RT-qPCR based determination of SARS-CoV-2 in health care workers, Cologne, Germany - A pre-delta/pre-omicron proof of principle field study

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), and SARS-CoV-2 variants pose an increased risk to global health. Therefore, monitoring of SARS-CoV-2 variants of concern (VOCs) is of high importance for the implementation of disease control methods, for timely public health decisions, and the development of vaccines against SARS-CoV-2 variants. In this study, which was performed before the delta and omicron variants of concern became dominant, a total of 111 SARS-CoV-2 positive samples from our hospital staff in Cologne, Germany, collected from March 2020 to May 2021 were analysed for VOCs. For determination of VOCs, mutation genotyping analysis (MGA) using mutation-specific simple (MSS) probes based on quantitative reverse transcription-polymerase chain reaction (RT-qPCR) of ten spike protein variants (SPVs) was performed. The MGA focuses on the detection of the spike protein mutation (SPM) of SPVs belonging to VOCs. By successful determination of SPV, the work concludes that 24.66 % of the samples belong to VOC B.1.1.7 and 1.37 % of the samples belong to VOC B.1.351. Based on these results, MGA proves to be a suitable alternative to sequencing technologies as it is a rapid, cost-effective, widely available, and feasible method that allows high sample throughput for the determination of circulating and monitored SARS-CoV-2 VOCs. With focus on the novel variants such as SARS-CoV-2 omicron BA.4 and BA.5 similar approaches could be used for a rapid initial screening, while, however, due to the increasing number of single nucleotide polymorphisms that determine the variants of concern in depth screening becomes more cost efficient by next generation sequencing.Copyright © 2022 AEPress, s.r.o.. All rights reserved.

Hybridoma-derived neutralizing monoclonal antibodies against Beta and Delta variants of SARS-CoV-2 in vivo.

Neutralizing monoclonal antibodies (mAb) are a major therapeutic strategy for the treatment of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. The continuous emergence of new SARS-CoV-2 variants worldwide has increased the urgency for the development of new mAbs. In this study, we immunized mice with the receptor-binding domain (RBD) of the SARS-CoV-2 prototypic strain (WIV04) and screened 35 RBD-specific mAbs using hybridoma technology. Results of the plaque reduction neutralization test showed that 25 of the mAbs neutralized authentic WIV04 strain infection. The 25 mAbs were divided into three categories based on the competitive enzyme-linked immunosorbent assay results. A representative mAb was selected from each category (RD4, RD10, and RD14) to determine the binding kinetics and median inhibitory concentration (IC50) of WIV04 and two variants of concern (VOC): B.1.351 (Beta) and B.1.617.2 (Delta). RD4 neutralized the B.1.617.2 variant with an IC50 of 2.67 â€‹ng/mL; however, it completely lost neutralizing activity against the B.1.351 variant. RD10 neutralized both variants with an IC50 exceeding 100 â€‹ng/mL; whereas RD14 neutralized two variants with a higher IC50 (>1 â€‹mg/mL). Animal experiments were performed to evaluate the protective effects of RD4 and RD10 against various VOC infections. RD4 could protect Adv-hACE2 transduced mice from B.1.617.2 infection at an antibody concentration of 25 â€‹mg/kg, while RD10 could protect mice from B.1.351 infection at an antibody concentration of 75 â€‹mg/kg. These results highlight the potential for future modifications of the mAbs for practical use.

TMPRSS2 Is Essential for SARS-CoV-2 Beta and Omicron Infection.

The COVID-19 pandemic remains a global health threat and novel antiviral strategies are urgently needed. SARS-CoV-2 employs the cellular serine protease TMPRSS2 for entry into lung cells, and TMPRSS2 inhibitors are being developed for COVID-19 therapy. However, the SARS-CoV-2 Omicron variant, which currently dominates the pandemic, prefers the endo/lysosomal cysteine protease cathepsin L over TMPRSS2 for cell entry, raising doubts as to whether TMPRSS2 inhibitors would be suitable for the treatment of patients infected with the Omicron variant. Nevertheless, the contribution of TMPRSS2 to the spread of SARS-CoV-2 in the infected host is largely unclear. In this study, we show that the loss of TMPRSS2 strongly reduced the replication of the Beta variant in the nose, trachea and lung of C57BL/6 mice, and protected the animals from weight loss and disease. The infection of mice with the Omicron variant did not cause disease, as expected, but again, TMPRSS2 was essential for efficient viral spread in the upper and lower respiratory tract. These results identify the key role of TMPRSS2 in SARS-CoV-2 Beta and Omicron infection, and highlight TMPRSS2 as an attractive target for antiviral intervention.

Immunogenicity of adjuvanted plant-produced SARS-CoV-2 Beta spike VLP vaccine in New Zealand white rabbits.

The outbreak of the SARS-CoV-2 global pandemic heightened the pace of vaccine development with various vaccines being approved for human use in a span of 24 months. The SARS-CoV-2 trimeric spike (S) surface glycoprotein, which mediates viral entry by binding to ACE2, is a key target for vaccines and therapeutic antibodies. Plant biopharming is recognized for its scalability, speed, versatility, and low production costs and is an increasingly promising molecular pharming vaccine platform for human health. We developed Nicotiana benthamiana-produced SARS-CoV-2 virus-like particle (VLP) vaccine candidates displaying the S-protein of the Beta (B.1.351) variant of concern (VOC), which triggered cross-reactive neutralising antibodies against Delta (B.1.617.2) and Omicron (B.1.1.529) VOCs. In this study, immunogenicity of the VLPs (5 µg per dose) adjuvanted with three independent adjuvants i.e. oil-in-water based adjuvants SEPIVAC SWETM (Seppic, France) and "AS IS" (Afrigen, South Africa) as well as a slow-release synthetic oligodeoxynucleotide (ODN) adjuvant designated NADA (Disease Control Africa, South Africa) were evaluated in New Zealand white rabbits and resulted in robust neutralising antibody responses after booster vaccination, ranging from 1:5341 to as high as 1:18204. Serum neutralising antibodies elicited by the Beta variant VLP vaccine also showed cross-neutralisation against the Delta and Omicron variants with neutralising titres ranging from 1:1702 and 1:971, respectively. Collectively, these data provide support for the development of a plant-produced VLP based candidate vaccine against SARS-CoV-2 based on circulating variants of concern.

A Spotlight on Novel Coronavirus (COVID - 19) with Various Types of Strains

Deadly COVID-19 viruses have raised a pandemic situation in the year 2019, causing serious and contagious respiratory infections in humans. SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the main causative agent for this disease outbreak. The pandemic created a critical impact on the global economy. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis that lasted about 11 months. Since, late 2020, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations. This resulted so far, in over 2.7 million deaths and near about 122 million infection cases. Most mutations in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome are either deleterious and swiftly purged or relatively neutral. As far as the concern is the variants it impacts the virus characteristics, including antigenicity and transmissibility in response to the modification of the human immune profile. In recent days, COVID-19 affected cases are rapidly increasing and it became difficult to inhibit this virus as they are continuously mutated in the host cell forming various new strains like B.1.1.7, B.1.351, P.1, P.2, B.1.1.529, etc. These monitoring, surveillance of variation, and sequencing efforts within the SARS-CoV-2 genome enabled the rapid identification of the first some of Variants of Concern (VOCs) in late 2020, where genome changes became the most observable impact on virus biology and disease transmission. In this review article, we tried to focus and spot the light on the genetic diversification of various strains, their nature, similarities and dissimilarities, mechanism of action, and the prophylactic interventions which could prevent this life-threatening disease in the long run.

DEVELOPMENT OF PCR TEST FOR DETECTION OF THE SARS-COV-2 GENETIC VARIANTS ALPHA, BETA, GAMMA, DELTA

The emergence of novel SARS-CoV-2 genetic variants with increased transmissivity and reduced antibody neutralization efficiency is a threat to global public health. Reverse transcription polymerase chain reaction (RT-PCR) with the use of fluorescent probes, which make it possible to detect the single nucleotide substitutions, is a technique suitable for screening the SARS-CoV-2 RNA-containing samples for the already known functionally significant mutations in the S-gene, identification of which allows to define and differentiate the most epidemiologically significant genetic variants. The study was aimed to develop an assay for the large-scale monitoring of the spread of the SARS-CoV-2 top-priority variants. Based on the whole-genome alignment of the SARS-CoV-2 sequences, deposited in the GISAID database, primers and LNA-modified probes were selected to detect mutations in the S gene, typical for the Alpha, Beta/Gamma and Delta variants of concern (VOC). The developed reagent kit for detection of the key mutations in the SARS-CoV-2 S gene by the real time RT-PCR has good analytical and diagnostic characteristics and was authorized as a medical device (reagent) for in vitro use. The results of detecting the VOC and the key mutations with the use of the developed reagent kit were consistent with the data of the whole genome sequencing of 1,500 SARS-CoV-2 RNA samples. The developed reagent kit and the subsequent SARS-CoV-2 RNA sequencing assay used to perform the epidemiological monitoring of SARS-CoV-2 variants made it possible to promptly report the emergence of the Delta genetic variant in Russia, and to trace the dynamic changes in the prevalence of Delta in Moscow Region in April-September 2021. © 2022 Obstetrics, Gynecology and Reproduction. All rights reserved.

Review of Concerned SARS-CoV-2 Variants Like Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), as well as Novel Methods for Reducing and Inactivating SARS-CoV-2 Mutants in Wastewater Treatment Facilities

The coronavirus known as COVID-19, which causes pandemics, is causing a global epidemic at a critical stage today. Furthermore, novel mutations in the SARS-CoV-2 spike protein have been discovered in an entirely new strain, impacting the clinical and epidemiological features of COVID-19. Variants of these viruses can increase the transmission in wastewater, lead to reinfection, and reduce immunity provided by monoclonal antibodies and vaccinations. According to the research, a large quantity of viral RNA was discovered in wastewater, suggesting that wastewater can be a crucial source of epidemiological data and health hazards. The purpose of this paper is to introduce a few basic concepts regarding wastewater surveillance as a starting point for comprehending COVID-19′s epidemiological aspects. Next, the observation of Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) in wastewater is discussed in detail. Secondly, the essential information for the initial, primary, and final treating sewage in SARS-CoV-2 is introduced. Following that, a thorough examination is provided to highlight the newly developed methods for eradicating SARS-CoV-2 using a combination of solar water disinfection (SODIS) and ultraviolet radiation A (UVA (315-400 nm)), ultraviolet radiation B (UVB (280-315 nm)), and ultraviolet radiation C (UVC (100-280 nm)) processes. SARS-CoV-2 eradication requires high temperatures (above 56°C) and UVC. However, SODIS technologies are based on UVA and operate at cooler temperatures (less than 45°C). Hence, it is not appropriate for sewage treatment (or water consumption) to be conducted using SODIS methods in the current pandemic. Finally, SARS-CoV-2 may be discovered in sewage utilizing the wastewater-based epidemiology (WBE) monitoring method.

COVID-19 outbreak trends in South Africa: A comparison of Omicron (B.1.1.529), Delta (B.1.617.2), and Beta (B.1.351) variants outbreak periods.

OBJECTIVES: We provided COVID-19 outbreak trends in South Africa during the Omicron (B.1.1.529), Delta (B.1.617.2), and Beta (B.1.351) variants outbreak periods from November 2020 to March 2022. METHODS: We used the time series summary data of the COVID-19 outbreak for South Africa available in the COVID-19 data repository created by the Center for System and Science and Engineering at Johns Hopkins University and the Our World in Data database by the University of Oxford from January 2020 to March 2022. We used the joinpoint regression model with a data-driven Bayesian information criterion method for analyzing the outbreak trends. In addition, we used density ellipses and partition modeling on the outbreak data. RESULTS: During the Omicron outbreak period, COVID-19 cases in South Africa significantly jumped by 4.7 times from December 01 to December 08, 2021. The average daily growth rate of incidence peaked at 23,000 cases/day until December 16, 2021, which was 18.6 % higher than the peak growth during the Delta outbreak period. South Africa experienced peak growth in COVID-19 cases with 18,611 cases/day (January 04 to January 14, 2021) during the Beta outbreak period and with 19,395 cases/day (July 01 to July 11, 2021) during the Delta outbreak period. Density ellipsoid showed a significant correlation between daily cases and daily death count during the Beta and Delta outbreak period which was not prominent in the Omicron outbreak period. Comparatively higher daily death tolls were reported in days with a recovery rate of less than 89.1 % and 91.9 % in the Beta and Delta outbreak period respectively. The backlog counts may be one of the reasons for the significant increase in daily death tolls during the Omicron period. CONCLUSIONS: During the Omicron period, COVID-19 cases peaked growth was 18.6 % higher than the peak growth during the Delta outbreak period. Despite that fact, growth in death trends in the Omicron outbreak period was found low which might be due to the low mortality rate and case fatality proportion. The emergence of the Omicron variant once again reminds us that- "no one is safe until everyone is safe".

Detection of SARS-CoV-2 N501Y mutation among SARS-CoV-2 variants of concern circulating in Northern Cyprus.

Aim: SARS-CoV-2 variants of concern (VOCs) carry signature mutations particularly in the spike protein. Most VOCs lineages that carry N501Y substitution have been reported to evade viral diagnostic tests and have impact on vaccine effectiveness. Therefore, monitoring the circulating variants represents a major requirement for a public health response worldwide. We aimed to investigate the prevalence of N501Y bearing SARS-CoV-2 samples in Northern Cyprus. Materials & methods: Reverse transcription quantitative PCR technique was used to identify N501Y mutation from 658 samples. Results: Our results indicate that the proportion of N501Y-bearing lineages increased significantly from January through May 2021 (45.2-75.5%) in the region. Conclusion: These results indicate that VOCs are dominant lineages in the country and highlight an alarming situation which require strict governmental measures to minimize COVID-19 morbidity and mortality.

The E484K Substitution in a SARS-CoV-2 Spike Protein Subunit Vaccine Resulted in Limited Cross-Reactive Neutralizing Antibody Responses in Mice.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially emerging variants, poses an increased threat to global public health. The significant reduction in neutralization activity against the variants such as B.1.351 in the serum of convalescent patients and vaccinated people calls for the design of new potent vaccines targeting the emerging variant. However, since most vaccines approved and in clinical trials are based on the sequence of the original SARS-CoV-2 strain, the immunogenicity and protective efficacy of vaccines based on the B.1.351 variant remain largely unknown. In this study, we evaluated the immunogenicity, induced neutralization activity, and protective efficacy of wild-type spike protein nanoparticle (S-2P) and mutant spike protein nanoparticle (S-4M-2P) carrying characteristic mutations of B.1.351 variant in mice. Although there was no significant difference in the induction of spike-specific IgG responses in S-2P- and S-4M-2P-immunized mice, neutralizing antibodies elicited by S-4M-2P exhibited noteworthy, narrower breadth of reactivity with SARS-CoV-2 variants compared with neutralizing antibodies elicited by S-2P. Furthermore, the decrease of induced neutralizing antibody breadth at least partly resulted from the amino acid substitution at position 484. Moreover, S-4M-2P vaccination conferred insufficient protection against live SARS-CoV-2 virus infection, while S-2P vaccination gave definite protection against SARS-CoV-2 challenge in mice. Together, our study provides direct evidence that the E484K substitution in a SARS-CoV-2 subunit protein vaccine limited the cross-reactive neutralizing antibody breadth in mice and, more importantly, draws attention to the unfavorable impact of this mutation in spike protein of SARS-CoV-2 variants on the induction of potent neutralizing antibody responses.

COVID-19 infection and neurodegeneration: Computational evidence for interactions between the SARS-CoV-2 spike protein and monoamine oxidase enzymes.

Although COVID-19 has been primarily associated with pneumonia, recent data show that its causative agent, the SARS-CoV-2 coronavirus, can infect many vital organs beyond the lungs, including the heart, kidneys and the brain. The literature agrees that COVID-19 is likely to have long-term mental health effects on infected individuals, which signifies a need to understand the role of the virus in the pathophysiology of brain disorders that is currently unknown and widely debated. Our docking and molecular dynamics simulations show that the affinity of the spike protein from the wild type (WT) and the South African B.1.351 (SA) variant towards MAO enzymes is comparable to that for its ACE2 receptor. This allows for the WT/SA⋅⋅⋅MAO complex formation, which changes MAO affinities for their neurotransmitter substrates, thereby impacting their metabolic conversion and misbalancing their levels. Knowing that this fine regulation is strongly linked with the etiology of various brain pathologies, these results are the first to highlight the possibility that the interference with the brain MAO catalytic activity is responsible for the increased neurodegenerative illnesses following a COVID-19 infection, thus placing a neurobiological link between these two conditions in the spotlight. Since the obtained insight suggests that a more contagious SA variant causes even larger disturbances, and with new and more problematic strains likely emerging in the near future, we firmly advise that the presented prospect of the SARS-CoV-2 induced neurological complications should not be ignored, but rather requires further clinical investigations to achieve an early diagnosis and timely therapeutic interventions.

The SARS-CoV-2 B.1.351 Variant Can Transmit in Rats But Not in Mice.

Previous studies have shown that B.1.351 and other variants have extended the host range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to mice. Sustained transmission is a prerequisite for viral maintenance in a population. However, no evidence of natural transmission of SARS-CoV-2 in wild mice has been documented to date. Here, we evaluated the replication and contact transmission of the B.1.351 variant in mice and rats. The B.1.351 variant could infect and replicate efficiently in the airways of mice and rats. Furthermore, the B.1.351 variant could not be transmitted in BALB/c or C57BL/6 mice but could be transmitted with moderate efficiency in rats by direct contact. Additionally, the B.1.351 variant did not transmit from inoculated Syrian hamsters to BALB/c mice. Moreover, the mouse-adapted SARS-CoV-2 strain C57MA14 did not transmit in mice. In summary, the risk of B.1.351 variant transmission in mice is extremely low, but the transmission risk in rats should not be neglected. We should pay more attention to the potential natural transmission of SARS-CoV-2 variants in rats and their possible spillback to humans.

A Bivalent COVID-19 Vaccine Based on Alpha and Beta Variants Elicits Potent and Broad Immune Responses in Mice against SARS-CoV-2 Variants.

With the emergence and rapid spread of new pandemic variants, especially variants of concern (VOCs), the development of next-generation vaccines with broad-spectrum neutralizing activities is of great importance. In this study, SCTV01C, a clinical stage bivalent vaccine based on trimeric spike extracellular domain (S-ECD) of SARS-CoV-2 variants Alpha (B.1.1.7) and Beta (B.1.351) with a squalene-based oil-in-water adjuvant was evaluated in comparison to its two corresponding (Alpha and Beta) monovalent vaccines in mouse immunogenicity studies. The two monovalent vaccines induced potent neutralizing antibody responses against the antigen-matched variants, but drastic reductions in neutralizing antibody titers against antigen-mismatched variants were observed. In comparison, the bivalent vaccine SCTV01C induced relatively higher and broad-spectrum cross-neutralizing activities against various SARS-CoV-2 variants, including the D614G variant, VOCs (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.1.529), variants of interest (VOIs) (C.37, B.1.621), variants under monitoring (VUMs) (B.1.526, B.1.617.1, B.1.429, C.36.3) and other variants (B.1.618, 20I/484Q). All three vaccines elicited potent Th1-biased T-cell immune responses. These results provide direct evidence that variant-based multivalent vaccines could play important roles in addressing the critical issue of reduced protective efficacy against the existing and emerging SARS-CoV-2 variants.

Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2.

Lipid nanoparticle (LNP)-mRNA vaccines offer protection against COVID-19; however, multiple variant lineages caused widespread breakthrough infections. Here, we generate LNP-mRNAs specifically encoding wild-type (WT), B.1.351, and B.1.617 SARS-CoV-2 spikes, and systematically study their immune responses. All three LNP-mRNAs induced potent antibody and T cell responses in animal models; however, differences in neutralization activity have been observed between variants. All three vaccines offer potent protection against in vivo challenges of authentic viruses of WA-1, Beta, and Delta variants. Single-cell transcriptomics of WT- and variant-specific LNP-mRNA-vaccinated animals reveal a systematic landscape of immune cell populations and global gene expression. Variant-specific vaccination induces a systemic increase of reactive CD8 T cells and altered gene expression programs in B and T lymphocytes. BCR-seq and TCR-seq unveil repertoire diversity and clonal expansions in vaccinated animals. These data provide assessment of efficacy and direct systems immune profiling of variant-specific LNP-mRNA vaccination in vivo.

Investigating Novel Coronavirus Through Statistical Methods for Biomedical Applications: An Engineering Student Perspective

The World of today is suffering from novel coronavirus (nCOV2). This is a respiratory infectious disease that has affected the entire globe. This respiratory infection is first originated in Wuhan, China. Today, it has many variants like the “United Kingdom (UK) variant called B.1.1.7,” “South African variant is called B.1.351,” “Brazilian variant is known as P.1,” etc. In this research work, we will discuss the Indian scenario to tackle nCOV2. We will also present an engineering student’s perspective to detect changes developed in the patient’s chest suffering from nCOV2 employing statistical methods. Among all the statistical techniques, GLCM-based texture analysis-based technique has gained popularity due to its diverse applications. It is used in many applications like remote sensing, image processing, biomedical applications, seismic data analysis. Thus in this research work, this methodology is used various changes in the before and after images of the patient suffering from the novel coronavirus. © 2022, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

Comparison of SARS-CoV-2 Variants of Concern Alpha (B.1.1.7) vs. Beta (B.1.351) in Critically Ill Patients: A Multicenter Cohort Study.

Objectives: The clinical outcomes of the Beta (B.1.351) variant of concern (VOC) of the SARS-CoV-2 virus remain poorly understood. In early 2021, northeastern France experienced an outbreak of Beta that was not observed elsewhere. This outbreak slightly preceded and then overlapped with a second outbreak of the better understood VOC Alpha (B.1.1.7) in the region. This situation allowed us to contemporaneously compare Alpha and Beta in terms of the characteristics, management, and outcomes of critically ill patients. Methods: A multicenter prospective cohort study was conducted on all consecutive adult patients who had laboratory confirmed SARS CoV-2 infection, underwent variant screening, and were admitted to one of four intensive care units (ICU) for acute respiratory failure between January 9th and May 15th, 2021. Primary outcome was 60-day mortality. Differences between Alpha and Beta in terms of other outcomes, patient variables, management, and vaccination characteristics were also explored by univariate analysis. The factors that associated with 60-day death in Alpha- and Beta-infected patients were examined with logistic regression analysis. Results: In total, 333 patients (median age, 63 years; 68% male) were enrolled. Of these, 174 and 159 had Alpha and Beta, respectively. The two groups did not differ significantly in terms of 60-day mortality (19 vs. 23%), 28-day mortality (17 vs. 20%), need for mechanical ventilation (60 vs. 61%), mechanical ventilation duration (14 vs. 15 days), other management variables, patient demographic variables, comorbidities, or clinical variables on ICU admission. The vast majority of patients were unvaccinated (94%). The remaining 18 patients had received a partial vaccine course and 2 were fully vaccinated. The vaccinated patients were equally likely to have Alpha and Beta. Conclusions: Beta did not differ from Alpha in terms of patient characteristics, management, or outcomes in critically ill patients. Trial Registration: ClinicalTrials.gov, identifier: NCT04906850.

A New Wave of COVID-19 in 2021 with Unique Genetic Characters - Present Global Scenario and Beholding Onwards.

After the first report of a coronavirus-associated pneumonia outbreak in December 2019, the virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) that causes the infection/disease (COVID-19) has developed into a pandemic, with >100 million people infected in over 210 countries along with two million people deceased from COVID-19 till today. Coronaviruses are positivestranded RNA viruses having restricted RNA polymerase proofreading ability thus it is very genetically susceptible to mutation. The evolution of SARS-CoV-2 from a single-point zoonotic introduction in Wuhan in November or December 2019 was widely expected, and viral sequence surveillance was developed as a result. When the first sequence of SARS-CoV-2 was released, a race to develop vaccines started, and several vaccines are now used worldwide. Independent SARS-CoV-2 lineages have recently been identified in the UK (B.1.1.7), Brazil (P.1), South Africa (B.1.351), and India (B.1.617). The recent appearance of several SARS-CoV-2 variant strains has shattered faith in the modern generation of vaccines' ability to provide enduring defense against infection. The risk of escaping natural and induced immunity has encouraged an urgency to comprehend the implications of these improvements, as well as a drive to develop new approaches to combat SARS-CoV-2 variants.

SARS-CoV-2 outbreak in a nursing home after vaccination with BNT162b2: A role for the quantification of circulating antibodies.

We describe an outbreak of SARS-CoV-2 (B.1.351) in a nursing home. At the outbreak onset 96% of residents and 76% of HCW had received two doses of BNT162b2. Twenty-eight residents (28/53) and six HCW (6/33) were infected. Infected residents had lower levels of anti-S antibodies compared to those who were not infected (157 vs 552 U/mL). Among 50 residents with available serological status, nineteen (19/25) with serum concentration < 300 U/mL and seven (7/25) with concentration > 300 U/mL acquired SARS-CoV-2 (RR 2.7 [95 %CI 1.4-5.3]). The quantification of circulating antibodies could be useful in detecting people with an impaired immune response who are at high risk of acquiring and spreading SARS-CoV-2.

Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant.

BACKGROUND: The COVID-19 pandemic is caused by the betacoronavirus SARS-CoV-2. In November 2021, the Omicron variant was discovered and immediately classified as a variant of concern (VOC), since it shows substantially more mutations in the spike protein than any previous variant, especially in the receptor-binding domain (RBD). We analyzed the binding of the Omicron RBD to the human angiotensin-converting enzyme-2 receptor (ACE2) and the ability of human sera from COVID-19 patients or vaccinees in comparison to Wuhan, Beta, or Delta RBD variants. METHODS: All RBDs were produced in insect cells. RBD binding to ACE2 was analyzed by ELISA and microscale thermophoresis (MST). Similarly, sera from 27 COVID-19 patients, 81 vaccinated individuals, and 34 booster recipients were titrated by ELISA on RBDs from the original Wuhan strain, Beta, Delta, and Omicron VOCs. In addition, the neutralization efficacy of authentic SARS-CoV-2 wild type (D614G), Delta, and Omicron by sera from 2× or 3× BNT162b2-vaccinated persons was analyzed. RESULTS: Surprisingly, the Omicron RBD showed a somewhat weaker binding to ACE2 compared to Beta and Delta, arguing that improved ACE2 binding is not a likely driver of Omicron evolution. Serum antibody titers were significantly lower against Omicron RBD compared to the original Wuhan strain. A 2.6× reduction in Omicron RBD binding was observed for serum of 2× BNT162b2-vaccinated persons. Neutralization of Omicron SARS-CoV-2 was completely diminished in our setup. CONCLUSION: These results indicate an immune escape focused on neutralizing antibodies. Nevertheless, a boost vaccination increased the level of anti-RBD antibodies against Omicron, and neutralization of authentic Omicron SARS-CoV-2 was at least partially restored. This study adds evidence that current vaccination protocols may be less efficient against the Omicron variant.