Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination

IgG antibodies against SARS-CoV-2 decay but persist 4 months after vaccination in a cohort of healthcare workers

BACKGROUND AND AIMS

Monitoring the immune response against SARS-CoV-2 is pivotal in the evaluation of long-term vaccine efficacy. Immunoglobulin G (IgG) antibodies represent an advisable tool to reach this goal, especially for the still poorly defined antibody trend induced by the new class of mRNA vaccines against SARS-CoV-2.

MATERIALS AND METHODS

Anti-Spike RBD IgG antibodies were monitored in a cohort of healthcare workers at CRO Aviano, National Cancer Institute, through MAGLUMI® chemiluminescence assay, at 1 and 4 months after full-schedule of BNT162b2 or mRNA-1273 vaccination.

RESULTS

At 1 month after vaccination, 99.9% of 767 healthcare workers showed a reactive antibody response, which was inversely correlated with age, and positively associated with a previous history of COVID-19, and mRNA-1273 vaccination. Serological response was maintained in 99.6% of the 516 subjects monitored also at follow-up. An antibody decay from 559.8 AU/mL (IQR 359.7-845.7) to 92.7 AU/mL (IQR 65.1-148.6; p < 0.001) was observed, independently from age and sex.

CONCLUSION

Our data supported the ability of SARS-CoV-2 mRNA vaccines to induce at least a 4 months-lasting IgG response, even outside the rules of clinical trials. The antibody decay observed at follow-up suggested to deepen the immune response characterization to identify subjects with low anti-SARS-CoV-2 immunity possibly requiring a vaccination boost.

Development and characterization of SARS-CoV-2 variant-neutralizing monoclonal antibodies

Vaccination and administration of monoclonal antibody cocktails are effective tools to control the progression of infectious diseases and to terminate pandemics such as COVID-19. However, the emergence of SARS-CoV-2 mutants with enhanced transmissibility and altered antigenicity requires broad-spectrum therapies. Here we developed a panel of SARS-CoV-2 specific mouse monoclonal antibodies (mAbs), and characterized them based on ELISA, Western immunoblot, isotyping, and virus neutralization. Six neutralizing mAbs that exhibited high-affinity binding to SARS-CoV-2 spike protein were identified, and their amino acid sequences were determined by mass spectrometry. Functional assays confirmed that three mAbs, F461G11, F461G15, and F461G16 neutralized four variants of concern (VOC): B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and B.1.617.2 (delta) These mAbs are promising candidates for COVID-19 therapy, and understanding their interactions with virus spike protein should support further vaccine and antibody development.

The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape

During the COVID-19 pandemic, SARS-CoV-2 variants have emerged and spread worldwide. The Delta (B.1.617.2) variant was first reported in India in October 2020 and was classified as a "variant of concern (VOC)" by the WHO on 11 May, 2021. Compared to the wild-type strain, several studies have shown that the Delta variant is more transmissible and has higher viral loads in infected samples. COVID-19 patients infected with the Delta variant have a higher risk of hospitalization, intensive care unit (ICU) admission, and mortality. The Delta variant is becoming the dominant strain in many countries around the world. This review summarizes and analyses the biological characteristics of key amino acid mutations, the epidemic characteristics, and the immune escape of the Delta variant. We hope to provide scientific reference for the monitoring and prevention measures of the SARS-CoV-2 Delta variant and the development strategy of a second-generation vaccine.

Evolution of the SARS-CoV-2 genome and emergence of variants of concern

The high transmission and mortality rates associated with SARS-CoV-2 have led to tragic consequences worldwide. Large-scale whole-genome sequencing of the SARS-CoV-2 genome since its identification in late 2019 has identified many sequence changes and the emergence of novel strains, each described by co-segregation of a particular set of sequence variations. Variants designated G, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) are important lineages that emerged sequentially and are considered variants of concern. A notable feature of the last four, each of which ultimately evolved from clade G, is the large number (≥ 20) of co-segregating sequence variations associated with them. Several variations are in the spike gene, and some variations are shared among or between strains. Meanwhile, observation of recurrent infections with the same or different SARS-CoV-2 lineages has raised concerns about the duration of the immune responses induced by the initial infection or the vaccine that was administered. While the alpha strain is sensitive to immune responses induced by earlier strains, the beta, gamma, and delta strains can escape antibody neutralization. Apart from random replication errors, intra-host RNA editing, chronic infections, and recombination are processes that may promote the accumulation of sequence changes in the SARS-CoV-2 genome. The known contribution of recombination to coronavirus evolution and recent data pertaining to SARS-CoV-2 suggest that recombination may be particularly important. Continued surveillance of the SARS-CoV-2 genome is imperative.

Immune response against SARS-CoV-2 variants: the role of neutralization assays

Since the emergence of the novel coronavirus SARS-CoV-2 in late 2019, the COVID-19 pandemic has hindered social life and global economic activity. As of July 2021, SARS-CoV-2 has caused over four million deaths. The rapid spread and high mortality of the disease demanded the international scientific community to develop effective vaccines in a matter of months. However, unease about vaccine efficacy has arisen with the spread of the SARS-CoV-2 variants of concern (VOCs). Time- and cost-efficient in vitro neutralization assays are widely used to measure neutralizing antibody responses against VOCs. However, the extent to which in vitro neutralization reflects protection from infection remains unclear. Here, we describe common neutralization assays based on infectious and pseudotyped viruses and evaluate their role in testing neutralizing responses against new SARS-CoV-2 variants. Additionally, we briefly review the recent findings on the immune response elicited by available vaccines against major SARS-CoV-2 variants, including Alpha, Beta, Gamma, and Delta.

A Systematic Review on COVID-19 Vaccine Strategies, Their Effectiveness, and Issues

COVID-19 vaccines are indispensable, with the number of cases and mortality still rising, and currently no medicines are routinely available for reducing morbidity and mortality, apart from dexamethasone, although others are being trialed and launched. To date, only a limited number of vaccines have been given emergency use authorization by the US Food and Drug Administration and the European Medicines Agency. There is a need to systematically review the existing vaccine candidates and investigate their safety, efficacy, immunogenicity, unwanted events, and limitations. The review was undertaken by searching online databases, i.e., Google Scholar, PubMed, and ScienceDirect, with finally 59 studies selected. Our findings showed several types of vaccine candidates with different strategies against SARS-CoV-2, including inactivated, mRNA-based, recombinant, and nanoparticle-based vaccines, are being developed and launched. We have compared these vaccines in terms of their efficacy, side effects, and seroconversion based on data reported in the literature. We found mRNA vaccines appeared to have better efficacy, and inactivated ones had fewer side effects and similar seroconversion in all types of vaccines. Overall, global variant surveillance and systematic tweaking of vaccines, coupled with the evaluation and administering vaccines with the same or different technology in successive doses along with homologous and heterologous prime-booster strategy, have become essential to impede the pandemic. Their effectiveness appreciably outweighs any concerns with any adverse events.

Correlates of neutralizing/SARS-CoV-2-S1-binding antibody response with adverse effects and immune kinetics in BNT162b2-vaccinated individuals

While mRNA vaccines against SARS-CoV-2 are exceedingly effective in preventing symptomatic infection, their immune response features remain to be clarified. In the present prospective study, 225 healthy individuals in Japan, who received two BNT162b2 doses, were enrolled. Correlates of BNT162b2-elicited SARS-CoV-2-neutralizing activity (50% neutralization titer: NT50; assessed using infectious virions) with various determinants were examined and the potency of sera against variants of concerns was determined. Significant rise in NT50s was seen in sera on day 28 post-1st dose. A moderate inverse correlation was seen between NT50s and ages, but no correlation seen between NT50s and adverse effects. NT50s and SARS-CoV-2-S1-binding-IgG levels on day 28 post-1st dose and pain scores following the 2nd dose were greater in women than in men. The average half-life of NT50s was ~ 68 days, and 23.6% (49 out of 208 individuals) failed to show detectable neutralizing activity on day 150. While sera from elite-responders (NT50s > 1,500: the top 4% among the participants) potently to moderately blocked all variants of concerns examined, some sera with low NT50s failed to block the B.1.351-beta strain. Since BNT162b2-elicited immunity against SARS-CoV-2 is short, an additional vaccine or other protective measures are needed.

Herd immunity to SARS-COV-2 in the population of the Southern regions of the Far East of Russia

The aim: to study the structure and dynamics of population immunity to SARSCoV-2 of the population of the Southern Regions of the Far East (SRFE): Khabarovsk, Primorsky Krai and Amur Region during the COVID-19 epidemic in 2020.

Materials and methods. The work was carried out according to the program for assessing population immunity to SARS -CoV-2 of the population of the Russian Federation according to the methodology developed by the Rospotrebnadzor with the  participation of the St.  Petersburg Pasteur Institute. The study was approved by  the  ethical committee of the St.  Petersburg Pasteur Institute. The selection of participants was carried out by a questionnaire method using cloud technologies. The  volunteers were randomized by age by stratification into 7  age groups: 1–17, 18–29, 30–39, 40–49, 50–59, 60–69, 70+ years old. Territorial randomization consisted in limiting the engaging of volunteers – no more than 30 people from one enterprise. After the initial cross-sectional study, a 3-stage seromonitoring was carried out, in which the same volunteers participated. Antibodies to the SARS-CoV-2 nucleocapsid were determined in peripheral blood serum by the enzyme immunoassay using an appropriate set of reagents produced by the State Scientific Center for Medical and Biological Sciences of the Rospotrebnadzor (Obolensk). Statistical analysis was performed using the Excel package. The confidence interval for the proportion was calculated using the A. Wald, J. Wolfowitz method with A. Agresti, B.A. Coull’s correction. The statistical significance of the differences was calculated online using a specialized calculator. The statistical significance of the differences was assessed with a probability of p˂ 0.05, unless otherwise indicated.

Results. In a comparative analysis, the highest morbidity was observed in the Khabarovsk Territory, the lowest – in the Primorsky Territory. The level of seroprevalence among the population of the region was 19.6 % (95 % CI: 18.2–21.1) in  the  Khabarovsk Territory, 19.6  % (95  %  CI: 18.1–21.2) in the Primorsky Territory19,6 % and 45,5 % (95 % CI: 43.7–47.3) in the Amur region. The highest seroprevalence was noted among 1–17 years old children, mainly due to the subgroup of 14–17-years-olds. The smallest proportion of seropositive was found among 40–49-year-olds in the Khabarovsk Territory (14.7 %, 95 % CI: 11.2–18.6), 18–28-yearolds in the Primorsky Territory (13.3 %, 95 % CI: 10.0–17.1) and 30–39-year-olds in the Amur Region (36.3  %, 95%  CI:  31.7–41.6). No statistically significant dependence of  seroprevalence on territorial and occupational factors has been established, with the exception of an increase in the proportion of seropositive medical workers in Primorsky Territory. In the process of 3-stage seromonitoring, a regular increase in the proportion of seropositive people was revealed in all SRFE. The resulting tendency is correctly described by a second-order polynomial. A relationship was revealed between the number of convalescents and persons in contact with them, which made it possible to calculate the base reproductive number (R0) in the range from 1.4 (Primorsky Territory) to 2.4 (Amur Region). Analysis of seroprevalent volunteers showed that the number of asymptomatic individuals varied from 94.1 % (95 % CI: 92.8–95.3) to 98.3 % (95 % CI: 98.8–99.2). This indicates that most of the volunteers had COVID-19 asymptomatically.

Conclusions. A comparative study showed the prevalence of seroprevalence in the Amur Region compared with the Khabarovsk and Primorsky Territories. The relationship between the number of convalescents and persons in contact with them was noted. The value of the base R0 is calculated. It has been shown that more than 90 % of seropositive individuals in the COVID-10 SRFE were asymptomatic.

Immunogenicity and Safety of an Intradermal BNT162b2 mRNA Vaccine Booster after Two Doses of Inactivated SARS-CoV-2 Vaccine in Healthy Population

Effective vaccine coverage is urgently needed to tackle the COVID-19 pandemic. Inactivated vaccines have been introduced in many countries for emergency usage, but have only provided limited protection. Heterologous vaccination is a promising strategy to maximise vaccine immunogenicity. Here, we conducted a phase I, randomised control trial to observe the safety and immunogenicity after an intradermal boost, using a fractional dosage (1:5) of BNT162b2 mRNA vaccine in healthy participants in Songkhla, Thailand. In total, 91 volunteers who had been administered with two doses of inactivated SARS-CoV-2 (CoronaVac) were recruited into the study, and then randomised (1:1:1) to received different regimens of the third dose. An intramuscular booster with a full dose of BNT162b2 was included as a conventional control, and a half dose group was included as reciprocal comparator. Both, immediate and delayed adverse events following immunisation (AEFI) were monitored. Humoral and cellular immune responses were examined to observe the booster effects. The intradermal booster provided significantly fewer systemic side effects, from 70% down to 19.4% (p < 0.001); however, they were comparable to local reactions with the conventional intramuscular booster. In the intradermal group after receiving only one fifth of the conventional dosage, serum Anti-RBD IgG was halved compared to the full dose of an intramuscular injection. However, the neutralising function against the Delta strain remained intact. T cell responses were also less effective in the intradermal group compared to the intramuscular booster. Together, the intradermal booster, using a fractional dose of BNT162b2, can reduce systemic reactions and provides a good level and function of antibody responses compared to the conventional booster. This favourable intradermal boosting strategy provides a suitable alternative for vaccines and effective vaccine management to increase the coverage during the vaccine shortage.

COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant, and implications for vaccination

BACKGROUND

The COVID-19 Delta pandemic wave in India surged and declined within 3 months; cases then remained low despite the continued spread of Delta elsewhere. Here we aim to estimate key epidemiological characteristics of the Delta variant based on data from India and examine the underpinnings of its dynamics.

METHODS

We utilize multiple datasets and model-inference methods to reconstruct COVID-19 pandemic dynamics in India during March 2020 - June 2021. We further use model estimates to retrospectively predict cases and deaths during July - mid-Oct 2021, under various vaccination and vaccine effectiveness (VE) settings to estimate the impact of vaccination and VE for non-Delta-infection recoverees.

FINDINGS

We estimate that Delta escaped immunity in 34.6% (95% CI: 0 - 64.2%) of individuals with prior wildtype infection and was 57.0% (95% CI: 37.9 - 75.6%) more infectious than wildtype SARS-CoV-2. Models assuming higher VE among those with prior non-Delta infection, particularly after the 1 ^st dose, generated more accurate predictions than those assuming no such increases (best-performing VE setting: 90/95% vs. 30/67% baseline for the 1 ^st /2 ^nd dose). Counterfactual modeling indicates that high vaccination coverage for 1 ^st vaccine-dose in India (∼50% by mid-Oct 2021) combined with the boosting of VE among recoverees averted around 60% of infections during July - mid-Oct 2021.

INTERPRETATION

Non-pharmaceutical interventions, infection seasonality, and high coverage of 1-dose vaccination likely all contributed to pandemic dynamics in India during 2021. Given the shortage of COVID-19 vaccines globally and boosting of VE, for populations with high prior infection rates, prioritizing the first vaccine-dose may protect more people.

RESEARCH IN CONTEXT

Evidence before this study: We searched PubMed for studies published through Nov 3, 2021 on the Delta (B.1.617.2) SARS-CoV-2 variant that focused on three areas: 1) transmissibility [search terms: ("Delta variant" OR "B.1.617") AND ("transmission rate" OR "growth rate" OR "secondary attack rate" OR "transmissibility")]; 2) immune response ([search terms: ("Delta variant" OR "B.1.617") AND ("immune evas" OR "immune escape")]; and 3) vaccine effectiveness ([search terms: ("Delta variant" OR "B.1.617") AND ("vaccine effectiveness" OR "vaccine efficacy" OR "vaccination")]. Our search returned 256 papers, from which we read the abstracts and identified 54 relevant studies.Forty-two studies addressed immune evasion and/or vaccine effectiveness. Around half (n=19) of these studies measured the neutralizing ability of convalescent sera and/or vaccine sera against Delta and most reported some reduction (around 2-to 8-fold) compared to ancestral variants. The remainder (n=23) used field observations (often with a test-negative or cohort-design) and reported lower VE against infection but similar VE against hospitalization or death. Together, these laboratory and field observations consistently indicate that Delta can evade preexisting immunity. In addition, five studies reported higher B-cell and/or T-cell vaccine-induced immune response among recovered vaccinees than naïve vaccinees, suggesting potential boosting of pre-existing immunity; however, all studies were based on small samples (n = 10 to 198 individuals).Sixteen studies examined transmissibility, including 1) laboratory experiments (n=6) showing that Delta has higher affinity to the cell receptor, fuses membranes more efficiently, and/or replicates faster than other SARS-CoV-2 variants, providing biological mechanisms for its higher transmissibility; 2) field studies (n=5) showing higher rates of breakthrough infections by Delta and/or higher viral load among Delta infections than other variants; and 3) modeling/mixed studies (n=5) using genomic or case data to estimate the growth rate or reproduction number, reporting a 60-120% increase. Only one study jointly estimated the increase in transmissibility (1.3-1.7-fold, 50% CI) and immune evasion (10-50%, 50% CI); this study also reported a 27.5% (25/91) reinfection rate by Delta.Added value of this study: We utilize observed pandemic dynamics and the differential vaccination coverage for two vaccine doses in India, where the Delta variant was first identified, to estimate the epidemiological properties of Delta and examine the impact of prior non-Delta infection on immune boosting at the population level. We estimate that Delta variant can escape immunity from prior wildtype infection roughly one-third of the time and is around 60% more infectious than wildtype SARS-CoV-2. In addition, our analysis suggests the large increase in population receiving their first vaccine dose (∼50% by end of Oct 2021) combined with the boosting effect of vaccination for non-Delta infection recoverees likely mitigated epidemic intensity in India during July - Oct 2021.Implications of all the available evidence: Our analysis reconstructs the interplay and effects of non-pharmaceutical interventions, infection seasonality, Delta variant emergence, and vaccination on COVID-19 pandemic dynamics in India. Modeling findings support prioritizing the first vaccine dose in populations with high prior infection rates, given vaccine shortages.

Partial resistance of SARS-CoV-2 Delta variants to vaccine-elicited antibodies and convalescent sera

Highly transmissible SARS-CoV-2 variants identified in India and designated B.1.617, Kappa (B.1.617.1), Delta (B.1.617.2), B.1.618, and B.1.36.29 contain spike mutations L452R, T478K, E484K, E484Q, and N440K located within the spike receptor-binding domain and thus could contribute to increased transmissibility and potentially allow re-infection or cause resistance to vaccine-elicited antibody. To address these issues, we used lentiviruses pseudotyped by variant spikes to measure their neutralization by convalescent sera, vaccine-elicited and Regeneron therapeutic antibodies, and ACE2 affinity. Convalescent sera and vaccine-elicited antibodies neutralized viruses with Delta spike with 2- to 5-fold decrease in titer in different donors. Regeneron antibody cocktail neutralized virus with the Delta spike with a 2.6-fold decrease in titer. Neutralization resistance to serum antibodies and monoclonal antibodies was mediated by L452R mutation. These relatively modest decreases in antibody neutralization titer for viruses with variant spike proteins suggest that current vaccines will remain protective against the family of Delta variants.

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Vaccine-elicited antibodies neutralize Delta spike with 4- to 5-fold decrease in titer

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Delta variant is resistant to REGN10933 monoclonal antibody

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Neutralization resistance is mediated by L452R

Why are some coronavirus variants more infectious?

Since the start of the pandemic, SARS-CoV-2 has infected almost 200 million human hosts and is set to encounter and gain entry in many more in the coming months. As the coronavirus flourish, the evolutionary pressure selects those variants that can complete the infection cycle faster and reproduce in large numbers compared to others. This increase in infectivity and transmissibility coupled with the immune response from high viral load may cause moderate to severe disease. Whether this leads to enhanced virulence in the prevalent Alpha and Delta variants is still not clear. This review describes the different types of SARS-CoV-2 variants that are now prevalent, their emergence, the mutations responsible for their growth advantages, and how they affect vaccine efficacy and increase chances of reinfection. Finally, we have also summarized the efforts made to recognize and predict the mutations, which can cause immune escape and track their emergence through impactful genomic surveillance.

A Paradigm Shift to Align Transmission Routes With Mechanisms

Current infection-control guidelines subscribe to a contact/droplet/airborne paradigm that is based on outdated understanding. Here, we propose to modify and align existing guidelines with a more accurate description of the different transmission routes. This will improve the effectiveness of control measures as more transmissible variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerge.

Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study

BACKGROUND

England's COVID-19 roadmap out of lockdown policy set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as vaccination roll-out continued, with step one starting on March 8, 2021. In this study, we assess the roadmap, the impact of the delta (B.1.617.2) variant of SARS-CoV-2, and potential future epidemic trajectories.

METHODS

This mathematical modelling study was done to assess the UK Government's four-step process to easing lockdown restrictions in England, UK. We extended a previously described model of SARS-CoV-2 transmission to incorporate vaccination and multi-strain dynamics to explicitly capture the emergence of the delta variant. We calibrated the model to English surveillance data, including hospital admissions, hospital occupancy, seroprevalence data, and population-level PCR testing data using a Bayesian evidence synthesis framework, then modelled the potential trajectory of the epidemic for a range of different schedules for relaxing NPIs. We estimated the resulting number of daily infections and hospital admissions, and daily and cumulative deaths. Three scenarios spanning a range of optimistic to pessimistic vaccine effectiveness, waning natural immunity, and cross-protection from previous infections were investigated. We also considered three levels of mixing after the lifting of restrictions.

FINDINGS

The roadmap policy was successful in offsetting the increased transmission resulting from lifting NPIs starting on March 8, 2021, with increasing population immunity through vaccination. However, because of the emergence of the delta variant, with an estimated transmission advantage of 76% (95% credible interval [95% CrI] 69-83) over alpha, fully lifting NPIs on June 21, 2021, as originally planned might have led to 3900 (95% CrI 1500-5700) peak daily hospital admissions under our central parameter scenario. Delaying until July 19, 2021, reduced peak hospital admissions by three fold to 1400 (95% CrI 700-1700) per day. There was substantial uncertainty in the epidemic trajectory, with particular sensitivity to the transmissibility of delta, level of mixing, and estimates of vaccine effectiveness.

INTERPRETATION

Our findings show that the risk of a large wave of COVID-19 hospital admissions resulting from lifting NPIs can be substantially mitigated if the timing of NPI relaxation is carefully balanced against vaccination coverage. However, with the delta variant, it might not be possible to fully lift NPIs without a third wave of hospital admissions and deaths, even if vaccination coverage is high. Variants of concern, their transmissibility, vaccine uptake, and vaccine effectiveness must be carefully monitored as countries relax pandemic control measures.

FUNDING

National Institute for Health Research, UK Medical Research Council, Wellcome Trust, and UK Foreign, Commonwealth and Development Office.

Effects of SARS-CoV-2 strain variation on virus neutralisation titres: therapeutic use of convalescent plasma

We compared neutralising antibody titres of convalescent samples collected before and after the emergence of novel strains of SARS-CoV-2, against the wild-type virus (WT), Alpha (B.1.1.7) and Beta (B.1.351) variants. Plasma collected in 2020 before emergence of variants showed reduced titres against the Alpha variants, and both sets of samples demonstrated significantly reduced titres against Beta. Comparison of microneutralisation titres to those obtained with pseudotype and HAT assays showed a good correlation of titres and effects of strain variation, supporting the use of these simpler assays for assessment of convalescent plasma potency against currently circulating and emerging strains of SARS-CoV-2.

SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity

The SARS-CoV-2 B.1.617 lineage variants, Kappa (B.1.617.1) and Delta (B.1.617.2, AY) emerged during the second wave of infections in India, but the Delta variants have become dominant worldwide and continue to evolve. The spike proteins of B.1.617.1, B.1.617.2, and AY.1 variants have several substitutions in the receptor binding domain (RBD), including L452R+E484Q, L452R+T478K, and K417N+L452R+T478K, respectively, that could potentially reduce effectiveness of therapeutic antibodies and current vaccines. Here we compared B.1.617 variants, and their single and double RBD substitutions for resistance to neutralization by convalescent sera, mRNA vaccine-elicited sera, and therapeutic neutralizing antibodies using a pseudovirus neutralization assay. Pseudoviruses with the B.1.617.1, B.1.617.2, and AY.1 spike showed a modest 1.5 to 4.4-fold reduction in neutralization titer by convalescent sera and vaccine-elicited sera. In comparison, similar modest reductions were also observed for pseudoviruses with C.37, P.1, R.1, and B.1.526 spikes, but seven- and sixteen-fold reduction for vaccine-elicited and convalescent sera, respectively, was seen for pseudoviruses with the B.1.351 spike. Four of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses due to the L452R substitution, whereas six of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.1 pseudoviruses due to either the E484Q or L452R substitution. Against AY.1 pseudoviruses, the L452R and K417N substitutions accounted for the loss of neutralization by four antibodies and one antibody, respectively, whereas one antibody lost potency that could not be fully accounted for by a single RBD substitution. The modest resistance of B.1.617 variants to vaccine-elicited sera suggest that current mRNA-based vaccines will likely remain effective in protecting against B.1.617 variants, but the therapeutic antibodies need to be carefully selected based on their resistance profiles. Finally, the spike proteins of B.1.617 variants are more efficiently cleaved due to the P681R substitution, and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants.

Understanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape

The global pandemic of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), places a heavy burden on global public health. Four SARS-CoV-2 variants of concern including B.1.1.7, B.1.351, B.1.617.2, and P.1, and two variants of interest including C.37 and B.1.621 have been reported to have potential immune escape, and one or more mutations endow them with worrisome epidemiologic, immunologic, or pathogenic characteristics. This review introduces the latest research progress on SARS-CoV-2 variants of interest and concern, key mutation sites, and their effects on virus infectivity, mortality, and immune escape. Moreover, we compared the effects of various clinical SARS-CoV-2 vaccines and convalescent sera on epidemic variants, and evaluated the neutralizing capability of several antibodies on epidemic variants. In the end, SARS-CoV-2 evolution strategies in different transmission stages, the impact of different vaccination strategies on SARS-CoV-2 immune escape, antibody therapy strategies and COVID-19 epidemic control prospects are discussed. This review will provide a systematic and comprehensive understanding of the secret of SARS-CoV-2 variants of interest/concern and immune escape.

High-Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild-Type and B.1.1.7 SARS-CoV-2 in Unprocessed Saliva

We report a simple and rapid saliva-based SARS-CoV-2 antigen test that utilizes a newly developed dimeric DNA aptamer, denoted as DSA1N5, that specifically recognizes the spike proteins of the wildtype virus and its Alpha and Delta variants with dissociation constants of 120, 290 and 480 pM, respectively, and binds pseudotyped lentiviruses expressing the wildtype and alpha trimeric spike proteins with affinity constants of 2.1 pM and 2.3 pM, respectively. To develop a highly sensitive test, DSA1N5 was immobilized onto gold electrodes to produce an electrochemical impedance sensor, which was capable of detecting 1000 viral particles per mL in 1:1 diluted saliva in under 10 min without any further sample processing. Evaluation of 36 positive and 37 negative patient saliva samples produced a clinical sensitivity of 80.5 % and specificity of 100 % and the sensor could detect the wildtype virus as well as the Alpha and Delta variants in the patient samples, which is the first reported rapid test that can detect any emerging variant of SARS-CoV-2.

An observational study of breakthrough SARS-CoV-2 Delta variant infections among vaccinated healthcare workers in Vietnam

BACKGROUND

Data on breakthrough SARS-CoV-2 Delta variant infections in vaccinated individuals are limited.

METHODS

We studied breakthrough infections among Oxford-AstraZeneca vaccinated healthcare workers in an infectious diseases hospital in Vietnam. We collected demographic and clinical data alongside serial PCR testing, measurement of SARS-CoV-2 antibodies, and viral whole-genome sequencing.

FINDINGS

Between 11th-25th June 2021 (7-8 weeks after the second dose), 69 staff tested positive for SARS-CoV-2. 62 participated in the study. Most were asymptomatic or mildly symptomatic and all recovered. Twenty-two complete-genome sequences were obtained; all were Delta variant and were phylogenetically distinct from contemporary viruses obtained from the community or from hospital patients admitted prior to the outbreak. Viral loads inferred from Ct values were 251 times higher than in cases infected with the original strain in March/April 2020. Median time from diagnosis to negative PCR was 21 days (range 8-33). Neutralizing antibodies (expressed as percentage of inhibition) measured after the second vaccine dose, or at diagnosis, were lower in cases than in uninfected, fully vaccinated controls (median (IQR): 69.4 (50.7-89.1) vs. 91.3 (79.6-94.9), p=0.005 and 59.4 (32.5-73.1) vs. 91.1 (77.3-94.2), p=0.002). There was no correlation between vaccine-induced neutralizing antibody levels and peak viral loads or the development of symptoms.

INTERPRETATION

Breakthrough Delta variant infections following Oxford-AstraZeneca vaccination may cause asymptomatic or mild disease, but are associated with high viral loads, prolonged PCR positivity and low levels of vaccine-induced neutralizing antibodies. Epidemiological and sequence data suggested ongoing transmission had occurred between fully vaccinated individuals.

FUNDING

Wellcome and NIH/NIAID.

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)¹. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.

Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern

COVID-19 vaccine design and vaccination rollout need to take into account a detailed understanding of antibody durability and cross-neutralizing potential against SARS-CoV-2 and emerging variants of concern (VOCs). Analyses of convalescent sera provide unique insights into antibody longevity and cross-neutralizing activity induced by variant spike proteins, which are putative vaccine candidates. Using sera from 38 individuals infected in wave 1, we show that cross-neutralizing activity can be detected up to 305 days pos onset of symptoms, although sera were less potent against B.1.1.7 (Alpha) and B1.351 (Beta). Over time, despite a reduction in overall neutralization activity, differences in sera neutralization potency against SARS-CoV-2 and the Alpha and Beta variants decreased, which suggests that continued antibody maturation improves tolerance to spike mutations. We also compared the cross-neutralizing activity of wave 1 sera with sera from individuals infected with the Alpha, the Beta or the B.1.617.2 (Delta) variants up to 79 days post onset of symptoms. While these sera neutralize the infecting VOC and parental virus to similar levels, cross-neutralization of different SARS-CoV-2 VOC lineages is reduced. These findings will inform the optimization of vaccines to protect against SARS-CoV-2 variants.

A Sanger sequencing protocol for SARS-CoV-2 S-gene

We describe a Sanger sequencing protocol for SARS-CoV-2 S-gene the Spike (S)-glycoprotein product of which, composed of receptor-binding (S1) and membrane fusion (S2) segments, is the target of vaccines used to combat COVID-19. The protocol can be used in laboratories with basic Sanger sequencing capabilities and allows rapid "at source" screening for SARS-CoV-2 variants, notably those of concern. The protocol has been applied for surveillance, with clinical specimens collected in either nucleic acid preservation lysis-mix or virus transport medium, and research involving cultured viruses, and can yield data of public health importance in a timely manner.

SARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its new variants reported in different countries have posed a serious threat to human health and social fabrics worldwide. In addition, these new variants hindered the efforts of vaccines and other therapeutic developments. In this review article, we explained the emergence of new variants of SARS-CoV-2, their transmission risk, mortality rate, and, more importantly, the impact of each new variant on the efficacy of the developed vaccines reported in different literature and findings. The literature reported that with the emergence of new variants, the efficacy of different vaccines is declined, hospitalization and the risk of reinfection is increased. The reports concluded that the emergence of a variant that entirely evades the immune response triggered by the vaccine is improbable. The emergence of new variants and reports of re-infections are creating a more distressing situation and therefore demands further investigation to formulate an effective therapeutic strategy.

Serological Assays for Assessing Postvaccination SARS-CoV-2 Antibody Response

Serological assays for measuring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies have crucial applications in the control and surveillance of the current COVID-19 pandemic. A large number of such assays have been developed and are now commercially available. However, there are limited studies evaluating the performance of these tests. We evaluated the performances of the following six commercially available serological assays for detecting SARS-CoV-2 antibodies: (i) Genscript cPass surrogate virus neutralization test (Genscript cPass), (ii) Diasorin-SARS-CoV-2 S1/S2 IgG detection (Diasorin-S1/S2 IgG), (iii) Alinity SARS-CoV-2 IgG II (Alinity IgG II), (iv) Diasorin-SARS-CoV-2 TrimericS IgG (Diasorin-TrimericS IgG), (v) Roche Elecsys anti-SARS-CoV-2-cobas (Roche Elecsys), and (vi) AESKU enzyme linked immunosorbent assay (AESKULISA). The results of these tests were compared against the gold standard plaque reduction neutralization test (PRNT). Roche Elecsys had the highest sensitivity, and the Genscript cPass had the highest specificity. Diasorin-TrimericS IgG had the best overall performance with the highest agreement with the PRNT results. Parallel testing of Genscript cPass with Diasorin-TrimericS IgG and Diasorin-S1/S2 IgG had the optimum performance. Based on the receiver operating characteristic (ROC) curve, lowering the cutoff from 30% to 20% in the Genscript cPass significantly increased the sensitivity and the overall agreement with the PRNT results. Commercially available serological assays are good alternatives to the standard PRNT. However, further studies on larger sample numbers are required for optimization of the assay cutoff values and for evaluation of cost effectiveness. IMPORTANCE Commercial serological assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are now widely available. This study adds new knowledge regarding the optimization of these assays for evaluating postvaccination antibodies status. It highlights the positive and negative aspects of each assay in terms of sensitivity, specificity, and positive and negative predictive values, compared to the gold standard neutralization test. When using serological assays to assess postvaccine immune status, a balance of all parameters needs to be considered and not simply the high specificity. This balance is particularly relevant in the current situation where countries are aiming to mass vaccinate their populations and bring this pandemic under control. Assays with good sensitivity will have a lower percentage of false negatives and thus provide confidence for vaccination. Understanding the strengths and limitations of commercially available serological assays is important, not only for better application of these tests but also to understand the immune response and the duration of protection postvaccination.

Development of an IgG-Fc fusion COVID-19 subunit vaccine, AKS-452

AKS-452 is a biologically-engineered vaccine comprising an Fc fusion protein of the SARS-CoV-2 viral spike protein receptor binding domain antigen (Ag) and human IgG1 Fc (SP/RBD-Fc) in clinical development for the induction and augmentation of neutralizing IgG titers against SARS-CoV-2 viral infection to address the COVID-19 pandemic. The Fc moiety is designed to enhance immunogenicity by increasing uptake via Fc-receptors (FcγR) on Ag-presenting cells (APCs) and prolonging exposure due to neonatal Fc receptor (FcRn) recycling. AKS-452 induced approximately 20-fold greater neutralizing IgG titers in mice relative to those induced by SP/RBD without the Fc moiety and induced comparable long-term neutralizing titers with a single dose vs. two doses. To further enhance immunogenicity, AKS-452 was evaluated in formulations containing a panel of adjuvants in which the water-in-oil adjuvant, Montanide™ ISA 720, enhanced neutralizing IgG titers by approximately 7-fold after one and two doses in mice, including the neutralization of live SARS-CoV-2 virus infection of VERO-E6 cells. Furthermore, ISA 720-adjuvanted AKS-452 was immunogenic in rabbits and non-human primates (NHPs) and protected from infection and clinical symptoms with live SARS-CoV-2 virus in NHPs (USA-WA1/2020 viral strain) and the K18 human ACE2-trangenic (K18-huACE2-Tg) mouse (South African B.1.351 viral variant). These preclinical studies support the initiation of Phase I clinical studies with adjuvanted AKS-452 with the expectation that this room-temperature stable, Fc-fusion subunit vaccine can be rapidly and inexpensively manufactured to provide billions of doses per year especially in regions where the cold-chain is difficult to maintain.

Data-driven analysis of amino acid change dynamics timely reveals SARS-CoV-2 variant emergence

Since its emergence in late 2019, the diffusion of SARS-CoV-2 is associated with the evolution of its viral genome. The co-occurrence of specific amino acid changes, collectively named ‘virus variant’, requires scrutiny (as variants may hugely impact the agent’s transmission, pathogenesis, or antigenicity); variant evolution is studied using phylogenetics. Yet, never has this problem been tackled by digging into data with ad hoc analysis techniques. Here we show that the emergence of variants can in fact be traced through data-driven methods, further capitalizing on the value of large collections of SARS-CoV-2 sequences. For all countries with sufficient data, we compute weekly counts of amino acid changes, unveil time-varying clusters of changes with similar—rapidly growing—dynamics, and then follow their evolution. Our method succeeds in timely associating clusters to variants of interest/concern, provided their change composition is well characterized. This allows us to detect variants’ emergence, rise, peak, and eventual decline under competitive pressure of another variant. Our early warning system, exclusively relying on deposited sequences, shows the power of big data in this context, and concurs to calling for the wide spreading of public SARS-CoV-2 genome sequencing for improved surveillance and control of the COVID-19 pandemic.

COVID-19 Risk Assessment for the Tokyo Olympic Games

Introduction: As of June 7, 2021, the outbreak of Coronavirus Disease 2019 (COVID-19) has spread to more than 200 countries. The global number of reported cases is more than 172.9 million, with more than 3.7 million deaths, and the number of infected individuals is still growing rapidly. Consequently, events and activities around the world were canceled or postponed, and the preparation for sporting events were greatly challenged. Under such circumstances, about 11,000 athletes from ~206 countries are arriving in Tokyo for the 32nd Summer Olympic Games. Therefore, it is urgently necessary to assess the occurrence and spread risk of COVID-19 for the Games. Objectives: To explore effective prevention and control measures for COVID-19 in large international events through simulations of different interventions according to risk assessment. Methods: We used a random model to calculate the number of initial infected patients and used Poisson distribution to determine the number of initial infected patients based on the number of countries involved. Furthermore, to simulate the COVID-19 transmission, the susceptible-exposed-symptomatic-asymptomatic-recovered-hospitalized (SEIARH) model was established based on the susceptible-exposed-infectious-recovered (SEIR) mathematical model of epidemic diseases. According to risk assessment indicators produced by different scenarios of the simulated interventions, the risk of COVID-19 transmission in Tokyo Olympic Games was assessed. Results: The current COVID-19 prevention measures proposed by the Japan Olympic Committee need to be enhanced. And large-scale vaccination will effectively control the spread of COVID-19. When the protective efficacy of vaccines is 78.1% or 89.8%, and if the vaccination rate of athletes reaches 80%, an epidemic prevention barrier can be established.

Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy

The widespread increase in multiple severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants is causing a significant health concern in the United States and worldwide. These variants exhibit increased transmissibility, cause more severe disease, exhibit evasive immune properties, impair neutralization by antibodies from vaccinated individuals or convalescence sera, and reinfection. The Centers for Disease Control and Prevention (CDC) has classified SARS-CoV-2 variants into variants of interest, variants of concern, and variants of high consequence. Currently, four variants of concern (B.1.1.7, B.1.351, P.1, and B.1.617.2) and several variants of interests (B.1.526, B.1.525, and P.2) are characterized and are essential for close monitoring. In this review, we discuss the different SARS-CoV-2 variants, emphasizing variants of concern circulating the world and highlight the various mutations and how these mutations affect the characteristics of the virus. In addition, we discuss the most common vaccines and the various studies concerning the efficacy of these vaccines against different variants of concern.

Adaptive immune determinants of viral clearance and protection in mouse models of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 160 million infections and more than 3 million deaths worldwide. Although effective vaccines are currently being deployed, the adaptive immune determinants that promote viral clearance and confer protection remain poorly defined. Using mouse models of SARS-CoV-2, we demonstrate that both humoral and cellular adaptive immunity contribute to viral clearance in the setting of primary infection. Furthermore, we find that either convalescent mice or mice that receive mRNA vaccination are protected from both homologous infection and infection with a variant of concern, B.1.351. In addition, we find that this protection is largely mediated by antibody response and not cellular immunity. These results highlight the in vivo protective capacity of antibodies generated to both vaccine and natural infection.

Robust Neutralizing Antibody Responses 6 Months Post Vaccination with BNT162b2: A Prospective Study in 308 Healthy Individuals

Elucidating long-term immunity following COVID-19 vaccination is essential for decision-making regarding booster shots. The aim of this study was to investigate the kinetics of neutralizing antibodies (Nabs) against SARS-CoV-2 up to six months after the second vaccination dose with the BNT162b2 mRNA vaccine. Nabs levels were measured on days 1 (before the first vaccine shot), 8, 22 (before the second shot), 36, 50, and 3 and 6 months after the second vaccination (NCT04743388). Three hundred and eight healthy individuals without malignant disease were included in this study. At six months, 2.59% of the participants had a Nabs value less than 30%, while 11.9% had Nabs values of less than 50%. Importantly, 58% of the subjects had Nabs values of more than 75%. Nabs were initially eliminated at a relatively slow rate, but after three months their elimination was 5.7 times higher. Older age was inversely associated with Nabs levels at all examined timepoints. Interestingly, a population modeling analysis estimated that half of the subjects will have Nabs values less than 73.8% and 64.6% at 9 and 12 months, respectively, post vaccination completion. In conclusion, we found a persistent but declining anti-SARS-CoV-2 humoral immunity at six months following full vaccination with BNT162b2 in healthy individuals, which was more pronounced among older persons. These data may inform the public health policies regarding the prioritization of booster vaccine shots.

B.1.617.2 enters and fuses lung cells with increased efficiency and evades antibodies induced by infection and vaccination

The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), B.1.617.2, emerged in India and has spread to over 80 countries. B.1.617.2 replaced B.1.1.7 as the dominant virus in the United Kingdom, resulting in a steep increase in new infections, and a similar development is expected for other countries. Effective countermeasures require information on susceptibility of B.1.617.2 to control by antibodies elicited by vaccines and used for coronavirus disease 2019 (COVID-19) therapy. We show, using pseudotyping, that B.1.617.2 evades control by antibodies induced upon infection and BNT162b2 vaccination, although to a lesser extent as compared to B.1.351. We find that B.1.617.2 is resistant against bamlanivimab, a monoclonal antibody with emergency use authorization for COVID-19 therapy. Finally, we show increased Calu-3 lung cell entry and enhanced cell-to-cell fusion of B.1.617.2, which may contribute to augmented transmissibility and pathogenicity of this variant. These results identify B.1.617.2 as an immune evasion variant with increased capacity to enter and fuse lung cells.

La variante Delta del SARS-CoV-2: características e implicaciones para la salud pública en Colombia

La variante Delta del SARS-CoV-2 se ha convertido en uno de los mayores desafíos en salud pública a nivel mundial, ya que, luego de su identificación en la India en diciembre de 2020, se ha extendido de manera rápida, afectando principalmente a los países con bajas tasas de vacunación, y aquellos que han flexibilizado las medidas de salud pública establecidas para controlar la pandemia por COVID-19. La variante Delta tiene una mayor capacidad de replicación y se asocia con cargas virales hasta 1.260 veces más altas en comparación con las de infecciones causadas por la cepa original, lo cual puede estar asociado a mayores probabilidades de hospitalización, ingreso a UCI, necesidad de oxigenoterapia, neumonía, o incluso muerte. Las personas con vacunación completa cuentan con una protección casi similar contra las variantes Delta y Alfa. Dado el impacto de Delta en los países afectados en los que es la variante dominante, es necesario que todos los países desarrollen planes de acción sistemáticos enfocados en implementar estrictas medidas de salud pública y sociales en el contexto de la pandemia por COVID-19 y aumentar la cobertura de vacunación.. Teniendo en cuenta lo anterior, el objetivo de esta reflexión es describir las principales características de la variante Delta, su impacto en la dinámica de la pandemia en algunos de los países en que ha sido detectada, la efectividad de las vacunas contra esta variante, y sus implicaciones para la salud pública en Colombia.

COVID-19 in fully vaccinated Everest trekkers in Nepal

COVID-19 in a fully mRNA-1273 vaccinated aspiring Everest summiteer and an Everest trekker who had two doses of ChAdOx1nCoV-19 are presented. Delta B.1.617.2 variant was sequenced in one of the cases. Travellers should be wary of starting up travel to under-vaccinated regions, particularly if they are at high risk for severe disease.

Nano-engineered tools in the diagnosis, therapeutics, prevention, and mitigation of SARS-CoV-2

The recent outbreak of SARS-CoV-2 has forever altered mankind resulting in the COVID-19 pandemic. This respiratory virus further manifests into vital organ damage, resulting in severe post COVID-19 complications. Nanotechnology has been moonlighting in the scientific community to combat several severe diseases. This review highlights the triune of the nano-toolbox in the areas of diagnostics, therapeutics, prevention, and mitigation of SARS-CoV-2. Nanogold test kits have already been on the frontline of rapid detection. Breath tests, magnetic nanoparticle-based nucleic acid detectors, and the use of Raman Spectroscopy present myriads of possibilities in developing point of care biosensors, which will ensure sensitive, affordable, and accessiblemass surveillance. Most of the therapeutics are trying to focus on blocking the viral entry into the cell and fighting with cytokine storm, using nano-enabled drug delivery platforms. Nanobodies and mRNA nanotechnology with lipid nanoparticles (LNPs) as vaccines against S and N protein have regained importance. All the vaccines coming with promising phase 3 clinical trials have used nano-delivery systems for delivery of vaccine-cargo, which are currently administered widely in many countries. The use of chemically diverse metal, carbon and polymeric nanoparticles, nanocages and nanobubbles demonstrate opportunities to develop anti-viral nanomedicine. In order to prevent and mitigate the viral spread, high-performance charged nanofiber filters, spray coating of nanomaterials on surfaces, novel materials for PPE kits and facemasks have been developed that accomplish over 90% capture of airborne SARS-CoV-2. Nano polymer-based disinfectants are being tested to make smart-transport for human activities. Despite the promises of this toolbox, challenges in terms of reproducibility, specificity, efficacy and emergence of new SARS-CoV-2 variants are yet to overcome.

Protection of BNT162b2 Vaccine Booster against Covid-19 in Israel

BACKGROUND

On July 30, 2021, the administration of a third (booster) dose of the BNT162b2 messenger RNA vaccine (Pfizer-BioNTech) was approved in Israel for persons who were 60 years of age or older and who had received a second dose of vaccine at least 5 months earlier. Data are needed regarding the effect of the booster dose on the rate of confirmed coronavirus 2019 disease (Covid-19) and the rate of severe illness.

METHODS

We extracted data for the period from July 30 through August 31, 2021, from the Israeli Ministry of Health database regarding 1,137,804 persons who were 60 years of age or older and had been fully vaccinated (i.e., had received two doses of BNT162b2) at least 5 months earlier. In the primary analysis, we compared the rate of confirmed Covid-19 and the rate of severe illness between those who had received a booster injection at least 12 days earlier (booster group) and those who had not received a booster injection (nonbooster group). In a secondary analysis, we evaluated the rate of infection 4 to 6 days after the booster dose as compared with the rate at least 12 days after the booster. In all the analyses, we used Poisson regression after adjusting for possible confounding factors.

RESULTS

At least 12 days after the booster dose, the rate of confirmed infection was lower in the booster group than in the nonbooster group by a factor of 11.3 (95% confidence interval [CI], 10.4 to 12.3); the rate of severe illness was lower by a factor of 19.5 (95% CI, 12.9 to 29.5). In a secondary analysis, the rate of confirmed infection at least 12 days after vaccination was lower than the rate after 4 to 6 days by a factor of 5.4 (95% CI, 4.8 to 6.1).

CONCLUSIONS

In this study involving participants who were 60 years of age or older and had received two doses of the BNT162b2 vaccine at least 5 months earlier, we found that the rates of confirmed Covid-19 and severe illness were substantially lower among those who received a booster (third) dose of the BNT162b2 vaccine.

Protection of BNT162b2 Vaccine Booster against Covid-19 in Israel

BACKGROUND

On July 30, 2021, the administration of a third (booster) dose of the BNT162b2 messenger RNA vaccine (Pfizer-BioNTech) was approved in Israel for persons who were 60 years of age or older and who had received a second dose of vaccine at least 5 months earlier. Data are needed regarding the effect of the booster dose on the rate of confirmed coronavirus 2019 disease (Covid-19) and the rate of severe illness.

METHODS

We extracted data for the period from July 30 through August 31, 2021, from the Israeli Ministry of Health database regarding 1,137,804 persons who were 60 years of age or older and had been fully vaccinated (i.e., had received two doses of BNT162b2) at least 5 months earlier. In the primary analysis, we compared the rate of confirmed Covid-19 and the rate of severe illness between those who had received a booster injection at least 12 days earlier (booster group) and those who had not received a booster injection (nonbooster group). In a secondary analysis, we evaluated the rate of infection 4 to 6 days after the booster dose as compared with the rate at least 12 days after the booster. In all the analyses, we used Poisson regression after adjusting for possible confounding factors.

RESULTS

At least 12 days after the booster dose, the rate of confirmed infection was lower in the booster group than in the nonbooster group by a factor of 11.3 (95% confidence interval [CI], 10.4 to 12.3); the rate of severe illness was lower by a factor of 19.5 (95% CI, 12.9 to 29.5). In a secondary analysis, the rate of confirmed infection at least 12 days after vaccination was lower than the rate after 4 to 6 days by a factor of 5.4 (95% CI, 4.8 to 6.1).

CONCLUSIONS

In this study involving participants who were 60 years of age or older and had received two doses of the BNT162b2 vaccine at least 5 months earlier, we found that the rates of confirmed Covid-19 and severe illness were substantially lower among those who received a booster (third) dose of the BNT162b2 vaccine.

Longitudinal Humoral Responses after COVID-19 Vaccination in Peritoneal and Hemodialysis Patients over Twelve Weeks

It has been demonstrated that patients on hemo- or peritoneal dialysis are particularly susceptible to SARS-CoV-2 infection and impaired seroconversion compared to healthy controls. Follow-up data on vaccination response in dialysis patients is limited but is greatly needed to individualize and guide (booster) vaccination strategies. In this prospective, multicenter study we measured anti-spike S1 and neutralizing antibodies in 124 hemodialysis patients, 41 peritoneal dialysis patients, and 20 age- and sex-matched healthy controls over 12 weeks after homologous BNT162b2 vaccination. Compared to healthy controls, both hemodialysis and peritoneal dialysis patients had lower anti-S1 IgG antibodies (median (IQR) 7.0 (2.8-24.3) and 21.8 (5.8-103.9) versus 134.9 (23.8-283.6), respectively; p < 0.001 and p < 0.05) and a reduced SARS-CoV-2 spike protein-ACE2 binding inhibition caused by vaccine-induced antibodies (median (IQR) 56% (40-81) and 77% (52-89) versus 96% (90-98), respectively; p < 0.001 and p < 0.01) three weeks after the second vaccination. Twelve weeks after the second vaccination, the spike protein-ACE2 binding inhibition significantly decreased to a median (IQR) of 45% (31-60) in hemodialysis patients and 55% (36-78) in peritoneal dialysis patients, respectively (p < 0.001 and p < 0.05). Peritoneal dialysis patients mounted higher antibody levels compared with hemodialysis patients at all time points during the 12-week follow-up. Individual booster vaccinations in high-risk individuals without seroconversion or rapidly waning neutralizing antibody levels are required and further data on the neutralization of emerging variants of concern in these patients are urgently needed.

Weak Cross-Lineage Neutralization by Anti SARS-CoV-2 Spike Antibodies after Natural Infection or Vaccination Is Rescued by Repeated Immunological Stimulation

After over one year of evolution, through billions of infections in humans, SARS-CoV-2 has evolved into a score of slightly divergent lineages. A few different amino acids in the spike proteins of these lineages can hamper both natural immunity against reinfection, and vaccine efficacy. In this study, the in vitro neutralizing potency of sera from convalescent COVID-19 patients and vaccinated subjects was analyzed against six different SARS-CoV-2 lineages, including the latest B.1.617.2 (or Delta variant), in order to assess the cross-neutralization by anti-spike antibodies. After both single dose vaccination, or natural infection, the neutralizing activity was low and fully effective only against the original lineage, while a double dose or a single dose of vaccine, even one year after natural infection, boosted the cross-neutralizing activity against different lineages. Neither binding, nor the neutralizing activity of sera after vaccination, could predict vaccine failure, underlining the need for additional immunological markers. This study points at the importance of the anamnestic response and repeated vaccine stimulations to elicit a reasonable cross-lineage neutralizing antibody response.

Breakthrough Infection With Severe Acute Respiratory Syndrome Coronavirus 2 Among Healthcare Workers in Delhi: A Single-Institution Study

Introduction This study aimed to determine the breakthrough infection rate of coronavirus disease 2019 (COVID-19) (severe acute respiratory syndrome coronavirus 2 {SARS-CoV-2}) infection in healthcare workers (HCWs) vaccinated with either BBV152 or AZD1222 (ChAdOx1-S) vaccine. Methods A cross-sectional analysis was conducted at a medical college and hospital complex in Delhi, India, through telephonic interviews among HCWs who had received at least one dose of a COVID-19 vaccine during January-March 2021. Breakthrough infections were operationally defined as the occurrence of COVID-19 infection ≥14 days after administration of two doses of either COVID-19 vaccine. Data were entered in Epidata 3.1 (Odense, Denmark: EpiData Association) (single entered) and analyzed with IBM SPSS version 25 (Armonk, NY: IBM Corp.). A p-value < 0.05 was considered statistically significant. Results We enrolled 325 HCWs with a mean (SD) age of 29.1 (9.9) years including 211 (64.9%) males and 114 (35.1%) females. A total of 37 (13.3%, 95% CI 9.8, 17.7) COVID-19 breakthrough infections were observed in the HCWs. Additionally, 20 (6.1%) non-breakthrough infections were reported in the HCWs who were vaccinated with at least a single dose of a COVID-19 vaccine, or both doses, but prior to 14 days since the administration of the second dose. Most breakthrough infections were mild without needing supplemental oxygen for recovery. Conclusion Nearly one in seven HCWs experienced a COVID-19 breakthrough infection in the present study. A history of SARS-CoV-2 natural infection followed by at least one dose of COVID-19 vaccination was associated with significant protection against breakthrough infections.

Assessment of Simulated Surveillance Testing and Quarantine in a SARS-CoV-2-Vaccinated Population of Students on a University Campus

Importance

The importance of surveillance testing and quarantine on university campuses to limit SARS-CoV-2 transmission needs to be reevaluated in the context of a complex and rapidly changing environment that includes vaccines, variants, and waning immunity. Also, recent US Centers for Disease Control and Prevention guidelines suggest that vaccinated students do not need to participate in surveillance testing.

Objective

To evaluate the use of surveillance testing and quarantine in a fully vaccinated student population for whom vaccine effectiveness may be affected by the type of vaccination, presence of variants, and loss of vaccine-induced or natural immunity over time.

Design Setting and Participants

In this simulation study, an agent-based Susceptible, Exposed, Infected, Recovered model was developed with some parameters estimated using data from the 2020 to 2021 academic year at Duke University (Durham, North Carolina) that described a simulated population of 5000 undergraduate students residing on campus in residential dormitories. This study assumed that 100% of residential undergraduates are vaccinated. Under varying levels of vaccine effectiveness (90%, 75%, and 50%), the reductions in the numbers of positive cases under various mitigation strategies that involved surveillance testing and quarantine were estimated.

Main Outcomes and Measures

The percentage of students infected with SARS-CoV-2 each day for the course of the semester (100 days) and the total number of isolated or quarantined students were estimated.

Results

A total of 5000 undergraduates were simulated in the study. In simulations with 90% vaccine effectiveness, weekly surveillance testing was associated with only marginally reduced viral transmission. At 50% to 75% effectiveness, surveillance testing was estimated to reduce the number of infections by as much as 93.6%. A 10-day quarantine protocol for exposures was associated with only modest reduction in infections until vaccine effectiveness dropped to 50%. Increased testing of reported contacts was estimated to be at least as effective as quarantine at limiting infections.

Conclusions and Relevance

In this simulated modeling study of infection dynamics on a college campus where 100% of the student body is vaccinated, weekly surveillance testing was associated with a substantial reduction of campus infections with even a modest loss of vaccine effectiveness. Model simulations also suggested that an increased testing cadence can be as effective as a 10-day quarantine period at limiting infections. Together, these findings provide a potential foundation for universities to design appropriate mitigation protocols for the 2021 to 2022 academic year.

Pregnancy Outcomes and Maternal Complications During the Second Wave of Coronavirus Disease 2019 (COVID-19) in India

Rates of severe coronavirus disease 2019 (COVID-19), intensive care unit admission, and maternal mortality increased among pregnant and postpartum women admitted for COVID-19 in the second wave compared with the first wave in India.

Severe Acute Respiratory Syndrome Coronavirus 2 Vaccination for Paediatric Patients With Inflammatory Bowel Diseases

In this communication, the members of the Porto group (the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN], inflammatory bowel diseases [IBD] working group) provide the current available evidence regarding vaccination of children and young adolescents with IBD against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our intent is to help provide meaningful answers to the concerns that parents and adolescents may have.

Optimizing testing regimes for the detection of COVID-19 in children and older adults

Introduction: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is a major pandemic and continuously emerging due to unclear prognosis and unavailability of reliable detection tools. Older adults are more susceptible to COVID-19 than children showing mature Angiotensin-Converting Enzyme 2 (ACE2), low concentration of immune targets, and comorbid conditions. Several detection platforms have been commercialized to date and more are in pipeline, however, the rate of false-positive results and rapid mutation of SARS-CoV-2 is increasing. Additionally, physiological, and geographical variations of affected individuals are also calling for diagnostic methods optimization.Areas Covered: Extensive information related to the optimization and usefulness of SARS-CoV-2 diagnostic methods based on sensitivity and specificity as definitive and feasible investigative tools is discussed. Moreover, an option of combining laboratory diagnostic methods to improve diagnostic strategies is also proposed and discussed in the comparative section of optimization studies.Expert Opinion: The review article explains the importance of optimization strategies for SARS-CoV-2 detection in children and older adults. There are advancements in COVID-19 detection including CRISPR-based, electrochemical, and optical-based sensing systems. However, the lack of sufficient studies on a comparative evaluation of standardized SARS-CoV-2 diagnostic methods among children and older adults, limit the authentication of commercialized kits.

Progress of the COVID-19 vaccine effort: viruses, vaccines and variants versus efficacy, effectiveness and escape

Where 2020 saw the development and testing of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at an unprecedented pace, the first half of 2021 has seen vaccine rollout in many countries. In this Progress article, we provide a snapshot of ongoing vaccine efficacy studies, as well as real-world data on vaccine effectiveness and the impact of virus variants of concern. Where they have been deployed in a high proportion of the adult population, the currently approved vaccines have been extremely effective in preventing COVID-19, particularly severe disease. Nonetheless, there are still significant challenges in ensuring equitable vaccine access around the globe and lessons that can be learned for controlling this pandemic and for the next pandemic.

Decisive conditions for strategic vaccination against SARS-CoV-2

While vaccines against severe acute respiratory syndrome coronavirus (SARS-CoV-2) are being administered, in many countries it may still take months until their supply can meet demand. The majority of available vaccines elicit strong immune responses when administered as prime-boost regimens. Since the immunological response to the first ("prime") dose may provide already a substantial reduction in infectiousness and protection against severe disease, it may be more effective-under certain immunological and epidemiological conditions-to vaccinate as many people as possible with only one dose instead of administering a person a second ("booster") dose. Such a vaccination campaign may help to more effectively slow down the spread of SARS-CoV-2 and reduce hospitalizations and fatalities. The conditions that make prime-first vaccination favorable over prime-boost campaigns, however, are not well understood. By combining epidemiological modeling, random-sampling techniques, and decision tree learning, we find that prime-first vaccination is robustly favored over prime-boost vaccination campaigns even for low single-dose efficacies. For epidemiological parameters that describe the spread of coronavirus disease 2019 (COVID-19), recent data on new variants included, we show that the difference between prime-boost and single-shot waning rates is the only discriminative threshold, falling in the narrow range of 0.01-0.02  day^-1 below which prime-first vaccination should be considered.