Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history

The Novel A-Type Proanthocyanidin-Rich Phytocomplex SP4™ Acts as a Broad-Spectrum Antiviral Agent against Human Respiratory Viruses

The appearance of new respiratory virus infections in humans with epidemic or pandemic potential has underscored the urgent need for effective broad-spectrum antivirals (BSAs). Bioactive compounds derived from plants may provide a natural source of new BSA candidates. Here, we investigated the novel phytocomplex formulation SP4™ as a candidate direct-acting BSA against major current human respiratory viruses, including coronaviruses and influenza viruses. SP4™ inhibited the in vitro replication of SARS-CoV-2, hCoV-OC43, hCoV-229E, Influenza A and B viruses, and respiratory syncytial virus in the low-microgram range. Using hCoV-OC43 as a representative respiratory virus, most of the antiviral activity of SP4™ was observed to stem primarily from its dimeric A-type proanthocyanidin (PAC-A) component. Further investigations of the mechanistic mode of action showed SP4™ and its PAC-A-rich fraction to prevent hCoV-OC43 from attaching to target cells and exert virucidal activity. This occurred through their interaction with the spike protein of hCoV-OC43 and SARS-CoV-2, thereby interfering with spike functions and leading to the loss of virion infectivity. Overall, these findings support the further development of SP4™ as a candidate BSA of a natural origin for the prevention of human respiratory virus infections.

Impact of the 2022 African Cup of Nations mass-gathering event on the COVID-19 epidemic in Garoua, Cameroon

BACKGROUND

The 2022 African Cup of Nations (AFCON) took place in Cameroon from January 9th to February 5th, 2022, including Garoua in the north. We aimed to measure the impact of this event on the local COVID-19 epidemic given the implementation of a preventive strategy based on a health pass.

METHODS

All players, staff and fans involved in the AFCON event were screened with PCR tests. Symptomatic cases were also continuously monitored in the general population and screened for variants of concern. Daily numbers of confirmed cases were compared to neighboring countries numbers retrieved from a public domain source.

RESULTS

In total, 1479 and 2481 tests were performed in the general population and on asymptomatic AFCON attendees, respectively. From the latter, 12.5% were PCR-positive; 97% were infected with Omicron, with no significant difference compared to the passive program (G-test, P value = 0.162). Surveillance indicated the AFCON did not increase the number of symptomatic PCR-positive cases in the general population compared to neighboring countries.

CONCLUSIONS

Though the COVID-19 epidemic was fueled by asymptomatic cases infected with the Omicron variant at the time, the non-therapeutic preventive measures implemented for AFCON mitigated an increase in the epidemic in the local population.

Antigenic Characterization of Circulating and Emerging SARS-CoV-2 Variants in the U.S. throughout the Delta to Omicron Waves

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into numerous lineages with unique spike mutations and caused multiple epidemics domestically and globally. Although COVID-19 vaccines are available, new variants with the capacity for immune evasion continue to emerge. To understand and characterize the evolution of circulating SARS-CoV-2 variants in the U.S., the Centers for Disease Control and Prevention (CDC) initiated the National SARS-CoV-2 Strain Surveillance (NS3) program and has received thousands of SARS-CoV-2 clinical specimens from across the nation as part of a genotype to phenotype characterization process. Focus reduction neutralization with various antisera was used to antigenically characterize 143 SARS-CoV-2 Delta, Mu and Omicron subvariants from selected clinical specimens received between May 2021 and February 2023, representing a total of 59 unique spike protein sequences. BA.4/5 subvariants BU.1, BQ.1.1, CR.1.1, CQ.2 and BA.4/5 + D420N + K444T; BA.2.75 subvariants BM.4.1.1, BA.2.75.2, CV.1; and recombinant Omicron variants XBF, XBB.1, XBB.1.5 showed the greatest escape from neutralizing antibodies when analyzed against post third-dose original monovalent vaccinee sera. Post fourth-dose bivalent vaccinee sera provided better protection against those subvariants, but substantial reductions in neutralization titers were still observed, especially among BA.4/5 subvariants with both an N-terminal domain (NTD) deletion and receptor binding domain (RBD) substitutions K444M + N460K and recombinant Omicron variants. This analysis demonstrated a framework for long-term systematic genotype to antigenic characterization of circulating and emerging SARS-CoV-2 variants in the U.S., which is critical to assessing their potential impact on the effectiveness of current vaccines and antigen recommendations for future updates.

Low antibody levels associated with significantly increased rate of SARS-CoV-2 infection in a highly vaccinated population from the US National Basketball Association

SARS-CoV-2 antibody levels may serve as a correlate for immunity and could inform optimal booster timing. The relationship between antibody levels and protection from infection was evaluated in vaccinated individuals from the US National Basketball Association who had antibody levels measured at a single time point from September 12, 2021, to December 31, 2021. Cox proportional hazards models were used to estimate the risk of infection within 90 days of serologic testing by antibody level (<250, 250-800, and >800 AU/mL1 ), adjusting for age, time since last vaccine dose, and history of SARS-CoV-2 infection. Individuals were censored on date of booster receipt. The analytic cohort comprised 2323 individuals and was 78.2% male, 68.1% aged ≤40 years, and 56.4% vaccinated (primary series) with the Pfizer-BioNTech mRNA vaccine. Among the 2248 (96.8%) individuals not yet boosted at antibody testing, 77% completed their primary vaccine series 4-6 months before testing and the median (interquartile range) antibody level was 293.5 (interquartile range: 121.0-740.5) AU/mL. Those with levels <250 AU/mL (adj hazard ratio [HR]: 2.4; 95% confidence interval [CI]: 1.5-3.7) and 250-800 AU/mL (adj HR: 1.5; 95% CI: 0.98-2.4) had greater infection risk compared to those with levels >800 AU/mL. Antibody levels could inform individual COVID-19 risk and booster scheduling.

RBD mutations at the residues K417, E484, N501 reduced immunoreactivity with antisera from vaccinated and COVID-19 recovered patients

Introduction

It is unclear whether induced spike protein-specific antibodies due to infections with SARS-CoV-2 or to the prototypic Wuhan isolate-based vaccination can immune-react with the emerging variants of SARS-CoV-2.

Aim/objectives

The main objective of the study was to measure the immunoreactivity of induced antibodies postvaccination with Covishield™ (ChAdOx1 nCoV-19 coronavirus vaccines) or infections with SARS-CoV-2 by using selected peptides of the spike protein of wild type and variants of SARS-CoV-2.

Methodology

Thirty patients who had recovered from SARS-CoV-2 infections and 30 individuals vaccinated with both doses of Covishield™ were recruited for the study. Venous blood samples (5 mL) were collected at a single time point from patients within 3-4 weeks of recovery from SARS-CoV-2 infections or receiving both doses of Covishield™ vaccines. The serum levels of total immunoglobulin were measured in both study groups. A total of 12 peptides of 10 to 24 amino acids length spanning to the receptor-binding domain (RBD) of wild type of SARS-CoV-2 and their variants were synthesized. The serum levels of immune-reactive antibodies were measured using these peptides.

Results

The serum levels of total antibodies were found to be significantly (p<0.001) higher in the vaccinated individuals as compared to COVID-19 recovered patients. Our study reported that the mutations in the RBD at the residues K417, E484, and N501 have been associated with reduced immunoreactivity with anti-sera of vaccinated people and COVID-19 recovered patients.

Conclusion

The amino acid substitutions at the RBD of SARS-CoV-2 have been associated with a higher potential to escape the humoral immune response.

Development of hybrid immunity during a period of high incidence of Omicron infections

BACKGROUND

Seroprevalence and the proportion of people with neutralizing activity (functional immunity) against SARS-CoV-2 variants were high in early 2022. In this prospective, population- based, multi-region cohort study, we assessed the development of functional and hybrid immunity (induced by vaccination and infection) in the general population during this period of high incidence of infections with Omicron variants.

METHODS

We randomly selected and assessed individuals aged ≥16 years from the general population in southern (n = 739) and north-eastern (n = 964) Switzerland in March 2022. We assessed them again in June/July 2022, supplemented with a random sample from western (n = 850) Switzerland. We measured SARS-CoV-2 specific IgG antibodies and SARS-CoV-2 neutralizing antibodies against three variants (ancestral strain, Delta, Omicron).

RESULTS

Seroprevalence remained stable from March 2022 (97.6%, n = 1894) to June/July 2022 (98.4%, n = 2553). In June/July, the percentage of individuals with neutralizing capacity against ancestral strain was 94.2%, against Delta 90.8% and against Omicron 84.9%, and 50.6% developed hybrid immunity. Individuals with hybrid immunity had highest median levels of anti-spike IgG antibodies titres [4518 World Health Organization units per millilitre (WHO U/mL)] compared with those with only vaccine- (4304 WHO U/mL) or infection- (269 WHO U/mL) induced immunity, and highest neutralization capacity against ancestral strain (hybrid: 99.8%, vaccinated: 98%, infected: 47.5%), Delta (hybrid: 99%, vaccinated: 92.2%, infected: 38.7%) and Omicron (hybrid: 96.4%, vaccinated: 79.5%, infected: 47.5%).

CONCLUSIONS

This first study on functional and hybrid immunity in the Swiss general population after Omicron waves showed that SARS-CoV-2 has become endemic. The high levels of antibodies and neutralization support the emerging recommendations of some countries where booster vaccinations are still strongly recommended for vulnerable persons but less so for the general population.

Spatiotemporal evolution of SARS-CoV-2 in the Bangkok metropolitan region, Thailand, 2020-2022: implications for future outbreak preparedness

Thailand experienced five waves of coronavirus disease 2019 (COVID-19) between 2020 and 2022, with the Bangkok Metropolitan Region (BMR) being at the centre of all outbreaks. The molecular evolution of the causative agent of the disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has previously been characterized in Thailand, but a detailed spatiotemporal analysis is still lacking. In this study, we comprehensively reviewed the development and timelines of the five COVID-19 outbreaks in Thailand and the public health responses, and also conducted a phylogenetic analysis of 27 913 SARS-CoV-2 genomes from Thailand, together with 7330 global references, to investigate the virus's spatiotemporal evolution during 2020 and 2022, with a particular focus on the BMR. Limited cross-border transmission was observed during the first four waves in 2020 and 2021, but was common in 2022, aligning well with the timeline of change in the international travel restrictions. Within the country, viruses were mostly restricted to the BMR during the first two waves in 2020, but subsequent waves in 2021 and 2022 saw extensive nationwide transmission of the virus, consistent with the timeline of relaxation of disease control measures employed within the country. Our results also suggest frequent epidemiological connections between Thailand and neighbouring countries during 2020 and 2021 despite relatively stringent international travel controls. The overall sequencing rate of the viruses circulating in the BMR was ~0.525 %, meeting the recommended benchmark, and our analysis supports that this is sufficient for tracking of the trend of the virus burden and genetic diversity. Our findings reveal insights into the local transmission dynamics of SARS-CoV-2 in Thailand, and provide a valuable reference for planning responses to future outbreaks.

Factors influencing neutralizing antibody response to the original SARS-CoV-2 virus and the Omicron variant in a high vaccination coverage country, a population-based study

The study compared immunity to the original SARS-CoV-2 virus (Wuhan) and the Omicron variant using neutralizing antibodies (NAbs), that provide a good approximation of protective immunity. The results might help determine immunization strategies.

DESIGN AND METHODS

Unlike previous studies, we analyzed NAbs in a random sample of 110 IgG positive sera from individuals who participated in a population-based seroprevalence transversal study, carried out in May 2022 in two Chilean cities, a country with high vaccination coverage.

RESULTS

Our findings indicate that 98.2% of individuals had NAbs against Wuhan, 65.5% against Omicron, and 32.7% tested positive for Wuhan but not Omicron. Factors influencing protective immunity included a prior natural infection and the number of vaccines received. NAbs titers against the original virus were high, demonstrating vaccine effectiveness in the population. However, the level of antibodies decreased when measuring NAbs against Omicron, particularly among older individuals, indicating a decline in vaccine protection. Previous COVID-19 episodes acted as a natural booster, increasing NAbs titers against both virus strains.

CONCLUSIONS

Protective immunity against the original Wuhan SARS-CoV-2 virus is reduced when compared to Omicron variant. Updating vaccine to target emerging variants and continued monitoring of effectiveness at the population level are necessary.

Neutralizing Activity of SARS-CoV-2 Antibodies in Patients with COVID-19 and Vaccinated Individuals

BACKGROUND

Serological diagnosis of COVID-19 is complex due to the emergence of different SARS-CoV-2 variants.

METHODS

164 serum samples from (I) patients who recovered from COVID-19 (n = 62) as well as (II) vaccinated individuals (n = 52) and (III) vaccinated individuals who were infected with different SARS-CoV-2 variants after vaccination (n = 50) were included. All samples were tested using EIA (binding antibodies) and a virus neutralization test (VNT) using the Wuhan strain (NT antibodies). Group III was further tested with a VNT using the Alpha/Delta/Omicron strains.

RESULTS

The highest antibody index (AI) was observed in vaccinated individuals infected with COVID-19 (median AI = 50, IQR = 27-71) and the lowest in vaccinated individuals (median AI = 19, IQR = 8-48). Similarly, NT antibody titer was highest in vaccinated individuals infected with COVID-19 (median 128; IQR = 32-256) compared to vaccinated individuals (median 32, IQR = 4-128) and patients with COVID-19 (median 32, IQR = 8-64). The correlation between AI and NT titer was strongly positive in vaccinated individuals and moderately positive in patients with COVID-19. No significant correlation was observed in vaccinated individuals infected with COVID-19. In patients infected with Alpha and Delta, the lowest VNT positivity rate was for the Omicron variant (85.0%/83.3%). Patients infected with the Alpha variant showed the lowest NT titer for the Omicron variant (median titer 32) compared to the Wuhan/Delta variants (64/128). Patients infected with the Delta variant had the lowest NT titer to the Omicron variant (median 32), compared to the Wuhan/Alpha variants (64/128). Patients infected with the Omicron variant showed similar titers to the Delta/Wuhan variants (128) and higher to the Alpha variant (256).

CONCLUSIONS

The cross-immunity to SARS-CoV-2 is lowest for the Omicron variant compared to the Alpha/Delta variants.

Comparing SARS-CoV-2 neutralizing antibody levels in convalescent unvaccinated, convalescent vaccinated, and naive vaccinated subjects

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 and spread rapidly. The purpose of this study was to compare neutralizing antibodies (NAbs) following the original booster vaccine in convalescent and naive vaccinated individuals and in a third comparison group consisting of unvaccinated convalescent plasma donors.

Methods

We assessed NAbs before and 2 months after a booster vaccine in 68 adults who had completed the initial vaccine series for SARS-CoV-2. Of these subjects, 58 had no history of prior infection (naïve vaccinated group) and 10 had been infected with SARS-COV-2 prior to the completing the first vaccine series (convalescent vaccinated group). A third comparison group included unvaccinated convalescent plasma donors (n = 55) from an earlier study with NAbs assessed approximately 2 months after a positive test for SARS-CoV-2.

Results

Prior to the booster, convalescent vaccinated subjects had higher NAbs compared to naive vaccinated subjects (p = 0.02). Two months following the booster, NAbs increased in both vaccinated groups. The naive vaccinated group increased more than the convalescent vaccinated group (p = 0.02). NAbs in the naive vaccinated group were almost four times higher than NAbs in the 55 unvaccinated subjects, while the convalescent vaccinated group had levels 2.5 times higher p < 0.01.

Conclusion

NAbs in both vaccinated/boosted groups were significantly higher than in the convalescent unvaccinated group (p < 0.01). Our data indicates that subjects with a single infection with SARS-CoV-2 did not have the same levels of neutralizing antibodies that we observed in subjects who were either in the convalescent vaccinated or the naive vaccinated groups.

Durability of ChAdOx1 nCoV-19 (AZD1222) vaccine and hybrid humoral immunity against variants including omicron BA.1 and BA.4 6 months after vaccination (COV005): a post-hoc analysis of a randomised, phase 1b-2a trial

BACKGROUND

COVID-19 vaccine rollout is lagging in Africa, where there has been a high rate of SARS-CoV-2 infection. We aimed to evaluate the effect of SARS-CoV-2 infection before vaccination with the ChAdOx-nCoV19 (AZD1222) vaccine on antibody responses through to 180 days.

METHODS

We did an unmasked post-hoc immunogenicity analysis after the first and second doses of AZD1222 in a randomised, placebo-controlled, phase 1b-2a study done in seven locations in South Africa. AZD1222 recipients who were HIV-uninfected, were stratified into baseline seropositive or seronegative groups using the serum anti-nucleocapsid (anti-N) immunoglobulin G (IgG) electroluminescence immunoassay to establish SARS-CoV-2 infection before the first dose of AZD1222. Binding IgG to spike (anti-S) and receptor binding domain (anti-RBD) were measured before the first dose (day 0), second dose (day 28), day 42, and day 180. Neutralising antibody (NAb) against SARS-CoV-2 variants D614G, beta, delta, gamma, and A.VOI.V2, and omicron BA1 and BA.4 variants, were measured by pseudovirus assay (day 28, day 42, and day 180). This trial is registered with ClinicalTrials.gov, NCT04444674, and the Pan African Clinicals Trials Registry, PACTR202006922165132.

FINDINGS

Of 185 individuals who were randomly assigned to AZD1222, we included 91 individuals who were baseline seropositive and 58 who were baseline seronegative, in the final analysis. In the seropositive group, there was little change of anti-S IgG (and anti-RBD IgG) or neutralising antibody (NAb) titres at day 42 compared with at day 28. Anti-S (and anti-RBD) IgG geometric mean concentrations (GMCs) were higher throughout in the seropositive compared with the seronegative group, including at day 180 (GMCs 517·8 [95% CI 411·3-651·9] vs 82·1 [55·2-122·3] BAU/mL). Also D614G NAb geometric mean titres (GMTs) were higher in the seropositive group than the seronegative group, as was the percentage with titres of at least 185 (80% putative risk reduction threshold [PRRT] against wild-type-alpha COVID-19), including at day 180 (92·0% [74·0-99·0] vs 18·2% [2·3-51·8). Similar findings were observed for beta, A.VOI.V2, and gamma. For delta, BA.1, and BA.4, NAb GMTs and the proportion with titres above the PRRT were substantially higher in the seropositive compared with seronegative group at day 28 and day 42, but no longer differed between the groups by day 180.

INTERPRETATION

A single dose of AZD1222 in the general African population, where COVID-19 vaccine coverage is low and SARS-CoV-2 seropositivity is 90%, could enhance the magnitude and quality of antibody responses to SARS-CoV-2.

FUNDING

The Bill & Melinda Gates Foundation, the South African Medical Research Council, the UK Research and Innovation, the UK National Institute for Health Research, and the South African Medical Research Council.

TRANSLATION

For the Zulu translation of the abstract see Supplementary Materials section.

Trajectories of Seroprevalence and Neutralizing Activity of Antibodies against SARS-CoV-2 in Southern Switzerland between July 2020 and July 2021: An Ongoing, Prospective Population-Based Cohort Study

OBJECTIVES

The COVID-19 pandemic continues, and evidence on infection- and vaccine-induced immunity is key. We assessed COVID-19 immunity and the neutralizing antibody response to virus variants across age groups in the Swiss population.

STUDY DESIGN

We conducted a cohort study in representative community-dwelling residents aged five years or older in southern Switzerland (total population 353,343), and we collected blood samples in July 2020 (in adults only, N = 646), November-December 2020 (N = 1457), and June-July 2021 (N = 885).

METHODS

We used a previously validated Luminex assay to measure antibodies targeting the spike (S) and the nucleocapsid (N) proteins of the virus and a high-throughput cell-free neutralization assay optimized for multiple spike protein variants. We calculated seroprevalence with a Bayesian logistic regression model accounting for the population's sociodemographic structure and the test performance, and we compared the neutralizing activity between vaccinated and convalescent participants across virus variants.

RESULTS

The overall seroprevalence was 7.8% (95% CI: 5.4-10.4) by July 2020 and 20.2% (16.4-24.4) by December 2020. By July 2021, the overall seroprevalence increased substantially to 72.5% (69.1-76.4), with the highest estimates of 95.6% (92.8-97.8) among older adults, who developed up to 10.3 more antibodies via vaccination than after infection compared to 3.7 times more in adults. The neutralizing activity was significantly higher for vaccine-induced than infection-induced antibodies for all virus variants (all p values < 0.037).

CONCLUSIONS

Vaccination chiefly contributed to the reduction in immunonaive individuals, particularly those in older age groups. Our findings on the greater neutralizing activity of vaccine-induced antibodies than infection-induced antibodies are greatly informative for future vaccination campaigns.

Serological Responses up to 9 Months following COVID-19 mRNA Vaccination in Residents and Health-Care Workers of Long-Term Care Facilities: A Multicenter Prospective Cohort Study in Northern Italy

Long-term care facilities (LTCFs) were severely affected by COVID-19, in particular in Northern Italy. We aimed to assess antibody responses among residents and healthcare workers (HCWs) of 13 LTCFs through serum samples collected at three time points: prior to, two weeks, and 9 months after receiving Pfizer/BNT162b2 SARS-CoV-2 mRNA vaccine (respectively t0, t1, and t2). IgG antibodies targeted towards the S1 domain of the spike protein were measured, and results were expressed in binding antibody units (BAU/mL). Friedman's average rank test was performed to compare antibody titres between the three time points. Two logistic regression models were built to identify independent predictors of (1) developing and (2) maintaining a significant antibody response to vaccination, using a previously identified threshold. In total, 534 subjects were enrolled (371 HCWs and 163 residents). The antibody titres at t1 were the highest; at t2, the IgG titres significantly decreased, remaining however 10 times higher compared to titres at t0. Previous infection was the only significant predictor of developing and maintaining a response over threshold in both models. Results of this study provided further insights on the humoral response elicited by vaccination, and on host factors determining variations in its magnitude and kinetics.

Antibody Response after SARS-CoV-2 Infection with the Delta and Omicron Variant

The SARS-CoV-2 virus caused a worldwide COVID-19 pandemic. So far, 6,120,834 confirmed cases of COVID-19 with 116,773 deaths have been reported in Poland. According to WHO, a total of 54,662,485 vaccine doses have been administered. New variants emerge that become dominant. The aim of this study was a comparison of antibody level after infection caused by Delta and Omicron variants. The study included 203 persons who underwent mild COVID-19 despite two doses of vaccine. The obtained results indicate that a significantly lower titer was observed in patients with the Omicron variant infection. Therefore, these patients may be at risk of reinfection with new strains of the Omicron variant. Due to the possibility of reinfection, booster vaccinations are necessary. Further epidemiological and clinical studies are necessary to develop new prevention strategies.

Seroprevalence of infection-induced SARS-CoV-2 antibodies among healthcare users of Northern Italy - results from two serosurveys (October-November 2019 - September-October 2021)

Objectives

The objective was to estimate the seroprevalence of SARS-CoV-2 in autumn 2019 (before case zero was identified in Italy) and 2021 among residual sera samples from health care users in the Piedmont region of northwestern Italy.

Methods

Two serosurveys were conducted. Using a semiquantitative method, samples were tested for the presence of immunoglobulin G (IgG) antibodies against the S1 domain of the spike protein. Samples with positive test results from the 2019 survey were independently retested using a multiplex panel to detect IgG antibodies against the receptor binding domain, S1 and S2 domains, and nucleocapsid. Samples with positive test results from the 2021 survey underwent repeat testing with enzyme-linked immunosorbent assay to detect anti-nucleocapsid IgG antibodies. Prevalence rates according to gender and age groups, together with their respective 95% confidence intervals (CIs), were calculated.

Results

Overall, the proportion of samples with positive test results was 2/353 in 2019 and 22/363 in 2021, with an estimated seroprevalence of 0.27% (95% CI 0-1.86) and 6.21% (95% CI 3.9-9.31) in 2019 and 2021 respectively.

Conclusion

Results of this study support the hypothesis that the virus was circulating in Italy as early as autumn 2019. The role of these early cases in broader transmission dynamics remains to be determined.