Neutralization potential of Covishield vaccinated individuals sera against B.1.617.1

Utility of COVID-19 Seropositive Plasma as Convalescent Plasma: An Immune and Neutralization Antibody Seroprevalence Analysis in Blood Donors for Future Potential Pandemic Readiness

OBJECTIVES

To analyze the seroprevalence of SARS-CoV-2 IgG antibodies and neutralizing antibodies in blood donors during the second wave of the pandemic and to explore the utility of COVID-19 seropositive plasma as convalescent plasma.

MATERIALS AND METHODS

In this study, 696 blood donors were tested for anti-SARS-CoV-2 IgG antibodies using a chemiluminescence assay. By blinding, 271 samples were chosen randomly for testing of neutralizing antibodies by enzyme-linked immunosorbent assay (ELISA) in duplicate among the 696 blood donors tested for anti-SARS-CoV-2 IgG antibodies, irrespective of the positivity or negativity of the result of the anti-SARS-CoV-2 IgG antibodies by chemiluminescence assay. IgG antibody levels were analyzed in signal-to-cutoff (S/Co), while neutralizing antibody levels were analyzed in percentage inhibition.

RESULTS

The seroprevalence of IgG antibodies based on the S/Co for the positive results ≥ 1.00 was 82.75%, while the seroprevalence of neutralizing antibodies based on the percentage inhibition for the positive results ≥ 30% was 89.59%. Frontline workers (FLWs) and Covishield-vaccinated individuals showed higher levels of the anti-SARS-CoV-2 IgG antibodies regarding higher S/Co. In comparison, levels of neutralization antibodies regarding percentage inhibition were higher only in FLWs. Covishield-vaccinated donors elicited a statistically higher seroprevalence of anti-SARS-CoV-2 IgG antibodies compared to the Covaxin-vaccinated, while the seroprevalence of neutralizing antibodies was not statistically different among this group. There was a positive correlation (0.762) between anti-SARS-CoV-2 IgG antibodies and neutralizing antibodies, and almost all donors' of S/Co ≥ 9.5 had neutralizing antibodies.

CONCLUSION

This study showed higher seroprevalence in the blood donor population compared to published seroprevalence in India's second wave of the pandemic. In the current study, 328 donors (47.12%) of the 696 screened donors were neither vaccinated nor had previous SARS-CoV-2 infection, but many had antibodies. The seroprevalence of neutralizing antibodies (96.42%) was higher than the seroprevalence of the anti-SARS-CoV-2 IgG antibodies (85.71%) in the donors who had previous infection of COVID-19. On the other hand, vaccinated donors showed similar immune responses for neutralizing antibodies and the anti-SARS-CoV-2 IgG antibodies. Higher IgG immune reactivity in S/Co showed a good correlation with neutralizing antibodies and can be used to screen whole blood donors for convalescent plasma donations.

Variable neutralizing antibody responses to 10 SARS-CoV-2 variants in natural infection with wild- type (B.1) virus, Kappa (B.1.617.1), and Delta (B.1.617.2) variants and COVISHIELD vaccine immunization in India: utility of the MSD platform

For the efficacy of COVID-19 vaccines, emergence of variants accumulating immune-escape mutations remains a major concern. We analyzed the anti-variant (n = 10) neutralization activity of sera from COVID-19 patients infected with Wuhan (B.1), Kappa, and Delta variants and COVISHIELD vaccine recipients with (prepositives) or without (prenegatives) prior antibody positivity using V- PLEX ACE2 Neutralization Kit from MSD. MSD and PRNT₅₀ correlated well (r = 0.76-0.83, p < 0.0001). Despite the least antibody positivity in Kappa patients, anti-variant neutralizing antibody (Nab) levels in the responders were comparable with Delta patients. Vaccinees sampled at 1 month (PD2-1) and 6 months (PD2-6) post-second dose showed the highest seropositivity and Nab levels against the Wuhan strain. At PD2-1, the responder rate was variant-dependent and 100% respectively in prenegatives and prepositives. Nab levels against B.1.135.1, B.1.620, B.1.1.7+E484K (both groups), AY.2 (prenegatives), and B.1.618 (prepositives) were lower than that of Wuhan. At PD2-6, positivity decreased to 15.6%-68.8% in the prenegatives; 3.5%-10.7% of prepositives turned negative for the same four variants. As against the decline in Nab levels in 9/10 variants (prenegatives), a further reduction was seen against the same four variants in the prepositives. These variants possess immune-evasion-associated mutations in the RBD/S region. In conclusion, our data show that the Nab response of patients to multiple variants depends on the infecting variant. We confirm superiority of hybrid immunity in neutralizing multiple variants. Depending on the infecting variant pre- or postvaccination, immune response to different vaccines in different populations will vary and impact protection against emerging variants. The MSD platform provides an excellent alternative to live virus/pseudovirus neutralization tests.

A SARS-CoV-2: Companion Animal Transmission and Variants Classification

The continuous emergence of novel viruses and their diseases are a threat to global public health as there have been three outbreaks of coronaviruses that are highly pathogenic to humans in the span of the last two decades, severe acute respiratory syndrome (SARS)-CoV in 2002, Middle East respiratory syndrome (MERS)-CoV in 2012, and novel SARS-CoV-2 which emerged in 2019. The unprecedented spread of SARS-CoV-2 worldwide has given rise to multiple SARS-CoV-2 variants that have either altered transmissibility, infectivity, or immune escaping ability, causing diseases in a broad range of animals including human and non-human hosts such as companion, farm, zoo, or wild animals. In this review, we have discussed the recent SARS-CoV-2 outbreak, potential animal reservoirs, and natural infections in companion and farm animals, with a particular focus on SARS-CoV-2 variants. The expeditious development of COVID-19 vaccines and the advancements in antiviral therapeutics have contained the COVID-19 pandemic to some extent; however, extensive research and surveillance concerning viral epidemiology, animal transmission, variants, or seroprevalence in diverse hosts are essential for the future eradication of COVID-19.

Advanced Plasmonic Nanoparticle-Based Techniques for the Prevention, Detection, and Treatment of Current COVID-19

Coronavirus is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2. Coronavirus disease 2019 known as COVID-19 is the worst pandemic since World War II. The outbreak of COVID-19 had a significant repercussion on the health, economy, politics, and environment, making coronavirus-related issues more complicated and becoming one of the most challenging pandemics of the last century with deadly outcomes and a high rate of the reproduction number. There are thousands of different types - or variants - of COVID circulating across the world. Viruses mutate all the time; it emphasizes the critical need for the designing of efficient vaccines to prevent virus infection, early and fast diagnosis, and effective antiviral and protective therapeutics. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis, and treatment of COVID-19. This review presents an outline of the platforms developed using plasmonic nanoparticles in the detection, treatment, and prevention of SARS-CoV-2. We select the best strategies in each of these approaches. The properties of metallic plasmon NPs and their relevance in the development of novel point-of-care diagnosis approaches for COVID-19 are highlighted. Also, we discuss the current challenges and the future perspectives looking towards the clinical translation and the commercial aspects of nanotechnology and plasmonic NP-based diagnostic tools and therapy to fight COVID-19 pandemic. The article could be of significance for researchers dedicated to developing suitable plasmonic detection tools and therapy approaches for COVID-19 viruses and future pandemics.

Bioinformatic Analysis of B- and T-cell Epitopes from SARS-CoV-2 Structural Proteins and their Potential Cross-reactivity with Emerging Variants and other Human Coronaviruses

Background

The mutations in SARS-CoV-2 variants of concern (VOC) facilitate the virus’ escape from the neutralizing antibodies induced by vaccines. However, the protection from hospitalization and death is not significantly diminished. Both vaccine boosters and infection improve immune responses and provide protection, suggesting that conserved and/or cross-reactive epitopes could be involved. While several important T- and B-cell epitopes have been identified, mainly in the S protein, the M and N proteins and their potential cross-reactive epitopes with other coronaviruses remain largely unexplored.

Aims

To identify and map new potential B- and T-cell epitopes within the SARS-CoV-2 S, M and N proteins, as well as cross-reactive epitopes with human coronaviruses.

Methods

Different bioinformatics tools were used to: i) Identify new and compile previously-reported B-and T-cell epitopes from SARS-CoV-2 S, M and N proteins; ii) Determine the mutations in S protein from VOC that affect B- and T-cell epitopes, and; iii) Identify cross-reactive epitopes with coronaviruses relevant to human health.

Results

New, potential B- and T-cell epitopes from S, M and N proteins as well as cross-reactive epitopes with other coronaviruses were found and mapped within the proteins’ structures.

Conclusion

Numerous potential B- and T-cell epitopes were found in S, M and N proteins, some of which are conserved between coronaviruses. VOCs present mutations within important epitopes in the S protein; however, a significant number of other epitopes remain unchanged. The epitopes identified here may contribute to augmenting the protective response to SARS-CoV-2 and its variants induced by infection and/or vaccination, and may also be used for the rational design of novel broad-spectrum coronavirus vaccines.

Facing the wrath of enigmatic mutations: a review on the emergence of severe acute respiratory syndrome coronavirus 2 variants amid coronavirus disease-19 pandemic

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging respiratory virus responsible for the ongoing coronavirus disease 19 (COVID-19) pandemic. More than a year into this pandemic, the COVID-19 fatigue is still escalating and takes hold of the entire world population. Driven by the ongoing geographical expansion and upcoming mutations, the COVID-19 pandemic has taken a new shape in the form of emerging SARS-CoV-2 variants. These mutations in the viral spike (S) protein enhance the virulence of SARS-CoV-2 variants by improving viral infectivity, transmissibility and immune evasion abilities. Such variants have resulted in cluster outbreaks and fresh infection waves in various parts of the world with increased disease severity and poor clinical outcomes. Hence, the variants of SARS-CoV-2 pose a threat to human health and public safety. This review enlists the most recent updates regarding the presently characterized variants of SARS-CoV-2 recognized by the global regulatory health authorities (WHO, CDC). Based on the slender literature on SARS-CoV-2 variants, we collate information on the biological implications of these mutations on virus pathology. We also shed light on the efficacy of therapeutics and COVID-19 vaccines against the emerging SARS-CoV-2 variants.

SARS-CoV-2 Kappa Variant Shows Pathogenicity in a Syrian Hamster Model

Objectives: The emergence of SARS-CoV-2 lineage B.1.617 variants in India has been associated with a surge in the number of daily infections. We investigated the pathogenic potential of Kappa (B.1.617.1) variant in Syrian golden hamsters. Methods: Two groups of Syrian golden hamsters (18 each) were inoculated intranasally with SARS-CoV-2 isolates, B.1 (D614G) and Kappa variant, respectively. The animals were monitored daily for the clinical signs and body weight. Throat swab, nasal wash, and organ samples (lungs, nasal turbinate, trachea) were collected and screened using SARS-CoV-2-specific RT-qPCR. Histopathologic evaluation of the lung samples was performed. Results: The hamsters infected with the Kappa variant demonstrated increased body weight loss compared to the B.1 lineage isolate. The highest viral RNA load was observed in the nasal turbinate and lung specimens of animals infected with both variants. A significantly higher sgRNA load was observed in the nasal swabs (7 DPI), trachea (3 DPI), and lungs (3 DPI) of hamsters infected with the Kappa variant. Neutralizing antibody response generated in the B.1 lineage-infected hamster sera were comparable against both B.1 and Kappa variant in contrast to Kappa variant-infected hamsters, which showed lower titers against B.1 lineage isolate. Gross and microscopic evaluation of the lung specimens showed severe lung lesions in hamsters infected with Kappa variant compared to B.1. Conclusions: The study demonstrates pathogenicity of Kappa variant in hamsters evident with reduced body weight, high viral RNA load in lungs, and pronounced lung lesions. Both Kappa variant- and B.1-infected hamsters produced neutralizing antibodies against both variants studied.

Characteristic analysis of Omicron‐included SARS‐CoV‐2 variants of concern

In view of the rapid development of the COVID‐19 pandemic and SARS‐CoV‐2 mutation, we characterized the emerging SARS‐CoV‐2 variants of concern (VOCs) by both bioinformatics methods and experiments. The representative genomic sequences of SARS‐CoV‐2 VOCs were first downloaded from NCBI, including the prototypic strain, Alpha (B.1.1.7) strain, Beta (B.1.351) strain, Delta (B.1.617.2), and Omicron (B1.1.529) strain. Bioinformatics analysis revealed that the D614G mutation led to formation of a protruding spike (S) in the tertiary structure of spike protein, which could be responsible for the enhanced binding to angiotensin‐converting enzyme 2 (ACE2) receptor. The epitope analysis further showed that the S protein antigenicity of the Omicron variant changed dramatically, which was possibly associated with its enhanced ability of immune escape. To verify the bioinformatics results, we performed experiments of pseudovirus infection and protein affinity assay. Notably, we found that the spike protein of Omicron variant showed the weakest infectivity and binding ability among all tested strains. Finally, we also proved this through virus infection experiments, and found that the cytotoxicity of Omicron seems to be not strong enough. The results in this study provide guidelines for prevention and control of COVID‐19.

Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe

The coronavirus disease-19 has left a permanent mark on the history of the human race. Severe acute respiratory syndrome coronavirus-2 is a positive-sense single-stranded RNA virus, first reported in Wuhan, China, in December 2019 and from there took over the world. Being highly susceptible to mutations, the virus's numerous variants started to appear, and some were more lethal and infectious than the parent. The effectiveness of the vaccine is also affected severely against the new variant. In this study, the infectious mechanism of the coronavirus is explained with a focus on different variants and their respective mutations, which play a critical role in the increased transmissibility, infectivity, and immune escape of the virus. As India has already faced the second wave of the pandemic, the future outlook on the likeliness of a third wave with respect to the Indian variants such as kappa, delta, and Delta Plus is also discussed. This review article aims to reflect the catastrophe of the variants of SARS-CoV-2 and the possibility of developing even more severe variants in the near future.

SARS CoV-2 Delta variant exhibits enhanced infectivity and a minor decrease in neutralization sensitivity to convalescent or post-vaccination sera

Since their identification, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Kappa and Delta have rapidly spread to become globally dominant. However, their infectivity and sensitivity to administered vaccines have not been documented. We monitored the neutralization potential of convalescent or BNT162b2 post-vaccination sera against Kappa and Delta SARS-CoV-2 pseudoviruses. We show that both variants were successfully neutralized by convalescent and post-vaccination sera, exhibiting a mild decrease in their neutralization sensitivity. Of the two variants, Delta presented enhanced infectivity levels compared with Kappa or wild-type SARS-CoV-2. Nevertheless, both variants were not as infectious or resistant to post-vaccination sera as the Beta variant of concern. Interestingly, the Delta plus variant (AY.1/B.1.617.2.1) exhibited high resistance to post-vaccination sera, similar to that of the Beta SARS-CoV-2. However, its infectivity levels were close to those of wild-type SARS-CoV-2. These results account for the worldwide prevalence of Delta variant of concern and confirm the efficacy of the BNT162b2 vaccine against circulating other Delta variants.

Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants

Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.

Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy

The SARS-CoV-2 variant of concern (VOC) "Delta" is currently defined by PANGOLIN as a cluster of 33 different AY sublineages. Delta (in particular B.1.617.2) is largely and rapidly replacing the Alpha VOC as the dominant clade in most countries. To date, variations in the Spike protein of the Delta VOC have largely been limited. We report here the results of a genomic surveillance programme from Northern Italy. We identified several Delta sublineages harbouring mutations previously reported in GISAID at extremely low frequencies and in different combinations. Two patients (one of them vaccinated) tested positive for a Delta sublineage harbouring S71F, T250I, T572I and K854N. More patients tested positive for G769 V plus C1248F, A352S, and R158G and C1248F, respectively. Genomic surveillance of Delta variants should be encouraged to anticipate immune escape and deploy countermeasures.

Robust Representation and Efficient Feature Selection Allows for Effective Clustering of SARS-CoV-2 Variants

The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail, unlike any virus before it. On the one hand, this will help biologists, policymakers, and other authorities to make timely and appropriate decisions to control the spread of the coronavirus. On the other hand, such studies will help to more effectively deal with any possible future pandemic. Since the SARS-CoV-2 virus contains different variants, each of them having different mutations, performing any analysis on such data becomes a difficult task, given the size of the data. It is well known that much of the variation in the SARS-CoV-2 genome happens disproportionately in the spike region of the genome sequence—the relatively short region which codes for the spike protein(s). In this paper, we propose a robust feature-vector representation of biological sequences that, when combined with the appropriate feature selection method, allows different downstream clustering approaches to perform well on a variety of different measures. We use such proposed approach with an array of clustering techniques to cluster spike protein sequences in order to study the behavior of different known variants that are increasing at a very high rate throughout the world. We use a k-mers based approach first to generate a fixed-length feature vector representation of the spike sequences. We then show that we can efficiently and effectively cluster the spike sequences based on the different variants with the appropriate feature selection. Using a publicly available set of SARS-CoV-2 spike sequences, we perform clustering of these sequences using both hard and soft clustering methods and show that, with our feature selection methods, we can achieve higher F1 scores for the clusters and also better clustering quality metrics compared to baselines.

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.

AK, Kumari MP, Biswas D, Iravane J, Raut S, Dutta S, Devi S, Barua P, Gupta P, Borkakoty B, Kalita D, Dhingra K, Fomda B, Joshi Y, Goyal K, John R, Munivenkatappa A, Dhodapkar R, Pandit P, Devi S, Dudhmal M, Kinariwala D, Khandelwal N, Tiwari YK, Khatri PK, Gupta A, Khatri H, Malhotra B, Nagasundaram M, Dar L, Sheikh N, Shastri J, Aggarwal N, Abraham P. Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India

From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.

Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India

From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.

SARS-CoV-2 Delta Variant Pathogenesis and Host Response in Syrian Hamsters

B.1.617 is becoming a dominant Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) lineage worldwide with many sublineages, of which B.1.617.2 is designated as a variant of concern. The pathogenicity of B.1.617.2 (Delta) and B.1.617.3 lineage of SARS-CoV-2 was evaluated and compared with that of B.1, an early virus isolate with D614G mutation in a Syrian hamster model. Viral load, antibody response, and lung disease were studied. There was no significant difference in the virus shedding pattern among these variants. High levels of SARS-CoV-2 sub genomic RNA were detected in the respiratory tract of hamsters infected with the Delta variant for 14 days, which warrants further transmission studies. The Delta variant induced lung disease of moderate severity in about 40% of infected animals, which supports the attributed disease severity of the variant. Cross neutralizing antibodies were detected in animals infected with B.1, Delta, and B.1.617.3 variant, but neutralizing capacity was significantly lower with B.1.351 (Beta variant).

[SARS-CoV-2 variants, a still unfinished story]

Mutations in the SARS-CoV-2 genome can affect the gene encoding the Spike (S) antigen, which interacts with the host cell specific receptor, selecting mutant variants with changes in their infective capacity, pathogenic potential and resistance to neutralizing antibodies. The nomenclature to design the variants uses a colloquial form referred to the country or place of detection, a code from the "Pangolin" database and one from the "Nextstrain" page. New variants that have spread include the British B.1.1.7 (20I/501Y.V1), the South African B.1.351 (20H/501.V2), the Brazilian P.1 (20J/501Y.V3), the Californians B.1.427 B.1.429 (20C/S:452R) and the most recent, the Indian B.1.617 (VUI-21APR-01).The gold standard for the identification of the variants is whole genome sequencing. However, real-time PCR techniques have already been developed for the detection of specific mutations that can facilitate their presumptive identification.The impact of these variants on global vaccination programs has raised concern. It is generally thought that, since the response evoked by the vaccine against the S antigen is directed at the entire protein and the mutations only affect specific regions, the escape effect of the vaccine antibodies will be limited. Among the future strategies proposed for immuno-protection, the increase in the number of doses, the alternation of vaccines and the development of specific vaccines against different variants has been suggested.

SARS-CoV-2 variants, a still unfinished story

Mutations in the SARS-CoV-2 genome can affect the gene encoding the Spike (S) antigen, which interacts with the host cell specific receptor, selecting mutant variants with changes in their infective capacity, pathogenic potential and resistance to neutralizing antibodies. The nomenclature to design the variants uses a colloquial form referred to the country or place of detection, a code from the “Pangolin” database and one from the “Nextstrain” page. New variants that have spread include the British B.1.1.7 (20I/501Y.V1), the South African B.1.351 (20H/501.V2), the Brazilian P.1 (20J/501Y.V3), the Californians B.1.427 B.1.429 (20C/S:452R) and the most recent, the Indian B.1.617 (VUI-21APR-01).

The gold standard for the identification of the variants is whole genome sequencing. However, real-time PCR techniques have already been developed for the detection of specific mutations that can facilitate their presumptive identification.

The impact of these variants on global vaccination programs has raised concern. It is generally thought that, since the response evoked by the vaccine against the S antigen is directed at the entire protein and the mutations only affect specific regions, the escape effect of the vaccine antibodies will be limited. Among the future strategies proposed for immuno-protection, the increase in the number of doses, the alternation of vaccines and the development of specific vaccines against different variants has been suggested.

Impact of SARS-CoV-2 variant-associated RBD mutations on the susceptibility to serum antibodies elicited by COVID-19 infection or vaccination

BACKGROUND

Several SARS-CoV-2 lineages with mutations at the spike protein receptor binding domain (RBD) have reduced susceptibility to antibody neutralization, and have been classified as Variants of Concern (VOCs) or Variants of Interest (VOIs). Here, we systematically compared the neutralization susceptibility and RBD binding of different VOCs/VOIs, including B.1.617.1 (kappa variant) and P.3 (theta variant) which were first detected in India and the Philippines, respectively.

METHODS

The neutralization susceptibility of the VOCs/VOIs (B.1.351, B.1.617.1 and P.3) and a non-VOC/VOI without RBD mutations (B.1.36.27) to convalescent sera from COVID-19 patients or BNT162b2 vaccinees was determined using a live virus microneutralization (MN) assay. Serum IgG binding to wild type and mutant RBDs were determined using an enzyme immunoassay.

RESULTS

The geometric mean neutralization titers (GMT) of B.1.351, P.3, and B.1.617.1 were significantly lower than that of B.1.36.27 for COVID-19 patients infected with non-VOCs/VOIs (3.4-5.7-fold lower) or individuals who have received 2 doses of BNT162b2 vaccine (4.4-7.3-fold lower). The GMT of B.1.351 or P.3 were lower than that of B.1.671.1. For the 4 patients infected with B.1.351 or B.1.617.1, the MN titer was highest for their respective lineage. RBD with E484K or E484Q mutation, either alone or in combination with other mutations, showed greatest reduction in serum IgG binding.

CONCLUSION

P.3 and B.1.617.1 escape serum neutralization induced by natural infection or vaccine. Infection with one variant do not confer cross protection for heterologous lineages. Immunogenicity testing for second generation COVID-19 vaccines should include multiple variant and "non-variant" strains.

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India

As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of "variants of concern" (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches were undertaken to identify possible new variants and gauge the fitness of the current circulating strains. Phylogenetic analysis revealed that newly identified lineages B.1.617.1 and B.1.617.2 were predominantly circulating. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Further in vitro/in vivo studies would help confirm the phenotypic changes of the mutant strains. Overall, the study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra. Lineage B.1.617.2 has been designated as a VOC delta and B.1.617.1 as a variant of interest kappa, and they are being widely reported in the rest of the country as well as globally. Continuous monitoring of these and emerging variants in India is essential.

Present variants of concern and variants of interest of severe acute respiratory syndrome coronavirus 2: Their significant mutations in S‐glycoprotein, infectivity, re‐infectivity, immune escape and vaccines activity

Newly arising variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are now a threat to global public health and are creating COVID‐19 surges in different countries. At the same time, there is limited knowledge about these emerging variants. Even if research data are available, it is varyingly scattered. In this review, we have discussed the appearance of significant alarming SARS‐CoV‐2 variants in the entire world. The study also discusses the properties of the substantial variant of concern (VOC) variants such as B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.427 (Epsilon) and B.1.429 (Epsilon). At the same time, the characteristic properties of some significant variant of interest (VOI) variants like B.1.525 (Eta), B.1.526 (Iota) (sublineage B.1.526.1), B.1.617 (sublineages B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3), P.2 (Zeta), P.3 (Theta), B.1.616 and B.1.427 have also been discussed. Here, we have explained some essential mutations for the VOC and VOI variants such as K417T/N, L452R, E484K, N501Y, D614G and P681R. Consecutively, we also highlighted the crucial clinical characteristics of the variants, such as transmissibility, infectivity, re‐infectivity, immune escape, vaccine activity and vaccine escape. Our comprehensive review will provide updated information on the newly appearing variants of SARS‐CoV‐2 and help the researchers to formulate strategies to curtail the COVID‐19 pandemic.

SARS-CoV-2 Variants: A Synopsis of In Vitro Efficacy Data of Convalescent Plasma, Currently Marketed Vaccines, and Monoclonal Antibodies

We summarize here in vitro evidences of efficacy for convalescent plasma, currently approved vaccines and monoclonal antibodies against SARS-CoV-2 variants of concern (VOC: B.1.1.7, B.1.351, P.1, and B.1.617.2), variants of interest (VOI: B.1.427/B.1.429, P.2, B.1.525, P.3, B.1.526, and B.1.671.1), and other strains (B.1.1.298 and B.1.258delta). While waiting from real world clinical efficacy, these data provide guidance for the treating physician.

Structure-function relations of the SARS-CoV-2 spike protein and impact of mutations in the variants of concern

This review covers the main features of the severe acquired respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, its interaction with the main entry receptor, the human angiotensin converting enzyme 2 (ACE2), and the subsequent membrane fusion step. The focus is on the structural organization of these proteins and mechanistic aspects of their interactions that lead to cytoplasmic release of the viral genome. The most potently neutralizing antibodies against SARS-CoV-2 were shown to interfere with the spike/ACE2 interaction. I thus also review the location and the potential impact of mutations in the spike protein observed in the variants of concern that emerged concomitantly with acquired immunity in the population after one year of virus circulation. Understanding how these interactions affect the spike/ACE2 interactions and the subsequent spike-protein-induced membrane fusion reaction is important to stay one step ahead of the virus evolution and develop efficient countermeasures.