Omicron variant (B.1.1.529) of SARS-CoV-2: Mutation, infectivity, transmission, and vaccine resistance

COVID-19 infection was associated with poor sperm quality: a cross-sectional and longitudinal clinical observation study

To ascertain whether COVID-19 infection affects sperm quality and measure the scale of the effects. A cross sectional study and a longitudinal study were conducted during the SARS-CoV-2 pandemic (from September 7th 2022 to late January 2023) in China. 604 patients participated in the cross sectional study; 140 in the longitudinal study with 149 unaffected natural controls. The cross sectional study included participants who produce semen sample after COVID-19. The longitudinal study included COVID-19 positive participants who could provide semen samples before and after the infection. In addition, patients unaffected by the infection who could provide two consecutive semen samples over the same period were included as controls for the longitudinal study. Conventional sperm quality parameters including sperm count, motility, morphology and more recent parameters such as sperm DNA fragmentation index (DFI) and sperm chromatin immaturity were observed. In the cross sectional study, the exposure group demonstrated significantly lower total sperm count (159.58 × 106 vs. 185.42 × 106, P = 0.042), lower percentage of grade A sperms (5.37% vs. 8.45%, P = 0.009), lower progressive motility (24.74 ± 14.96% vs. 28.73 ± 16.65%, P = 0.023), lower total motility (32.04 ± 18.03% vs. 36.91 ± 20.86%, P = 0.022), and higher sperm DFI (17.50% vs. 11.75%, P = 0.030) than the controls. In the longitudinal study, after the infection, patients showed lower total sperm count (131.80 × 106 vs. 173.63 × 106, Δd = -20.49 × 106, P = 0.018 ), lower percentage of grade A sperms ( 2.61% vs. 8.50%, Δd = -3.18%, P < 0.001), lower progressive motility (19.82 ± 13.68% vs. 24.88 ± 14.97%, Δd = -5.07 ± 11.94%, P < 0.001) and lower total motility (26.64 ± 17.35% vs. 32.25 ± 18.69%, Δd = -5.62 ± 14.30%, P < 0.001) and higher DFI (32.10 ± 21.30% vs. 26.49 ± 18.54%, Δd = 5.61 ± 13.71%, P < 0.039) than before the infection, while the negative controls showed the opposite changes. Finally, in the longitudinal study, after the infection, 59.29% of the COVID-19 positive patients showed deteriorated sperm concentration, 57.86% deteriorated total sperm count, 71.43% Grade A sperm, 65.00% progressive motility, 69.29% total motility, and 75.00% sperm DFI, while the changes in negative controls were all less than 40% (P < 0.002). COVID-19 was associated with poor sperm quality. The findings would be useful for clinicians to manage men with fertility problems who suffered COVID-19.

Tracking the evolution of serum antibody levels and influencing factors post-SARS-CoV-2 infection among community residents in Fuzhou City

Objective

To track the level of serum antibodies in Fuzhou residents and analyze the possible influencing factors of serum antibodies, so as to provide a scientific basis for the adjustment of population immunity and prevention and control strategies.

Methods

Residents in the Fuzhou community who had symptoms of covid-19 infection or who had tested positive for nucleic acid or antigen since December 2022 were selected for the questionnaire survey and their sera were collected to analyze the trend of antibody changes, the antibody level was divided into high antibody group and low antibody group according to the literature data. The possible influencing factors of serum antibody level was analyzed by multivariate logistic regression model.

Results

A total of 2,521 Fuzhou residents were adopted in the study, including 223 in the high antibody group and 194 in the low antibody group. A univariate analysis showed that, there were significant differences in age (Z=-4.028, P<0.00), occupation (χ2 = 18.591, P=0.005), typical symptoms after the first infection (χ2 = 9.784, P=0.002), history of surgery (χ2 = 29.542, P<0.001), symptoms lasting more than 2 weeks after the first infection (χ2 = 4.887, P=0.027), smoking (χ2 = 18.524, P<0.001) and drinking (χ2 = 19.578, P<0.001) between the high antibody group and the low antibody group. Multivariate regression models show that, age (OR= 1.011, 95%CI: 1.002~1.020, P=0.017), history of surgery (OR=4.956,95%CI: 2.606~9.423, P<0.001),smoking (OR=2.089, 95%CI: 1.002~4.355, P=0.049), drinking (OR=2.214, 95%CI: 1.066~4.600, P=0.033) were the risk factors affecting antibody level. Typical symptoms after the first infection (OR=0.224, 95%CI: 0.086~0.579, P=0.002) and symptoms lasting more than 2 weeks after the first infection (OR=0.432, 95%CI: 0.258~0.723, P=0.001) were protective factors. By observing the trend of antibody changes in 3, 6 and 9 months, we found that the level of IgG antibody showed a decreasing trend.

Conclusions

The high level of protection was more likely to occur in young adults, people without operation history, people without smoking history, people without drinking history, people with typical symptoms after the first infection and symptoms lasting more than 2 weeks after the first infection. The level of IgG antibody was decreased in general, so it is necessary to strengthen immunization.

Epidemic evolutionarily stable strategies within an age-structured host population

To understand infectious disease dynamics, we need to understand the inextricably intertwined nature of the ecology and evolution of pathogens and hosts. Epidemiological dynamics of many infectious diseases have highlighted the importance of considering the demographics of the societies in which they spread, particularly with respect to age structure. In addition, the waves of the recent COVID-19 pandemic driven by variant replacements at an unprecedented speed show that it is vital to consider the evolutionary aspects. The classic trade-off theory of virulence addresses aspects of pathogen evolution, but here we explore in more detail the possibility of society-specific evolutionarily stable strategies (ESS) during an unfolding pandemic. Theory posits the existence under some conditions of an ESS representing the evolutionary endpoint of change. By using a demographically realistic model incorporating infection rates that vary with age, we outline which evolutionary scenarios are plausible. Focusing on the rate of infection and duration of infectivity, we ask whether an ESS exists, what characterizes it, and as a result which long-term public-health consequences may be expected. We demonstrate that the ESS of an evolving pathogen depends upon the background age-dependent frailty and mortality rates. Our findings shed important light on the plausible long-term trajectories of highly evolvable novel pathogens.

SARS-CoV-2 Genetic Variants Identified in Selected Regions of Ethiopia Through Whole Genome Sequencing: Insights from the Fifth Wave of COVID-19

BACKGROUND

The COVID-19 pandemic highlighted SARS-CoV-2 variants with increased transmissibility and immune evasion. In Ethiopia, where cases surged, the understanding of the virus's dynamics was limited. This study analyzed SARS-CoV-2 variants during the fifth wave, crucial for guiding vaccines, therapeutics, diagnostics, and understanding disease severity.

METHOD

From June to August 2022, 150 SARS-CoV-2-positive samples were randomly selected from the Ethiopian Public Health Institute repository. Sixty-three high-quality genome sequences were analyzed.

RESULTS

Of the 63 sequences, 70% were from males and 30% from females, with a median age of 34. Omicron dominated (97%, 61/63), primarily clade 22A (64%, 40/63), followed by 22B (18%, 11/63) and 21K (14%, 9/63). Delta accounted for 3.2% (2/63). Omicron was identified in all (25) vaccinated study participants. Ethiopian sequences showed limited evolutionary divergence and lower genetic diversity compared to global sequences.

CONCLUSION

Omicron was the predominant variant during Ethiopia's fifth wave, indicating recent community transmission. Despite minor genetic diversity differences, ongoing surveillance remains critical for tracking variants and informing public health interventions.

Cracking the code of a correlate of protection against SARS-CoV-2 breakthrough infection in cancer patients

The level of protection against SARS-CoV-2 breakthrough infections conferred by the presence of anti-S1 SARS-CoV-2 antibodies (IgGs) in cancer patients is still understudied. This work examines the existence of an anti-S1 immunoglobulin G (IgG) -based correlate of protection (CoP) established by prospectively collected observational data about breakthrough infections with different SARS-CoV-2 variants in a large cohort study with vaccinated cancer patients. 760 cancer patients were longitudinally followed-up, starting before first vaccination until six months after second booster. Anti-S1 SARS-CoV-2 IgGs were quantified in serum samples (N = 2958) and breakthrough infections were monitored using questionnaires, routine COVID-19 testing and medical chart review. A Generalized Estimating Equations approach was used to model the binary infection status as endpoint in relation to anti-S1 IgG titers. It is observed that higher anti-S1 IgG titers correspond to a lower probability of breakthrough infection. For the early pandemic phase, a protective anti-S1 IgG titer above 20.42 BAU/mL was observed. However, with the emergence of the Omicron variant, higher anti-S1 IgG titers are required to be protective, but no clear CoP could be identified.

Genomic evolution of SARS-CoV-2 in Morocco: Insights from whole genome sequences collected from 2020 to 2024

This study investigates the evolution and genetic diversity of SARS-CoV-2 strains circulating in Morocco to track the spread, clade distributions and mutations of the virus across various regions from February 2020 to June 2024. The genome sequences were retrieved from the GISAID database. A total of 2630 SARS-CoV-2 genome sequences were analyzed using bioinformatic tools such as Nextclade, followed by phylogenetic and statistical analyses. The study highlights the predominance of the GRA clade (Omicron variant) since November 2021, while clades such as G, GH, GR, and GRY were identified earlier. The GRA clade exhibited the highest number of non-synonymous mutations, particularly in the Spike (S) gene, suggesting strong evolutionary pressure. The correlation analysis between structural and non-structural proteins revealed key interactions between S and NSP5, providing insights into the viral replication and assembly processes. This work gives new insights to the dynamics of SARS-CoV-2 in Morocco and underscores the importance of ongoing genomic surveillance to respond to emerging variants and potential future outbreaks.

Inhibition potential of natural flavonoids against selected omicron (B.1.19) mutations in the spike receptor binding domain of SARS-CoV-2: a molecular modeling approach

The omicron (B.1.19) variant of contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is considered a variant of concern (VOC) due to its increased transmissibility and highly infectious nature. The spike receptor-binding domain (RBD) is a hotspot of mutations and is regarded as a prominent target for screening drug candidates owing to its crucial role in viral entry and immune evasion. To date, no effective therapy or antivirals have been reported; therefore, there is an urgent need for rapid screening of antivirals. An extensive molecular modelling study has been performed with the primary goal to assess the inhibition potential of natural flavonoids as inhibitors against RBD from a manually curated library. Out of 40 natural flavonoids, five natural flavonoids, namely tomentin A (-8.7 kcal/mol), tomentin C (-8.6 kcal/mol), hyperoside (-8.4 kcal/mol), catechin gallate (-8.3 kcal/mol), and corylifol A (-8.2 kcal/mol), have been considered as the top-ranked compounds based on their binding affinity and molecular interaction profiling. The state-of-the-art molecular dynamics (MD) simulations of these top-ranked compounds in complex with RBD exhibited stable dynamics and structural compactness patterns on 200 nanoseconds. Additionally, complexes of these molecules demonstrated favorable free binding energies and affirmed the docking and simulation results. Moreover, the post-simulation validation of these interacted flavonoids using principal component analysis (PCA) revealed stable interaction patterns with RBD. The integrated results suggest that tomentin A, tomentin C, hyperoside, catechin gallate, and corylifol A might be effective against the emerging variants of SARS-CoV-2 and should be further evaluated using in-vitro and in-vivo experiments.Communicated by Ramaswamy H. Sarma.

Prospective clinical performance of CoVarScan in identifying SARS-CoV-2 Omicron subvariants

The purpose of this work was to evaluate the performance of CoVarScan, a multiplex fragment analysis approach, in identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of the Omicron lineage rapidly and accurately. The ability to identify variants with high fidelity and low turnaround time is important both epidemiologically and clinically for pandemic monitoring and therapeutic monoclonal antibody (mAb) selection. Currently, the gold-standard test for this task is whole-genome sequencing (WGS), which is prohibitively expensive and/or inaccessible due to equipment requirements for many laboratories. Omicron variants have been closely related, so the ability of genotyping tests to differentiate them is an important, outstanding question. CoVarScan uses PCR targeting eight SARS-CoV-2 mutational hot spots. In total, 4,918 SARS-CoV-2-positive cases between 17 December 2021 and 31 January 2024 were included in the analysis. CoVarScan achieved 96.5% concordance with WGS and could detect unique mutational signatures for BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, XBB, and BA.2.86. These are the major variants of concern (VOCs) that have dominated since Omicron originally appeared in December 2021. Lastly, based on panel design, we predict a unique mutational pattern for the newly emergent, highly mutated variant BA.2.87. CoVarScan can rapidly, accurately, and cost-effectively identify all Omicron variants in a scalable manner. Furthermore, CoVarScan does not require design alterations to detect new VOCs. CoVarScan performs as accurately as WGS with higher sensitivity, allowing its use as a tool to quickly identify variants for epidemiological surveillance and clinical decision-making in the selection of effective therapeutic mAbs.IMPORTANCEAlmost 5 years since the start of the pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern continue to emerge, with mutations conferring new properties like increased transmissibility and resistance to therapeutic monoclonal antibodies and vaccines. Conventionally, whole-genome sequencing (WGS) has characterized new SARS-CoV-2 variants, but results come too late for clinical actionability. WGS suffers from high failure rates for samples with low viral RNA and is inaccessible for lower-resource laboratories. As new variants like Omicron appear, it is necessary to develop rapid and accurate testing to distinguish between variants. Fast and accurate identification of sensitive viral lineages would allow tailored use of monoclonal antibodies that may otherwise have been pulled from the market due to rising overall resistance. Rapid results also allow public health officials to make policy decisions in time to reduce morbidity and mortality for sensitive populations such as patients who are immunocompromised or have significant medical comorbidities.

Clinical characteristics and prediction model of re-positive nucleic acid tests among Omicron infections by machine learning: a real-world study of 35,488 cases

BACKGROUND

During the Omicron BA.2 variant outbreak in Shanghai, China, from April to May 2022, PCR nucleic acid test re-positivity (TR) occurred frequently, yet the risk factors and predictive models for TR remain unclear. This study aims to identify the factors influencing Omicron TR and to develop machine learning models to predict TR risk. Accurately predicting re-positive patients is crucial for identifying high-risk individuals, optimizing resource allocation, and developing personalized treatment and management plans, thereby effectively controlling the spread of the epidemic, reducing community burden, and ensuring public health.

METHODS

A retrospective study was conducted among individuals infected with Omicron BA.2 variant from April 12 to May 25, 2022, in the largest Shanghai Fangcang shelter hospital. Five machine learning models were compared, including k-nearest-neighbors (KNN), logistic regression (logistic), bootstrap aggregation (bagging), error back-propagation (BP) neural network, and support vector machines (SVM), to select the best prediction model for the TR risk factors.

RESULTS

A total of 35,488 cases were included in this real-world study. The TR and control groups comprised of 6,171 and 29,317 cases respectively, with a re-positive rate of 17.39%. Higher occurrence of TR was observed in young age, males, those with obvious symptoms, underlying diseases, and a low Ct value. The KNN model proved to be the best in predicting the prognosis in the overall evaluation (accuracy = 0.8198, recall = 0.8026, and AUC = 0.8110 in the test set).

INTERPRETATION

Higher TR risk was found in infected cases who were underage or with underlying diseases; vaccine brand and inoculation status were not significantly associated with TR. KNN was the most effective machine learning model to predict TR occurrence in isolation.

Comparative Effectiveness of Antivirals and Monoclonal Antibodies for Treating COVID-19 Patients Infected With Omicron Variant: A Systematic Review and Network Meta-Analysis

Antiviral drugs likely remain effective against the SARS-CoV-2 Omicron variant, while monoclonal antibody (mAb) therapies have experienced drops in neutralizing ability. This systematic review and network meta-analysis aims to estimate the comparative effectiveness of antivirals and mAb therapies for treating COVID-19 patients infected with Omicron, capturing primarily acute outcomes. We searched multiple databases from July 4 to July 19, 2022, with updates through November 4, 2022. Studies comparing the effectiveness of antivirals or mAb to either nonuser controls or other treatments were included. Risk of bias was assessed using the Cochrane RoB 2 and ROBINS-I tools. Data extraction and verification involved five independent researchers. Among 39 studies (727,893 individuals with COVID-19, including 38 nonrandomized trials), nirmatrelvir/ritonavir and sotrovimab were associated with lower risks of mortality (HR = 0.317, 95% credible intervals [CrI] = 0.144-0.678; HR = 0.176, 95%CrI = 0.052-0.527) and hospitalization (HR = 0.479, 95%CrI = 0.319-0.711; HR = 0.489, 95%CrI = 0.293-0.797) compared with nonuser controls. Remdesivir users were associated with a lower risk of hospitalization (HR = 0.367, 95%CrI = 0.147-0.868) but not mortality. Molnupiravir and bebtelovimab showed no significant benefits for these outcomes. In conclusion, among individuals infected with COVID-19 during the Omicron wave, mortality risk was lower with nirmatrelvir/ritonavir or sotrovimab use, whereas hospitalization was reduced with nirmatrelvir/ritonavir, remdesivir, or sotrovimab. Sotrovimab and nirmatrelvir/ritonavir were effective against Omicron B.1.1.529/BA.1 and BA.2/BA.4/BA.5 subvariants, respectively. A key limitation is that findings rely on data from the last search and may be impacted by potential changes in mortality risk due to immune evasion by emerging variants, highlighting the need for ongoing randomized trials across variants and populations. TRIAL REGISTRATION: The study was registered on PROSPERO, CRD42022351508.

Research progress of spike protein mutation of SARS-CoV-2 mutant strain and antibody development

The coronavirus disease 2019 (COVID-19) is a respiratory disease with a very high infectious rate caused by the Severe Acute Respiratory Syndrome Coronavirus-2(SARS-CoV-2). Because SARS-CoV-2 is easy to mutate, the continuous emergence of SARS-CoV-2 variant strains not only enhances the infectivity of the SARS-CoV-2 but also brings great obstacles to the treatment of COVID-19. Neutralizing antibodies have achieved good results in the clinical application of the novel coronavirus pneumonia, which can be used for pre-infection protection and treatment of novel coronavirus patients. This review makes a detailed introduction to the mutation characteristics of SARS-CoV-2, focusing on the molecular mechanism of mutation affecting the infectivity of SARS-CoV-2, and the impact of mutation on monoclonal antibody therapy, providing scientific reference for the prevention of SARS-CoV-2 variant strains and the research and development of antibody drugs.

Engineered bispecific antibodies with enhanced breadth and potency against SARS-CoV-2 variants and SARS-related coronaviruses

The concern of COVID-19 persists due to the continuous emergence of variants and the potential spillover of animal coronaviruses. The broad-spectrum neutralizing antibodies play a pivotal role in the prevention and treatment of coronavirus (CoV) infections. Here, we constructed 18 bi-specific antibodies (bsAbs) using 9 antibodies isolated from COVID-19 convalescents and vaccinated individuals, designed as dual variable domain immunoglobulin (DVD-Ig). A bsAb 5-HI showed a high binding capability to the S1 subunit of spike and exhibited breadth and potency against pseudotyped SARS-CoV-2 variants of concerns (VOCs) and SARS-related-CoVs (SARSr-CoVs), with half maximal effective concentration (EC50) of 0.028-3.444 nM and 50% inhibitory concentration (IC50) of 0.008-0.800 nM. In addition, it retained neutralization potency against the peudotyped virus of recently prevalent JN.1 strain (IC50, 12.74 nM). We found that the parental antibodies showed weak or no binding to the receptor binding domain (RBD) of the SARS-CoV, EG.5.1, and JN.1. However, the 5-HI maintained the binding with RBD and prevented the binding between hACE2 and RBD (IC50 for the RBD of SARS-CoV, 1.067 nM; EG.5.1, 0.423 nM; JN.1, 0.223 nM). In neutralization assays with the authentic virus, we found that the 5-HI effectively neutralized Omicron variants XBB.1.5 (IC50, 0.308 nM), EG.5.1 (IC50, 0.129 nM), and JN.1 (IC50, 13.692 nM), while its parental antibodies showed weakened or no neutralization. Therefore, the 5-HI represents a promising candidate for further development in the treatment and prevention of ongoing evolved SARS-CoV-2 VOCs and other SARSr-CoVs that potentially emerge in the future.

Local effects of non-pharmaceutical interventions on mitigation of COVID-19 spread through decreased human mobilities in Japan: a prefecture-level mediation analysis

To control the COVID-19 epidemic, the Japanese government and the local governments have repeatedly implemented non-pharmaceutical interventions (NPIs) throughout 2020-2022. Using Bayesian state-space mediation models, we examined the effect of repeated NPIs on infection spread mitigation, mediated by human mobility changes in each prefecture during three epidemic phases: from April 1, 2020 to February 28, 2021; from March 1, 2021 to December 16, 2021; and from December 17, 2021 to December 31, 2022. In the first phase, controlling downtown populations at nighttime was effective in mitigating the infection spread in almost all prefectures. In the second and third phases, the effect was not clear, especially in metropolitan prefectures. Controlling visitors from the central prefectures of metropolitan areas was effective in mitigating infection spread in the surrounding prefectures during all phases. These results suggest that the local spread of infection can be mitigated by focusing on nighttime human mobility control in downtown areas before the epidemic spreads widely and transmission routes become more diverse, and that the geospatial spread of infection can be prevented by controlling the flows of people from large cities to other areas.

Characteristics and outcomes of ICU-admitted COVID-19 patients in the Omicron and Alpha-dominated periods

BACKGROUND

Comparing the outcomes of intensive care unit (ICU) admitted COVID-19 patients during the Alpha and Omicron-dominated periods.

METHODS

Patients with critical COVID-19 disease, requiring ICU admission from May to September 2021 and February to August 2022, were enrolled from a single medical center in Northern Taiwan. Clinical demographics, comorbidities, disease severity, and management strategies were recorded. The 28-day mortality from the two periods were compared both in the original and propensity score (PS)-matched cohort.

RESULTS

Of 231 patients, 72 (31.2%) were from the Alpha period and 159 (68.8%) from the Omicron period. Patients in the Omicron period were older, had a lower body mass index, more comorbidities, higher disease severities, and increased 28-day mortality (26.4% vs. 13.9%, p = 0.035). In multivariable analysis, the Omicron-dominated period was not identified as an independent factor associated with increased 28-day mortality. COVID-19 patients in Alpha- and Omicron-dominated periods had comparable 28-day mortality in PS-matched cohort (12.1% vs. 18.2%, p = 0.733). Independent factors associated with 28-day mortality were a lower PF ratio (PF ratio <100, adjusted odds ratio [aOR] 2.68, 95% confidence interval, CI 1.21-5.94), septic shock ([aOR] 2.39, 95% CI 1.12-5.09) and absence of remdesivir ([aOR] 0.36, 95% CI 0.16-0.83).

CONCLUSION

While patients in the Omicron period exhibited greater severity, the variant was not independently linked to higher 28-day mortality in ICU-admitted patients.

Serious Game Development for Public Health: Participatory Design Approach to COVID-19 Quarantine Policy Education

Background

Public health education plays a crucial role in effectively addressing infectious diseases such as COVID-19. However, existing educational materials often provide only foundational information, and traditional group education faces challenges due to social distancing policies.

Objective

Addressing these gaps, our study introduces a serious game called "Flattening the Curve." This interactive experience immerses learners in the role of quarantine policy managers, offering unique insights into the effects and challenges of social distancing policies.

Methods

The development of the game adhered to the SERES framework, ensuring a scientifically designed foundation. To achieve its learning objectives, the game incorporated learning and game mechanics including an agent-based infection model, a social distancing policy model, and an economic model, which were developed based on previous literature. After defining a broad concept of scientific and design foundations, we used a participatory design process. This study included 16 undergraduates and took place over one semester. Participants played the game, gave feedback, and answered surveys. The game was improved based on participants' feedback throughout the process. Participants' feedback was analyzed based on the Design, Play, and Experience framework. Surveys were conducted before and after the activity and analyzed to assess participants' evaluation of and satisfaction with the game.

Results

The game successfully achieved its learning objectives, encompassing a comprehensive understanding of infectious disease characteristics; the disease transmission process; the necessity and efficacy of quarantine policies and their delicate balance with economic factors; and the concept of flattening the curve. To achieve this, the game includes the following: (1) an agent-based infection model based on the modified Susceptible-Exposed-Infectious-Hospitalized-Recovered (SEIHR) model with five infectious disease scenarios; (2) a quarantine policy model with social distancing, travel control, and intensive care unit management; and (3) an economic model that allows users to consider the impact of quarantine policies on a community's economy. In response to participatory design feedback, the game underwent meticulous modifications, including refining game systems, parameters, design elements, the user interface, and interactions. Key feedback included requests for more scenarios and engaging yet simple game elements, as well as suggestions for improving the scoring system and design features. Notably, concerns about the fairness of the outcome evaluation system (star rating system), which could incentivize prioritizing economic activity over minimizing casualties, were raised and addressed by replacing the star rating system with a progress-based vaccine development system. Quantitative evaluation results reflect participants' positive assessments of the game through the learner-centric approach.

Conclusions

The serious game "Flattening the Curve," developed through a participatory design approach, emerges as a valuable tool for public health education, particularly concerning social distancing policies. The game and its source code are openly accessible online, enabling widespread use for research and educational purposes.

Younger and rural children are more likely to be hospitalized for SARS-CoV-2 infections

PURPOSE

To identify characteristics of SARS-CoV-2 infection that are associated with hospitalization in children initially evaluated in a Pediatric Emergency Department (ED).

METHODS

We identified cases of SARS-CoV-2 positive patients seen in the Arkansas Children's Hospital (ACH) ED or hospitalized between May 27, 2020, and April 28, 2022, using ICD-10 codes within the Pediatric Hospital Information System (PHIS) Database. We compared infection waves for differences in patient characteristics and used logistic regressions to examine which features led to a higher chance of hospitalization.

FINDINGS

We included 681 pre-Delta cases, 673 Delta cases, and 970 Omicron cases. Almost 17% of patients were admitted to the hospital. Compared to Omicron-infected children, pre-Delta and Delta-infected children were twice as likely hospitalized (OR = 2.2 and 2.0, respectively; p<0.0001). Infants under one year were >3 times as likely to be hospitalized than children ages 5-14 years regardless of wave (OR = 3.42; 95%CI = 2.36-4.94). Rural children were almost three times as likely than urban children to be hospitalized across all waves (OR = 2.73; 95%CI = 1.97-3.78). Finally, those with a complex condition had nearly a 15-fold increase in odds of admission (OR = 14.6; 95%CI = 10.6-20.0).

CONCLUSIONS

Children diagnosed during the pre-Delta or Delta waves were more likely to be hospitalized than those diagnosed during the Omicron wave. Younger and rural patients were more likely to be hospitalized regardless of the wave. We suspect lower vaccination rates and larger distances from medical care influenced higher hospitalization rates.

Structural and genomic evolutionary dynamics of Omicron variant of SARS-CoV-2 circulating in Madhya Pradesh, India

The SARS-CoV-2 Omicron (B.1.1.529) variant emerged in early November 2021 and its rapid spread created fear worldwide. This was attributed to its increased infectivity and escaping immune mechanisms. The spike protein of Omicron has more mutations (>30) than any other previous variants and was declared as the variant of concern (VOC) by the WHO. The concern among the scientific community was huge about this variant, and a piece of updated information on circulating viral strains is important in order to better understand the epidemiology, virus pathogenicity, transmission, therapeutic interventions, and vaccine development. A total of 710 samples were processed for sequencing and identification up to a resolution of sub-lineage. The sequence analysis revealed Omicron variant with distribution as follows: B.1.1, B.1.1.529, BA.1, BA.2, BA.2.10, BA.2.10.1, BA.2.23, BA.2.37, BA.2.38, BA.2.43, BA.2.74, BA.2.75, BA.2.76, and BA.4 sub-lineages. There is a shift noted in circulating lineage from BA.1 to BA.2 to BA.4 over a period from January to September 2022. Multiple signature mutations were identified in S protein T376A, D405N, and R408S mutations, which were new and common to all BA.2 variants. Additionally, R346T was seen in emerging BA.2.74 and BA.2.76 variants. The emerging BA.4 retained the common T376A, D405N, and R408S mutations of BA.2 along with a new mutation F486V. The samples sequenced were from different districts of Madhya Pradesh and showed a predominance of BA.2 and its variants circulating in this region. The current study identified circulation of BA.1 and BA.1.1 variants during initial phase. The predominant Delta strain of the second wave has been replaced by the Omicron variant in this region over a period of time. This study successfully deciphers the dynamics of the emergence and replacement of various sub-lineages of SARS-CoV-2 in central India on real real-time basis.

Neutralizing Antibodies against 10 SARS-CoV-2 Variants at Two Years Post-COVISHIELD Vaccination with Special Reference to Omicron Subvariants and Booster Administration

To study the durability of neutralizing antibodies (NAbs) against ten SARS-CoV-2 variants among COVISHIELD vaccine recipients from Pune, India, 184 vaccinee samples with (pre-positives) or without (pre-negatives) prior antibody positivity were evaluated. To estimate NAb levels, a validated ten-plex MSD ACE2 neutralization assay was used. NAbs against Alpha, Beta, Delta, and Omicron/subvariants were assessed at 1 month (PD2-1) and 6 months (PD2-6) post-vaccination, post-booster dose, and 2 years (2Y) post-vaccination. In pre-negatives, the seropositivity declined from PD2-1 to PD2-6 for all variants (Omicron variants: 14-54% to 0%; non-Omicron variants: 66-100% to 8-44%). In pre-positives, the decline in seropositivity from PD2-1 to PD2-6 was seen only for Omicron variants (14-39%). At PD2-6, a significant reduction in NAb levels was observed in all vaccinees against all the variants. Irrespective of prior exposure, the diminished anti-variant antibody levels at PD2-6 increased significantly following the administration of the booster. In conclusion, the COVISHIELD vaccine booster dose did provide cross-neutralizing antibodies against broad-range SARS-CoV-2 variants with improved durability up to [16 (15-18)] months post-booster dose and two years post-vaccination.

Clinical characteristics and severity markers in hospitalized COVID-19 patients from western Mexico: a comparative analysis of Delta and Omicron variants

Introduction

COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus notable for its rapid mutation rate, which has led to the emergence of various variants such as Delta and Omicron, each with potentially different levels of transmissibility and virulence. Therefore, this study aims to compare clinical charactheristics and markers associated with the severity of COVID-19 in hospitalized patients from western Mexico who were infected with the Delta and Omicron variants of SARS-CoV-2.

Methods

This cross-sectional study involved 66 patients hospitalized for COVID-19, diagnosed by RT-qPCR. SARS-CoV-2 variants were identified through whole genome sequencing using the COVIDseq platform from Illumina. Upon admission, patients underwent a clinical history assessment, blood gas analysis, and blood biometry. Additionally, several tests and markers were measured, including the percentage of neutralizing antibodies, erythrocyte sedimentation rate (ESR), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNFα), D-dimer, lactate dehydrogenase (LDH), C-reactive protein (CRP), and ferritin.

Results and discussion

Patients hospitalized with the Omicron were found to be older, compared to those infected with the Delta (64 vs. 54 years, p = 0.006). Additionally, a higher proportion of male patients were observed in the Omicron compared to the Delta (p = 0.029). Both Omicron and Delta variants were associated with lymphopenia, although the lymphocyte count was lower in Omicron (0.9 vs. 0.56 10x3/L; p = 0.007). The COVID-GRAM scale indicated a high risk for severe disease in both groups, but the score was higher in Omicron compared to Delta (157 vs. 128 points; p = 0.0004). Patients infected with Omicron exhibited a lower percentage of neutralizing antibodies than those with Delta (35.99 vs. 81%; p < 0.05), regardless of their vaccination status. Among the markers assessed, globular ESR was found to be lower in Omicron compared to Delta (30.5 vs. 41.5 mm/h; p = 0.001), while ferritin levels were higher in patients infected with the Omicron (1,359 vs. 960.6 μg/L; p = 0.007). In patients with severe COVID-19, markers such as lymphopenia, neutralizing antibody levels, ferritin, and COVID-GRAM scores are elevated in the Omicron variant, while only the leukocyte count and ESR for the Delta variant.

COVID-19 in a common woolly monkey (Lagothrix lagothricha): First evidence of fatal outcome in a nonhuman primate after natural SARS-CoV-2 infection

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a pandemic by the World Health Organization in March 2020. Since then, viral spread from humans to animals has occurred worldwide. Nonhuman primates (NHPs) have been found to be susceptible to reverse-zoonosis transmission of SARS-CoV-2, but initial research suggested that platyrrhine primates are less susceptible than catarrhine primates. Here we report the natural SARS-CoV-2 infection of a common woolly monkey (Lagothrix lagothricha) from a wildlife rehabilitation center in Ecuador. The course of the disease, the eventual death of the specimen, and the pathological findings are described. Our results show the susceptibility of a new platyrrhine species to SARS-CoV-2 and provide evidence for the first time of a COVID-19-associated death in a naturally infected NHP. The putative route of transmission from humans, and implications for captive NHPs management, are also discussed. Given that common woolly monkeys are at risk of extinction in Ecuador, further understanding of the potential threat of SARS-CoV-2 to their health should be a conservation priority. A One Health approach is the best way to protect NHPs from a new virus in the same way that we would protect the human population.

Disposable graphene-oxide screen-printed electrode integrated with portable device for detection of SARS-CoV-2 in clinical samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis is the need of the hour, as cases are persistently increasing, and new variants are constantly emerging. The ever-changing nature of the virus leading to multiple variants, has brought an imminent need for early, accurate and rapid detection methods. Herein, we have reported the design and fabrication of Screen-Printed Electrodes (SPEs) with graphene oxide (GO) as working electrode and modified with specific antibodies for SARS-CoV-2 Receptor Binding Domain (RBD). Flexibility of design, and portable nature has made SPEs the superior choice for electrochemical analysis. The developed immunosensor can detect RBD as low as 0.83 fM with long-term storage capacity. The fabricated SPEs immunosensor was tested using a miniaturized portable device and potentiostat on 100 patient nasopharyngeal samples and corroborated with RT-PCR data, displayed 94 % sensitivity. Additionally, the in-house developed polyclonal antibodies detected RBD antigen of the mutated Omicron variant of SARS-CoV-2 successfully. We have not observed any cross-reactivity/binding of the fabricated immunosensor with MERS (cross-reactive antigen) and Influenza A H1N1 (antigen sharing common symptoms). Hence, the developed SPEs sensor may be applied for bedside point-of-care diagnosis of SARS-CoV-2 using miniaturized portable device, in clinical samples.

A global study of screening intensity and economic status on epidemic control performance during various epidemic periods of COVID-19 mutant strains

This study analyzed global data on epidemic control measures and economic conditions in different countries during different mutant strain epidemic periods, including the Alpha, Delta, and Omicron strains. The study estimated the elasticity coefficient through a log-log model, which represents the percent change of the confirmed case number with respect to a percent change in the total number of screening tests in a country for epidemic control. The 7-day rolling data of screening tests and confirmed cases from the Our World in Data database for the pandemic periods of Alpha strain in 2020, Delta strain in 2021, and Omicron strain in 2022, suggest that the magnitude of the elasticity was associated with the economic condition of a country. Compared with the results during either Alpha or Delta pandemic period, the Omicron pandemic has a much higher estimated elasticity coefficient of 1.317 (Alpha: 0.827 and Delta: 0.885). Further examining economic conditions categorized by quartile ranges, the results indicate that the elasticity is statistically significantly lower in countries with gross domestic product (GDP) per capita between $11,354 and $26,651, and in countries with GDP per capita above $26,651 than in countries with GDP per capita below $3,335. These results suggest that countries should consider not only epidemiological measures but also economic conditions when formulating epidemic control strategies. This study highlights the importance of assessing the appropriateness of epidemic control strategies within a country and provides valuable insights into the effectiveness of such strategies, particularly in the context of community screening.

Complexity and Diversity of the Neurological Spectrum of SARS-CoV-2 over Three Waves of COVID-19

Background/Objectives: SARS-CoV-2 continually mutates, with five identified variants. Many neurological manifestations were observed during the COVID-19 pandemic, with differences between virus variants. The aim of this study is to assess the frequency and characteristics of neurological manifestations during COVID-19 in hospitalized patients over three waves in Poland with comparison and analysis correlation with the course of infection. Methods: This retrospective single-center study included 600 consecutive adults with confirmed COVID-19, hospitalized during 3 waves (pre-Delta, Delta and Omicron) in Poland. Demographic and clinical information and neurological manifestations were collected and compared across three periods. Results: The median age of the study group was 68, lower during the Delta wave. In the Omicron period, the disease severity at admission and inflammatory markers concentration were the lowest. Neurological manifestations were observed in 49%. The most common were altered mentation, headache, myalgia, mood disorder, ischemic stroke and encephalopathy. Smell and taste disturbances (STDs) were less frequent in the Omicron period. Neurological complications were predominant in the pre-Delta and Omicron periods. Ischemic stroke was observed more often in pre-Delta period. Altered mentation was related to higher severity at admission, worse lab test results, higher admission to ICU and mortality, while headache reduced mortality. Pre-existing dementia was related to higher mortality. Conclusions: Neurological manifestations of COVID-19 are frequent, with a lower rate of STDs in the Omicron period and more often cerebrovascular diseases in the pre-Delta period. Headache improves the course of COVID-19, while altered mentation, stroke and neurological comorbidities increase severity and mortality.

Incidence and risk factors of COVID-19 in a tertiary hospital and the effectiveness of booster vaccination among health care workers: A retrospective cohort study, January 2020 to June 2022

BACKGROUND

Health care workers (HCWs) face a higher risk of infection and may transmit pathogens to patients during a pandemic. This study aims to evaluate infection-control measures by analyzing the incidence and risk factors of COVID-19 and estimating vaccine effectiveness (VE) at a tertiary hospital in Seoul, Republic of Korea.

METHODS

This study included 2,516 HCWs from January 1, 2020, to June 30, 2022. Data were analyzed to determine the incidence density and cumulative incidence; the results were compared by the age- and gender-specific standardized incidence ratios (SIR). VE was estimated with multivariate Cox proportional-hazard models as 1-adjusted hazard ratio × 100%.

RESULTS

SIR indicated a lower COVID-19 risk in the hospital population than in the general Korean population (SIR, 0.81; 95% confidence interval [CI]: 0.76-0.87). Multivariate Cox analysis indicated that, compared to doctors, nonmedical service supporters and other HCWs (excluding doctors and nurses) were high-risk groups (adjusted hazard ratio [95% CI], 1.72 [1.04-2.83] and 1.76 [1.20-2.58], respectively). Compared to the outpatient unit, the emergency department was a high-risk department (1.70 [1.16-2.50]). The VE of the booster dose was 55.47%, compared to no or incomplete vaccination (95% CI: 22.63-74.37).

CONCLUSIONS

Besides encouraging HCWs vaccination, effective infection-control measures should target high-risk groups and departments.

Mechanistic study of the transmission pattern of the SARS-CoV-2 omicron variant

The omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) characterized by 30 mutations in its spike protein, has rapidly spread worldwide since November 2021, significantly exacerbating the ongoing COVID-19 pandemic. In order to investigate the relationship between these mutations and the variant's high transmissibility, we conducted a systematic analysis of the mutational effect on spike-angiotensin-converting enzyme-2 (ACE2) interactions and explored the structural/energy correlation of key mutations, utilizing a reliable coarse-grained model. Our study extended beyond the receptor-binding domain (RBD) of spike trimer through comprehensive modeling of the full-length spike trimer rather than just the RBD. Our free-energy calculation revealed that the enhanced binding affinity between the spike protein and the ACE2 receptor is correlated with the increased structural stability of the isolated spike protein, thus explaining the omicron variant's heightened transmissibility. The conclusion was supported by our experimental analyses involving the expression and purification of the full-length spike trimer. Furthermore, the energy decomposition analysis established those electrostatic interactions make major contributions to this effect. We categorized the mutations into four groups and established an analytical framework that can be employed in studying future mutations. Additionally, our calculations rationalized the reduced affinity of the omicron variant towards most available therapeutic neutralizing antibodies, when compared with the wild type. By providing concrete experimental data and offering a solid explanation, this study contributes to a better understanding of the relationship between theories and observations and lays the foundation for future investigations.

COVID-19 in the Arab countries: Three-year study

Background

Twenty-two Arab countries share a common language, history, and culture. Nevertheless, governmental policies, healthcare systems, and resources differ from one Arab country to another. We have been following Coronavirus (COVID-19) from the beginning in each Arab country. In the present study, we aimed to assess the prevalence of COVID-19 in the Arab world and to compare these findings with other significantly affected countries.

Methods

Websites of the World Health Organization, World COVID-vaccinations tracker, Worldometer, and Ministries of Health were used to extract COVID-19 data in all Arab countries between the period January 2020 to December 2022.

Results

All Arab countries had 14,218,042 total confirmed COVID-19 cases, 13,384,924 total recovered cases and 173,544 total related deaths. The trend demonstrated that the third quarter of 2021 recorded the highest death toll and the first quarter of 2022 recorded the highest number of confirmed and recovered cases. Compared to the top 15 affected countries, the Arab world ranked last as it had the lowest overall incidence per million population (PMP) of 31,609. The data on total deaths PMP showed that India had the lowest number of deaths with only 377 cases followed by the Arab world with 386 cases.

Conclusions

Although the number of confirmed, death, and recovered cases of COVID-19 have greatly reduced in the last quarter of 2022 in most Arab countries, many Arab countries still need to re-campaign about COVID-19 vaccines and raise awareness programs about boosters. COVID-19 has had a relatively smaller impact on Arab countries than on other countries that have been significantly affected.

Vertical transmission of SARS-CoV-2 delta-variant in a preterm infant

BACKGROUND

As SARS-CoV-2 continues to be relevant and cause illnesses, the effect of emerging virus variants on perinatal health remains to be elucidated. It was demonstrated that vertical transmission of SARS-CoV-2 is a relatively rare event in the original SARS-CoV-2 strain. However, very few reports describe vertical transmission related to the delta-variant.

CASE PRESENTATION

We report a case of a preterm male neonate born to a mother with positive SARS-CoV-2 and mild respiratory complications. The neonate was born by cesarean section due to fetal distress. The rupture of the amniotic membrane was at delivery. The neonate had expected prematurity-related complications. His nasopharyngeal swabs for RT-PCR were positive from birth till three weeks of age. RT-ddPCR of the Placenta showed a high load of the SARS-CoV-2 virus with subgenomic viral RNA. RNAscope technique demonstrated both the positive strand of the S gene and the orf1ab negative strand. Detection of subgenomic RNA and the orf1ab negative strand indicats active viral replication in the placenta.

CONCLUSIONS

Our report demonstrates active viral replication of the SARS-CoV-2 delta-variant in the placenta associated with vertical transmission in a preterm infant.

Site-directed neutralizing antibodies targeting structural sites on SARS-CoV-2 spike protein

'Epivolve' (epitope evolution) is an innovative paratope-evolving technology using a haptenated peptide or protein immunogen as a means of directing the in vivo immune response to specifically targeted sites at a one amino acid residue resolution. Guided by protein structural analysis, Epivolve technology was tested to develop site-directed neutralizing antibodies (nAbs) in a systematic fashion against the SARS-CoV-2 Receptor Binding Domain (RBD). Thirteen solvent-exposed sites covering the ACE2 receptor-binding interface were targeted. Immunogens composed of each targeted site were used to immunize rabbits in separate cohorts. In vivo site-directed immune responses against all 13 targets were demonstrated by B cell secreted IgG and recombinant IgG testing. One site, SL13 (Y505) which mutates from tyrosine to histidine in the SARS-CoV-2 Omicron variant, was chosen as a proof-of-concept (PoC) model for further functional monoclonal antibody development. Epivolve technology demonstrated the capabilities of generating pan-variant antibodies and nAbs against the SARS-CoV-2 primary strain and the Omicron variant.

Investigation of epidemiological and clinical characteristics of people infected with SARS-CoV-2 during the second pandemic of COVID-19 in Chengdu, China

Objective

This study investigated the epidemiological and clinical characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infected patients during the second pandemic of COVID-19 (coronavirus disease of 2019) in Chengdu, China. Furthermore, the differences between first infection and re-infection cases were also compared and analyzed to provide evidence for better prevention and control of SARS-CoV-2 re-infection.

Methods

An anonymous questionnaire survey was conducted using an online platform (wjx.cn) between May 20, 2023 to September 12, 2023.

Results

This investigation included 62.94% females and 32.97% of them were 18-30 years old. Furthermore, 7.19-17.18% of the participants either did not receive vaccination at all or only received full vaccination, respectively. Moreover, 577 (57.64%) participants were exposed to cluster infection. The clinical manifestations of these patients were mainly mild to moderate; 78.18% of participants had a fever for 1-3 days, while 37.84% indicated a full course of disease for 4-6 days. In addition, 40.66% of the participants had re-infection and 72.97% indicated their first infection approximately five months before. The clinical symptoms of the first SARS-CoV-2 infection were moderate to severe, while re-infection indicated mild to moderate symptoms (the severity of symptoms other than diarrhea and conjunctival congestion had statistically significant differences) (p < 0.05). Moreover, 70.53 and 59.21% of first and re-infection cases had fever durations of 3-5 and 0-2 days, respectively. Whereas 47.91 and 46.40% of first and re-infection cases had a disease course of 7-9 and 4-6 days.

Conclusion

The SARS-CoV-2 infected individuals in Chengdu, China, during the second pandemic of COVID-19 had mild clinical symptoms and a short course of disease. Furthermore, compared with the first infection, re-infection cases had mild symptoms, low incidences of complications, short fever duration, and course of disease.

Blood Count and Renal Functionality Assessments in the Emergency Section Disclose Morbidity and Mortality in Omicron COVID-19 Patients: A Retrospective Study

Background: SARS-CoV-2 is the coronavirus responsible for the COVID-19 pandemic. Even though we are no longer in a pandemic situation, people are still getting infected, some of them need hospitalization and a few of them die. Methods: We conducted a retrospective study including 445 patients who accessed the Emergency Section of Policlinico Umberto I, Rome, Italy, where they had routine blood exams. In this study, we focused on the complete blood count, serum creatinine and azotemia. The data were analyzed using ANOVA, Spearman correlation and ROC analyses. They were divided into four groups based on their clinical outcomes: (1) the emergency group (patients who had mild forms and were quickly discharged); (2) the hospital ward group (patients who were admitted to the emergency section and were then hospitalized in a COVID-19 ward); (3) the intensive care unit (ICU) group (patients who required intensive assistance after the admission in the emergency section); (4) the deceased group (patients who had a fatal outcome after admission to the emergency section). Results: We found significant changes for creatinine, azotemia, hematocrit, mean corpuscular hemoglobin concentration, basophils, monocytes, red blood cell distribution width, hemoglobin, hematocrit and red blood cell numbers using ANOVA according to their clinical outcomes, particularly for the deceased group. Also, we found linear correlations of clinical outcomes with eosinophils, hemoglobin, hematocrit, mean corpuscular hemoglobin concentration, lymphocyte, neutrophil, platelet and red blood cell number and red blood cell distribution width. Conclusions: This study discloses an early association between "classical" routine blood biomarkers and the severity of clinical outcomes in Omicron patients.

Effectiveness of COVID-19 mRNA vaccine in preventing infection against Omicron strain: Findings from the Hiroshima Prefecture COVID-19 version J-SPEED for PCR center

BACKGROUND AND PURPOSE

Despite the widespread adoption of various preventive measures since the spread of COVID-19, there remains a lack of consensus on universally acknowledged best practices. However, the significance of vaccination has risen to prominence as a paramount preventive strategy. Numerous investigations have demonstrated vaccine effectiveness against the omicron strain in severe disease and symptomatic disease, however, the scope of research pertaining to vaccine effectiveness in preventing infection is presently limited. Therefore, the current study aimed to evaluate COVID-19 mRNA (Pfizer-BioNTech BNT162b2 or Moderna mRNA-1273) vaccine effectiveness in preventing infection.

METHODS

We conducted a test-negative case-control study using a dataset of 117,335 individuals. These data were collected through the COVID-19 J-SPEED form in the PCR center at Hiroshima Prefecture, Japan from 1 February to 17 March 2022. We estimated propensity score matching for vaccine status based on participants' demographic characteristics. Subsequently, odds ratio was calculated from logistic regression to determine the association between vaccination status and test positivity rate adjusting for symptoms, exposure to close contact, and previous infection history. Vaccine effectiveness was defined as (1 -aORs) ×100%.

RESULTS

The PCR test positivity rates were 7.9%, 4.5%, and 2.8% for the non-vaccinated (non-vaccinated, vaccinated with a single dose, and vaccinated with two doses less than 14 days ago), vaccinated with two doses (vaccinated over 14 days ago), and three doses, respectively. In unadjusted and adjusted analyses, vaccine effectiveness of two doses against infection were 38.5% (95% confidence interval [CI]: 32.8%-43.8%) and 34.7% (95%CI: 28.4%-40.4%), respectively, compared to non-vaccinated group. Vaccine effectiveness of three doses were 33.8% (95%CI: 25.0%-41.5%) and 26.4% (95%CI: 16.4%-35.2%), respectively, compared to those vaccinated with two doses.

CONCLUSIONS

These results illustrate the protective effect of mRNA vaccines against Omicron strain infections and emphasize the significance of completing the suggested vaccination schedule.

Assessing SARS-CoV-2 Testing Adherence in a University Town: Recurrent Event Modeling Analysis

BACKGROUND

Healthy Davis Together was a program launched in September 2020 in the city of Davis, California, to mitigate the spread of COVID-19 and facilitate the return to normalcy. The program involved multiple interventions, including free saliva-based asymptomatic testing, targeted communication campaigns, education efforts, and distribution of personal protective equipment, community partnerships, and investments in the local economy.

OBJECTIVE

This study identified demographic characteristics of individuals that underwent testing and assessed adherence to testing over time in a community pandemic-response program launched in a college town in California, United States.

METHODS

This study outlines overall testing engagement, identifies demographic characteristics of participants, and evaluates testing participation changes over 4 periods of the COVID-19 pandemic, distinguished by the dominant variants Delta and Omicron. Additionally, a recurrent model is employed to explore testing patterns based on the participants' frequency, timing, and demographic characteristics.

RESULTS

A total of 770,165 tests were performed between November 18, 2020, and June 30, 2022, among 89,924 (41.1% of total population) residents of Yolo County, with significant participation from racially or ethnically diverse participants and across age groups. Most positive cases (6351 of total) and highest daily participation (895 per 100,000 population) were during the Omicron period. There were some gender and age-related differences in the pattern of recurrent COVID-19 testing. Men were slightly less likely (hazard ratio [HR] 0.969, 95% CI 0.943-0.996) to be retested and more likely (HR 1.104, 95% CI 1.075-1.134) to stop testing altogether than women. People aged between 20 and 34 years were less likely to be retested (HR 0.861, 95% CI 0.828-0.895) and more likely to stop testing altogether (HR 2.617, 95% CI 2.538-2.699). However, older age groups were less likely to stop testing, especially those aged between 65-74 years and 75-84 years, than those aged between 0 and 19 years. The likelihood of stopping testing was lower (HR 0.93, 95% CI 0.889-0.976) for the Asian group and higher for the Hispanic or Latino (HR 1.185, 95% CI 1.148-1.223) and Black or African American (HR 1.198, 95% CI 1.054-1.350) groups than the White group.

CONCLUSIONS

The unique features of a pandemic response program that supported community-wide access to free asymptomatic testing provide a unique opportunity to evaluate adherence to testing recommendations and testing trends over time. Identification of individual and group-level factors associated with testing behaviors can provide insights for identifying potential areas of improvement in future testing initiatives.

A mini review of reinfection with the SARS-CoV-2 Omicron variant

Background

COVID-19 has caused severe morbidity and mortality worldwide. After the end of the dynamic zero-COVID policy in China in December, 2022, concerns regarding reinfection were raised while little was known due to the lack of surveillance data in this country.

Aims

This study reviews the probability, risk factors, and severity of severe acute respiratory syndrome coronavirus 2 Omicron variant reinfection, as well as the interval between infections, risk of onward transmission by reinfected cases, and the role of booster vaccination against reinfection.

Sources

References for this review were identified through searches of PubMed and Web of Science up to September 24, 2023.

Results

The rate of reinfection ranges from 3.1% to 13.0%. Factors associated with a higher risk of reinfection include being female, having comorbidities, and being unvaccinated. Reinfection with the BA.4 or BA.5 variant occurs approximately 180 days after the initial infection. Reinfections are less clinically severe than primary infections, and there is evidence of lower transmissibility. The debate surrounding the effectiveness and feasibility of booster vaccinations in preventing reinfection continues.

Conclusions

The reinfection rate during the Omicron epidemic is significantly higher than in previous epidemic periods. However, the symptoms and infectivity of reinfection were weaker than those of the prior infection. Medical staff and individuals at high risk of reinfection should be vigilant. The efficacy of booster vaccinations in reducing reinfection is currently under debate.

Lipid Nanoparticle-Based Inhibitors for SARS-CoV-2 Host Cell Infection

Purpose

The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the lingering threat to public health has fueled the search for effective therapeutics to treat SARS-CoV-2. This study aimed to develop lipid nanoparticle (LNP) inhibitors of SARS-CoV-2 entry to reduce viral infection in the nose and upper airway.

Methods

Two types of LNP formulations were prepared following a microfluidic mixing method. The LNP-Trap consisted of DOPC, DSPC, cholesterol, and DSPE-PEG-COOH modified with various spike protein binding ligands, including ACE2 peptide, recombinant human ACE2 (rhACE2) or monoclonal antibody to spike protein (mAb). The LNP-Trim consisted of ionizing cationic DLin-MC3-DMA, DSPC, cholesterol, and DMG-PEG lipids encapsulating siACE2 or siTMPRSS2. Both formulations were assayed for biocompatibility and cell uptake in airway epithelial cells (Calu-3). Functional assessment of activity was performed using SARS-CoV-2 spike protein binding assays (LNP-Trap), host receptor knockdown (LNP-Trim), and SARS-CoV-2 pseudovirus neutralization assay (LNP-Trap and LNP-Trim). Localization and tissue distribution of fluorescently labeled LNP formulations were assessed in mice following intranasal administration.

Results

Both LNP formulations were biocompatible based on cell impedance and MTT cytotoxicity studies in Calu-3 cells at concentrations as high as 1 mg/mL. LNP-Trap formulations were able to bind spike protein and inhibit pseudovirus infection by 90% in Calu-3 cells. LNP-Trim formulations reduced ACE2 and TMPRSS2 at the mRNA (70% reduction) and protein level (50% reduction). The suppression of host targets in Calu-3 cells treated with LNP-Trim resulted in over 90% inhibition of pseudovirus infection. In vivo studies demonstrated substantial retention of LNP-Trap and LNP-Trim in the nasal cavity following nasal administration with minimal systemic exposure.

Conclusion

Both LNP-Trap and LNP-Trim formulations were able to safely and effectively inhibit SARS-CoV-2 pseudoviral infection in airway epithelial cells. These studies provide proof-of-principle for a localized treatment approach for SARS-CoV-2 in the upper airway.

Multivalent and Sequential Heterologous Spike Protein Vaccinations Effectively Induce Protective Humoral Immunity against SARS-CoV-2 Variants

The emergence of new SARS-CoV-2 variants continues to cause challenging problems for the effective control of COVID-19. In this study, we tested the hypothesis of whether a strategy of multivalent and sequential heterologous spike protein vaccinations would induce a broader range and higher levels of neutralizing antibodies against SARS-CoV-2 variants and more effective protection than homologous spike protein vaccination in a mouse model. We determined spike-specific IgG, receptor-binding inhibition titers, and protective efficacy in the groups of mice that were vaccinated with multivalent recombinant spike proteins (Wuhan, Delta, Omicron), sequentially with heterologous spike protein variants, or with homologous spike proteins. Trivalent (Wuhan + Delta + Omicron) and sequential heterologous spike protein vaccinations were more effective in inducing serum inhibition activities of receptor binding to spike variants and virus neutralizing antibody titers than homologous spike protein vaccination. The higher efficacy of protection was observed in mice with trivalent and sequential heterologous spike protein vaccination after a challenge with a mouse-adapted SARS-CoV-2 MA10 strain compared to homologous spike protein vaccination. This study provides evidence that a strategy of multivalent and sequential heterologous variant spike vaccination might provide more effective protection against emerging SARS-CoV-2 variants than homologous spike vaccination and significantly alleviate severe inflammation due to COVID-19.

Prevalence of SARS-CoV-2 variants in Prague wastewater determined by nanopore-based sequencing

The early detection of upcoming disease outbreaks is essential to avoid both health and economic damage. The last four years of COVID-19 pandemic have proven wastewater-based epidemiology is a reliable system for monitoring the spread of SARS-CoV-2, a causative agent of COVID-19, in an urban population. As this monitoring enables the identification of the prevalence of spreading variants of SARS-CoV-2, it could provide a critical tool in the fight against this viral disease. In this study, we evaluated the presence of variants and subvariants of SARS-CoV-2 in Prague wastewater using nanopore-based sequencing. During August 2021, the data clearly showed that the number of identified SARS-CoV-2 RNA copies increased in the wastewater earlier than in clinical samples indicating the upcoming wave of the Delta variant. New SARS-CoV-2 variants consistently prevailed in wastewater samples around a month after they already prevailed in clinical samples. We also analyzed wastewater samples from smaller sub-sewersheds of Prague and detected significant differences in SARS-CoV-2 lineage progression dynamics among individual localities studied, e.g., suggesting faster prevalence of new variants among the sites with highest population density and mobility.

Neutralization antibody titer and change in 50% protection after the third dose of the COVID-19 vaccine

BACKGROUND

The new COVID-19 variant outbreak is the present global public health problem. The omicron variant of SARS-CoV-2 has several subvariants and causes outbreaks worldwide. Because of the increasing genetic heterogeneity of SARS-CoV-2, it is expected that using COVID-19 immunization to prevent and control disease will be problematic.

AIM

The aim of the study was to study neutralization of antibody titer and change in 50% protection after the third dose of the COVID-19 vaccine.

MATERIALS AND METHODS

In this report, the authors determine the expected neutralization antibody titer against omicron subvariants and the change in 50% protection against infection after the third dose of the immunization.

RESULTS

The change due to subvariant B.4 or B.5 is substantially higher than that due to the other subvariants. The efficacy of using viral vector vaccine boosters is questionable since viral vector COVID-19 boosters fail to generate enough antibodies to achieve the mean convalescent plasma level.

CONCLUSION

Higher antibody levels than the typical convalescent level and that needed for half protective property are still possible with the mRNA vaccine booster shot. In addition, compared to the half-dose regimen, the full-dose regimen produces a higher antibody level. As a booster shot, the mRNA COVID-19 vaccine is recommended.

Evaluation of Real and Perceived Risk to Health Care Workers Caring for Patients With the Omicron Variant of the SARS-CoV-2 Virus in Surgery and Obstetrics

OBJECTIVES

The Omicron variant of the SARS-CoV-2 virus is described as more contagious than previous variants. We sought to assess risk to health care workers (HCWs) caring for patients with COVID-19 in surgical/obstetrical settings, and the perception of risk among this group.

METHODS

From January to April 2022, reverse transcription polymerase chain reaction was used to detect the presence of SARS-CoV-2 viral ribonucleic acid in patient, environmental (floor, equipment, passive air) samples, and HCWs' masks (inside surface) during urgent surgery or obstetrical delivery for patients with SARS-CoV-2 infection. The primary outcome was the proportion of HCWs' masks testing positive. Results were compared with our previous cross-sectional study involving obstetrical/surgical patients with earlier variants (2020-2021). HCWs completed a risk perception electronic questionnaire.

RESULTS

Eleven patients were included: 3 vaginal births and 8 surgeries. In total, 5/108 samples (5%) tested positive (SARS-CoV-2 Omicron) viral ribonucleic acid: 2/5 endotracheal tubes, 1/22 floor samples, 1/4 patient masks, and 1 nasal probe. No samples from the HCWs' masks (0/35), surgical equipment (0/10), and air (0/11) tested positive. No significant differences were found between the Omicron and 2020/21 patient groups' positivity rates (Mann-Whitney U test, P = 0.838) or the level of viral load from the nasopharyngeal swabs (P = 0.405). Nurses had a higher risk perception than physicians (P = 0.038).

CONCLUSION

No significant difference in contamination rates was found between SARS-CoV-2 Omicron BA.1 and previous variants in surgical/obstetrical settings. This is reassuring as no HCW mask was positive and no HCW tested positive for COVID-19 post-exposure.

Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been evolving rapidly causing emergence of new variants and health uncertainties. Monitoring the evolution of the virus was of the utmost importance for public health interventions and the development of national and global mitigation strategies. Here, we report national data on the emergence of new variants, their distribution, and dynamics in a 3-year study conducted from March 2020 to the end of January 2023 in the Republic of Serbia. Nasopharyngeal and oropharyngeal swabs from 2,398 COVID-19-positive patients were collected and sequenced using three different next generation technologies: Oxford Nanopore, Ion Torrent, and DNBSeq. In the subset of 2,107 SARS-CoV-2 sequences which met the quality requirements, detection of mutations, assignment to SARS-CoV-2 lineages, and phylogenetic analysis were performed. During the 3-year period, we detected three variants of concern, namely, Alpha (5.6%), Delta (7.4%), and Omicron (70.3%) and one variant of interest-Omicron recombinant "Kraken" (XBB1.5) (<1%), whereas 16.8% of the samples belonged to other SARS-CoV-2 (sub)lineages. The detected SARS-CoV-2 (sub)lineages resulted in eight COVID-19 pandemic waves in Serbia, which correspond to the pandemic waves reported in Europe and the United States. Wave dynamics in Serbia showed the most resemblance with the profile of pandemic waves in southern Europe, consistent with the southeastern European location of Serbia. The samples were assigned to sixteen SARS-CoV-2 Nextstrain clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F and six different Omicron recombinants (XZ, XAZ, XAS, XBB, XBF, and XBK). The 10 most common mutations detected in the coding and untranslated regions of the SARS-CoV-2 genomes included four mutations affecting the spike protein (S:D614G, S:T478K, S:P681H, and S:S477N) and one mutation at each of the following positions: 5'-untranslated region (5'UTR:241); N protein (N:RG203KR); NSP3 protein (NSP3:F106F); NSP4 protein (NSP4:T492I); NSP6 protein (NSP6: S106/G107/F108 - triple deletion), and NSP12b protein (NSP12b:P314L). This national-level study is the most comprehensive in terms of sequencing and genomic surveillance of SARS-CoV-2 during the pandemic in Serbia, highlighting the importance of establishing and maintaining good national practice for monitoring SARS-CoV-2 and other viruses circulating worldwide.

Comparison of azvudine, molnupiravir, and nirmatrelvir/ritonavir in adult patients with mild-to-moderate COVID-19: a retrospective cohort study

This study aimed to explore the effectiveness and safety of azvudine, nirmatrelvir/ritonavir, and molnupiravir in adult patients with mild-to-moderate COVID-19. This retrospective cohort study included patients with mild-to-moderate COVID-19 (asymptomatic, mild, and common types) at the First Hospital of Changsha (Hunan Province, China) between March and November 2022. Eligible patients were classified into the azvudine, nirmatrelvir/ritonavir, or molnupiravir groups according to the antiviral agents they received. The outcomes were the times to nucleic acid negative conversion (NANC). This study included 157 patients treated with azvudine (n = 66), molnupiravir (n = 66), or nirmatrelvir/ritonavir (n = 25). There were no statistically significant differences in the time from diagnosis to NANC among the azvudine, molnupiravir, and nirmatrelvir/ritonavir groups [median, 9 (95% CI 9-11) vs. 11 (95% CI 10-12) vs. 9 (95% CI 8-12) days, P = 0.15], time from administration to NANC [median, 9 (95% CI 8-10) vs. 10 (95% CI 9.48-11) vs. 8.708 (95% CI 7.51-11) days, P = 0.50], or hospital stay [median, 11 (95% CI 11-13) vs. 13 (95% CI 12-14) vs. 12 (95% CI 10-14) days, P = 0.14], even after adjustment for sex, age, COVID-19 type, comorbidities, Ct level, time from diagnosis to antiviral treatment, and number of symptoms. The cumulative NANC rates in the azvudine, molnupiravir, and nirmatrelvir/ritonavir groups were 15.2%/12.3%/16.0% at day 5 (P = 0.858), 34.8%/21.5%/32.0% at day 7 (P = 0.226), 66.7%/52.3%/60.0% at 10 days (P = 0.246), and 86.4%/86.2%/80.0% at day 14 (P = 0.721). No serious adverse events were reported. Azvudine may be comparable to nirmatrelvir/ritonavir and molnupiravir in adult patients with mild-to-moderate COVID-19 regarding time to NANC, hospital stay, and AEs.

Comparative analysis of symptom profile and risk of death associated with infection by SARS-CoV-2 and its variants in Hong Kong

The recurrent multiwave nature of coronavirus disease 2019 (COVID-19) necessitates updating its symptomatology. We characterize the effect of variants on symptom presentation, identify the symptoms predictive and protective of death, and quantify the effect of vaccination on symptom development. With the COVID-19 cases reported up to August 25, 2022 in Hong Kong, an iterative multitier text-matching algorithm was developed to identify symptoms from free text. Multivariate regression was used to measure associations between variants, symptom development, death, and vaccination status. A least absolute shrinkage and selection operator technique was used to identify a parsimonious set of symptoms jointly associated with death. Overall, 70.9% (54 450/76 762) of cases were symptomatic with 102 symptoms identified. Intrinsically, the wild-type and delta variant caused similar symptoms among unvaccinated symptomatic cases, whereas the wild-type and omicron BA.2 subvariant had heterogeneous patterns, with seven symptoms (fatigue, fever, chest pain, runny nose, sputum production, nausea/vomiting, and sore throat) more frequent in the BA.2 cohort. With ≥2 vaccine doses, BA.2 was more likely than delta to cause fever among symptomatic cases. Fever, blocked nose, pneumonia, and shortness of breath remained jointly predictive of death among unvaccinated symptomatic elderly in the wild-type-to-omicron transition. Number of vaccine doses required for reducing occurrence varied by symptoms. We substantiate that omicron has a different clinical presentation compared to previous variants. Syndromic surveillance can be bettered with reduced reliance on symptom-based case identification, increased weighing on symptoms predictive of death in outcome prediction, individual-based risk assessment in care homes, and incorporating free-text symptom reporting.

The Efficacy and Safety of Nirmatrelvir/Ritonavir Against COVID-19 in Elderly Patients

Objective

To assess the key factors influencing the effectiveness of nirmatrelvir/ritonavir in treating elderly patients with COVID-19.

Methods

This study was conducted on patients aged ≥60 who were admitted to the Second Affiliated Hospital of Soochow University for COVID-19 infection and were treated with nirmatrelvir/ritonavir. Clinical information was collected from patients and steady-state blood concentrations of nirmatrelvir and ritonavir were measured. Factors associated with treatment effects were searched by univariate and multivariate analysis.

Results

A total of 68 (51 males and 17 females) patients had a median age of 80 (73.0-84.8) years were enrolled in this study. The blood concentration measurements (trough concentrations) of nirmatrelvir and ritonavir were 5.1 (2.6-7.1) and 0.4 (0.2-0.9) μg/mL, respectively. Adverse drug reaction was reported in 4 (5.9%) patients. Univariate analysis showed that age, clinical classification, APACHE II score, total bilirubin (TBil), aspartate transaminase (AST), lactate dehydrogenase (LDH), and total cholesterol (TC) were significantly associated with the effectiveness of treatment (P value <0.05). Concentration of nirmatrelvir was also associated with treatment outcome (P value <0.1). Based on the results of univariate analysis, the above factors were introduced into the multiple linear regression equation as independent variables, and the results showed that clinical classification was included in the regression equation model and was the most important factor affecting the treatment outcome. By receiver operating characteristic curve analysis, the area under curve of age + biochemical indicators + APACHE II score + clinical classification was 0.968 (95% CI = 0.919-1.000; P <0.0001). Among the 68 patients included in the study, 4 cases experienced adverse drug reactions.

Conclusion

Age, clinical classification, APACHE II score, TBil, AST, LDH, and TC were significantly associated with the effectiveness of treatment in elderly patients with COVID-19.

Challenges in Emerging Vaccines and Future Promising Candidates against SARS-CoV-2 Variants

Since the COVID-19 outbreak, the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) virus has evolved into variants with varied infectivity. Vaccines developed against COVID-19 infection have boosted immunity, but there is still uncertainty on how long the immunity from natural infection or vaccination will last. The present study attempts to outline the present level of information about the contagiousness and spread of SARS-CoV-2 variants of interest and variants of concern (VOCs). The keywords like COVID-19 vaccine types, VOCs, universal vaccines, bivalent, and other relevant terms were searched in NCBI, Science Direct, and WHO databases to review the published literature. The review provides an integrative discussion on the current state of knowledge on the type of vaccines developed against SARS-CoV-2, the safety and efficacy of COVID-19 vaccines concerning the VOCs, and prospects of novel universal, chimeric, and bivalent mRNA vaccines efficacy to fend off existing variants and other emerging coronaviruses. Genomic variation can be quite significant, as seen by the notable differences in impact, transmission rate, morbidity, and death during several human coronavirus outbreaks. Therefore, understanding the amount and characteristics of coronavirus genetic diversity in historical and contemporary strains can help researchers get an edge over upcoming variants.

The intention to get COVID-19 booster vaccination and its association with cognitive and emotional factors: A survey of Chinese COVID-19 infected people in Hong Kong

BACKGROUND

Although the pandemic has ended officially, COVID-19 remains impactful. Booster COVID-19 vaccination is still needed to protect individuals against COVID-19 and the disease's harmful consequences. This study investigated the prevalence of the intention to get booster COVID-19 vaccination after receiving the COVID-19 diagnosis and its associated factors among people reporting prior COVID-19.

METHODS

A population-based anonymous telephone survey was conducted in Hong Kong, China from June to August 2022 among Chinese people reporting prior COVID-1 between February and August 2022 and having taken up ≥2 doses of COVID-19 vaccines prior to COVID-19 diagnosis.

RESULTS

The prevalence of the intention to get booster vaccination was 59.2 %. Older age (>60 years), being currently married, not employed full-time, and having chronic diseases were positively associated with the intention to get booster vaccination. Adjusted for the background factors, higher levels of the cognitive factors of perceived susceptibility to COVID-19, perceived acquired moderate-to-strong immunity against COVID-19, and perceived adequate knowledge of COVID-19 were positively associated with the intention to get booster vaccination; stronger perceived severity of prior infection despite vaccination was negatively associated with the intention outcome. In contrast, stronger mental distress due to COVID-19, illness concern, and emotional representation were positively associated with the intention. Self-perceived long COVID status was not a significant factor.

DISCUSSION

The prevalence of the intention to get booster COVID-19 vaccination was limited, especially among younger people reporting prior COVID-19. Health promotion is still required among people reporting prior COVID-19 and may emphasize the significant cognitive factors positively associated with the intention. Future studies are needed to confirm the findings, clarify the role of emotional factors on booster vaccination, and explore other factors of the intention to get booster vaccination among people reporting prior COVID-19.

Transmission characteristics and inactivated vaccine effectiveness against transmission of the SARS-CoV-2 Omicron BA.2 variant in Shenzhen, China

We conducted a retrospective cohort study to evaluate the transmission risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 variant and the effectiveness of inactivated COVID-19 vaccine boosters in Shenzhen during a BA.2 outbreak period from 1 February to 21 April 2022. A total of 1,248 individuals were infected with the BA.2 variant, and 7,855 close contacts were carefully investigated. The risk factors for the high secondary attack rate of SARS-CoV-2 infection were household contacts [adjusted odds ratio (aOR): 1.748; 95% confidence interval (CI): 1.448, 2.110], younger individuals aged 0-17 years (aOR: 2.730; 95% CI: 2.118, 3.518), older persons aged ≥60 years (aOR: 1.342; 95% CI: 1.135, 1.588), women (aOR: 1.442; 95% CI: 1.210, 1.718), and the subjects exposed to the post-onset index cases (aOR: 8.546; 95% CI: 6.610, 11.050), respectively. Compared with the unvaccinated and partially vaccinated individuals, a relatively low risk of secondary attack was found for the individuals who received booster vaccination (aOR: 0.871; 95% CI: 0.761, 0.997). Moreover, a high transmission risk was found for the index cases aged ≥60 years (aOR: 1.359; 95% CI: 1.132, 1.632), whereas a relatively low transmission risk was observed for the index cases who received full vaccination (aOR: 0.642; 95% CI: 0.490, 0.841) and booster vaccination (aOR: 0.676; 95% CI: 0.594, 0.770). Compared with full vaccination, booster vaccination of inactivated COVID-19 vaccine showed an effectiveness of 24.0% (95% CI: 7.0%, 37.9%) against BA.2 transmission for the adults ≥18 years and 93.7% (95% CI: 72.4%, 98.6%) for the adults ≥60 years, whereas the effectiveness was 51.0% (95% CI: 21.9%, 69.3%) for the individuals of 14 days to 179 days after booster vaccination and 51.2% (95% CI: 37.5%, 61.9%) for the non-household contacts. The estimated mean values of the generation interval, serial interval, incubation period, latent period, and viral shedding period were 2.7 days, 3.2 days, 2.4 days, 2.1 days, and 17.9 days, respectively. In summary, our results confirmed that the main transmission route of Omicron BA.2 subvariant was household contact, and booster vaccination of the inactivated vaccines was relatively effective against BA.2 subvariant transmission in older people.

COVID-19 Crisis in Brazil: Post-Vaccination Seroprevalence and Infection in More and Less Vaccinated Municipalities in a Northeastern State

BACKGROUND

Given the impact of the pandemic in Brazil, vaccination is essential to prevent illness and death. Thus, this study sought to compare, after vaccination, the circulation of SARS-CoV-2 and the response to vaccination in the least and most vaccinated municipalities of a Brazilian state during the height of the pandemic when the Omicron variant was dominant.

METHODS

We tested for the SARS-CoV-2 antigen and confirmed infection using an RT-qPCR and measured IgM and IgG antibodies in fully vaccinated participants from municipalities with higher and lower vaccination rates.

RESULTS

We showed that participants from the least vaccinated municipalities were more likely to have detectable IgM antibodies and a positive antigen/RT-qPCR result for SARS-CoV-2 than participants from the most vaccinated municipalities. There were no differences between the vaccines used (BNT162b2, Ad26.COV2.S, AZD1222, and CoronaVac) and antibody production.

CONCLUSIONS

Our study evaluated municipal vaccination coverage and its effects on mortality, infections, and anti-SARS-CoV-2 antibodies during a critical phase of the pandemic. The results suggest that higher vaccination coverage reduces acute cases and confers higher memory antibody levels against SARS-CoV-2. Even with a full vaccination schedule, individuals living in places with low vaccination rates are more susceptible to infection.

Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon

BACKGROUND

Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country.

METHODS

A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology.

RESULTS

Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42).

CONCLUSIONS

The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.

Mild Neurological Manifestations Associated With Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Hospitalized Children During the Omicron Wave in Singapore: A Retrospective Cohort Review

BACKGROUND

Neurological complications with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant have been reported in adults; however, there are little data in the pediatric population. We aimed to report on the prevalence and clinical characteristics of children with neurological symptoms during the SARS-CoV-2 omicron wave.

METHODS

This was a single-center, retrospective cohort review of children (<18 years old) hospitalized for SARS-CoV-2 infection from December 2, 2021, to June 30, 2022.

RESULTS

During the study period, 455 children (mean age 4.8 years, range 0.67 to 18, male 58.9%) were hospitalized with SARS-CoV-2 infection. A total of 108 (23.7%) children experienced neurological symptoms; most common were seizures (62.0%), headaches (32.4%) and giddiness (14.8%). Seizures included febrile seizures (64.1%), acute symptomatic seizures (17.9%), and breakthrough seizures in known epileptics (17.9%). Children with neurological manifestations were older (7.3 vs 4.0 years, P < 0.00001), more likely to have underlying epilepsy (9.3% vs 1.2%, P = 0.0002) or neurodevelopmental disorders (17.6% vs 1.7%, P < 0.00001), and presented earlier in their illness (2.1 vs 2.8 days, P < 0.00001), compared with those without neurological manifestations. Neurological symptoms fully resolved in all but one patient at discharge. There were no mortalities and no difference in duration of hospitalization (3.1 vs 3.7 days, P = 0.5) between the groups.

CONCLUSIONS

One in four hospitalized children with SARS-CoV-2 infection when omicron variant was dominant experienced mild neurological symptoms. Overall risk factors for neurological symptoms associated with SARS-CoV-2 included older age, pre-existing febrile seizures/epilepsy and neurodevelopmental disorders.

Impaired T-cell response to mRNA vaccination heralds risk of COVID-19 in long-term allogeneic hematopoietic stem cell transplantation survivors

Not available.

A non-autonomous time-delayed SIR model for COVID-19 epidemics prediction in China during the transmission of Omicron variant

<abstract><p>With the continuous evolution of the coronavirus, the Omicron variant has gradually replaced the Delta variant as the prevalent strain. Their inducing epidemics last longer, have a higher number of asymptomatic cases, and are more serious. In this article, we proposed a nonautonomous time-delayed susceptible-infected-removed (NATD-SIR) model to predict them in different regions of China. We obtained the maximum and its time of current infected persons, the final size, and the end time of COVID-19 epidemics from January 2022 in China. The method of the fifth-order moving average was used to preprocess the time series of the numbers of current infected and removed cases to obtain more accurate parameter estimations. We found that usually the transmission rate $ \beta(t) $ was a piecewise exponential decay function, but due to multiple bounces in Shanghai City, $ \beta(t) $ was approximately a piecewise quadratic function. In most regions, the removed rate $ \gamma(t) $ was approximately equal to a piecewise linear increasing function of (a*t+b)*H(t-k), but in a few areas, $ \gamma(t) $ displayed an exponential increasing trend. For cases where the removed rate cannot be obtained, we proposed a method for setting the removed rate, which has a good approximation. Using the numerical solution, we obtained the prediction results of the epidemics. By analyzing those important indicators of COVID-19, we provided valuable suggestions for epidemic prevention and control and the resumption of work and production.</p></abstract>