A tabulated summary of the evidence on humoral and cellular responses to the SARS-CoV-2 Omicron VOC, as well as vaccine efficacy against this variant

Unpacking adverse events and associations post COVID-19 vaccination: a deep dive into vaccine adverse event reporting system data

INTRODUCTION

The rapid development of COVID-19 vaccines has provided crucial tools for pandemic control, but the occurrence of vaccine-related adverse events (AEs) underscores the need for comprehensive monitoring.

METHODS

This study analyzed the Vaccine Adverse Event Reporting System (VAERS) data from 2020-2022 using statistical methods such as zero-truncated Poisson regression and logistic regression to assess associations with age, gender groups, and vaccine manufacturers.

RESULTS

Logistic regression identified 26 System Organ Classes (SOCs) significantly associated with age and gender. Females displayed especially higher odds in SOC 19 (Pregnancy, puerperium and perinatal conditions), while males had higher odds in SOC 25 (Surgical and medical procedures). Older adults (>65) were more prone to symptoms like Cardiac disorders, whereas those aged 18-65 showed susceptibility to AEs like Skin and subcutaneous tissue disorders. Moderna and Pfizer vaccines induced fewer SOC symptoms compared to Janssen and Novavax. The zero-truncated Poisson regression model estimated an average of 4.243 symptoms per individual.

CONCLUSION

These findings offer vital insights into vaccine safety, guiding evidence-based vaccination strategies and monitoring programs for precise and effective outcomes.

Correlative analysis of wastewater trends with clinical cases and hospitalizations through five dominant variant waves of COVID-19

Wastewater-based epidemiology (WBE) has been utilized to track community infections of Coronavirus Disease 2019 (COVID-19) by detecting RNA of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), within samples collected from wastewater. The correlations between community infections and wastewater measurements of the RNA can potentially change as SARS-CoV-2 evolves into new variations by mutating. This study analyzed SARS-CoV-2 RNA, and indicators of human waste in wastewater from two sewersheds of different scales (University of Miami (UM) campus and Miami-Dade County Central District wastewater treatment plant (CDWWTP)) during five internally defined COVID-19 variant dominant periods (Initial, Pre-Delta, Delta, Omicron and Post-Omicron wave). SARS-CoV-2 RNA quantities were compared against COVID-19 clinical cases and hospitalizations to evaluate correlations with wastewater SARS-CoV-2 RNA. Although correlations between documented clinical cases and hospitalizations were high, prevalence for a given wastewater SARS-CoV-2 level varied depending upon the variant analyzed. The correlative relationship was significantly steeper (more cases per level found in wastewater) for the Omicron-dominated period. For hospitalization, the relationships were steepest for the Initial wave, followed by the Delta wave with flatter slopes during all other waves. Overall results were interpreted in the context of SARS-CoV-2 virulence and vaccination rates among the community.

Mathematical Modeling of SARS-CoV-2 Omicron Wave under Vaccination Effects

Over the course of the COVID-19 pandemic millions of deaths and hospitalizations have been reported. Different SARS-CoV-2 variants of concern have been recognized during this pandemic and some of these variants of concern have caused uncertainty and changes in the dynamics. The Omicron variant has caused a large amount of infected cases in the US and worldwide. The average number of deaths during the Omicron wave toll increased in comparison with previous SARS-CoV-2 waves. We studied the Omicron wave by using a highly nonlinear mathematical model for the COVID-19 pandemic. The novel model includes individuals who are vaccinated and asymptomatic, which influences the dynamics of SARS-CoV-2. Moreover, the model considers the waning of the immunity and efficacy of the vaccine against the Omicron strain. This study uses the facts that the Omicron strain has a higher transmissibility than the previous circulating SARS-CoV-2 strain but is less deadly. Preliminary studies have found that Omicron has a lower case fatality rate compared to previous circulating SARS-CoV-2 strains. The simulation results show that even if the Omicron strain is less deadly it might cause more deaths, hospitalizations and infections. We provide a variety of scenarios that help to obtain insight about the Omicron wave and its consequences. The proposed mathematical model, in conjunction with the simulations, provides an explanation for a large Omicron wave under various conditions related to vaccines and transmissibility. These results provide an awareness that new SARS-CoV-2 variants can cause more deaths even if their fatality rate is lower.

Dynamic behavior analysis of an SVIR epidemic model with two time delays associated with the COVID-19 booster vaccination time

Since the outbreak of COVID-19, there has been widespread concern in the community, especially on the recent heated debate about when to get the booster vaccination. In order to explore the optimal time for receiving booster shots, here we construct an SVIR model with two time delays based on temporary immunity. Second, we theoretically analyze the existence and stability of equilibrium and further study the dynamic properties of Hopf bifurcation. Then, the statistical analysis is conducted to obtain two groups of parameters based on the official data, and numerical simulations are carried out to verify the theoretical analysis. As a result, we find that the equilibrium is locally asymptotically stable when the booster vaccination time is within the critical value. Moreover, the results of the simulations also exhibit globally stable properties, which might be more beneficial for controlling the outbreak. Finally, we propose the optimal time of booster vaccination and predict when the outbreak can be effectively controlled.

The Omicron-transformer: Rise of the subvariants in the age of vaccines

Introduction: Omicron is the latest SARS-CoV-2 variant of concern, the pathogen that causes COVID-19. Since its emergence in late 2021, Omicron has displaced other circulating variants and caused successive waves of infection worldwide throughout 2022. Omicron is characterised by the rapid emergence of many subvariants and high rates of infection in people with vaccine- and/or infection-induced immunity. This review article will consolidate current knowledge regarding Omicron subvariants, the role of boosters, and future vaccine development. Method: This narrative review is based on a literature search using PubMed. Search terms related to Omicron were used and priority was given to published peer-reviewed articles over pre-prints. Results: Studies indicate that vaccinations and boosters are important to reduce disease severity, hospitalisation and death from Omicron. A variety of factors, such as differing host factors, circulating variants, and forces of infection, can influence the benefit of repeated booster administration. Next-generation bivalent vaccines have now been approved in some countries including Singapore and have demonstrated the ability to induce broad variant protection. Future third-generation vaccines involving mucosal vaccines and/or pan-sarbecovirus vaccines may provide broader and longer-lasting protection. Conclusion: Due to current high levels of vaccine- and infection-induced immunity, it is likely that rates of severe illness, hospitalisation, and death due to Omicron will continue to moderate. Nevertheless, the virus is ever-changing, and public health policies, especially those related to vaccinations, will also have to continually evolve and adapt as COVID-19 transitions to endemicity. Keywords: Booster, COVID-19, infectious diseases, Omicron, vaccine

Intranasal delivery of a rationally attenuated SARS-CoV-2 is immunogenic and protective in Syrian hamsters

Few live attenuated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are in pre-clinical or clinical development. We seek to attenuate SARS-CoV-2 (isolate WA1/2020) by removing the polybasic insert within the spike protein and the open reading frames (ORFs) 6-8, and by introducing mutations that abolish non-structural protein 1 (Nsp1)-mediated toxicity. The derived virus (WA1-ΔPRRA-ΔORF6-8-Nsp1^K164A/H165A) replicates to 100- to 1000-fold-lower titers than the ancestral virus and induces little lung pathology in both K18-human ACE2 (hACE2) transgenic mice and Syrian hamsters. Immunofluorescence and transcriptomic analyses of infected hamsters confirm that three-pronged genetic modifications attenuate the proinflammatory pathways more than the removal of the polybasic cleavage site alone. Finally, intranasal administration of just 100 PFU of the WA1-ΔPRRA-ΔORF6-8-Nsp1^K164A/H165A elicits robust antibody responses in Syrian hamsters and protects against SARS-CoV-2-induced weight loss and pneumonia. As a proof-of-concept study, we demonstrate that live but sufficiently attenuated SARS-CoV-2 vaccines may be attainable by rational design.

Effectiveness of Second mRNA COVID-19 Booster Vaccine in Immunocompromised Persons and Long-Term Care Facility Residents

We used a nationwide population registry in South Korea to estimate the effect of a second booster dose of mRNA COVID-19 vaccine on the risk for laboratory-confirmed SARS-CoV-2 infection, critical infection, and death in immunocompromised persons and long-term care facility (LTCF) residents. During February 16-May 7, 2022, among 972,449 eligible persons, 736,439 (75.7%) received a first booster and 236,010 (24.3%) persons received a second booster. Compared with the first booster group, at 30-53 days, the second booster recipients had vaccine effectiveness (VE) against all infections of 22.28% (95% CI 19.35%-25.11%), VE against critical infection of 56.95% (95% CI 29.99%-73.53%), and VE against death of 62.96% (95% CI 34.18%-79.15%). Our findings provide real-world evidence that a second booster dose of mRNA vaccine substantially increases protection against critical infection and death in these high-risk population groups.

Prerequisite for COVID-19 Prediction: A Review on Factors Affecting the Infection Rate

Since the year 2020, coronavirus disease 2019 (COVID-19) has emerged as the dominant topic of discussion in the public and research domains. Intensive research has been carried out on several aspects of COVID-19, including vaccines, its transmission mechanism, detection of COVID-19 infection, and its infection rate and factors. The awareness of the public related to the COVID-19 infection factors enables the public to adhere to the standard operating procedures, while a full elucidation on the correlation of different factors to the infection rate facilitates effective measures to minimize the risk of COVID-19 infection by policy makers and enforcers. Hence, this paper aims to provide a comprehensive and analytical review of different factors affecting the COVID-19 infection rate. Furthermore, this review analyses factors which directly and indirectly affect the COVID-19 infection risk, such as physical distance, ventilation, face masks, meteorological factor, socioeconomic factor, vaccination, host factor, SARS-CoV-2 variants, and the availability of COVID-19 testing. Critical analysis was performed for the different factors by providing quantitative and qualitative studies. Lastly, the challenges of correlating each infection risk factor to the predicted risk of COVID-19 infection are discussed, and recommendations for further research works and interventions are outlined.

Long-term monitoring of SARS-CoV-2 RNA in sewage samples from specific public places and STPs to track COVID-19 spread and identify potential hotspots

Coronavirus pandemic started in March 2020 and since then has caused millions of deaths worldwide. Wastewater-based epidemiology (WBE) can be used as an epidemiological surveillance tool to track SARS-CoV-2 dissemination and provide warning of COVID-19 outbreaks. Considering that there are public places that could be potential hotspots of infected people that may reflect the local epidemiological situation, the presence of SARS-CoV-2 RNA was analyzed by RT-qPCR for approximately 16 months in sewage samples from five public places located in the metropolitan area of Belo Horizonte, MG, Brazil: the sewage treatment plant of Confins International Airport (AIR), the main interstate bus terminal (BUS), an upscale shopping centre (SHC1), a popular shopping centre (SHC2) and a university institute (UNI). The results were compared to those of the influent sewage of the two main sewage treatment plants of Belo Horizonte (STP1 and STP2). Viral monitoring in the STPs proved to be an useful regional surveillance tool, reflecting the trends of COVID-19 cases. However, the viral concentrations in the samples from the selected public places were generally much lower than those of the municipal STPs, which may be due to the behaviour of the non-infected or asymptomatic people, who are likely to visit these places relatively more than the symptomatic infected ones. Among these places, the AIR samples presented the highest viral concentrations and concentration peaks were observed previously to local outbreaks. Therefore, airport sewage monitoring can provide an indication of the regional epidemiological situation. For the other places, particularly the UNI, the results suggested a greater potential to detect the infection and trace cases especially among employees and regular attendees. Taken together, the results indicate that for a regular and permanent sentinel sewage surveillance the sewage from STPs, AIR and UNI could be monitored.

Long-term monitoring of SARS-CoV-2 RNA in sewage samples from specific public places and STPs to track COVID-19 spread and identify potential hotspots

Coronavirus pandemic started in March 2020 and since then has caused millions of deaths worldwide. Wastewater-based epidemiology (WBE) can be used as an epidemiological surveillance tool to track SARS-CoV-2 dissemination and provide warning of COVID-19 outbreaks. Considering that there are public places that could be potential hotspots of infected people that may reflect the local epidemiological situation, the presence of SARS-CoV-2 RNA was analyzed by RT-qPCR for approximately 16 months in sewage samples from five public places located in the metropolitan area of Belo Horizonte, MG, Brazil: the sewage treatment plant of Confins International Airport (AIR), the main interstate bus terminal (BUS), an upscale shopping centre (SHC1), a popular shopping centre (SHC2) and a university institute (UNI). The results were compared to those of the influent sewage of the two main sewage treatment plants of Belo Horizonte (STP1 and STP2). Viral monitoring in the STPs proved to be an useful regional surveillance tool, reflecting the trends of COVID-19 cases. However, the viral concentrations in the samples from the selected public places were generally much lower than those of the municipal STPs, which may be due to the behaviour of the non-infected or asymptomatic people, who are likely to visit these places relatively more than the symptomatic infected ones. Among these places, the AIR samples presented the highest viral concentrations and concentration peaks were observed previously to local outbreaks. Therefore, airport sewage monitoring can provide an indication of the regional epidemiological situation. For the other places, particularly the UNI, the results suggested a greater potential to detect the infection and trace cases especially among employees and regular attendees. Taken together, the results indicate that for a regular and permanent sentinel sewage surveillance the sewage from STPs, AIR and UNI could be monitored.

Immune responses in Omicron SARS-CoV-2 breakthrough infection in vaccinated adults

The SARS-CoV-2 Omicron variant has more than 15 mutations in the receptor binding domain of the Spike protein enabling increased transmissibility and viral escape from antibodies in vaccinated individuals. It is unclear how vaccine immunity protects against Omicron infection. Here we show that vaccinated participants at a super-spreader event have robust recall response of humoral and pre-existing cellular immunity induced by the vaccines, and an emergent de novo T cell response to non-Spike antigens. Individuals with Omicron SARS-CoV-2 breakthrough infections have significantly increased activated SARS-CoV-2 wild type Spike-specific cytotoxic T cells, activated follicular helper (TFH) cells, functional T cell responses, boosted humoral responses, and rapid release of Spike and RBD-specific IgG+ B cell plasmablasts and memory B cells into circulation. Omicron breakthrough infection affords significantly increased de novo memory T cell responses to non-Spike viral antigens. Concerted T and B cell responses may provide durable and broad immunity.

Predictors of Willingness of the General Public to Receive a Second COVID-19 Booster Dose or a New COVID-19 Vaccine: A Cross-Sectional Study in Greece

Given the concerns of waning immunity from the primary COVID-19 vaccines and the first booster dose, we conducted an online cross-sectional study in May 2022 to investigate willingness to receive a second COVID-19 booster dose or a new COVID-19 vaccine and its associated factors. Overall, 62% of the participants were willing to be vaccinated, 25.8% were unsure, and 12.3% were unwilling to be vaccinated. The main reasons against accepting a second COVID-19 booster dose/new COVID-19 vaccine were concerns about the side effects and the effectiveness and the opinion that further vaccination is unnecessary. Males, younger individuals, participants without a previous COVID-19 diagnosis, and those with good/very good self-perceived physical health were significantly more frequently willing to receive a second COVID-19 booster dose or a new COVID-19 vaccine. Additionally, increased fear of the COVID-19, increased trust in COVID-19 vaccinations, and decreased fear of a second booster dose or a new COVID-19 vaccine was associated with increased willingness. Our results show some hesitancy and unwillingness toward further COVID-19 vaccination and indicate that the fear of COVID-19 and trust in COVID-19 vaccination affects public opinion.

Recapping the Features of SARS-CoV-2 and Its Main Variants: Status and Future Paths

Over the two years that we have been experiencing the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic, our challenges have been the race to develop vaccines and the difficulties in fighting against new variants due to the rapid ability of the virus to evolve. In this sense, different organizations have identified and classified the different variants that have been emerging, distinguishing between variants of concern (VOC), variants of interest (VOI), or variants under monitoring (VUM). The following review aims to describe the latest updates focusing on VOC and already de-escalated variants, as well as to describe the impact these have had on the global situation. Understanding the intrinsic properties of SARS-CoV-2 and its interaction with the immune system and vaccination is essential to make out the underlying mechanisms that have led to the appearance of these variants, helping to determine the next steps for better public management of this pandemic.

An Update on Protective Effectiveness of Immune Responses After Recovery From COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibits variable immunity responses among hosts based on symptom severity. Whether immunity in recovered individuals is effective for avoiding reinfection is poorly understood. Determination of immune memory status against SARS-CoV-2 helps identify reinfection risk and vaccine efficacy. Hence, after recovery from COVID-19, evaluation of protective effectiveness and durable immunity of prior disease could be significant. Recent reports described the dynamics of SARS-CoV-2 -specific humoral and cellular responses for more than six months in convalescent SARS-CoV-2 individuals. Given the current evidence, NK cell subpopulations, especially the memory-like NK cell subset, indicate a significant role in determining COVID-19 severity. Still, the information on the long-term NK cell immunity conferred by SARS-CoV-2 infection is scant. The evidence from vaccine clinical trials and observational studies indicates that hybrid natural/vaccine immunity to SARS-CoV-2 seems to be notably potent protection. We suggested the combination of plasma therapy from recovered donors and vaccination could be effective. This focused review aims to update the current information regarding immune correlates of COVID-19 recovery to understand better the probability of reinfection in COVID-19 infected cases that may serve as guides for ongoing vaccine strategy improvement.

Turning point: A new global COVID-19 wave or a signal of the beginning of the end of the global COVID-19 pandemic?

A new variant named Omicron (B.1.1.529), first identified in South Africa, has become of considerable interest to the World Health Organization. This variant differs from the other known major variants, as it carries a large number of unusual mutations, particularly in the spinous process protein and receptor binding domains. Some specific mutation sites make it vaccine resistant, highly infectious, and highly pathogenic. The world fears that the Omicron variant could be even more harmful than the previous major variant, given that it has emerged amid fierce competition to trigger a new global pandemic peak as infections in South Africa rise. However, some epidemiological evidence has emerged that the Omicron variant may produce milder patient symptoms. We speculate if the virulence of the Omicron variant will diminish as transmissibility increases, thereby signaling the beginning of the end for the global COVID-19 pandemic. Based on this view, we make recommendations for COVID-19 mitigation in the present and future. However, it will take a few weeks to determine the true threat posed by the Omicron variant and we need to be fully prepared for future outbreaks, regardless of their severity.