Mapping of SARS-CoV-2 Spike Protein Evolution During the First and Second Waves of COVID-19 Infections in India

Rajpal, Vijay Rani; Sharma, Shashi; Kumar, Akhilesh; Vaishnavi, Samantha; Singh, Apekshita; Sehgal, Deepmala; Tiwari, Mugdha; Goel, Shailendra; Raina, S. N.

doi:10.2217/fvl-2021-0267

Cited by 3 publications

(3 citation statements)

References 33 publications

(49 reference statements)

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“…Indeed, in SARS-CoV-2, the Orf3a protein may work in coordination with the E protein, another highly conserved essential structural protein with viroporin function (52), to help release the virion from the host cell through the modification of the membrane permeability (53). The identification of novel antigenic peptides from non-spike regions is a result of interest because most of the studies on SARS-CoV-2 evolvability and antigenicity have been focusing on S protein (19,20). The NIP AI platform has been previously used to demonstrate the high level of conservation of predicted T cell epitopes among all mutated peptides identified in variants of concern (VOCs) (54).…”

Section: Discussionmentioning

confidence: 99%

“…From all the SARS−CoV−2 hotspots identified by the NIP algorithm (1), we selected a group of 101 peptides with lengths of 9 to 10 amino acids predicted to preferentially stimulate response in CD8 + T cells (18). Although the relevance of non-spike regions in SARS-CoV-2 evolution has not been as extensively investigated as done for the S protein (19,20), the peptide selection used in this study included a significant number of epitopes from those regions because their inclusion in vaccines is expected to broaden and boost protective T cell memory response (21). Using flow cytometry and PBMC isolated from previously infected and/or vaccinated patients, we tested the antigenicity of these peptides by quantifying the expression of activation-induced markers (AIMs) CD137, CD40L, IFNg, and TNF as previously shown (2)(3)(4).…”

Section: Introductionmentioning

confidence: 99%

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Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence

Federico,

Malone,

Tennøe

et al. 2023

Front. Immunol.

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During the COVID-19 pandemic we utilized an AI-driven T cell epitope prediction tool, the NEC Immune Profiler (NIP) to scrutinize and predict regions of T cell immunogenicity (hotspots) from the entire SARS-CoV-2 viral proteome. These immunogenic regions offer potential for the development of universally protective T cell vaccine candidates. Here, we validated and characterized T cell responses to a set of minimal epitopes from these AI-identified universal hotspots. Utilizing a flow cytometry-based T cell activation-induced marker (AIM) assay, we identified 59 validated screening hits, of which 56% (33 peptides) have not been previously reported. Notably, we found that most of these novel epitopes were derived from the non-spike regions of SARS-CoV-2 (Orf1ab, Orf3a, and E). In addition, ex vivo stimulation with NIP-predicted peptides from the spike protein elicited CD8+ T cell response in PBMC isolated from most vaccinated donors. Our data confirm the predictive accuracy of AI platforms modelling bona fide immunogenicity and provide a novel framework for the evaluation of vaccine-induced T cell responses.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence

Federico,

Malone,

Tennøe

et al. 2023

Front. Immunol.

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“…Another mutation found within the spike region was A67T (isolate #123), associated with the Eta (B.1.525) VOI according to the WHO classification based on amino acid substitutions observed in 303,250 spike-protein sequences [ 39 ]. The G1267R (isolate #36) and V915I (isolate #38) substitutions were previously seen in SARS-CoV-2 spike-protein sequences analyzed from Indian isolates in different domains, cytoplasmic regions, and Heptad repeat region 1 (HR1), respectively [ 43 ]. The HR1, contained in the S2 domain, is usually more conserved than other regions of the S protein and is a candidate to inhibit virus fusion [ 44 ].…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month

Marascio

Çilburunoğlu

TORUN>

et al. 2023

Viruses

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The SARS-CoV-2 pandemic has seriously affected the population in Turkey. Since the beginning, phylogenetic analysis has been necessary to monitor public health measures against COVID-19 disease. In any case, the analysis of spike (S) and nucleocapsid (N) gene mutations was crucial in determining their potential impact on viral spread. We screened S and N regions to detect usual and unusual substitutions, whilst also investigating the clusters among a patient cohort resident in Kahramanmaraş city, in a restricted time span. Sequences were obtained by Sanger methods and genotyped by the PANGO Lineage tool. Amino acid substitutions were annotated comparing newly generated sequences to the NC_045512.2 reference sequence. Clusters were defined using phylogenetic analysis with a 70% cut-off. All sequences were classified as Delta. Eight isolates carried unusual mutations on the S protein, some of them located in the S2 key domain. One isolate displayed the unusual L139S on the N protein, while few isolates carried the T24I and A359S N substitutions able to destabilize the protein. Phylogeny identified nine monophyletic clusters. This study provided additional information about SARS-CoV-2 epidemiology in Turkey, suggesting local transmission of infection in the city by several transmission routes, and highlighting the necessity to improve the power of sequencing worldwide.

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Repurposing of Plant-based Antiviral Molecules for the Treatment of COVID-19

Khazir,

Ahmed,

Thakur

et al. 2024

CTMC

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COVID-19, stemming from SARS-CoV-2, poses a formidable threat to global healthcare, with a staggering 77 million confirmed cases and 690,067 deaths recorded till Decem-ber 24, 2023. Given the absence of specific drugs for this viral infection, the exploration of novel antiviral compounds becomes imperative. High-throughput technologies are actively engaged in drug discovery, and there is a parallel effort to repurpose plant-based molecules with established antiviral properties. In this context, the review meticulously delves into the potential of plant-based folk remedies and existing molecules. These substances have showcased substantial viral inhibition in diverse in vivo, in silico, and in vitro studies, particularly against critical viral protein targets, including SARS-CoV-2. The findings position these plant-based molecules as promising antiviral drug candidates for the swift advancement of treatments for COVID-19. It is noteworthy that the inherent attributes of these plant-based molecules, such as their natural origin, potency, safety, and cost-effectiveness, contribute to their appeal as lead candidates. The review advocates for further exploration through comprehensive in vivo studies conducted on animal models, em-phasizing the potential of plant-based compounds to help in the ongoing quest to develop effec-tive antivirals against COVID-19.

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Mapping of SARS-CoV-2 Spike Protein Evolution During the First and Second Waves of COVID-19 Infections in India

Cited by 3 publications

References 33 publications

Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence

Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence

Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month

Repurposing of Plant-based Antiviral Molecules for the Treatment of COVID-19

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