Vaccine effectiveness against onward transmission of SARS-CoV2-infection by variant of concern and time since vaccination, Belgian contact tracing, 2021

A platform for the rapid screening of equine immunoglobins F (ab)2 derived from single equine memory B cells able to cross-neutralize to influenza virus

Single B cells-based antibody platforms offer an effective approach for the discovery of useful antibodies for therapeutic or research purposes. Here we present a method for screening equine immunoglobins F(ab)2, which offers the potential advantage of reacting with multiple epitopes on the virus. Using equine influenza virus (EIV) as model, a hemagglutinin (HA) trimer was constructed to bait B cells in vaccinated horses. We screened 370 HA-specific B cells from 1 × 106 PBMCs and identified a diverse set of equine variable region gene sequences of heavy and light chains and then recombined with humanized Ig Fc. Recombinant equine Ig was then self-assembled in co-transfected 293 T cells, and subsequently optimized to obtain HA binding B-cell receptor (s). The recombinant antibodies exhibited a high binding affinity to the HA protein. Antibody H81 exhibited the highest cross neutralizing activities against EIV strains in vitro. Furthermore, it effectively protected EIV-challenged mice, resulting in significantly improved survival, reduced pulmonary inflammation and decreased viral titers. In silico predication identified a functional region of H81 comprising 27 key amino acids cross the main circulating EIV strains. The 12 amino acid residues in this region with the highest binding affinities were screened. Notably, the predicted epitopes of H81 encompassed the documented equine HA receptor binding site, validating its cross-neutralization. In summary, a rapid platform was successfully established to investigate the profiling of equine antigen-recognizing receptors (BCRs) following infection. This platform has the potential to optimize the screening of virus-neutralizing antibodies and aid in vaccine design.

Inducing Long Lasting B Cell and T Cell Immunity Against Multiple Variants of SARS-CoV-2 Through Mutant Bacteriophage Qβ-Receptor Binding Domain Conjugate

More than 3 years into the global pandemic, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a significant threat to public health. Immunities acquired from infection or current vaccines fail to provide long term protection against subsequent infections, mainly due to their fast-waning nature and the emergence of variants of concerns (VOCs) such as Omicron. To overcome these limitations, SARS-CoV-2 Spike protein receptor binding domain (RBD)-based epitopes are investigated as conjugates with a powerful carrier, the mutant bacteriophage Qβ (mQβ). The epitope design is critical to eliciting potent antibody responses with the full length RBD being superior to peptide and glycopeptide antigens. The full length RBD conjugated with mQβ activates both humoral and cellular immune systems in vivo, inducing broad spectrum, persistent, and comprehensive immune responses effective against multiple VOCs including Delta and Omicron variants, rendering it a promising vaccine candidate.

Prevalence of SARS-CoV-2 antibodies and associated factors in the adult population of Belgium: a general population cohort study between March 2021 and April 2022

BACKGROUND

This study assessed seroprevalence trends of SARS-CoV-2 antibodies in the Belgian adult population between March 2021 and April 2022, and explored factors associated with seropositivity and seroreversion among the vaccinated and unvaccinated population.

METHODS

A prospective longitudinal surveillance study was conducted within a random sample of the general population (18 + years) in Belgium, selected from the national register through a multistage sampling design. Participants provided a saliva sample and completed a survey questionnaire on three occasions: at baseline and in two follow-up waves. Outcome variables included (1) seropositivity, defined as the presence of SARS-CoV-2 antibodies, assessed with a semi-quantitative measure of anti-RBD (Receptor Binding Domain) IgG ELISA and (2) seroreversion, defined as passing from a positive to a negative antibody test between two measurements. Trends in SARS-CoV-2 antibody prevalence were assessed using binary logistic regression with contrasts applying post-stratification. Potential determinants of seropositivity were assessed through multilevel logistic regressions.

RESULTS

In total 6,178 valid observations were obtained from 2,768 individuals. SARS-CoV-2 antibody prevalence increased from 25.1% in the beginning of the study period to 92.3% at the end. Among the vaccinated population, factors significantly associated with higher seropositivity rates were being younger, having a bachelor diploma, living with others, having had a vaccine in the last 3 months and having received a nucleic-acid vaccine or a combination. Lower seropositivity rates were observed among vaccinated people with a neurological disease and transplant patients. Factors significantly associated with higher seropositivity rates among the unvaccinated population were having non-O blood type and being non-smoker. Among vaccinated people, the seroreversion rate was much lower (0.3%) in those who had received their latest vaccine in the last 3 months compared to those who had received their latest vaccine more than 3 months ago (2.7%) (OR 0.13; 95%CI 0.04-0.42).

CONCLUSIONS

The rapid increase in antibody seropositivity in the general adult population in Belgium during the study period was driven by the vaccination campaign which ran at full speed during this period. Among vaccinated people, seropositivity varied in function of the time since last vaccine, the type of vaccine, sociodemographic features and health status.

Vaccine Mandates: Weighing the Common Good vs Personal Conscience and Autonomy

COVID-19 is a serious illness with significant morbidity and mortality. Vaccines to immunize against it were developed in record time. Mandates followed. The question to be considered is when mandates are ethical. Mandates can be used to prevent spread of an infection, prevent overwhelming the healthcare system, or protect public safety, thereby protecting the vulnerable and allowing for full flourishing of the common good. At the same time, one must be careful about respecting autonomy by allowing those who consciences do not allow them to be vaccinated to refuse. Because COVID-19 knowledge is rapidly changing as more information is known and the virus mutates, the conditions under which mandates are ethical change as well. At present, since vaccines prevent severe infection and death in high-risk individuals with added benefit for those who are vaccinated and have a history of infection, mandates can be imposed on those individuals. With an estimated 95% of the US population believed to have been infected and prior history of infection shown to be as effective as vaccination, with immunity lasting at least 500 days, and ability to prevent spread unknown at present but limited at best in the past, the vaccines therefore cannot be ethically mandated for those who are low risk for the versions released September 2023 based on information as of October 2023.

Association between SARS-CoV-2 variants and post COVID-19 condition: findings from a longitudinal cohort study in the Belgian adult population

BACKGROUND

While many studies on the determinants of post-COVID-19 conditions (PCC) have been conducted, little is known about the relationship between SARS-CoV-2 variants and PCC. This study aimed to assess the association between different SARS-CoV-2 variants and the probability of having PCC three months after the infection.

METHODS

This study was a longitudinal cohort study conducted between April 2021 and September 2022 in Belgium. In total, 8,238 adults with a confirmed SARS-CoV-2 infection were followed up between the time of their infection and three months later. The primary outcomes were the PCC status three months post infection and seven PCC symptoms categories (neurocognitive, autonomic, gastrointestinal, respiratory, musculoskeletal, anosmia and/or dysgeusia, and other manifestations). The main exposure variable was the type of SARS-CoV-2 variants (i.e. Alpha, Delta, and Omicron), extracted from national surveillance data. The association between the different SARS-CoV-2 variants and PCC as well as PCC symptoms categories was assessed using multivariable logistic regression.

RESULTS

The proportion of PCC among participants infected during the Alpha, Delta, and Omicron-dominant periods was significantly different and respectively 50%, 50%, and 37%. Participants infected during the Alpha- and Delta-dominant periods had a significantly higher odds of having PCC than those infected during the Omicron-dominant period (OR = 1.61, 95% confidence interval [CI] = 1.33-1.96 and OR = 1.73, 95%CI = 1.54-1.93, respectively). Participants infected during the Alpha and Delta-dominant periods were more likely to report neurocognitive, respiratory, and anosmia/dysgeusia symptoms of PCC.

CONCLUSIONS

People infected during the Alpha- and Delta-dominant periods had a higher probability of having PCC three months after infection than those infected during the Omicron-dominant period. The lower probability of PCC with the Omicron variant must also be interpreted in absolute figures. Indeed, the number of infections with the Omicron variant being higher than with the Alpha and Delta variants, it is possible that the overall prevalence of PCC in the population increases, even if the probability of having a PCC decreases.

COVID-19 contact tracing at work in Belgium - how tracers tweak guidelines for the better

BACKGROUND

When conducting COVID-19 contact tracing, pre-defined criteria allow differentiating high-risk contacts (HRC) from low-risk contacts (LRC). Our study aimed to evaluate whether contact tracers in Belgium followed these criteria in practice and whether their deviations improved the infection risk assessment.

METHOD

We conducted a retrospective cohort study in Belgium, through an anonymous online survey, sent to 111,763 workers by email. First, we evaluated the concordance between the guideline-based classification of HRC or LRC and the tracer's classification. We computed positive and negative agreements between both. Second, we used a multivariate Poisson regression to calculate the risk ratio (RR) of testing positive depending on the risk classification by the contact tracer and by the guideline-based risk classification.

RESULTS

For our first research question, we included 1105 participants. The positive agreement between the guideline-based classification in HRC or LRC and the tracer's classification was 0.53 (95% CI 0.49-0.57) and the negative agreement 0.70 (95% CI: 0.67-0.72). The type of contact tracer (occupational doctors, internal tracer, general practitioner, other) did not significantly influence the results. For the second research question, we included 589 participants. The RR of testing positive after an HRC compared to an LRC was 3.10 (95% CI: 2.71-3.56) when classified by the contact tracer and 2.24 (95% CI: 1.94-2.60) when classified by the guideline-based criteria.

CONCLUSION

Our study indicates that contact tracers did not apply pre-defined criteria for classifying high and low risk contacts. Risk stratification by contact tracers predicts who is at risk of infection better than guidelines only. This result indicates that a knowledgeable tracer can target testing better than a general guideline, asking for a debate on how to adapt the guidelines.

Key risk factors associated with fractal dimension based geographical clustering of COVID-19 data in the Flemish and Brussels region, Belgium

Introduction

COVID-19 remains a major concern globally. Therefore, it is important to evaluate COVID-19's rapidly changing trends. The fractal dimension has been proposed as a viable method to characterize COVID-19 curves since epidemic data is often subject to considerable heterogeneity. In this study, we aim to investigate the association between various socio-demographic factors and the complexity of the COVID-19 curve as quantified through its fractal dimension.

Methods

We collected population indicators data (ethnic composition, socioeconomic status, number of inhabitants, population density, the older adult population proportion, vaccination rate, satisfaction, and trust in the government) at the level of the statistical sector in Belgium. We compared these data with fractal dimension indicators of COVID-19 incidence between 1 January - 31 December 2021 using canonical correlation analysis.

Results

Our results showed that these population indicators have a significant association with COVID-19 incidences, with the highest explanatory and predictive power coming from the number of inhabitants, population density, and ethnic composition.

Conclusion

It is important to monitor these population indicators during a pandemic, especially when dealing with targeted interventions for a specific population.

Impact of prior SARS-COV-2 infection and vaccination on COVID-19 hospital admission and mortality amongst nursing home residents

BACKGROUND

Nursing home residents (NHRs) have experienced disproportionately high risk of severe outcomes due to COVID-19 infection.

AIM

We investigated the impact of COVID-19 vaccinations and previous SARS-CoV-2 episodes in preventing hospitalization and mortality in NHRs.

METHODS

Retrospective study of a cohort of all NHRs in our area who were alive at the start of the vaccination campaign. The first three doses of SARS-CoV-2 vaccine and prior COVID-19 infections were registered. The main outcomes were hospital admission and mortality during each follow up. Random effects time-varying Cox models adjusted for age, sex, and comorbidities were fitted to estimate hazard ratios (HRs) according to vaccination status.

RESULTS

COVID-19 hospitalization and death rates for unvaccinated NHRs were respectively 2.39 and 1.42 per 10,000 person-days, falling after administration of the second dose (0.37 and 0.34) and rising with the third dose (1.08 and 0.8). Rates were much lower amongst people who had previously had COVID-19. Adjusted HRs indicated a significant decrease in hospital admission amongst those with a two- and three-dose status; those who had had a previous COVID-19 infection had even lower hospital admission rates. Death rates decreased as NHRs received two and three doses, and the probability of death was much lower among those who had previously had the infection.

CONCLUSIONS

The effectiveness of current vaccines against severe COVID-19 disease in NHRs remains high and SARS-CoV-2 episodes prior to vaccination entail a major reduction in hospitalization and mortality rates. The protection conferred by vaccines appears to decline in the following months.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT04463706.

Mutational Analysis of Circulating Omicron SARS-CoV-2 Lineages in the Al-Baha Region of Saudi Arabia

Purpose

Omicron (B.1.1.529) is one of the highly mutated variants of concern of SARS-CoV-2. Lineages of Omicron bear a remarkable degree of mutations leading to enhanced pathogenicity and upward transmission trajectory. Mutating Omicron lineages may trigger a fresh COVID-19 wave at any time in any region. We aimed at the whole-genome sequencing of SARS-CoV-2 to determine variants/subvariants and significant mutations which can foster virus evolution, monitoring of disease spread, and outbreak management.

Methods

We used Illumina-NovaSeq 6000 for SARS-CoV-2 genome sequencing, MEGA 10.2 and nextstrain tools for phylogeny; CD-HIT program (version 4.8.1) and MUSCLE program for clustering and alignment. At the same time, UCSF Chimera was employed for protein visualization.

Results

Predominant Omicron pango lineages in Al-Baha were BA.5.2/B22 (n=4, 57%), and other lineages were BA.2.12/21L (n=1, 14.28%), BV.1/22B (n=1, 14.28%) and BA.5.2.18/22B (n=1, 14.28%). 22B nextstrain clade was predominant, while only one lineage showed 21L. BA.5.2/22B, BA.5.2/22B harbored a maximum of n=24 mutations in the spike region. Twelve crucial RBD mutations: D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, and Y505H were identified except the lineage BA.5.2/22B in which F486V mutation was not observed. Critical deletions S106 in membrane protein NSP6, E31in nucleocapsid, and L24 in spike region were observed in all the lineages. Furthermore, we identified common mutations of Omicron variants of SARS-CoV-2 in therapeutic hot spot spike region: T19I, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, A653V, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K, D1146D, L452R, F486V, N679K and D796Y. The effect of RBD-targeted mutations on neutralizing (NAbs) binding was considerable.

Conclusion

The outcome of this first report on SARS-CoV-2 variants identification and mutation in the Al-Baha region could be used to lay down the policies to manage and impede the regional outbreak of COVID-19 effectively.

The impact of national and international travel on spatio-temporal transmission of SARS-CoV-2 in Belgium in 2021

BACKGROUND

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread over the world and caused tremendous impacts on global health. Understanding the mechanism responsible for the spread of this pathogen and the impact of specific factors, such as human mobility, will help authorities to tailor interventions for future SARS-CoV-2 waves or newly emerging airborne infections. In this study, we aim to analyze the spatio-temporal transmission of SARS-CoV-2 in Belgium at municipality level between January and December 2021 and explore the effect of different levels of human travel on disease incidence through the use of counterfactual scenarios.

METHODS

We applied the endemic-epidemic modelling framework, in which the disease incidence decomposes into endemic, autoregressive and neighbourhood components. The spatial dependencies among areas are adjusted based on actual connectivity through mobile network data. We also took into account other important factors such as international mobility, vaccination coverage, population size and the stringency of restriction measures.

RESULTS

The results demonstrate the aggravating effect of international travel on the incidence, and simulated counterfactual scenarios further stress the alleviating impact of a reduction in national and international travel on epidemic growth. It is also clear that local transmission contributed the most during 2021, and municipalities with a larger population tended to attract a higher number of cases from neighboring areas.

CONCLUSIONS

Although transmission between municipalities was observed, local transmission was dominant. We highlight the positive association between the mobility data and the infection spread over time. Our study provides insight to assist health authorities in decision-making, particularly when the disease is airborne and therefore likely influenced by human movement.

COVID-19 vaccine effectiveness against symptomatic infection and hospitalisation in Belgium, July 2021 to May 2022

BackgroundThe Belgian COVID-19 vaccination campaign aimed to reduce disease spread and severity.AimWe estimated SARS-CoV-2 variant-specific vaccine effectiveness against symptomatic infection (VEi) and hospitalisation (VEh), given time since vaccination and prior infection.MethodsNationwide healthcare records from July 2021 to May 2022 on testing and vaccination were combined with a clinical hospital survey. We used a test-negative design and proportional hazard regression to estimate VEi and VEh, controlling for prior infection, time since vaccination, age, sex, residence and calendar week of sampling.ResultsWe included 1,932,546 symptomatic individuals, of whom 734,115 tested positive. VEi against Delta waned from an initial estimate of 80% (95% confidence interval (CI): 80-81) to 55% (95% CI: 54-55) 100-150 days after the primary vaccination course. Booster vaccination increased initial VEi to 85% (95% CI: 84-85). Against Omicron, an initial VEi of 33% (95% CI: 30-36) waned to 17% (95% CI: 15-18), while booster vaccination increased VEi to 50% (95% CI: 49-50), which waned to 20% (95% CI: 19-21) 100-150 days after vaccination. Initial VEh for booster vaccination decreased from 96% (95% CI: 95-96) against Delta to 87% (95% CI: 86-89) against Omicron. VEh against Omicron waned to 73% (95% CI: 71-75) 100-150 days after booster vaccination. While recent prior infections conferred higher protection, infections occurring before 2021 remained associated with significant risk reduction against symptomatic infection. Vaccination and prior infection outperformed vaccination or prior infection only.ConclusionWe report waning and a significant decrease in VEi and VEh from Delta to Omicron-dominant periods. Booster vaccination and prior infection attenuated these effects.

Expectations and disappointments relative to COVID-19 passes: results from a voluntary mixed-methods study in French-speaking Belgium

Objectives

Belgium enacted a coronavirus disease 2019 (COVID-19) pass - the 'COVID Safe Ticket' (CST) - in October 2021. This study aimed to understand the expectations and reasons given by those supporting this policy measure.

Methods

This mixed methods study was based on a voluntary online survey among 9444 French-speaking residents in Belgium.

Results

Most respondents were not very supportive of the CST, with only 617 respondents (7%) being pro-CST. Compared with other respondents, the pro-CST sample comprised more males, older people, people scared of COVID-19, people who had confidence in the COVID-19 vaccines, and highly educated people. A qualitative analysis was undertaken to identify the reasons why respondents supported the CST. Two lines of argument were related to personal comfort (individual protection and means of 'recovering freedom'), and two other lines were related to collective protection (controlling the pandemic and incentivizing vaccination). Pro-CST respondents also indicated some limitations of the CST.

Conclusions

The expectations regarding the CST were high, diverse and not entirely rational. Some contradictions and frustration emerged from the respondents' comments. The CST may have exacerbated the social divide in society. The high expectations risk leading to comparably high levels of disappointment, resulting in potential distrust towards future public health interventions.

Hybrid Immunity to SARS-CoV-2 from Infection and Vaccination-Evidence Synthesis and Implications for New COVID-19 Vaccines

COVID-19 has taken a severe toll on the global population through infections, hospitalizations, and deaths. Elucidating SARS-CoV-2 infection-derived immunity has led to the development of multiple effective COVID-19 vaccines and their implementation into mass-vaccination programs worldwide. After ~3 years, a substantial proportion of the human population possesses immunity from infection and/or vaccination. With waning immune protection over time against emerging SARS-CoV-2 variants, it is essential to understand the duration of protection, breadth of coverage, and effects on reinfection. This targeted review summarizes available research literature on SARS-CoV-2 infection-derived, vaccination-elicited, and hybrid immunity. Infection-derived immunity has shown 93-100% protection against severe COVID-19 outcomes for up to 8 months, but reinfection is observed with some virus variants. Vaccination elicits high levels of neutralizing antibodies and a breadth of CD4+ and CD8+ T-cell responses. Hybrid immunity enables strong, broad responses, with high-quality memory B cells generated at 5- to 10-fold higher levels, versus infection or vaccination alone and protection against symptomatic disease lasting for 6-8 months. SARS-CoV-2 evolution into more transmissible and immunologically divergent variants has necessitated the updating of COVID-19 vaccines. To ensure continued protection against SARS-CoV-2 variants, regulators and vaccine technical committees recommend variant-specific or bivalent vaccines.

Humoral immunity to SARS-CoV-2 elicited by combination COVID-19 vaccination regimens

The SARS-CoV-2 pandemic prompted a global vaccination effort and the development of numerous COVID-19 vaccines at an unprecedented scale and pace. As a result, current COVID-19 vaccination regimens comprise diverse vaccine modalities, immunogen combinations, and dosing intervals. Here, we compare vaccine-specific antibody and memory B cell responses following two-dose mRNA, single-dose Ad26.COV.2S, and two-dose ChAdOx1, or combination ChAdOx1/mRNA vaccination. Plasma-neutralizing activity, as well as the magnitude, clonal composition, and antibody maturation of the RBD-specific memory B cell compartments, showed substantial differences between the vaccination regimens. While individual monoclonal antibodies derived from memory B cells exhibited similar binding affinities and neutralizing potency against Wuhan-Hu-1 SARS-CoV-2, there were significant differences in epitope specificity and neutralizing breadth against viral variants of concern. Although the ChAdOx1 vaccine was inferior to mRNA and Ad26.COV.2S in several respects, biochemical and structural analyses revealed enrichment in a subgroup of memory B cell neutralizing antibodies with distinct RBD-binding properties resulting in remarkable potency and breadth.

Structural and Phylogenetic Analysis of SARS-CoV-2 Spike Glycoprotein from the Most Widespread Variants

The SARS-CoV-2 pandemic, reported for the first time at the end of 2019 in the city of Wuhan (China), has spread worldwide in three years; it lead to the infection of more than 500 million people and about six million dead. SARS-CoV-2 has proved to be very dangerous for human health. Therefore, several efforts have been made in studying this virus. In a short time, about one year, the mechanisms of SARS-CoV-2 infection and duplication and its physiological effect on human have been pointed out. Moreover, different vaccines against it have been developed and commercialized. To date, more than 11 billion doses have been inoculated all over the world. Since the beginning of the pandemic, SARS-CoV-2 has evolved; it has done so by accumulating mutations in the genome, generating new virus versions showing different characteristics, and which have replaced the pre-existing variants. In general, it has been observed that the new variants show an increased infectivity and cause milder symptoms. The latest isolated Omicron variants contain more than 50 mutations in the whole genome and show an infectivity 10-folds higher compared to the wild-type strain. Here, we analyse the SARS-CoV-2 variants from a phylogenetic point of view and hypothesize a future scenario for SARS-CoV-2, by following its evolution to date.