BRIEF REPORT | doi:10.20944/preprints202307.0840.v2
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Vaccine adverse event; Covid-19; spike protein; diagnosis
Online: 29 August 2023 (09:18:30 CEST)
Delineating the epidemic of vaccine injury from the coterminous condition long covid is a challenging prospect, but one with many implications not just for treatment, but also has important legal considerations for settlements of vaccine injury. The shared etiological factor of the spike protein in both vaccine injury and long covid make differentiation difficult, and while treatment is largely similar between vaccine injury and long covid, there are important distinctions. Furthermore, diagnostics are important for monitoring treatment progress and assessing the extent of subclinical vaccine injury in population having received a covid-19 vaccine. The development of rigorous diagnostics is an important step towards the recognition of both long covid and vaccine injury, as those suffering these conditions have faced immense challenges in having their conditions recognized, treated, and compensated by insurance companies or national health services.
REVIEW | doi:10.20944/preprints202306.1903.v1
Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: Fasting; autophagy; long-COVID; post-vaccination syndrome; spike protein; mitochondria; mitophagy
Online: 27 June 2023 (12:33:46 CEST)
Fasting, a practice with historical roots in various cultures, has recently garnered significant interest in the field of medicine. In this article, we delve into the mechanisms underlying fasting-induced autophagy and its therapeutic applications for spike protein associated pathology. We explore the therapeutic potential of fasting on spike protein-related pathology and the role of interventions to upregulate autophagy, including compounds like spermidine, resveratrol, rapamycin, and metformin. In conclusion, fasting, coupled with an understanding of its nuances, holds promise as a therapeutic intervention for spike protein related diseases; with broad implications for human health. This review presents the therapeutic possibility of using autophagy to treat spike protein related diseases, and details the interventions to deploy this therapeutic modality.
ARTICLE | doi:10.20944/preprints202006.0184.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS; spike; variants; structure
Online: 14 June 2020 (16:00:35 CEST)
Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human endothelial cells of the respiratoty system for the virus to be engulfed causing COVID-19 disease after priming by type II transmembrane protease TMPRSS2 and then binding with the angiotensin-converting enzyme 2 (ACE2). Therefore, mutations and amino acid variants analysis are essential in understanding the mechanism of binding of spike protein with its receptor to have an insights on possibilities to design a peptide or nucleotide-based vaccine for COVID-19. Here, we employed Iterative Threading Assembly Refinement (I-TASSER) and Multiple Alignment using Fast Fourier Transform (MAFFT) to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 and to analyze the amino acid variants for protein sequences from GISAID database for samples collected from Jordan in a try to find an explanation for the low confirmed number of COVID-19 in Jordan. Our Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) findings showed four single amino acid variants (SAV) found in 20 samples of SARS-CoV-2. What is equal to 5% of samples showed tyrosine deletion at Y144 located in the SARS-CoV-like_Spike_S1_NTD (N terminal domain), 62% showed aspartate substitution to glycine at D614G located in the SARS-CoV-2_Spike_S1_RBD (spike recognition binding site), 5% showed aspartate substitution to tyrosine at D1139Y and 5% showed glycine substitution to serine at G1167S both located in the Corona_S2 domain. The findings have shown lower mutational sensitivity in all variants that might not affect the function of spike glycoprotein except for D614G, which has the highest mutational sensitivity score (5 out of 9) indicating a higher likelihood to affect the function of the spike protein. This might suggest, in general, a reduced transmitability of SARS-CoV-2 in Jordan.
REVIEW | doi:10.20944/preprints202306.1306.v1
Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: Fasting; autophagy; long-COVID; post-vaccination syndrome; spike protein; mitochondria; mitophagy
Online: 19 June 2023 (07:39:57 CEST)
Fasting, a practice with historical roots in various cultures, has recently garnered significant interest in the field of medicine. In this article, we delve into the mechanisms underlying fasting-induced autophagy and its therapeutic applications for spike protein associated pathology. We explore the therapeutic potential of fasting on spike protein-related pathology. Additionally, we discuss factors that affect fasting, such as duration, type (dry vs. water), and the role of specific compounds like spermidine, resveratrol, rapamycin, and metformin. Furthermore, we analyse the interactions between fasting and other practices such as exercise, and highlight important considerations regarding participant characteristics, including pregnancy, breastfeeding, medication interactions, and metabolic disorders. In conclusion, fasting, coupled with an understanding of its nuances, holds promise as a therapeutic intervention with broad implications for human health.
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-Cov-2; main protease; Spike protein; RIN
Online: 15 June 2020 (06:27:35 CEST)
Motivation: The SARS-Cov-2 pandemic has gripped the entire world and a race to find either a cure or a vaccine for this pandemic is on. The public databases have a deluge of information in terms of genomic sequences and protein structures making it possible to study the minute details in terms of conserved motifs and super-motifs in its proteins. In this study we have identified the hidden features of the Spike protein and the Main protease (Mpro) of SARS-Cov2. These domains have been identified using the standard bioinformatics tools and the pfam database. We found four domains reported in the pfam database are present in the spike protein and the Mpro of SARS-Cov2 but have not been reported earlier. These domains are specific to human strains of SARS-Cov2 and are not present in SARS-Cov or the coronaviruses of other animals. Using RIN we also identified the motifs and super-motifs in these two proteins that are important in understanding species wise changes as well as evolution driven variation in amino acids. Our results highlight several interesting features of the spike protein and Mpro of SARS-Cov2 that can be exploited for the development of various drug and vaccine therapies.
CONCEPT PAPER | doi:10.20944/preprints202004.0282.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Penicillamine; spike protein; docking
Online: 16 April 2020 (15:44:39 CEST)
Purpose: Pandemic Novel Coronavirus (SARS-CoV-2) has emerger centered from wuhan, China. Structurally homologous spike protein of SARS-CoV-2 receptor is taxonomically homologous with SARS-Cov and SARS associated bat coronavirus. Still now scientists are trying to find out proper vaccine and treatments for this disease. Methods: Systematically we modeled and compared the structure of SARS-CoV-2 spike protein along with Bat Cov, Bat SARS Cov and SARS Cov Urbani. S1 and S2 unit of the coronavirus (SARS-CoV-2) are attached with ACE2 and furin, here we docked 5 Ca+ chelating drugs with these two proteins. Results: Structural comparison with all these spike proteins revealed that less significant but not negligible difference exists among them. Inserted stable nucleotide sequences and corresponding surface exposed peptidal region may be considered as epitope. Docking result with Toxicokinetics and half life of Penicillamine can effectly inhibit the attachment site of spike protein of coronavirus (SARS-CoV-2). Conclusions: Docking summery and the pharmacokinetics with toxicokinetics index recommend that Penicillamine can able to inhibit the infection of SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202304.1094.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; Monocyte; Spike protein; Morphology.
Online: 28 April 2023 (03:29:08 CEST)
Background: This study investigated the biological effects on circulating monocytes after challenge with SARS-CoV-2 recombinant spike protein. Methods: Whole blood collected form seven ostensibly healthy healthcare workers was incubated for 15 min with 2 and 20 ng/mL recombinant spike protein of Ancestral, Alpha, Delta and Omicron variants. Samples were analyzed with Sysmex XN and DI-60 analyzers. Results: Cellular complexity (i.e., presence of granules, vacuoles and other cytoplasmic inclusions) increased in all samples challenged with the recombinant spike protein of Ancestral, Alpha and Delta variants, but not in those containing Omicron. The cellular content of nucleic acids was constantly decreased in most samples, achieving statistical significance in those containing 20 ng/mL of Alpha and Delta recombinant spike proteins. The heterogeneity of monocyte volumes significantly increased in all samples, achieving statistical significance in those containing 20 ng/mL of recombinant spike protein of Ancestral, Alpha and Delta variants. The monocyte morphological abnormalities after spike protein challenge included dysmorphia, granulation, intense vacuolization, platelet phagocytosis, development of aberrant nuclei and cytoplasmic extrusions. Conclusions: The SARS-CoV-2 spike protein triggers important monocyte morphological abnormalities, more evident in cells challenged with spike protein of the more clinically severe Alpha and Delta variants.
ARTICLE | doi:10.20944/preprints202007.0132.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: coronavirus; spike protein; database; sequence alignment; mutation; homology model; hydrophobic amino acids
Online: 7 July 2020 (16:49:04 CEST)
Analysis of SARS-CoV-2 spike protein sequences of over 19 countries from biological databases submitted around the globe was carried out with help of bioinformatics tools and structure prediction databases. Initial data analysis showed entry of virus into different geographic regions started in the month of January 2020. Meanwhile, alignment of spike protein sequences of SARS-CoV-2 isolates from China and other countries revealed a critical mutation of D614G. Surprisingly, mutation D614G was not seen in early samples submitted in the month of January but gradually it started appearing globally from the month of March 2020. However, the mutations of amino acids in the spike protein other than D614G exhibiting similar pI and altered polarity were found to be specific to geographical regions. Besides, prediction of homology model for interaction of spike protein showed predominant role of chain C of trimeric spike protein in adhering receptor binding domain (RBD) of human ACE2 receptor. Furthermore, the prediction of glycosylation points has revealed that there are about 20 N-glycosylation potential sites on spike protein. We believe that the information present here would not only help in thorough understanding of infectivity but also enhance the knowledge of the scientific community in developing prophylactics and/or therapeutics for SARS-CoV19-2 virus.
ARTICLE | doi:10.20944/preprints202210.0245.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Spike; Cysteine; proteolysis; brefeldin A
Online: 18 October 2022 (03:52:19 CEST)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds to the cell receptor angiotensin-converting enzyme-2 (ACE2) as the first step in viral cell entry. SARS-CoV-2 spike protein expression in ACE2-expressing cell surface induces cell–cell membrane fusion, thus forming syncytia. To exert its fusiogenic activity, the spike protein is typically processed at a specific site (S1/S2 site) by cellular proteases such as furin. The C488 residue, located at the spike–ACE2 interacting surface, is critical for the fusiogenic and infectious roles of the SARS-CoV-2 spike protein. We further demonstrated that the C488 residue of spike protein is involved in subcellular targeting and S1/S2 processing. C488 mutant spike localization to the Golgi apparatus and cell surface were impaired. Consequently, the S1/S2 processing of the spike protein, probed by anti-Ser-686-cleaved spike antibody, markedly decreased in C488 mutant spike proteins. Moreover, brefeldin A-mediated endoplasmic reticulum-to-Golgi traffic suppression also suppressed spike protein S1/S2 processing. As brefeldin A treatment and C488 mutation inhibited S1/S2 processing and syncytia formation, the C488 residue of spike protein is required for functional spike protein processing.
ARTICLE | doi:10.20944/preprints202003.0409.v2
Subject: Biology And Life Sciences, Virology Keywords: angiotensin-converting enzyme 2; SARS-CoV-2; spike protein; COVID-19
Online: 9 April 2020 (09:59:37 CEST)
Objectives Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has high infectivity in humans, attributed to the strong affinity of its spike (S) protein to human angiotensin-converting enzyme 2 (ACE2). Here, we analyzed the structural similarity of the S protein between SARS-CoV-2 and other SARS-related coronaviruses (CoVs). Methods We performed multiple alignment analysis of nine amino acid sequences of CoV S proteins from NCBI with MAFFT web-based software, followed by phylogeny analysis. Three-dimensional structure modeling was performed by SWISS-MODEL. We calculated the template modeling score between the S protein of SARS-CoV-2 and that of other SARS-related CoVs. Results The S1 domain of the unclassified CoV RaTG13 (the host of which is the intermediate horseshoe bat) was structurally very similar to that of SARS-CoV-2, implying that RaTG13 could be the origin of SARS-CoV-2. In addition, the folding property of the entire S protein was nearly the same between SARS-CoV-2 and RaTG13 after the PRRA amino acid insertion was removed from SARS-CoV-2. Conclusions RaTG13 could have a high binding affinity to ACE2, similar to SARS-CoV-2, and it is therefore highly likely to infect other animals. Therefore, massive research and monitoring of CoVs in animals is necessary to prevent future COVID-19-like disasters.
COMMUNICATION | doi:10.20944/preprints202106.0238.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Immunoinformatics; Molecular dynamics simulation; mutation; SARS-CoV-2; Spike protein; Virus structure
Online: 8 June 2021 (13:57:03 CEST)
It has been more than a year since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found. This coronavirus has infected more than 110 million people worldwide by the end of February, 2021, and several virulent as well as more spreadable mutant forms of SARS-CoV-2 have emerged subsequently. In the latter group, three variants B.1.1.7, B.1.351, and P1 lineages, have been reported. Using computer simulation, the present paper investigates the structural differences between the wild type SARS-CoV-2 spike protein and its Asn501Tyr (N501Y) mutant variant. Time-based structural changes between the receptor binding domains of these two species are also examined. The N501Y mutation is common to all the three aforesaid mutant variants.
REVIEW | doi:10.20944/preprints202307.1081.v1
Subject: Medicine And Pharmacology, Clinical Medicine Keywords: Long COVID; mRNA vaccines side effects; immunothrombosis; spike protein
Online: 17 July 2023 (09:33:51 CEST)
Abstract Long COVID syndrome, known as Long COVID, refers to a series of debilitating symptoms that arise after infection with the SARS-CoV-2 virus. These symptoms are similar to those experienced by some people after vaccination with vaccines based on mRNA platforms (Pfizer, Moderna). With more than 200 million Long COVID patients worldwide and an increase in cases of moderate to severe reactions after administration of mRNA vaccines (VSITV), the effects on quality of life and economics are significant, for what is necessary to pay urgent attention to understand its pathophysiology and to provide an adequate diagnosis and treatment. In this article, we describe our perspective that both Long COVID and common side effects of mRNA vaccines (VSITV) induce persistent and prolonged expression of the spike protein (SPIKE) in various tissues and organs of the body. This would induce coagulopathy, microscopic vasculitis, and endothelitis as the main drivers of the disease, and may also cause or worsen other common pathologies in Long COVID, such as mast cell activation syndrome, dysautonomia, and sudden deaths due to arrhythmias and heart attacks, reports of which continue to rise. Given that the SARS-CoV-2 spike protein can independently induce fibrinoid microclot formation, platelet activation, and endothelitis, we predict that the persistence of the spike protein will be a key mechanism driving ongoing coagulopathy in Long COVID and in the VSITV. We discuss various treatment goals to address coagulopathy, endothelitis, and vasculitis and predict that treatment, especially if given early, with a combination of anticoagulants, antiplatelets, corticosteroids, and rapamycin/everolimus, will provide significant relief for many patients.
REVIEW | doi:10.20944/preprints202301.0388.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Vaccine; Spike protein; Mutation; Conserved epitopes
Online: 23 January 2023 (02:03:42 CET)
Abstract: Over the years, several distinct pathogenic coronaviruses have emerged, including the pandemic SARS-CoV-2 which is difficult to curtail despite the availability of licensed vaccines. The difficulty in managing SARS-CoV-2 is linked to changes in the variants’ proteins, especially in the spike protein (S) used for viral entry. These mutations, especially in the S, enable the virus to evade the immune responses induced by natural infection or vaccination. However, some parts of the SP in the S1 subunit and the S2 subunit are considered conserved among coronaviruses. In this review, we will discuss the epitopes in the SARS-CoV-2 S1 and S2 subunit proteins that have been demonstrated by various studies to be conserved among coronaviruses and may be immunogenic for the development of vaccine. Considering the higher conservancy of the S2, we will further discuss the likely challenges that could limit the S2 subunit from inducing robust immune responses and the promising approaches to increase their immunogenicity.
ARTICLE | doi:10.20944/preprints202007.0251.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; Spike protein; Mutant; Genome
Online: 12 July 2020 (12:03:16 CEST)
The severity of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), greatly varies from patient to patient. In the present study, we explored and compared mutation profiles of SARS-CoV-2 isolated from mildly affected and severely affected COVID-19 patients in order to explore any relationship between mutation profile and disease severity. Genomic sequences of SARS-CoV-2 were downloaded from GISAID database. With the help of Genome Detective Coronavirus Typing Tool, genomic sequences were aligned with the Wuhan seafood market pneumonia virus reference sequence and all the mutations were identified. Distribution of mutant variants was then compared between mildly and severely affected groups. Among the numerous mutations detected, 14,408C>T and 23,403A>G mutations resulting in RNA-dependent RNA polymerase (RdRp) P323L and spike protein D614G mutations, respectively, were found predominantly in severely affected group (>82%) compared with mildly affected group (<46%, p<0.001). The 241C>T mutation in the non-coding region of the genome was also found predominantly in severely affected group. The 3,037C>T, a silent mutation, also appeared in relatively high frequency in severely affected group. We concluded that RdRp P323L and spike protein D614G mutations predominate in severely affected COVID-19 patients. Further studies will be required to explore whether these mutations have any impact on the severity of COVID-19.
ARTICLE | doi:10.20944/preprints202305.1749.v1
Subject: Biology And Life Sciences, Virology Keywords: Marine sulfated glycans; SARS-CoV-2; Omicron XBB.1.5; Spike protein; Heparin
Online: 25 May 2023 (07:12:52 CEST)
Keywords: Marine sulfated glycans; SARS-CoV-2; Omicron XBB.1.5, Spike protein; Heparin
ARTICLE | doi:10.20944/preprints202008.0447.v1
Subject: Biology And Life Sciences, Virology Keywords: spike protein; SARS-CoV-2; mutation; drug repurposing; digitoxin
Online: 20 August 2020 (08:24:41 CEST)
Novel SARS-CoV-2, a bat based virus originated in Wuhan, China that caused a global pandemic in December, 2019 belongs to the Betacorona virus family and contains single stranded genome of ~29Kbp. The host cell invasion of SARS-CoV-2 is facilitated by interaction of C-Terminal Domain (CTD) of Spike (S) protein of virus and host ACE2 receptor in the presence of TMPRSS seine protease secreted by the host cell. In this study the mutation hotspots of S-protein will be identified and the impact of such mutation in the binding affinity will be studied. Additionally, the lead molecule which can bind to the mutated protein also will be identified. Multiple sequence alignment of the spike protein sequence of SARS-CoV-2 shows the number of single amino acid mutation hotspots such as L5F, R214L, R408I, G476S, V483A, H519Q, A520S, T572I, D614G and H655Y. Among these mutations D614G has 57.5% occurrence and G476S, V483A has 7.5% occurrence. The mutated proteins were modelled based on wild type homolog and docked to ACE2 receptor. When the mutated S protein is docked, the ∆G (binding free energy) value is very minimal in mutated protein showed the stability of variants. By the drug repurposing method, 1000 FDA approved drugs were virtually screened for its binding to RBD of S1 domain. Among these drugs Digitoxin, Gliquidone and Zorubicin Hcl binds to spike proteins with higher docking score (lesser than -8.5 Kcal/mol) to both wild type and mutants.
ARTICLE | doi:10.20944/preprints202002.0447.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; ACE2; RGD; Spike protein; therapeutic drugs
Online: 28 February 2020 (16:26:53 CET)
Pneumonia caused by a new coronavirus SARS-CoV-2 has caused serious harm to people's lives and health in Wuhan, China. By February 26, 2020, over 80,000 people were infected and 2,814 died from the infection. The initial route of infection is the binding of the spike protein (S protein) of the virus to the angiotensin-converting enzyme 2 (ACE2). From bioinformatics analysis, we found that the S protein of SARS-CoV-2 produced an evolutionary mutation of K403R compared with the S protein of SARS-CoV, forming an adjacent RGD motif at the interaction surface. As the RGD motif is considered as a ligand for many cell surface integrins, we proposed that the binding of S protein of SARS-CoV-2 with integrins may facilitate the infection process of the virus. Therefore, high-throughput virtual screening was performed by choosing the key residues of S protein interface of SARS-CoV-2 and the adjacent RGD motif as potential binding site, to search for the potential agents targeting interaction of S protein of SARS-CoV-2 with both ACE2 and integrins as potential therapeutic drugs. Various libraries including the FDA-approved drugs etc. were screened, and Nadide, Losartan, 9'''-Methyllithospermate B and Leonurine etc. were identified as representative potential drugs candidate for COVID-19.
ARTICLE | doi:10.20944/preprints202002.0071.v1
Subject: Biology And Life Sciences, Virology Keywords: 2019-nCoV; novel corona virus; Wuhan virus; drug; vaccine; spike protein; epitope; vaccine design
Online: 5 February 2020 (15:34:15 CET)
The recent outbreak of the new virus in Wuhan city, China from the sea food market has led to the identification of a new strain called the corona virus and named as novel corona virus (2019-nCoV) belonging to Coronaviridae family. This has created major havoc and concern due to the mortality of 250 persons and affecting more than 10,000 people. This virus causes sudden fever, pneumonia and also kidney failure. In this study a computational approach is proposed for drug and vaccine design. The spike protein sequences were collected from a protein database and analysed with various bioinformatics tools to identify suitable natural inhibitors for the N-terminal receptor binding domain of spike protein. Also, it is attempted to identify suitable vaccine candidates by identifying B-Cell and T-cell epitopes. In the drug design, the tanshinone Iia and methyl Tanshinonate were identified as natural inhibitors based on the docking score. In the vaccine design, B-cell epitope VLLPLVSSQCVNLTTRTQLPPAYTN was found to have the highest antigenicity. FVFLVLLPL of MHC class-I allele and FVFLVLLPL of MHC class-II allele were identified as best peptides based on a number of alleles and antigencity scores. The present study identifies natural inhibitors and putative antigenic epitopes which may be useful as effective drug and vaccine candidates for the eradication of novel corona virus.
REVIEW | doi:10.20944/preprints202009.0420.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: COVID-19; SARS-CoV-2; ACE2 receptor; spike glycoprotein; S glycoprotein immunogenic sequences; ACE2 polymorphism
Online: 18 September 2020 (04:56:02 CEST)
Pneumonia cases of unknown etiology in Wuhan, China, were reported to the WHO on 31st of December 2019. Later the pathogen was reported to be a novel coronavirus designated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that causes Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 is a novel pathogenic beta coronavirus that infects humans causing severe respiratory illness. However, multifarious factors can contribute to the susceptibility to COVID-19 related morbidity and mortality such as age, gender and underlying comorbidities. Importantly, SARS-CoV and SARS-CoV-2 entry into the host cells is mediated via ACE2 receptor. However, ACE2 receptor binding affinity to SARS-CoV-2 is 4 folds higher than that to SARS-CoV. Identification of different aspects such as binding affinity, differential antigenic profiles of spike glycoproteins, and ACE2 polymorphisms might influence the investigation of potential therapeutic strategies targeting SARS-CoV-2/ACE2 binding interface. Here we aim to elaborate on SARS-CoV-2 S1/ACE2 ligand that facilitates viral internalization as well as to highlight the differences between SARS-CoVs binding affinity to ACE2. We also discuss the possible immunogenic sequences of spike glycoprotein and the effect of ACE2 polymorphism on viral binding/infectivity and host susceptibility to disease. Furthermore, targeting of ACE2 will be discussed to understand its role in therapeutics.
ARTICLE | doi:10.20944/preprints201808.0529.v1
Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: orcine epidemic diarrhea virus; coronavirus; spike protein; virulence; gnotobiotic piglets; reverse genetics
Online: 30 August 2018 (14:35:03 CEST)
Base on the sequence of S genes, which encode spike proteins, we previously identified three different types (North American, S INDEL and S large-DEL types) of porcine epidemic diarrhea virus (PEDV) that have re-emerged in Japan since 2013. Base on experimental infections with the North American and S large-DEL types, we also hypothesized that PEDV virulence may be linked to the S1 subunit of the S protein. To test this hypothesis, we have now assayed in gnotobiotic piglets various recombinant PEDVs generated by reverse genetics. Piglets inoculated with CV777 maintained in National Institute of Animal Health, along with piglets infected with a recombinant form of the same virus, developed subclinical to mild diarrhea. In contrast, severe watery diarrhea, dehydration, weight loss, astasia, and high mortality were observed in piglets inoculated with recombinant strains in which the S gene was partially or fully replaced with corresponding sequences from the highly virulent Japanese PEDV isolate OKN-1/JPN/2013. Indeed, symptoms resembled those in piglets inoculated with the OKN-1/JPN/2013, and were especially pronounced in younger piglets. Collectively, the data demonstrate that the S1 subunit of the S protein is an important determinant of PEDV virulence, and advance development of new vaccine candidate.
ARTICLE | doi:10.20944/preprints202006.0032.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; Spike protein; COVID-19; Mutation; hACE2 Receptor; Real-time PCR; Vaccine
Online: 4 June 2020 (08:48:03 CEST)
Currently, entire world is crumbled due to COVID-19 caused by novel SARS-CoV-2. Globally, over 5 million people are infected by SARS-CoV-2 with 6% fatality rate. The surface spike (S) protein plays a key role in the pathogenesis of SARS-CoV-2 by mediating viral entry through human angiotensin converting enzyme 2 (hACE2) receptors on the host cell and there is a big global race to find viral neutralizing antibodies and vaccine against S protein of SARS-CoV-2. Since SARS-CoV-2 evolved into 10 different clades in a very short span, a study on sipke protein mutation is essential to have effective vaccine coverage globally. Based on the mutation analysis of S protein from 166 Indian SARS-CoV-2 genome, a total of 40 different SNPs comprising of 14 synonymous and 26 non-synonymous mutations were observed, and notably, Indian S protein diverged into two major clusters, D614 and G614, with 11 different types. Majority of Indian strains fall in A2a and O clusters. Alarmingly, we have observed six SNPs at RBD and notably two of them at RBM (S438F and S494P). S494P SNP, similar to Bat–SARS like-CoV, may indicate a low ACE2 binding affinity. Interestingly 38% of Indian strains harbor a characteristic D614G SNP which was found predominantly in A2a cluster, mostly comprising USA and European strains with high disease severity. The association of disease severity with D614G SNP is well-correlated in states with high death rate except Maharashtra. Notably, more than 50% of D614G mutation were observed in Northern part of India and 14% in Southern part but not in Kerala and Tamil Nadu strains. Highly conserved motif, D614 (608-VAVLYQDVNCT-618) in upstream and also few downstream, of S1/S2 furin cleavage site may indicate specific key role in efficient interaction with host proteases in pathogenesis. Further studies are warranted to clarify the impact of SD614G SNP association to disease severity . Interestingly, C2367T (Y789Y) synonymous SNP is observed in 37% of Indian strains and notably similar SNPs with degeneracy bases were observed which is a key indication for the possibility of misdiagnosis by Real-Time PCR and revised strategies are needed for the precise diagnosis. Circulation of high number of signature SNPs [D614G and C2367T (Y789Y)] in certain states may be an early indication of emergence of community transmission in India. Further large genome sequence data from India will aid in deep understanding on the diversity of circulating SASR-Cov-2 and its impact on disease severity, origin of imported cases to India, community spread, effect on diagnosis and vaccine coverage.
ARTICLE | doi:10.20944/preprints202310.1181.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: recombinant probiotic -based vaccines; probiotic strain E. faecium L3; mucosal vaccines; SARS-CoV-2 spike protein; vaccine efficacy.
Online: 18 October 2023 (11:29:09 CEST)
The COVID-19 pandemic was declared in March 2020 and is still ongoing. The course of the epidemic remains uncertain, and mutations in the coronavirus, as well as the emergence of new variants of concern, make it possible that there will be periodic surges in the number of cases. Moreover, it is not clear how quickly and to what extent the effectiveness of vaccination will decline as the virus continues to mutate. One possible solution to combat the rapidly mutating coronavirus is the development of pan-coronavirus vaccines that stimulate the production of antibodies against conserved elements of the virus. Another approach could be the creation of safe vaccine platforms that can be rapidly adapted to deliver new, specific antigens in response to viral mutations. Recombinant probiotic microorganisms that can produce viral antigens by inserting specific viral DNA fragments into their genome show promise as a platform and vector for mucosal vaccine antigen delivery. With a well-established safety profile and the ability to transform into vaccine candidates, probiotic bacteria have significant research potential. The authors of this study have developed a convenient and universal technique for inserting the DNA sequences of pathogenic bacteria and viruses into the gene that encodes the pili protein of the probiotic strain E. faecium L3. The paper presents data on the immunogenic properties of two E. faecium L3 vaccine strains, which produce two different fragments of the coronavirus S1 protein, and provides an assessment of the protective efficacy of these oral vaccines against coronavirus infection in Syrian hamsters.
ARTICLE | doi:10.20944/preprints202206.0255.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: coronaviruses; SARS-CoV-2; variant; Omicron; SLiMs; spike protein; motifs; covid-19
Online: 17 June 2022 (13:49:02 CEST)
Short Linear Motifs (SLiMs) are short linear sequences that can mediate protein-protein interaction. Mimicking eukaryotic SLiMs to compete with extra or intracellular binding partners or to sequester host proteins is the crucial strategy of viruses to pervert the host system. The evolved proteins in viruses facilitate minimal protein-protein interactions that significantly affect intracellular signaling networks. Unfortunately, very little information about the SARS-CoV-2 SLiMs is known, especially across the SARS-CoV-2 variants. Through ELM database-based sequence analysis of spike protein from all the major SARS-CoV-2 variants, we identified four overriding SLiMs in the SARS-CoV-2 Omicron variant including LIG_TRFH_1, LIG_REV1ctd_RIR_1, LIG_CaM_NSCaTE_8, and MOD_LATS_1. These SLiMs are highly likely to interfere with various immune functions, interact with host intracellular proteins, regulate cellular pathways, and lubricate viral infection and transmission. These cellular interactions possibly serve as potential therapeutic targets for these variants, and this approach can be further exploited to combat emerging SARS-CoV-2 variants.
ARTICLE | doi:10.20944/preprints202107.0295.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 spike protein; ACE2 host receptor; nanobodies; molecular dynamics; mutational sensitivity; binding free energy; allosteric interactions; signal transmission
Online: 13 July 2021 (11:18:02 CEST)
Structural and biochemical studies have recently revealed a range of rationally engineered nanobodies with efficient neutralizing capacity against SARS-CoV-2 virus and resilience against mutational escape. In this work, we combined atomistic simulations and conformational dynamics analysis with the ensemble-based mutational profiling of binding interactions for a diverse panel of SARS-CoV-2 spike complexes with nanobodies. Using this computational toolkit, we identified dynamic signatures and binding affinity fingerprints for the SARS-CoV-2 spike protein complexes with nanobodies Nb6 and Nb20, VHH E, a pair combination VHH E+U, a biparatopic nanobody VHH VE, and a combination of CC12.3 antibody and VHH V/W nanobodies. Through ensemble-based deep mutational profiling of stability and binding affinities, we identify critical hotspots and characterize molecular mechanisms of SARS-CoV-2 spike protein binding with single ultra-potent nanobodies, nanobody cocktails and biparatopic nanobodies. By quantifying dynamic and energetic determinants of the SARS-CoV-2 S binding with nanobodies, we also examine the effects of circulating variants and escaping mutations. We found that mutational escape mechanisms may be controlled through structurally and energetically adaptable binding hotspots located in the host receptor-accessible binding epitope that are dynamically coupled to the stability centers in the distant epitope targeted by VHH U/V/W nanobodies. The results of this study suggested a mechanism in which through cooperative dynamic changes, nanobody combinations and biparatopic nanobody can modulate the global protein response and induce the increased resilience to common escape mutants.
HYPOTHESIS | doi:10.20944/preprints202004.0247.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS CoV-2; COVID 19; pandemic global-outbreak; Spike glycoprotein; ACE2; PatchDock; hydroxychloroquine
Online: 15 April 2020 (10:50:13 CEST)
SARS CoV-2 or COVID-19 pandemic global-outbreak created the most unstable situation of human health-economy. Last two decades different parts of the word experienced smaller or bigger outbreak related to human-coronaviruses. The spike-glycoproteins of the COVID-19 (similar to SARS-CoV) attach to the angiotensin-converting-enzyme (ACE-2) and transit over a stabilized open-state for the viral-internalization to the host-cells and propagate with great efficacy. Higher rate of mutability makes this virus unpredictable/less-sensitive to the protein/nucleic-acid based-drugs. In this emergent situation, drug-induced destabilization of spike-binding to RBD could be a good strategy. In the current study we demonstrated by Bioinformatics (CASTp: Computed-Atlas-of-Surface-Topography, PyMol: molecular-visualization) and Molecular docking (PatchDock) experiments that tea flavonoids catechin-products mainly EGCG or other like theaflavin gallate demonstrated higher Atomic Contact Energy (ACE), surface area and more amino-acid interactions than hydroxychloroquine (HCQ) during binding in the central channel of the spike-protein. Moreover, out of three distinct binding-sites (I, II and III) of spike core when HCQ binds only with site III (farthest from the vCoV-RBD of ACE2 contact), EGCG and TG bind all three sites. As because site I and II is in closer contact with open state location and viral-host contact area so these drugs might have significant effects. Taking into account the toxicity/side-effects by CQ/HCQ, present drugs may be important. Our laboratory is working on tea flavonoids and other phytochemicals in the protection from toxicity, DNA/mitochondrial damage, inflammation etc. The present data might be helpful for further analysis of flavonoids in this emergent pandemic situation.
ARTICLE | doi:10.20944/preprints202311.0123.v1
Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; Spike protein; structural stability; Molecular dynamics simulations; Electric fields
Online: 2 November 2023 (08:12:44 CET)
In its prefusion state, the SARS-CoV-2 Spike protein (similarly to other class I viral fusion proteins) is metastable, which is considered to be an important feature for optimizing or regulating their functions. After the binding process of its S1 subunit (S1) with the ACE2, the Spike protein (S) suffers a dramatic conformational change where S1 splits from the S2 subunit, which then penetrates the membrane of the host cell, promoting the fusion of the viral and cell membranes. This results in the infection of the host cell. In a previous work, we showed -using large scale molecular dynamics simulations- that the application of external electric fields (EF) induces drastic changes and damage in the receptor-binding domain (RBD) of the wild type Spike protein, as well of the Alpha, Beta and Gamma variants, leaving a structure which cannot be recognized any more by ACE2. In this work, we first extend the study to the Delta and Omicron variants and confirm the high sensitivity and extreme vulnerability of S to moderate EF (as weak as 104 V m-1), but, more importantly, we also show that, in contrast, the postfusion state of the spike protein does not suffer structural damage even if electric field intensities four orders of magnitude higher are applied. These results provide a solid scientific basis to confirm the prefusion state metastability roots of the SARS-CoV-2 Spike protein susceptibility to be damaged by EF. After the virus docks to the ACE2 receptor, the stable and robust postfusion conformation develops, which exhibits a similar resistance to EF (damage threshold higher than 108 V m-1) like most globular proteins.
ARTICLE | doi:10.20944/preprints202311.0296.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: SARS-CoV-2; Variants; Spike Glycoprotein; Receptor Binding Motif, Receptor Binding Domain; Neutralizing Antibodies; Ig subclasses; IgG; IgA
Online: 7 November 2023 (11:27:48 CET)
Global economic and social burden was caused by the SARS-CoV-2 spread worldwide. Despite the end of the pandemic, there is a concern about virulent evolving variants of the virus which can bypass the humoral immune response induced by vaccination or infection. Crucial to the viral entrance, amino acid residues in the RBM region, which interacts with cellular receptor ACE2, can elicit neutralizing antibody response. Herein we determine the immunogenicity of one-dose or heterologous dose vaccinated serum against wild-type and mutated RBM region. Despite low antibody response to wild-type SARS-CoV-2 RBM, omicron variants possess four mutations in RBM (S477N, T478K, E484A, F486V) that induce even less antibody titers. The most predominant responses were against IgA and IgG. While neutralizing antibodies (nAbs) predominantly target the RBD, our investigation revealed a diminished seroreactivity within the RBD's crucial region, the receptor-binding motif (RBM), potentially impacting the production of protective nAbs. S1WT and S2WT RBM peptides binding to nAbs were evaluated through microscale thermophoresis, and higher affinity (35 nM) was obtained for sequence S2WT (GSTPCNGVEGFNCYF), containing the FNCY patch. Our data indicates that SARS-CoV-2 RBM is not an immunodominant region in vaccinated individuals. Understanding the intricate dynamics of the humoral response and its interplay with viral evolution and host genetics is essential for the formulation of effective vaccination strategies, not only against SARS-CoV-2 but also for future emerging coronaviruses.
BRIEF REPORT | doi:10.20944/preprints202301.0137.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Covid-19; SARS-CoV-2 Spike protein; vaccine; HIV; IgA; IgG; neutralization
Online: 9 January 2023 (03:30:30 CET)
Vaccines against SARS-CoV-2 have been pivotal in overcoming the Covid-19 pandemic yet understanding the subsequent outcomes and immunological effects remain crucial, especially for at-risk groups e.g. people living with human immunodeficiency virus (HIV) (PLWH). In this study we report the longitudinal IgA and IgG antibody titers, as well as antibody-mediated angiotensin converting enzyme 2 (ACE2) binding blockade, against the SARS-CoV-2 spike (S) proteins after 1 and 2 doses of the ChAdOx1 nCoV-19 vaccine in a population of Black PLWH. Here, we report that PLWH (N = 103) did not produce an anti-S IgA response after infection or vaccination, however, anti-S IgG was detected in response to vaccination and infection, with the highest level detected for infected vaccinated participants. The anti-IgG and ACE2 blockade assays revealed that both vaccination and infection resulted in IgG production, however, only vaccination resulted in a moderate increase in ACE2 binding blockade to the ancestral S protein. Vaccination with a previous infection results in the greatest anti-S IgG and ACE2 blockade for the ancestral S protein. In conclusion, PLWH produce an anti-S IgG response to the ChAdOx1 nCoV-19 vaccine and/or infection, and ChAdOx1 nCoV-19 vaccination with a previous infection produced more neutralizing antibodies than vaccination alone.
ARTICLE | doi:10.20944/preprints202002.0265.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: SARS-CoV; Spike protein; Electrostatic hot spots; Angiotensin-converting enzyme 2 (ACE2); Neutralizing antibody
Online: 18 February 2020 (11:03:10 CET)
The spike protein of SARS coronavirus (SARS-CoV) attaches the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2), which is mediated by the receptor binding domain (RBD) of the spike protein. Recently, an analysis based on decade-long structural studies of SARS was reported to illustrate with atomic-level details receptor recognition by the novel coronavirus from Wuhan, i.e., 2019-nCoV. Here, this article reports a comprehensive set of structural electrostatic analysis of all SARS-CoV spike protein RBD-related structures as of February 13, 2020, aiming at identifying the electrostatic hot spots for SARS-CoV spike protein to be complexed with ACE2 and its neutralizing antibodies. First, this article identified a structural action mechanism of the F26G19 antibody (of SARS-CoV spike protein), where its Asp56 residue binds to the Arg426 of the SARS-CoV spike protein RBD against the formation of the interfacial Arg426-Glu329 salt bridges between ACE2 and the SARS-CoV spike protein RBD. Second, a hypothesis is reported that a pair of electrostatic clips exist at the interface between ACE2 and the SARS-CoV spike protein RBD, including both Arg426-Glu329 and His445-Glu23-Lys447 salt bridges. Last, this article reports a structurally identified interfacial Glu35-Arg479 salt bridge which helps stabilize the complex structure of ACE2 and the SARS-CoV spike protein RBD. Overall, the structurally identified electrostatic hot spots reported here may be useful for the design of SARS-CoV-neutralizing antibodies in future.
BRIEF REPORT | doi:10.20944/preprints202007.0488.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV; SARS-CoV; COVID-19; Sarbecovirus; D614G; Spike glycoprotein; Coronavirus; Alignment-free
Online: 21 July 2020 (12:47:13 CEST)
Conservation history of D614 residue is valuable in predicting the consequences of D614G mutation in the SARS-CoV-2 spike glycoprotein (SGP). We report here that the D614 belonged to an extraordinarily conserved, densely hydrophobic eleven amino acid peptide-motif vavlyqdvnct (11-aa), in the Sarbecovirus group and the variant carrying vavlyqdvnct had appeared in Chinese samples and became predominant in several geographical hotspots in late March, 2020. Interestingly a 2009 annotation of SARS-CoV contained the same mutation.
REVIEW | doi:10.20944/preprints202308.0520.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; spike protein; mutations; viral infectivity; pathogenesis; vaccine efficacy; immune evasion; antibody neutralization; T-cell response; therapeutic targeting
Online: 7 August 2023 (10:12:28 CEST)
The SARS-CoV-2 virus, which is responsible for the COVID-19 pandemic which emerged and spread, has sparked intense research on its spike protein, which is essential for viral entrance into host cells. Viral reproduction and transmission, host immune response regulation, receptor recognition and host cell entrance mechanisms, as well as structural and functional effects have all been linked to mutations in the spike protein. Spike protein mutations can also result in immune evasion mechanisms that impair vaccine effectiveness and escape, and they are linked to illness severity and clinical consequences. Numerous studies have been conducted to determine the effects of these mutations on the spike protein structure and how it interacts with host factors. These results have important implications for the design and development of medicines and vaccines based on spike proteins as well as for the assessment of those products' efficiency against newly discovered spike protein mutations. The paper gives a general overview of how spike protein mutations are categorized and named, as well as the genomic and phylogenetic techniques that have been used to track their genesis and dissemination. Additionally, it looks at the links between spike protein mutations and clinical outcomes, illness severity, unanswered problems, and future research prospects. Additionally, explored are the effects of these mutations on vaccine effectiveness as well as the possible therapeutic targeting of spike protein mutations.
ARTICLE | doi:10.20944/preprints202310.0497.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; vaccine; hACE2 transgenic mice; intranasal route; spike protein; cationic liposome; CpG-ODNs; heterologous immunity
Online: 9 October 2023 (11:43:57 CEST)
Mucosal vaccination appears to be suitable to protect against SARS-CoV-2 infection. In this study, we tested an intranasal mucosal vaccine candidate to COVID-19 constituted of a cationic liposome containing a trimeric SARS-CoV-2 spike protein and CpG-ODNs, a Toll-like receptor 9 agonist, as adjuvant. In vitro and in vivo experiments indicated the absence of toxicity following the intranasal administration of this vaccine formulation. First, we found that subcutaneous or intranasal vaccination protected hACE-2 transgenic mice from infection with the wild-type (Wuhan) SARS-CoV-2 strain, as shown by weight lost and mortality indicators. However, when compared to the subcutaneous administration, the intranasal route was more effective in the pulmonary clearance of the virus and induced higher neutralizing antibodies and anti-S IgA titers. In addition, the intranasal vaccination afforded protection against gamma, delta and omicron virus variants of concern. Furthermore, the intranasal vaccine formulation was superior to intramuscular vaccination with a recombinant, replication-deficient chimpanzee adenovirus vector encoding the SARS-CoV-2 spike glycoprotein (Oxford/AstraZeneca) in terms of virus lung clearance and production of neutralizing antibodies in serum and bronchial alveolar lavage (BAL). Finally, the intranasal liposomal formulation boosted heterologous immunity induced by previous intramuscular vaccination with the Oxford/AstraZeneca vaccine that was more robust than homologous immunity.
ARTICLE | doi:10.20944/preprints202005.0407.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; spike protein; D614G mutation; genotype distribution; furin cleavage site; secondary structure; sequence analysis; homology modeling
Online: 24 May 2020 (20:31:16 CEST)
We analyzed the SARS-CoV-2 spike (S) protein amino acid sequence extracted from 11,542 viral genomic sequences submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database through April 27, 2020. Consistent with prior reports, we found a major S protein mutation, D614 to G614, that was represented in 56% of all the analyzed sequences. All other mutations combined were less than 10%. After parsing the data geographically, we found most of the Chinese patient samples showed D614 (97%). By contrast, most patient samples in many European countries showed G614 (51 to 88%). In the United States, the genotypic distribution in California and Washington was similar to Asian countries, while the distribution in other US states was comparable to Europe. We observed a dramatic increase in the frequency of G614 over time in multiple regions, surpassing D614 when both were present, suggesting G614 S protein virus outcompetes D614 S protein virus. To gain insight into the consequences of the D614G mutation, homology modeling using a multi-template threading mechanism with ab initio structural refinement was performed for a region of the S protein (S591 to N710) spanning the D614G mutation and the S1 furin cleavage site. Molecular models of this region containing D614 or G614 revealed a major difference in secondary structure at the furin domain (RRARS, R682 to S686). The D614 model predicted a random coil structure in the furin domain whereas the G614 model predicted an alpha helix. Critical residues in the cleavage domain of G614 model were found to better align with the PDB structure of a furin inhibitor. Thus, homology modeling studies suggest a potential mechanism whereby the D614G mutation may confer a competitive advantage at the furin binding domain that may contribute to the rise of the D614G SARS-CoV-2 mutant.
ARTICLE | doi:10.20944/preprints202308.2083.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; SARS-CoV-2 spike protein 1 (S1); methylglyoxal; MG-H1; Glyoxalase 1; RAGE; inflammation; Nrf2; BEAS-2B; A549
Online: 30 August 2023 (12:02:02 CEST)
The pathogenesis of coronavirus disease 2019 (COVID-19) is associated with a hyperinflammatory response. The mechanisms of SARS-CoV-2-induced inflammation are scantly known. Methylglyoxal (MG) is a glycolysis-derived by-product, endowed with a potent glycating action, leading to the formation of advanced glycation end products (AGEs), the major of which is MG-H1. MG-H1 exerts strong pro-inflammatory effects, frequently mediated by the receptor for AGEs (RAGE). Here, we investigated the involvement of MG-H1/RAGE axis as a potential novel mechanism in SARS-CoV-2-induced inflammation by resorting to human bronchial (BEAS-2B) and alveolar (A549) epithelial cells, expressing different levels of ACE2 receptor (R), exposed to SARS-CoV-2 spike protein 1 (S1). Interestingly, we found in BEAS-2B cells that do not express ACE2-R, that S1 exerted a pro-inflammatory action through a novel MG-H1/RAGE-based pathway. RAGE expression levels in nasopharyngeal swabs from SARS-Cov-2 positive and negative individuals, as well as glyoxalase 1 expression, the major scavenging enzyme of MG, seem to support the results obtained in vitro. Altogether, our findings reveal a novel mechanism involved in the inflammation triggered by S1, paving the way to the study of MG-H1/RAGE inflammatory axis in SARS-CoV-2 infection as a potential therapeutic target to mitigate COVID-19 associated pathogenic inflammation.
ARTICLE | doi:10.20944/preprints202308.1603.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Multiplicity of infection; cell density at infection; SARS-CoV-2; Spike S1 glycoprotein; Receptor binding domain; Sf9 cells
Online: 23 August 2023 (07:53:03 CEST)
To map Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV 2) spreading and evaluate immune responses variations against this virus, it was essential to locally set up efficient serological tests. The SARS-CoV2 immunogenic proteins were very expensive and not affordable mainly for Low and Middle Income Countries (LMICs). For this purpose, the commonly used antigen, Re-ceptor-Binding Domain (RBD) of Spike S1 protein (S1RBD), was produced using the the Baculovirus Expression Vector System (BEVS) . During the current study, the expression of S1RBD was monitored using western blot under different culture conditions. Different parameters were studied: Multiplicity Of Infection (MOI), cell density at infection and harvest time. Hence, optimal conditions for efficient S1RBD production were identified: MOI 3; cell density at infection 2-3x 106 cells/mL and time post-infection (tpi or harvest time) of 72h and 72-96 h successively for expression in shake-flasks and 7L-bioreactor. A high production yield of S1RBD varying between 4mg and 70 mg per liter of crude cell culture supernatant was achieved, respectively, in shake-flasks and in 7L-bioreactor. Moreover, the produced S1RBD showed an excellent antigenicity potential against COVID-19 patient sera evaluated by western blot. Thus, additional serological assays, such as ELISA, were developed using the purified S1RDB (published by other research groups).
ARTICLE | doi:10.20944/preprints202206.0010.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: COVID-19; ARDS; Cytokine Storm; Spike S1 protein; SARS-CoV-2, Long COVID; ACE2; A549 cells; Caco-2 cells
Online: 1 June 2022 (09:49:27 CEST)
The Coronavirus disease 2019 (COVID-19) pandemic began in Jan. 2020 in Wuhan, China with a new coronavirus designated SARS-CoV-2. The principle cause of death from COVID-19 disease quickly emerged as Acute Respiratory Distress Syndrome (ARDS). A key ARDS pathogenic mechanism is the “Cytokine Storm”. This is a dramatic increase in the blood of inflammatory cytokines. In the last 2 years of the pandemic new pathology has emerged in COVID-19 survivors in which a variety of long-term symptoms emerge. This condition is called “Long COVID”. The spike protein on the surface of the virus (target for the new mRNA/DNA vaccines) is composed of joined S1-S2 subunits. Upon S1 bind-ing to the human ACE2 receptor on cells, the S1 subunit is cleaved and the S2 subunit me-diates entry of the virus. The S1 protein is then released into the blood, which might be one of the pivotal triggers for initiation and/or perpetuation of the cytokine storm. In this study, we tested the hypothesis that the spike S1 protein may activate inflammatory sig-naling and cytokine production independent of the virus. Our data support a potential role for spike S1 activation of inflammatory signaling and cytokine production in human lung and intestinal epithelial cells in culture. These data support a potential role for the SARS-CoV-2 spike S1 protein in COVID-19 pathogenesis.
BRIEF REPORT | doi:10.20944/preprints202004.0154.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV2; spike glycoprotein; mutation
Online: 9 April 2020 (13:15:21 CEST)
SARS-CoV2 popularly known as (COVID-19) has presently received worldwide attention. It has been considered a pandemic by the World Health Organisation. Owing to its high transmittance factor the virus has brought about many deaths and spread to all the major countries of the world. Scientists and Researchers worldwide are giving their full efforts to develop a vaccine. In our present study, we have included the comparative analysis of the different spike glycoprotein sequences of the patients suffering from COVID-19 from different countries where this pandemic has occurred. Spike glycoproteins are the structural proteins that bring about the binding of the SARS-CoV-2 viral molecule to the ACE2 receptor of the host following which infection occurs. Through this data, we have shown the different point mutations in the spike glycoproteins that occurred over time in different countries as the disease progressed.
BRIEF REPORT | doi:10.20944/preprints202309.0211.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARSCoV-2 virus; Long Covid; Spike protein
Online: 5 September 2023 (05:11:54 CEST)
The collective considerations presented here lead to a crucial question: What truly constitutes the primary public health challenge posed by SARSCoV-2 infection and its variants?The findings of Bowen et al.(1) and Noé et al.(4) have offered us new insights into the actual repercussions of SARSCoV-2 virus infections on public health. They unmistakably point to the late sequelae and complications arising as secondary effects of the viral infection, causing severe and long-term damage to global public health. Rather than the acute infection which has a very low mortality rate in the general population, as initially and commonly believed.
BRIEF REPORT | doi:10.20944/preprints202103.0551.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Telomere attrition in covid19; telomerase and spike RNA
Online: 22 March 2021 (15:48:20 CET)
In this letter we investigate if SARS-CoV-2 RNA is involved in the increased ageing of alveolar cells. Our in silico study is explorative. With the results we are able to outline experiments with AEC2 repair of bleomycin damaged alveolar cells. If AEC2 repair capability is diminished by spike RNA then perhaps this result provides a first step on a route to treat immortal lung cancer cells.
ARTICLE | doi:10.20944/preprints202005.0020.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: COVID-19; , 2019-nCoV; Heparin; Ivermectin; Spike Shielding
Online: 2 May 2020 (16:21:32 CEST)
The disease of COVID-19 comprises the most serious against human health worldwide with a high rate of virulence and mortality. The disease is caused by the 2019-nCoV virus from the beta coronavirus family. The virus makes use of its surface glycoprotein named S protein or spike to enter the human cells. The virus attached to its receptor named angiotensin-converting enzyme 2 on host cells surface via its receptor-binding domain and its fusion is mediated by cleavage at S2' site that is carried out by surface protease. Vaccines or drugs interfering with S protein binding or cleavage sites could be considered as drugs to get rid of the infection. In the current work and though docking and molecular dynamic experiments we have checked more than 100 drugs with high enough molecular weights for their shielding potency toward S protein binding sites and processing S2' sites. Our results indicate the shielding potency of: fidaxomicin > ivermectin > heparin > azithromycin > clarithromycin > eryhthromycin > niclosamide > ritonavir. Considering affluent reports regarding the complex disturbance in the immune system and multi-organ involvement in the disease there is no single or binary drug regime for cure expectedly and instead, we claim the multi-drug regime should be the choice in this context. Accordingly, we suggest our extracted drugs as an adjuvant for clinical trials.
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: SARS-CoV2; spike; receptor–ligand docking; super infection
Online: 20 March 2020 (08:30:40 CET)
SARS-CoV2 (corona virus) has spread globally at an unprecedented rate; so far, increasing SARS-CoV2-infected individuals have been identified. Although the situation in China is improving and is currently under control, the outbreak in other countries and its pandemic management is only beginning to develop. Based on 154 SARS-CoV2 genome sequence analyses, we used receptor–ligand docking to identify one potential point mutation (V354F) on the spike structure which enhances spike binding to ACE2 receptors underlying potential super infection. Importantly, the V354F site on spike S1 had been identified in 5/10 infected French patients living in Paris, who sharing 100% identical SARS-CoV2 genomes. With Covid-19 cases increasing rapidly in France that could lead to a new explosion, we suggest that the French government should identify all potential super spreaders and treat them accordingly. In summary, our study provides on of the measures to avoid the potential second worldwide explosion of SARS-CoV2.
ARTICLE | doi:10.20944/preprints202005.0026.v1
Subject: Biology And Life Sciences, Virology Keywords: coronavirus; SARS-CoV-2; Spike protein; Nucleocapsid protein; MSA
Online: 3 May 2020 (06:27:36 CEST)
SARS-CoV-2 is a novel and highly pathogenic coronavirus, which was first diagnosed in Wuhan city, China, in 2019, and spread to 185 countries and territories, and as of April 29, 2020, more than 3.11 million cases were recorded, and more than 217,000 people were killed. Despite all worldwide efforts, there is currently no vaccine, any drugs available to protect people against deadly SARS-CoV-2 coronavirus. The world urgently needs a SARS-CoV-2 coronavirus vaccine or effective antiviral drugs to relieve the human suffering associated with the pandemic that kills thousands of people every day. The SARS-CoV-2 genome encode a non-structural proteins named as ORF1a/b, and structural proteins such as spike (S) glycoprotein, nucleocapsid protein (N), small envelop protein (E) and matrix protein (M). A number of studies have been shown that CoV spike (S) glycoprotein and nucleocapsid protein (N) could be promising targets for vaccine, antibodies and therapeutic drug development to combat with deadly, pandemic SARS-CoV-2. Purposes of the present paper is the sequence analysis and amino acid variations of structural proteins deduced from novel coronavirus SARS-CoV-2 strains, isolated in different countries. Multiple sequence alignment of S, N and E proteins from four different coronavirus species, are also described. It is expected that the data from these studies will be very useful for the the designing and development of vaccines, antibodies and therapeutic agents that can be used to combat with the highly pathogenic SARS-CoV-2 coronavirus worldwide.
ARTICLE | doi:10.20944/preprints202004.0369.v2
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; spike protein; ACE1; ACE2; host-virus interaction; drug repurposing
Online: 2 August 2020 (09:23:18 CEST)
Respiratory transmission is the primary route of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Angiotensin I converting enzyme 2 (ACE2) is the known receptor of SARS-CoV-2 surface spike glycoprotein for entry into human cells. A recent study reported absent to low expression of ACE2 in a variety of human lung epithelial cell samples. Three bioprojects (PRJEB4337, PRJNA270632 and PRJNA280600) invariably found abundant expression of ACE1 (a homolog of ACE2 and also known as ACE) in human lungs compared to very low expression of ACE2. In fact, ACE1 has a wider and more abundant tissue distribution compared to ACE2. Although it is not obvious from the primary sequence alignment of ACE1 and ACE2, comparison of X-ray crystallographic structures show striking similarities in the regions of the peptidase domains (PD) of these proteins, which is known (for ACE2) to interact with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Critical amino acids in ACE2 that mediate interaction with the viral spike protein are present and organized in the same order in the PD of ACE1. In silico analysis predicts comparable interaction of SARS-CoV-2 spike protein with ACE1 and ACE2. In addition, this study predicts from a list of 1263 already approved drugs that may interact with ACE2 and/or ACE1, potentially interfere with the entry of SARS-CoV-2 inside the host cells and alleviate the symptoms of Coronavirus disease (COVID-19).
HYPOTHESIS | doi:10.20944/preprints202003.0042.v2
Subject: Biology And Life Sciences, Virology Keywords: Flue; Virus; COVID19; SARS CoV-2; Spike Protein; Virtual Screening; dgitoxin; anthracycline; rolitetracycline; E-155
Online: 23 March 2020 (10:19:17 CET)
The novel coronavirus (SARS-CoV-2) is a human pathogen recently emerged in China, causing a global pandemic of severe respiratory illness (COVID19). SARS-CoV-2 makes entry into human cells through its spike (S) protein that binds to cell surface receptors. Widespread of SARS-CoV-2 has been attributed to high affinity of S protein to its receptor. A homology model of the receptor binding domain of SARS-CoV-2 S protein (RBD) was built. RBD- receptor docking and published molecular dynamics data were used to map the key RBD-receptor interaction hotspot (RBDhp) on the RBD. Primary virtual screening was carried out against RBDhp using more than 3300 compounds approved by U.S Food and Drug Administration (FDA) and other authorities for human use. Compounds that bind to hpRBD with a binding energy ≤ - 6.5 kcal/mol were subjected to secondary screening using a recently published cryo EM (2.9 Å) structure of RBD. A cardiac glycoside (dgitoxin), two anthracyclines (zorubicin and aclarubicin), a tetracycline derivative (rolitetracycline), a cephalosporin (cefoperazone) and a food dye (E-155) were predicted to be most potent inhibitors of RBD – receptor interaction. An anti-asthmatic drug (zafirlukast) and several other drugs (itrazol, fazadinium, troglitazone, gliquidone, Idarubicin, Oxacillin) were found to be high affinity binders that may have a potential to inhibit RBD – receptor interaction.
ARTICLE | doi:10.20944/preprints201903.0091.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: image analysis; pattern recognition; algorithms; computer vision; wheat spike
Online: 7 March 2019 (12:06:15 CET)
Spike shape and morphometric characteristics are among the key characteristics of cultivated cereals associated with their productivity. Identification of the genes controlling these traits requires morphometric data harvesting and analysis for numerous plants, which is automatable using technologies of digital image analysis. A method for wheat spike morphometry utilizing 2D image analysis is proposed. Digital images are acquired in two variants: a spike on a table (one projection) or fixed with a clip (four projections). The method identifies spike and awns in the image and estimates their quantitative characteristics (area in image, length, width, circularity, etc.). Models of sections, quadrilaterals, and radial model are proposed for describing spike shape. Parameters of these models are used to predict spike shape type (spelt, normal, or compact) by machine learning. The mean error in spike density prediction for the images in one projection is 4.61 (~18%) versus 3.33 (~13%) for the parameters obtained using four projections. F1 measure in automated spike classification into three types is 0.78 using logistic regression (one projection) and 0.85 using random forest method (four projections). The proposed method is implemented in Java; examples of images and user guide are available at http://wheatdb.org/werecognizer.
ARTICLE | doi:10.20944/preprints202305.0661.v1
Subject: Chemistry And Materials Science, Electrochemistry Keywords: Memristor; Polyaniline; neural network; spike; Red-ox front; solid electrolyte
Online: 9 May 2023 (12:58:21 CEST)
We observed and studied the phenomenon of the redox front propagation in different polyaniline (PAni) deposited samples interfaced with liquid or solid polymeric electrolyte. The front of electrochemical conversion, in which the insulator and the conductor parts of PAni are interfaced, is studied observing the temporal evolution of the conductivity of PAni samples. The propagation of redox front was studied in electrochemically obtained thick (2 µm) and in thin (50 nm) poly-aniline films, obtained using Langmuir-Blodgett (LB) method. In the configuration that we tested, the speed of the red-ox front propagation for the thin LB films was found to be 200 micron/sec opening the way for the manufacturing large neural networks, realized using PAni based memristive devices, in which the memristance can be quickly changed in the programmable manner. The prototypes of the spiking neuron connections were manufactured on the basis of lithographically developed gold contacts, bridged by electrochemically grown polyaniline and placed under polymer electrolyte layer with only one counter electrode (gate) for the whole manifold of pseudo-two-terminal memristor bridges. The spike propagation was studied in such gold-polyaniline systems. The research opens the possibility of miniature spike or rate-based neural network circuits manufacture, based on metal pads and polyaniline.
REVIEW | doi:10.20944/preprints202303.0140.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; genetic vaccines; adverse reactions; autoimmunity; immunohistochemistry; spike protein
Online: 8 March 2023 (02:57:33 CET)
As a result of the spread of SARS-CoV-2, a global pandemic was declared. Indiscriminate COVID-19 vaccination has been extended to include age groups and naturally immune people with minimal danger of suffering serious complications due to COVID-19. Solid immuno-histopathological evidence demonstrates that the COVID-19 genetic vaccines can display an off-target distribution in tissues that are terminally differentiated, triggering autoimmune reactions. These include the heart and brain, which may incur in situ production of spike protein eliciting a strong autoimmunological inflammatory response. Due to the fact that every human cell which synthesizes non-self antigens becomes inevitably the target of the immune system, and since the human body is not a strictly compartmentalized system, accurate pharmacokinetic and pharmacodynamic studies are needed in order to determine precisely which tissues can be harmed. Therefore, our article aims to draw the attention of the scientific and regulatory communities on the critical need of bio-distribution studies for the genetic vaccines against COVID-19, as well as of rational harm-benefit assessments by age group.
ARTICLE | doi:10.20944/preprints202203.0155.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Omicron variant; Monoclonal antibody; Neutralization; Spike protein
Online: 10 March 2022 (14:30:25 CET)
SARS-CoV-2 Omicron variants contain many mutations in its spike receptor binding domain, the target of all authorized monoclonal antibodies (mAbs). Determining the extent to which Omicron variants reduced mAb susceptibility is critical to preventing and treating COVID-19. We systematically reviewed PubMed and three preprint servers, last updated February 22, 2022, of the in vitro activity of authorized mAbs against the Omicron variants. Thirty-three studies were eligible including 33 containing Omicron BA.1 susceptibility data and five that also contained Omicron BA.2 susceptibility data. The first two authorized mAb combinations, bamlanivimab/etesevimab and casirivimab/imdevimab, were inactive against the Omicron BA.1 and BA.2 variants. In 24 studies, sotrovimab (third authorized mAb) displayed a median 4.1-fold (IQR: 2.4-7.6) reduced activity against Omicron BA.1 and, in four studies, a median 26-fold (IQR:16-35) reduced activity against Omicron BA.2. In 18 studies, cilgavimab and tixagevimab independently displayed median reductions in activity of >300-fold against Omicron BA.1, while in ten studies, the cilgavimab/tixagevimab combination (fourth authorized mAb preparation) displayed a median 63-fold (IQR: 26-145) reduced activity against Omicron BA.1. In two studies, cilgavimab was approximately 100-fold more susceptible to BA.2 than to BA.1. In two studies, bebtelovimab, the most recently authorized mAb, was fully active against both the Omicron variants. Disparate results between assays were common as evidenced by a median 42-fold range (IQR: 25-625) in IC50 between assays for the eight authorized individual mAbs and three authorized mAb combinations. Highly disparate results between published assays indicates a need for improved mAb susceptibility test standardization or inter-assay calibration.
REVIEW | doi:10.20944/preprints202005.0519.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Angiotensin-Converting Enzyme 2; Spike glycoprotein; TMPRESS2; Furin; Malayan pangolin
Online: 31 May 2020 (21:41:44 CEST)
The outbreak of a novel coronavirus (SARS-CoV2) associated with acute respiratory disease called COVID-19 marked the introduction of the third spillover of an animal CoV to humans in the last 2 decades. The SARS-CoV2 genome analysis with various bioinformatics tools revealed that it belongs to beta CoVs genera, with highly similar genome as bat coronavirus and receptor binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS-CoV2 is likely to be originated from bat derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further spike protein S1/S2 cleavage site of SARS-CoV2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS-CoV2, roles of virus proteins in pathogenesis, commonalities and differences between different corona viruses. We have also highlighted the evidences regarding the potential drugs and vaccine candidates with their modes of action to cope with this viral outbreak. Our review provides comprehensive up-dated information on molecular aspects of the SARS-CoV2.
COMMUNICATION | doi:10.20944/preprints202005.0401.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: SARS-CoV-2; Peptide Vaccine; Spike Protein; Vaccinomics; Epitope Prediction
Online: 24 May 2020 (19:11:19 CEST)
SARS-CoV-2 has been the talk of the town ever since the beginning of 2020. The pandemic has brought the complete world on a halt. Every country is trying all possible steps to combat the disease ranging from shutting the complete economy of the country to repurposing of drugs and vaccine development. The rapid data analysis and widespread tools, software and databases have made bioinformatics capable of giving new insights to the researchers to deal with the current scenario more efficiently. Vaccinomics, the new emerging field of bioinformatics uses concepts of immunogenetics and immunogenomics with in silico tools to give promising results for wet lab experiments. This approach is highly validated for the designing and development of potent vaccines. The present in-silico study was attempted to identify peptide fragments from spike surface glycoprotein that can be efficiently used for the designing and development of epitope-based vaccine designing approach. Both B-cell and T-cell epitopes are predicted using integrated computational tools. VaxiJen server was used for prediction of protective antigenicity of the protein. NetCTL was studied for analyzing most potent T cell epitopes and its subsequent MHC-I interaction through tools provided by IEDB. 3D structure prediction of peptides and MHC-I alleles (HLA-C*03:03) was further done to carry out docking studies using AutoDock4.0. Various tools from IEDB were used to predict B-cell epitopes on the basis of different essential parameters like surface accessibility, beta turns and many more. Based on results interpretation, the peptide sequence from 1138-1145 amino acid and sequence WTAGAAAYY and YDPLQPEL were obtained as a potential B-cell epitope and T-cell epitope respectively. This in-silico study will help us to identify novel epitope-based peptide vaccine target in spike protein of SARS-CoV-2. Further, in-vitro and in-vivo study needed to validate the findings.
ARTICLE | doi:10.20944/preprints202004.0535.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2 RNA Secondary Structure; Spike Protein; Furin; TMPRSS2
Online: 30 April 2020 (14:13:36 CEST)
Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) has claimed nearly 180,000 lives and continues to spread. There are currently no approved medications or vaccines for this new coronavirus. Studies have shown that the positive RNA genome of SARS-CoV-2 contains unique features, including a 12-base sequence inserted between the two subunits of viral receptor protein Spike. This inserted sequence facilitates the cleavage of Spike by the cellular proteases Furin and TMPRSS2, leading to the fusion of virus and host cell membranes. Current studies are mostly focused on the SARS-CoV-2 Spike protein and its interacting cellular proteins ACE2, Furin, and TMPRSS2. RNA structural studies are limited and little is known about the potential impact of the 12-base sequence insert on the secondary structure of SARS-CoV-2 genomic RNA and/or its transcripts. Here, by using local and global RNA secondary structure predictions, we show that the novel 12-base insert of SARS-CoV-2 genome likely induces a major RNA secondary structure change.
Subject: Biology And Life Sciences, Virology Keywords: ACE2; Spike protein; SARS-CoV2; death rate; polymorphism; isoform variant; CD157, sankramikogenomics
Online: 17 May 2020 (14:51:39 CEST)
The 2019-Novel Coronavirus has currently gripped the world in terror, affecting 210 countries and territories. Originating from Wuhan, Hubei province, China, the virus has spread so rapidly throughout the world and has already claimed 308,927 lives and is currently afflicting 4.6 million people. The US has over 1.48 million confirmed cases of COVID-19, followed by Spain, Italy, France, UK, Germany, Turkey, Russia, Iran, and China. On careful inspection of the COVID-19 statistics, a peculiar unsettling trend becomes apparent. Western European countries and the US appear to have difficulties in overcoming the catastrophe. In contrast, countries in East Asia, Middle East and mid-Europe have sorted out the situation. Here, we will highlight this trend and propose the importance of infection-genomics (sankramikogenomics), in understanding the susceptibility to COVID-19 and the severity of disease progress. More detailed, systematic evaluation may also identify more susceptible populations. We will also highlight mere 12-fold lower affinity is insufficient to ignore CD147, as interactions occur between tens of spike proteins and equal number of cell surface ACE2 and/or CD147. Thus, both receptors are important to understand sankramikogenomics and severity of COVID-19. The observed ethnic differences in COVID severities may be due to variations in structure or tissue-specific expression (alternate splicing and accessibility) of both the target receptors. Research on both receptors may help in designing improved therapeutic strategies to fight COVID-19. Similar to pharmacogenomics to drug development and precision medicine, Sankramikogenomics will become an important field in other infectious diseases and pathogenicity.
ARTICLE | doi:10.20944/preprints202304.0563.v1
Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Hevein-lectins; Selaginella moellendorffii; SARS-CoV-2, Spike protein; Docking; Variants
Online: 19 April 2023 (07:44:58 CEST)
Multidisciplinary research efforts on potential COVID-19 vaccine and therapeutic candidates have increased since the pandemic outbreak of SARS-CoV-2 in 2019. This search has become imperative due to the increasing emergences and limited widely available medicines. The presence of bioactive anti-SARS-CoV-2 molecules was examined from various plant sources. Among them is a group of proteins called lectins that can bind carbohydrate moieties. In this article, we present ten novel, chitin-specific Hevein-like lectins that were derived from Selaginella moellendorffii v1.0's genome. The capacity of these lectin homologs to bind with the spike protein of SARS-CoV-2 was examined. Using the HDOCK server, 3D-modeled Hevein-domains were docked to the spike protein's receptor binding domain (RBD). The Smo446851, Smo125663, and Smo99732 interacted with Asn343-located complex N-glycan and RBD residues, respectively, with binding free energies of -17.5, -13.0, and -26.5 Kcal/mol. The normal-state analyses via torsional coordinate association for the Smo99732-RBD complex using iMODS is characterized by overall higher stability and minimum deformity than the other lectin complexes. The three lectins interacting with carbohydrates were docked against five individual mutations that frequently occur in major SARS-CoV-2 variants. These were in the spike protein’s receptor-binding motif (RBM), while Smo125663 and Smo99732 only interacted with the spike glycoprotein in a protein-protein manner. The precursors for the Hevein-like homologs underwent additional characterization and their expressional profile in different tissues was studied. These in-silico findings offered potential lectin candidates targeting key N-glycan sites crucial to the virus's virulence and infection.
ARTICLE | doi:10.20944/preprints202304.0360.v1
Subject: Computer Science And Mathematics, Probability And Statistics Keywords: quantile regression; Spike-and-Slab prior; variational Bayesian; high-dimensional data
Online: 14 April 2023 (09:36:47 CEST)
Quantile regression model is widely used in variable relationship research of general size data, due to strong robustness and more comprehensive description of the response variables' characteristics. With the increase of data size and data dimension, there have been some studies on high-dimensional quantile regression under the classical statistical framework, including higher-efficient frequency perspective, which is however at cost of randomness quantification, or lower-efficient Bayesian method based on MCMC sampling. To overcome these problems, we propose the high-dimensional quantile regression with Spike-and-Slab Lasso penalty based on variational Bayesian (VBSSLQR), which can not only improve the computational efficiency but also measure the randomness via variational distributions. The simulation studies and real data analysis illustrate that the proposed VBSSLQR method is superior to or equivalent to other quantile and non-quantile regression methods (including Bayesian and non-Bayesian methods), and its efficiency is higher than any other method.
ARTICLE | doi:10.20944/preprints202203.0182.v1
Subject: Computer Science And Mathematics, Probability And Statistics Keywords: cumulative logit; penalized models; LASSO; variable inclusion indicators; spike-and-slab
Online: 14 March 2022 (10:04:52 CET)
Stage of cancer is a discrete ordinal response that indicates aggressiveness of disease and is often used by physicians to determine the type and intensity of treatment to be administered. For example, the FIGO stage in cervical cancer is based on the size and depth of the tumor as well as the level of spread. It may be of clinical relevance to identify molecular features from high-throughput genomic assays that are associated with stage of cervical cancer, to elucidate pathways related to tumor aggressiveness, identify improved molecular features that may be useful for staging, and identify therapeutic targets. High-throughput RNA-Seq data and corresponding clinical data (including stage) for cervical cancer patients has been made available through The Cancer Genome Atlas Project (TCGA). We recently described penalized Bayesian ordinal response models that can be used for variable selection for over-parameterized datasets such as the TCGA-CESC dataset. Herein, we describe our ordinalbayes R package, available from the Comprehensive R Archive Network (CRAN), which is capable of fitting cumulative logit models when the outcome is ordinal and the number of predictors exceeds the sample size, P>N, such as for TCGA data. We demonstrate use of this package through application to TCGA cervical cancer dataset. Our ordinalbayes package can be used to fit models to high-dimensional dataset and effectively performs variable selection.
ARTICLE | doi:10.20944/preprints202108.0011.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Transformer; spike; neural decoding; CNN; RNN; LSTM; deep learning; information; neuroscience
Online: 2 August 2021 (09:51:43 CEST)
Neural decoding from spiking activity is an essential tool for understanding the information encoded in population neurons, especially in applications like brain-computer interface (BCI). Various quantitative methods have been proposed and have shown superiorities under different scenarios respectively. From the machine learning perspective, the decoding task is to map the high-dimensional spatial & temporal neuronal activity to the low-dimensional physical quantities (e.g., velocity, position). Because of the complex interactions and the abundant dynamics among neural circuits, good decoding algorithms usually have the capability of capturing flexible spatiotemporal structures embedded in the input feature space. Recently, the Transformer-based models are widely used in processing natural languages and images due to its superior performances in handling long-range and global dependencies. Hence, in this work we examine the potential applications of Transformers in neural decoding and introduce two Transformer-based models. Besides adapting the Transformer to neuronal data, we also propose a data augmentation method for overcoming the data shortage issue. We test our models on three experimental datasets and their performances are comparable to the previous state-of-the-art (SOTA) RNN-based methods. In addition, Transformer-based models show increased decoding performances when the input sequences are longer, while LSTM-based models deteriorate quickly. Our research suggests that Transformer-based models are important additions to the existing neural decoding solutions, especially for large datasets with long temporal dependencies.
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: vaccine; adenovirus; COVID-19; spike; endothelial; vector; coagulation; clot; thrombopenia; platelet
Online: 15 April 2021 (14:05:48 CEST)
Prothrombotic thrombocytopathy mimicking heparin-induced thrombocytopenia has been observed in patients with severe COVID-19 and after immunisation with the Vaxzevria vaccine. Herein, we discuss the pathogenesis of this disorder focusing on the possible involvement of anti-platelet factor 4 (PF4) autoantibodies.
ARTICLE | doi:10.20944/preprints202103.0647.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: American Mink; COVID-19; Neovison vison; SARS-CoV-2; Spike; wildlife
Online: 25 March 2021 (16:39:13 CET)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19 , is considered a pathogen with animal origin, mainly transmitted human to human. It has been experimentally and naturally demonstrated that several animals can be infected by SARS-CoV-2. There are strong evidences that minks are highly susceptible to SARS-CoV-2 infection, since several cases of human to mink infection have been reported, and it has been suggested mink to human infection exists, which so far it is the most reliable example of a zoonotic event of COVID-19 . However, all these cases reported are form mink farms, with the exception of one case in the USA in which the virus was detected in a mink located in the wild, but it was demonstrated that the animal was infected on a fur farm. In the present work, we have detected SARS-CoV-2 RNA in two wild American minks (Neovison vison) in Valencian Community (Eastern Spain) during invasive species trapping campaigns. The animals were trapped from areas known for harbouring self-sustained populations, far away from the nearest fur farm. SARS-CoV-2 RNA was detected in mesenteric lymph nodes samples by RT-PCR. A partial region of the Spike protein gene was amplified and sequence obtaining a 397 nt size sequence. Phylogenetic analysis shown that both sequences were identical to the consensus variant SARS CoV-2 sequence (from Wuhan). This research describes the first infection report of a true wild American mink not related to infected fur farms or direct contact with humans, which is believed to be the first example of wild animals in which SARS-CoV-2 has been detected.
ARTICLE | doi:10.20944/preprints202007.0297.v1
Subject: Computer Science And Mathematics, Probability And Statistics Keywords: information source; information transmission rate; fluctuations; entropy; standard deviation; spike-trains
Online: 14 July 2020 (10:57:02 CEST)
(1) Background: In nervous system information is conveyed by a sequence of action potentials, called spikes-trains. As MacKay and McCulloch proposed, spike-trains can be represented as bits sequences coming from Information Sources. Previously, we studied relations between Information Transmission Rates (ITR) carried out by the spikes, their correlations, and frequencies. Here, we concentrate on the problem of how spikes fluctuations affect ITR. (2) Methods: The Information Theory Method developed by Shannon is applied. Information Sources are modeled as stationary stochastic processes. We assume such sources as two states Markov processes. As a spike-trains' fluctuation measure, we consider the Standard Deviation sigma, which, in fact, measures average fluctuation of spikes around the average spike frequency. (3) Results: We found that character of ITR and signal fluctuations relation strongly depends on the parameter s which is a sum of transitions probabilities from no spike state to spike state and vice versa. It turned out that for smaller s (s<1) the quotient ITR\sigma has a maximum and can tend to zero depending on transition probabilities. While for s large enough (1<s) the ITR\sigma is separated from 0 for each s. Similar behavior was observed also when we replaced Shannon entropy terms in Markov entropy formula by their approximation with polynomials. We also show that the ITR quotient by Variance behaves in a completely different way. (4) Conclusions: Our results show that for large transition parameter s the Information Transmission Rate by sigma will never decrease to zero. Specifically, for 1<s<1.7 the ITR will be always, independently on transition probabilities which form this s, above the level of fluctuations, i.e. in this case we have sigma<ITR. Thus, we conclude that in a more noisy environment, to get appropriate reliability and efficiency of transmission, Information Sources with higher tendency of transition from the state no spike to spike state and vice versa should be applied.
ARTICLE | doi:10.20944/preprints202003.0242.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; spike protein; multiepitope vaccine; molecular modeling
Online: 15 March 2020 (12:45:54 CET)
The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the world health organization declared it pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. In this urgency situation, development of SARS-CoV-2 based vaccines is immediately required. Immunoinformatic and molecular modelling are generally used time-efficient methods to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines is proved to be a promising immunization strategy against viruses and pathogens, which induce more comprehensive protective immunity. The current study demonstrated a comprehensive in-silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in-silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in E. Coli. Despite this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can present to be a better prophylactic solution against COVID-19.
REVIEW | doi:10.20944/preprints202009.0395.v1
Subject: Biology And Life Sciences, Virology Keywords: Spike protein, V483A, substitution mutation, virus-host cell interaction, high transmission, infectivity.
Online: 17 September 2020 (10:43:02 CEST)
Exploring the biological significance of mutations in SARS-CoV-2 coronavirus, causing the COVID–19 pandemic, has recently become an area of paramount interest for many researchers, who are pouring their tremendous efforts, in cracking the COVID–19 pandemic code. One of many such mutations that have occurred in the viral genome is V483A mutation, which is a part of the receptor-binding motif (RBM), present in the S1 domain of the spike protein. V483A mutant virus is becoming popular in North America with 36 cases so far, due to its frequent occurrences in recent days. In this review, we have assembled all information, currently available on V483A mutation, and have made a critical analysis based on the perspectives of many researchers all around the world. Comparison is made between the wild type and the V483A mutants to analyze certain factors like the type of interaction between the virus and host cell interface, binding affinity, stability, partition energy, hydrophobicity, occurrence rate, and transmissibility. Insilico dynamic analysis shows minimal alteration in the receptor-binding domain (RBD) of V483A mutant protein in free-state and no significant change of mutant tertiary structure of RBM upon binding to the ACE2 receptor. Comprehensive details about infectivity and evasion of the immune system by the virus are discussed. This information can in turn be of monumental importance in the field of vaccine and drug development because the mutants are becoming resistant to the vaccines and monoclonal antibodies.
ARTICLE | doi:10.20944/preprints202004.0102.v3
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Medicinal plants; Mpro; 3CLpro; spike (S) glycoprotein; COVID-19; SARS-CoV-2
Online: 1 July 2020 (08:37:49 CEST)
Since the outbreak of the COVID-19 (Coronavirus Disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants by using a molecular docking approach to inhibit the Main Protease (Mpro) and Spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina as a docking engine. A rule of five (RO5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was done by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding / ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine and hydroxychloroquine sulfate (anti-malarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir, but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. These plant compounds have the potential to be developed as specific therapeutic agents against COVID-19. Several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate which so far are recommended in the treatment of COVID-19. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development lead compounds to treat infections caused by SARS-CoV-2.
ARTICLE | doi:10.20944/preprints201907.0230.v1
Subject: Computer Science And Mathematics, Mathematics Keywords: non-equilibrium steady states; maximum entropy principle; spike train statistics; entropy production
Online: 22 July 2019 (04:44:16 CEST)
Although most biological processes are characterized by a strong temporal asymmetry, several popular mathematical models neglect this issue. Maximum entropy methods provide a principled way of addressing time irreversibility, which leverages powerful results and ideas from the3literature of non-equilibrium statistical mechanics. This article provides a comprehensive overview of these issues, with a focus in the case of spike train statistics. We provide a detailed account of the5mathematical foundations and work out examples to illustrate the key concepts and results from non-equilibrium statistical mechanics
ARTICLE | doi:10.20944/preprints202006.0165.v2
Subject: Biology And Life Sciences, Virology Keywords: Conserved signature indels (CSIs) specific for SARS and SARS-CoV-2-related viruses. Molecular markers distinguishing different clades of Sarbecovirus, Evolutionary relationships between SARS and SARS-CoV-2-related viruses, Origin of SARS-CoV-2 and Pangolin CoV_MP789 viruses, Novel sequence and structural features of spike and nucleocapsid proteins. Genetic recombination.
Online: 26 August 2020 (10:17:16 CEST)
Both SARS-CoV-2 (COVID-19) and SARS coronaviruses (CoVs) are members of the subgenus Sarbecovirus. To understand the origin of SARS-CoV-2, protein sequences from sarbecoviruses were analyzed to identify highly-specific molecular markers consisting of conserved inserts or deletions (termed CSIs) in the spike (S) and nucleocapsid (N) proteins that are specific for either particular clusters/lineages of these viruses or are commonly shared by specific lineages. Three novel CSIs in the N-terminal domain of the spike protein S1-subunit (S1-NTD) are uniquely shared by the SARS-CoV-2, BatCoV-RaTG13 and most pangolin CoVs, distinguishing this cluster of viruses (SARS-CoV-2r) from all others. In the same positions, where these CSIs are found, related CSIs are also present in two other sarbecoviruses (viz. CoVZXC21 and CoVZC45 forming CoVZC cluster), which form an out group of the SARS-CoV-2r cluster. These three CSIs are not found in the SARS-CoVs. However, both SARS and SARS-CoV-2r CoVs contain two large CSIs in the C-terminal domain of S1 (S1-CTD), which binds the human ACE-2 receptor, that are absent in the CoVZC cluster of CoVs. These results indicate that while the S1-NTD of the SARS-CoV-2r viruses possesses the sequence characteristics of the CoVZC cluster of CoVs, their S1-CTD resembles the SARS viruses. Thus, the spike protein of SARS-CoV-2r viruses has likely originated from a recombination event between the S1-NTD of the CoVZC viruses and the S1-CTD of SARS viruses. This inference is also supported by the amino acid sequence similarity of the S1-NTD and S1-CTD from SARS-CoV-2 compared to the CoVZC and SARS CoVs. We also present evidence that one of the pangolin-CoV_MP789, whose receptor-binding domain is most similar to the SARS-CoV-2, is also derived by a recent recombination between the S1-NTD of the CoVZC CoVs and the S1-CTD of a SARS-CoV-2 related virus. Several other identified CSIs are specific for others clusters of sarbecoviruses including a clade consisting of bat SARS-CoVs (BM48-31/BGR/2008 and SARS_BtKY72). Structural mappings studies show that the identified CSIs are located within surface-exposed loops and form distinct patches on the surface of the spike protein. These surface loops/patches are predicted to interact with other host components and play important role in the biology/pathology of SARS-CoV-2 virus. Lastly, the CSIs specific for the SARS-CoV-2r clade provide novel means for development of new diagnostic and therapeutic targets for these viruses.
REVIEW | doi:10.20944/preprints202301.0133.v2
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19 vaccination; mRNA vaccines; Clinical Trials; Safety Assessment; Novel Technologies; Spike protein
Online: 12 January 2023 (03:16:56 CET)
Pharmacovigilance databases are showing evidence of injury in the context of the COVID-19 modified mRNA shots. According to recent publications, adverse event reports linked to the mRNA COVID-19 products largely point to the spike protein as an aetiological agent of adverse events, but we propose that the platform itself may be culpable. To assess the safety of current and future mRNA vaccines, further analysis on the risks due to the platform itself, and not specifically the expressed antigen. If harm can be exclusively and conclusively attributed to the spike protein, then it is possible that future mRNA vaccines expressing other antigens will be safe. If harms are attributable to the platform itself, then regardless of the toxicity, or lack thereof, of the chosen payload therein, the platform may be inherently unsafe, pending modification. In this work, we examine previous studies of RNA-based delivery by a lipid nanoparticle and break down the possible etiological elements of harm.
ARTICLE | doi:10.20944/preprints202105.0750.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2 genomics; spike protein; epitope prediction; coronavirus comparative genomics
Online: 31 May 2021 (11:36:29 CEST)
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenges include understanding what triggered SARS-CoV-2 emergence, how this RNA virus is evolving or how the genomic variability may impact the primary structure of proteins that are targets for vaccine. We analyzed 19471 SARS-CoV-2 genomes and 199,984 spike glycoprotein sequences available at the GISAID database from all over the world and 3335 genomes of other Coronoviridae family members available at Genbank, collecting SARS-CoV-2 high-quality genomes and distinct Coronoviridae family genomes. Here, we identify a SARS-CoV-2 emerging cluster containing 13 closely related genomes isolated from bat and pangolin that showed evidence of recombination, which may have contributed to the emergence of SARS-CoV-2. The analyzed SARS-CoV-2 genomes presented 9632 single nucleotide polymorphisms (SNPs) corresponding to a variant density of 0.3 over the genome, and a clear geographic distribution. SNPs are unevenly distributed throughout the genome and hotspots for mutations were found for the spike gene and ORF 1ab. We describe a set of predicted spike protein epitopes whose variability is negligible. All predicted epitopes for the structural E, M and N proteins are highly conserved. This result favors the continuous efficacy of the available vaccines.
REVIEW | doi:10.20944/preprints202008.0166.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: COVID-19, seroconversion, neutralizing antibody, spike protein, SARS-CoV-2, convalescent plasma, vaccine
Online: 6 August 2020 (12:16:11 CEST)
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people and caused tremendous morbidity and mortality worldwide. Effective treatment for coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 infection is lacking and different therapeutic strategies are under testing. Host humoral and cellular immunity to SARS-CoV-2 infection is a critical determinant for patients’ outcome. SARS-CoV-2 infection results in seroconversion and production of anti-SARS-CoV-2 antibodies. The antibodies may suppress viral replication through neutralization but also might also participate in COVID-19 pathogenesis through a process termed antibody-dependent enhancement. Rapid progress has been made in the research of antibody response and therapy in COVID-19 patients including characterization of the clinical features of antibody responses in different populations infected by SARS-CoV-2, treatment of COVID-19 patients with convalescent plasma and intravenous immunoglobin products, isolation and characterization of a large panel of monoclonal neutralizing antibodies, as well as preliminary clinical results from several COVID-19 vaccine candidates. In this review, we summarize the recent progress and discuss the implications of these findings in vaccine development.
ARTICLE | doi:10.20944/preprints202004.0439.v1
Subject: Biology And Life Sciences, Biophysics Keywords: SARS-CoV-2; COVID-19; spike glycoprotein; variability; molecular docking; molecular dynamics; inhibitors
Online: 24 April 2020 (11:42:01 CEST)
An important stage in SARS-CoV-2 life cycle is the fusion of spike(S) protein with the ACE2 host-cell receptor. Therefore, to explore conserved features in S protein dynamics and to identify potentially novel regions for drugging, we measured variability derived from 791 viral genomes and studied its properties by MD simulation. The findings indicated that S2 subunit (HR1, CH, and CD domains) showed low variability, low fluctuations in MD, and displayed a trimer cavity. By contrast, the RBD domain, which is typically targeted in drug discovery programmes, exhibits more sequence variability and flexibility. Interpretations from MD suggest that the monomer is in constant motion showing transitions up-to-down state, and the trimer cavity may function as a 'bouncing spring' that may facilitates S protein interactions with ACE2. Feasibility of trimer cavity for potential drug target was examined by SBVS screening. Several hits that have already been validated or suggested to inhibit the SARS-CoV-2 virus in cell systems were identified; in particular, the data suggest an action mechanism for such molecules including Chitosan and macrolide types. These findings identify a novel binding-site formed by the S protein, that might assist in future drug discovery programmes aimed at targeting the CoV family of viruses.
REVIEW | doi:10.20944/preprints202311.1883.v1
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: COVID-19 vaccines; mRNA vaccine; SARS-CoV-2 spike; myocarditis; ACE2; renin-angiotensin system
Online: 29 November 2023 (12:20:42 CET)
Myocarditis has been recognized as a possible rare complication of COVID-19 mRNA vaccination. It concerns between one and five vaccinated people per 100,000 in the general population, with increased incidence in adolescent and young adult men. Most often, cases of myocarditis have been reported in the days following the second dose of vaccine mainly in younger male patients. This rare complication of vaccination usually resolves within days or weeks. However, the pathophysiological events responsible for the increase in frequency of myocarditis after COVID-19 vaccination remain unclear. Several recent reports have highlighted that free spike proteins circulating in the blood of patients at high levels appear to play a major role in myocarditis. Here, we review the most relevant data that partly lift the veil on the molecular mechanisms of the induction of myocarditis following mRNA-based COVID-19 vaccination. We hypothesize that a mechanism of molecular mimicry of the viral spike triggers transient dysregulation of angiotensin-converting enzyme 2, leading to increased soluble angiotensin II binding to the transmembrane receptor angiotensin II type I receptor, similar to what is observed during SARS-CoV-2 infection. We suggest to standardize management of suspected cases of mRNA-based COVID-19 vaccine-induced myocarditis, including angiotensin II and spike antigenemia monitoring.
ARTICLE | doi:10.20944/preprints202310.1836.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2 immunity; ELISA; Spike-RBD; SARS-CoV-2 variants; Omicron; virus neutralizing
Online: 30 October 2023 (07:06:58 CET)
We have developed a simple, rapid, high-throughput RBD-based ELISA to assess the humoral immunity against emerging SARS-CoV-2 virus variants. The cDNAs of the his-tagged RBD proteins of the virus variants were stably engineered into HEK cells secreting the protein into the supernatant, and RBD purification was performed by Ni-chromatography and buffer exchange by membrane filtration. The simplified assay uses single dilutions of sera from finger-pricked native blood samples, purified RBD in 96-well plates, and a chromogenic dye for development. The results of this RBD-ELISA were confirmed to correlate with those of a commercial immunoassay measuring antibodies against the Wuhan strain, as well as direct virus neutralization assays assessing the cellular effects of the Wuhan and the Omicron (BA.5) variants. Here we document the applicability of this ELISA to assess the variant-specific humoral immunity in vaccinated and convalescent patients, as well as to follow the time course of selective vaccination response. This simple and rapid assay, easily modified to detect humoral immunity against emerging SARS-CoV-2 virus variants, may help to assess the level of antiviral protection after vaccination or infection.
ARTICLE | doi:10.20944/preprints202308.0296.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: 3D NAND flash memory; noncircular cell; spike; TCAD simulation; threshold voltage variation; trapped charge
Online: 3 August 2023 (10:41:05 CEST)
Variations in threshold voltage (VTH) and charge distributions in noncircular cells of three-dimensional (3D) NAND flash memory are investigated. The electric field difference in the circular and spike regions causes nonuniform trapped electron density in the charge trap layer (CTL) and influences the VTH variation. Such less-trapped electron (LT) regions in CTL between the circular and spike regions exhibit a lower electric field during the program, resulting in a higher current flow through that region. For the two-spike cells, the charge distribution and VTH variation are analyzed at different heights (HSpike) and angles between spikes. These irregular cells decrease VTH as the HSpike increases.
ARTICLE | doi:10.20944/preprints202010.0616.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Spike-and-wave; Generalized Gaussian distribution; EEG; Morlet wavelet; k-nearest neighbors classifier; Epilepsy
Online: 29 October 2020 (14:05:54 CET)
Spike-and-wave discharge (SWD) pattern detection in electroencephalography (EEG) signals is a key signal processing problem. It is particularly important for overcoming time-consuming, difficult, and error-prone manual analysis of long-term EEG recordings. This paper presents a new SWD method with a low computational complexity that can be easily trained with data from standard medical protocols. Precisely, EEG signals are divided into time segments for which the Morlet 1-D decomposition is applied. The generalized Gaussian distribution (GGD) statistical model is fitted to the resulting wavelet coefficients. A k-nearest neighbors (k-NN) self-supervised classifier is trained using the GGD parameters to detect the spike-and-wave pattern. Experiments were conducted using 106 spike-and-wave signals and 106 non-spike-and-wave signals for training and another 96 annotated EEG segments from six human subjects for testing. The proposed SWD classification methodology achieved 95 % sensitivity (True positive rate), 87% specificity (True Negative Rate), and 92% accuracy. These results set the path to new research to study causes underlying the so-called absence epilepsy in long-term EEG recordings.
ARTICLE | doi:10.20944/preprints202004.0347.v1
Subject: Biology And Life Sciences, Virology Keywords: antiviral peptides; COVID-19; SARS-CoV-2; nCoV-19; peptide design; ACE2; Spike protein
Online: 19 April 2020 (13:21:44 CEST)
Background: There are no known medicines or vaccines to control the COVID-19 pandemic caused by SARS-CoV-2 (nCoV). Antiviral peptides are superior to conventional drugs and may also be effective against COVID-19. Hence, we investigated the SARS-CoV-2 Spike RBD (nCoV-RBD) that interacts with hACE2 for viral attachment and entry. Methods: Three strategies and bioinformatics approaches were employed to design potential nCoV-RBD - hACE2 interaction-blocking peptides that may restrict viral attachment and entry. Firstly, the key residues interacting with nCoV-RBD - hACE2 are identified and hACE2 sequence based peptides are designed. Second, peptides from five antibacterial peptide databases that block nCoV-RBD are identified; finally, a chimeric peptide design approach is used to design peptides that can bind to key nCoV-RBD residues. The final peptides are selected based on their physiochemical properties, numbers and positions of key residues binding, binding energy, and antiviral properties. Results: We found (i) three amino acid stretches in hACE2 interact with nCoV-RBD; (ii) effective peptides must bind to three key positions of nCoV-RBD: Gly485/Phe486/Asn487, Gln493, and Gln498/Thr500/Asn501; (iii) Phe486, Gln493, and Asn501 are critical residues; (iv) AC20 and AC23 derived from hACE2 may block two key critical positions; (iv) DBP6 identified from databases can block the three sites of the nCoV-RBD interacting with one critical position Gln498; (v) seven chimeric peptides were considered promising among which cnCoVP-3, cnCoVP-4, and cnCoVP-7 are the top three; and (vi) cnCoVP-4 meets all the criteria and is the best peptide. Conclusion: All the ten peptides need experimental validation for their therapeutic efficacy.
ARTICLE | doi:10.20944/preprints201711.0052.v1
Subject: Physical Sciences, Thermodynamics Keywords: information entropy production; Discrete Markov Chains; spike train statistics; Gibbs measures; maximum entropy principle
Online: 8 November 2017 (04:25:12 CET)
Experimental recordings of the collective activity of interacting spiking neurons exhibit random behavior and memory effects, thus the stochastic process modeling the spiking activity is expected to show some degree of time irreversibility. We use the thermodynamic formalism to build a framework, in the context of spike train statistics, to quantify the degree of irreversibility of any parametric maximum entropy measure under arbitrary constraints, and provide an explicit formula for the information entropy production of the inferred Markov maximum entropy process. We provide examples to illustrate our results and discuss the importance of time irreversibility for modeling the spike train statistics.
BRIEF REPORT | doi:10.20944/preprints202307.0613.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID19; SARS-CoV-2; Variants of Concern; Diagnosis; LC-MS/MS; Mass-Spectrometry; Spike; Nucleocapsid
Online: 11 July 2023 (03:01:19 CEST)
The spread of SARS-CoV-2 variants of concern (VOCs), is of great importance to the whole community, since their genetic changes may increase transmissibility, disease severity and reduce effectiveness of vaccines. Moreover, these changes may lead to failure of diagnostic measures, thus variant-specific diagnostic methods are essential. To date, genetic sequencing is the gold standard method to discriminate between variants, however it is time consuming (several days) and expensive. Therefore, the development of rapid diagnostic methods for SARS-CoV-2 in accordance with its genetic modification is of great importance. In this study, we introduce a Mass-Spectrometry (MS)-based methodology for the diagnosis of SARS-CoV-2 in clinical specimens, a methodology which enables universal identification, alongside with variant-specific discrimination. The universal identification of SARS-CoV-2 is based on conserved markers shared by all variants, while the identification of the specific variant relies on variant-specific markers. Determining a specific set of peptides for a given variant consists of a multistep procedure, starting with in-silico search for variant-specific tryptic peptides, followed by tryptic digest of a cell-cultured SARS-CoV-2 variant and identification of these markers by HR-LC-MS/MS analysis. As a proof of concept, this approach was demonstrated for four representative VOCs, in comparison with the wild-type Wuhan reference strain. For each variant, at least two unique markers, derived mainly from the spike (S) and nucleocapsid (N) viral proteins, were identified. This methodology is specific, rapid, easy to perform and inexpensive, therefore can be applied as a general diagnostic tool of pathogenic variants.
ARTICLE | doi:10.20944/preprints202203.0375.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; spike glycoprotein; epitope; electrochemical biosensor; point of care; immunological diagnostic
Online: 29 March 2022 (08:39:31 CEST)
The coronavirus disease of 2019, COVID-19, is caused by an infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It was recognized in late 2019 and has since spread worldwide leading to a pandemic with unprecedented health and financial consequences. There remains an enormous demand for new diagnostic methods that can deliver fast, low-cost, and easy-to-use confirmation of a SARS-CoV-2 infection. We have developed an affordable electrochemical biosensor for the rapid detection of serological immunoglobulin (Ig) G antibody in sera against the Spike protein. Materials and Methods: A previously identified linear B-cell epitope (EP) specific to SARS-CoV-2 spike glycoprotein and recognized by IgG in patient sera was selected for the target molecule. After synthesis, the EP was immobilized onto the surface of the working electrode of a commercially available screen-printed electrode (SPE). The capture of SARS-CoV-2 specific IgGs allowed the formation of an immunocomples that was measured by square wave voltammetry from its generation of hydroquinone (HQ). Results: An evaluation of the performance of the EP-based biosensor presented a selectivity and specificity for COVID-19 of 93% and 100%, respectively. No cross-reaction was observed to antibodies against other diseases that included Chagas disease, Chikungunya, Leishmaniosis, and Dengue. Differentiation of infected and non-infected individuals was possible even at high dilution factor that decreased the required sample volumes to a few microliters. Conclusion: The final device proved suitable for diagnosing COVID-19 assaying actual serum samples and the results displayed good agreement with the molecular biology diagnoses. The flexibility to conjugate other EPs to SPEs suggests that this technology could be rapidly adapted to diagnose new variants of SARS-CoV-2 or other pathogens.
REVIEW | doi:10.20944/preprints202106.0725.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mRNA vaccine; viral vector vaccine; Spike protein; antigen presentation; polyethylene glycol; platelet factor 4; thrombosis
Online: 30 June 2021 (09:46:15 CEST)
Infection with Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which has reached pandemic proportions. A number of effective vaccines have been produced, including mRNA vaccines and viral vector vaccines, which are now being implemented on a large scale in order to control the pandemic. The mRNA vaccines are composed of the Spike S1 protein encoding mRNA, incorporated in a lipid nanoparticle, stabilized by polyethylene glycol (PEG). mRNA vaccines are novel in many respects, including cellular uptake, the intracellular routing, processing, and secretion of the viral protein. Viral vector vaccines have incorporated DNA sequences encoding the SARS-CoV-2 Spike S1 protein into (attenuated) adenoviruses. The antigen presentation routes in MHC class I and class II, in relation to induction of virus neutralizing antibodies and cytotoxic T-lymphocytes will be reviewed. In rare cases, mRNA vaccines induce unwanted immune mediated side effects. mRNA based vaccines may lead to an anaphylactic reaction. This reaction may be triggered by PEG. The intracellular routing of PEG, and potential presentation in the context of CD1 will be discussed. Adenovirus vector based vaccines have been associated with thrombocytopenic thrombosis events. The anti-platelet factor 4 antibodies found in these patients could be generated due to conformational changes of relevant epitopes presented to the immune system.
REVIEW | doi:10.20944/preprints202106.0060.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; COVID-19; variants; vaccines; immune dysregulated; comorbidities; antibody; Spike protein; biomolecules; coronavirus
Online: 2 June 2021 (09:56:14 CEST)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic which has been a topic of major concern to global human health. The challenge to restrain the COVID-19 pandemic is further compounded by the emergence of several SARS-CoV-2 variants viz. B.1.1.7, B.1.351, P1 and, B.1.617., which show in-creased transmissibility and resistance towards vaccines and therapies. Importantly, the likelihood of susceptibility to SARS-CoV-2 infection among individuals with dysregulated immune response or comorbidities needs greater attention. Herein, we provide a comprehensive perspective regarding ongoing vaccine (mRNA, protein-based, viral vector based etc.) and therapeutic (mono-clonal antibodies, small molecules, plasma therapy, etc.) modalities designed to curb the COVID-19 pandemic. We also discuss in detail the challenges posed by different SARS-CoV-2 variants of concern (VOC) identified across the globe and their effects on therapeutic and prophylactic interventions.
BRIEF REPORT | doi:10.20944/preprints202005.0084.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Vitamin D; Ivermectin; RNA-dependent-RNA polymerase; Spike glycoprotein; Knowledge based docking
Online: 5 May 2020 (15:18:30 CEST)
COVID-19 has emerged as deadly pandemic worldwide with no vaccine or suitable antiviral drugs to prevent or cure the disease. Because of the time-consuming process to develop new vaccines or antiviral agents, there has been a growing interest in repurposing some existing drugs to combat SARS-CoV-2. Vitamin D is known to be protective against acute respiratory distress syndrome (ARDS), pneumonia and cytokine storm. Recently it has been used as a repurposed drug for the treatment of H5N1 virus-induced lung injury. Circumstantial evidences indicate that people with low level of vitamin D are more susceptible to SARS-CoV-2. Although, vitamin D was suggested to interfere with viral replication, its interaction with any SARS-CoV-2 protein is unexplored yet. Beside this, ivermectin, a well-known anti-parasitic agent, exhibits potent anti-viral activities in vitro against viruses such as HIV-1 and dengue. Very recently, ivermectin has been found to reduce viral load of SARS-CoV-2 in vitro. We have analyzed available structures of SARS-CoV-2 proteins to identify probable binding partner(s) of vitamin D and ivermectin through knowledge-based docking studies and figured out possible implication of their binding in SARS-CoV-2 infection. Our observations suggest that the non-structural protein nsp7 possesses a potential site to house 25-hydroxyvitamin D3 (VDY) or the active form of Vitamin D, calcitrol. Binding of vitamin D with nsp7 likely to hamper the formation of nsp7-nsp8 complex which is required to bind with RNA dependent RNA polymerase (RdRP), nsp12 for optimal function. On the other hand, potential binding site of ivermectin has been identified in the S2 subunit of trimeric spike(S) glycoprotein of SARS-CoV-2. We propose that deeply inserted mode of ivermectin binding at three inter-subunit junctions may restrict large scale conformational changes of S2 helices which is necessary for efficient fusion of viral and host membrane. Our study, therefore, opens up avenues for further investigations to consider vitamin D and ivermectin as potential drugs against SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202003.0159.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: bat SARS-like CoV; SARS-CoV; 2019-nCoV; phylogeny; spike protein; viral and host fusion
Online: 10 March 2020 (03:49:10 CET)
A novel coronavirus (2019-nCoV) that is initially found to trigger human severe respiratory illness in Wuhan City of China, 2019, has been recognized as a public health emergency of international concern. In the past two months, this deadly agent has caused 77,785 cases with 2,666 deaths via rapid person-to-person transmission and reached at least 25 countries. However, its evolutionary origin is poorly understood. Here we show integrative evidence that 2019-nCoV is a possible progenitor for SARS-CoV with bat origin. Our finding underscores the importance of tracing origin in the efficient monitoring, and effectively preventing the interspecies transmission of such emerging/re-emerging coronaviruses.
COMMUNICATION | doi:10.20944/preprints202307.1638.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: recombinant spike protein; human PBMCs; lung microvascular endothelial cells; cytokines; chemokines; lipid droplets; lipid metabolism genes
Online: 25 July 2023 (08:14:12 CEST)
Intracellular lipid droplets (LDs) can occur in response to inflammation, metabolic stresses, and other physiological/pathological processes. Herein, we investigated whether spike proteins of SARS-CoV-2 induce LDs in human peripheral blood mononuclear cells (PBMCs) and in pulmonary microvascular endothelial cells (HPMEC). PBMCs or HPMEC were incubated alone or with endotoxin-free recombinant variants of trimeric spike glycoproteins (Alpha, Beta, Delta, and Omicron, 12 µg/ml). Afterwards, cells were stained with Oil Red O for LDs, cytokine release was determined by ELISA, and the gene expression was analyzed by real-time PCR using TaqMan assays. Our data show that spikes induce LDs in PBMCs but not in HPMEC. In line, in PBMCs spike proteins lower expression of genes involving lipid metabolism and LDs formation, such as SREBF1, HMGCS1, LDLR, and CD36. On the other hand, PBMCs exposed to spikes for 6 or 18 h did not increase in IL-1β, IL-6, IL-8, MCP-1, and TNFα release or expression as compared to non-treated controls. Thus, spike-induced LDs formation in PBMCs seems to be not related to cell inflammatory activation. Further detailed studies are warranted to investigate in which specific immune cells spikes induce LDs, and what are pathophysiological mechanisms and consequences of this induction in vivo.
BRIEF REPORT | doi:10.20944/preprints202212.0219.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2 breakthrough infections; vaccines; anti-spike antibody levels; humoral response; IgG specific salivary antibodies
Online: 13 December 2022 (02:28:02 CET)
SARS-CoV-2 breakthrough infections, associated with waning immunity, increase systemic antibody levels. In this study, we analyzed the impact of the infection timing on the magnitude of the systemic humoral response and whether breakthrough infections also boost antibody levels in the salivary compartment. We observed that the combination of infection plus vaccination, regardless of infection timing, produced a sharp increase of systemic antibodies, being higher in subjects infected after third doses. Moreover, despite high systemic antibody levels, breakthrough infections after dose 3 occurred and boosted antibody levels in the salivary compartment. These results lead to rethink the current vaccination strategies against COVID-19 and the use of salivary anti-SARS-CoV-2 antibodies for disease surveillance and vaccination follow-up.
ARTICLE | doi:10.20944/preprints202203.0236.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; BBIBP-CorV; children 3-12 years old; the anti-spike; Anti-nucleocapsid; Neutralizing antibody
Online: 16 March 2022 (15:24:51 CET)
Background and Objectives: In the current Covid-19 pandemic, children below the age of 12 could manifest Covid-19 symptoms and serve as a reservoir for the virus in the community. The present study was conducted to evaluate the reactogenicity, and immunogenicity of BBIBP-CorV, prior to involving this age group in the vaccination program in the kingdom of Bahrain. Subjects and Methods: The study included 582 children from 3 to 12 years old of Bahraini and non-Bahraini nationality, all of which contributed to the reactogenicity study. Of those, 401 contributed to the immunogenicity study. All children received 2 doses of BBIBP-CorV inactivated virus 3 weeks apart. To assess reactogenicity, children were followed up for 5 weeks to evaluate any vaccine-related adverse events (AE). To assess immunogenicity, blood was collected on day 0 and day 35 to assess antibody titer against S, N, and neutralizing antibody. Results: Of the 582 participants, (45.4%) were female, (54.61%) were male, with 49% in 9-12 age group. Of the 401 children contributing to the immunogenicity study, 274 (68.3%) had no prior exposure to Covid-19. The overall incidence of AE was 27.7%. No significant difference was found among different age groups. The most frequent AE was local (at the injection site) and occurred in 16% of children, followed by fever in 9.3%. No serious adverse events were reported. The Seroconversion rate was 100% among children with no prior exposure to Covid-19. Children with previous Covid-19 exposure had higher averages of anti-S (2379 U/ml compared to 409.1), anti-N (177.6 U/ml compared to 30.9) and neutralizing antibody (93.7 U/ml compared to 77.1) than children with no prior exposure at day 35. Conclusions: Two doses of COVID-19 BBIBP-CorV on the subjects aged between 3 to 12 has good safety and tolerance and can induce an effective immune response and neutralizing antibody titer.
BRIEF REPORT | doi:10.20944/preprints202004.0024.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-nCoV-2; vaccine; antibody; immune escape; variant; spike protein; genomic drift; convalescent plasma
Online: 3 April 2020 (04:24:52 CEST)
New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat the COVID-19 disease. Several approaches are being used by scientists for investigation including 1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease and 2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. As the disease has grown to become a pandemic, new B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries such as the Netherlands, Switzerland and France.
REVIEW | doi:10.20944/preprints202310.1717.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; murky origins; furin like cleavage sites (FLCS); spike; combination multi-epitope vaccines
Online: 26 October 2023 (14:39:52 CEST)
Globally, we are undergoing compelling changes in virtually every branch of the society and every aspect of our daily lives over the last couple of years due to the COVID-19 pandemic. In the words of Melinda Gates, the famous American Philanthropist, the pandemic has literally “magnified every existing inequality”. There has been much talk and an ongoing debate on the origin of SARS-CoV-2 (or, the novel coronavirus) as to whether have evolved purely naturally or has the contaminating element of human intervention somewhere in its trajectory. Proponents of the pure ‘natural evolution theory’, some of whom are bigshots in the field of virology have seem to take up great effort to stamp their authority right from the very early days of the pandemic on the slow natural evolution of the virus from its ancestrors by several publications in high-profile journals. These well-cited papers however provide rationals that are somewhat contradictory and are backed up with data which maybe argued as far from being complete and/or all-inclusive. As time progressed, alternative theories to that of the pure natural evolution of the virus emerged with strong counter-logics and gradually compiling genomic and epidemiological data along with detailed structural studies of relevant molecular interactions. All said and done, till date, compelling evidences lack on either end of the spectrum making the COVID origin debate still very mucg wide open. Regardless of whether purely natural or human-intervented the damage caused by the virus is unmistakable and has been an alarming concern to medical science lately. To that end, a section of the scientific community is devoting committed efforts using immuno-informatics to design and develop possible multi-epitope combination vaccines to cover a plethora of viral antigens and their plausible future mutations, alongside with the vaccines that are currently available.
BRIEF REPORT | doi:10.20944/preprints202105.0526.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 virus; complete genome sequencing; COVID-19 RT-PCR testing; Spike protein; vi-ral variants
Online: 21 May 2021 (15:12:17 CEST)
A growing number of emerging SARS-CoV-2 variants is being identified worldwide, potentially impacting the effectiveness of current vaccines. We report the data obtained in several Italian regions involved in the SARS-CoV-2 variant monitoring from the beginning of the epidemic and spanning the period from October 2020 to March 2021.
BRIEF REPORT | doi:10.20944/preprints202008.0148.v1
Subject: Biology And Life Sciences, Virology Keywords: Alignment-free software tool; Coronavirus; COVID-19; D614G mutation; Sarbecovirus; SARS-CoV; SARS-CoV-2; Spike glycoprotein
Online: 6 August 2020 (10:12:00 CEST)
As reported by us and others previously (1, 2), the D614G mutation appeared in the spike glycoprotein (SPG) of the SARS-CoV-2 (the pathogen behind COVID-19) at the early stages of the pandemic and then G614 containing variant of SARS-CoV-2 became the predominant strain in most human populations across the world. However, one of the most recent reports from India (3) stated the incidence of G614 to be only 26% in the Indian population. This report is contradictory to the information available through the GenBank (4) SARS-CoV-2 sequence deposits made by various laboratories from India. The above stated report currently circulating in the Indian media is likely to create a public perception that the Indian strain is less contagious and such a notion could be harmful to people’s welfare. In view of this concern we have re-evaluated, updated and recalculated the incidence of the G614 variant in the Indian population by analyzing 395 Indian SARS-CoV-2 genomic sequences available in the GenBank as of June 26, 2020. In our analysis we have categorized the samples by the month in which the samples were collected. We have used an alignment-free software tool named Compare (5, 6), and the Basic Local Alignment Search Tool (BLAST) (7) in the present analysis. We finally inspected each of the 395 sequences physically for the presence of aspartic acid (D) or glycine (G) at the 614th position of the spike glycoprotein. We analyzed an Australian cohort in parallel for comparison. We have found that the prevalence of G614 variant in the Indian samples for the month of June 2020 is 90.6%. The trends are similar with the Australian samples.
ARTICLE | doi:10.20944/preprints202305.2014.v1
Subject: Medicine And Pharmacology, Other Keywords: ABCB5; biodistribution; cell therapy; HSSATA17 sequence; mesenchymal stromal cells; quantitative polymerase chain reaction; spike recovery; tissue matrix effects
Online: 29 May 2023 (12:50:39 CEST)
Quantitative polymerase chain reaction (qPCR) has emerged as an important bioanalytical method for assessing the pharmacokinetics of human cell-based medicinal products after xenotransplantation into immunodeficient mice. A particular challenge in bioanalytical qPCR studies is that the different tissues of the host organism can affect amplification efficiency and amplicon detection to varying degrees, and ignoring these matrix effects can easily cause a significant underestimation of the true number of target cells in a sample. Here we describe the development and drug regulatory-compliant validation of a TaqMan® qPCR assay for quantification of mesenchymal stromal cells in the range of 125 to 20,000 cells/200 µl lysate by amplification of a human-specific, highly repetitive αsatellite DNA sequence of the chromosome 17 centromere region HSSATA17. Assessment of matrix effects in 14 different mouse tissues and blood revealed a wide range of spike recovery rates across the different tissue types from 11 to 174%. Based on these observations, we propose to perform systematic spike-and-recovery experiments during assay validation and to correct for the effects of the different tissue matrices on cell quantification in subsequent bioanalytical studies by multiplying the back-calculated cell number by tissue-specific factors derived from the inverse of the validated percent recovery rate.
ARTICLE | doi:10.20944/preprints202001.0345.v2
Subject: Biology And Life Sciences, Biophysics Keywords: stream of consciousness; quantum mechanics; decoherence theory; synaptic transmission; spike; action potential; neural code; neural correlate of consciousness
Online: 4 March 2020 (04:54:40 CET)
In previous work, a quantum mathematical formalism associated an element of experience with a single sensory neuron, as a local reduction of a global mental state. In contrast to the binary objective states of neuronal polarisation/depolarisation, neuronal experience was modeled as a continuous variable, the instantaneous value of which could only be estimated statistically from an ensemble of evoked responses to stereotyped stimulus presentation. In the present work, the quantum operations formalism of energy dissipation through amplitude damping is adopted to explain how smooth evolution of conscious experience might arise from discrete spikes and discontinuous synaptic transmission between neurons.
ARTICLE | doi:10.20944/preprints202307.1790.v1
Subject: Biology And Life Sciences, Virology Keywords: Spike protein; B-cell epitope mapping; COVID-19; DENV; SARS-CoV-2 variants; Vaccination; Cross-reactivity; Antibody-mediated enhancement.
Online: 26 July 2023 (09:41:31 CEST)
Despite successful vaccination efforts, the emergence of new SARS-CoV-2 variants poses ongoing challenges to control COVID-19. Understanding humoral responses concerning SARS-CoV-2 infections and their impact is crucial for developing future vaccines that are effective worldwide. Here, we identified 41 immunodominant linear IgG B-cell epitopes in its Spike glycoprotein with a SPOT synthesis peptide array probed with a pool of serum from hospitalized COVID-19 patients. Bioinformatics showed a restricted set of epitopes unique to SARS-CoV-2 compared to other coronavirus family members. Potential crosstalk was also detected with Dengue virus (DENV), confirmed by screening individuals infected with DENV before the COVID-19 pandemic in a commercial ELISA assay for anti-SARS-CoV-2 antibodies. Higher reactivity indices were often measured in individuals with a pre-pandemic dengue infection than those with COVID-19. A high-resolution evaluation of antibody reactivity against peptides representing epitopes in the spike protein identified ten sequences in the NTD, RBD, and S2 domains. Functionally, antibody-dependent enhancement (ADE) in SARS-CoV-2 infection of monocytes was observed with pre-pandemic dengue-positive sera. A significant increase in viral load was measured compared to controls, with no detectable neutralization or considerable cell death, suggesting its role in viral entry. This study highlights the importance of identifying the epitopes generated during the humoral response to a pathogenic infection to understand the potential interplay of previous and future conditions on disease. Vaccine development and optimization strategies should be mindful of the potential for A.D.E. that could differ geographically due to endemic biological risks.
ARTICLE | doi:10.20944/preprints202004.0390.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; SARS-CoV; ACE2; spike protein; phosphorylation; O-β-GlcNAcylation; molecular docking; chloroquine; 2-hydroxybenzohydrazine
Online: 22 April 2020 (06:01:00 CEST)
The novel coronavirus COVID- 19 disease is extremely contagious and has been spread worldwide. First COVID-19 case was identified in December, 2019 and within three months, more than one million affected cases and over 65,000 deaths have been reported. SARS-coronavirus 2 (SARS-CoV-2) also known as 2019-nCoV is a causative agent of COVID-19 disease and belongs to the SARS CoV (Severe Acute Respiratory Syndrome corona virus) family. The SARS-CoV-2 enters the human body by binding its viral surface spike protein with the host angiotensin-converting enzyme 2 (ACE2) receptors and cause infection. To prevent the virus entry and its transmission in the human body, we focused on the two domains of ACE2: i) the N-terminal extracellular binding domain (18-740 residues) reported for coronavirus spike interaction, and ii) the C-terminal cytoplasmic region (762-805 residues) to prevent the virus transmission. Therefore, we proposed: i) inhibition of receptor binding domain (RBD) of SARS-CoV-2 and human ACE2 protein may prevent the virus entry to the host and ii) inhibition of phosphorylation at Ser-787 of ACE2 protein may prevent the transmission of the virus in the COVID-19 patients. In the past, the critical role of Ser 787 in human ACE2 protein has been experimentally verified in SARS-CoV transmission, that upon binding to the receptor, SARS- CoV induces CKII- mediated phosphorylation of ACE2 at Ser-787 that in-turn facilitate virus entry to host cells, followed by replication and activation of ACE2, initiates downstream signaling leading to lung fibrosis. Therefore, in this study, we have suggested post-translational modification (PTM) O-β-GlcNAcylation, and two compounds Chloroquine and 2-hydroxybenzohydrazine might share the common pathways to prevent the COVID-19 infection in human. The addition of O-β-GlcNAcylation at same or neighboring Ser/ Thr residues results in phosphorylation inhibition and a change in protein structural and functional confirmations. Thereby, using neural networking methods, we have identified Ser/ Thr residues in ACE2 that are potential sites for phosphorylation and / or O-β-GlcNAcylation. Molecular docking showed that UDP-GlcNAc has more binding affinity with Ser-787 than the phosphoryl group. Moreover, chloroquine and 2-hydroxybenzohydrazine also showed great potential to bind at Ser-787 that may result in inhibition of Ser-787 phosphorylation and downstream signaling. Furthermore, O-β-GlcNAcylation, chloroquine and 2-hydroxybenzohydrazine showed their high affinity at ACE2-SARS-CoV-2receptor binding domain that may prevent the entry of SARS-CoV-2 into human body. In conclusion, inhibition of human ACE2 phosphorylation at Ser-787 and ACE2-SARS-CoV-2 binding domain could be promising targets against SARS-CoV-2 infection.
ARTICLE | doi:10.20944/preprints202003.0320.v1
Subject: Biology And Life Sciences, Virology Keywords: envelope protein; furin cleavage site; hydrophobic aggregation and rapid transmission; immediate ancestor; pangolins coronaviruses; SARS-CoV-2; spike protein
Online: 23 March 2020 (00:42:35 CET)
We are witnessing the severe third outbreak mediated by coronaviruses affecting global public health with unprecedented economic consequences. A better understanding of its phylogenetics, exploration of sequence features and mutational changes could unveil its genealogy to gain insights into the mechanism of transmission and development of possible interventions. Our comparative genomic analyses of >160 isolates of SARS-CoV-2 reveal phylogenetic kinship with other coronaviruses and emergence of evolutionary divergence in clinical isolates. t-SNE-based clustering revealed different clades but no continent specific clusters. Amino acid substitutions at RBD of spike protein provide possible reasons for rapid transmission. Few proteins specific to SARS-CoV-2 were identified which could have implications as therapeutic targets and diagnostic biomarkers. Virtual screening identified repurposed drugs, known nutraceuticals, for specific interventions. These phylogenetic observations reveal the ancestry and computational studies reveal the emergency measures to interject this emerging pathogen that pose threat to whole of mankind.
HYPOTHESIS | doi:10.20944/preprints202310.2100.v1
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Alzheimer’s disease; Angiotensin II; Angiotensin-converting enzyme 2; COVID-19; Brain; Dementia; Furin; Neurological disorders; SARS-CoV-2; Spike protein.
Online: 31 October 2023 (14:53:01 CET)
Neurological disorders have been reported to occur in a large number of coronavirus disease 2019 (COVID-19) patients, suggesting that this disease may also exert long-term adverse neurological consequences. COVID-19 occurs due to the infection by a positive-sense single-stranded RNA virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The membrane fusion protein of SARS-CoV-2, the spike protein, binds to its human host receptor, angiotensin-converting enzyme 2 (ACE2), to initiate membrane fusion between the virus and host cell. The spike protein of SARS-CoV-2 contains the furin protease recognition site and its cleavage enhances the infectivity of this virus. The binding of SARS-CoV-2 to the ACE2 receptor has been shown to downregulate ACE2, thereby increasing the levels of pathogenic angiotensin II (Ang II). The furin protease cleaves between S1 subunit of the spike protein with the binding domain toward ACE2 and S2 subunit with transmembrane domain that anchors to the viral membrane, and this activity releases the S1 subunit into the blood circulation. The released S1 subunit of the spike protein would also bind to and downregulate ACE2, in turn, increasing the level of Ang II. Considering that a viral particle contains a number of the spike protein molecules, furin-dependent cleavage would release a large number of free S1 proteins each of which can downregulate ACE2, while the infection with a viral particle only affects one ACE2 molecule. Therefore, the furin-dependent release of S1 protein would dramatically amplify the ability to downregulate ACE2 and produce Ang II. We hypothesize that this amplification mechanism that the virus possesses, but not the infection per se, is the major driving force behind the neurological disorders.
ARTICLE | doi:10.20944/preprints201806.0114.v1
Subject: Computer Science And Mathematics, Applied Mathematics Keywords: computational neuroscience; spike train statistics; maximum entropy principle; large deviation theory; out-of-equilibrium statistical mechanics; thermodynamic formalism; entropy production
Online: 7 June 2018 (11:06:22 CEST)
We consider the maximum entropy Markov chain inference approach to characterize the collective statistics of neuronal spike trains, focusing on the statistical properties of the inferred model. We review large deviations techniques useful in this context to describe properties of accuracy and convergence in terms of sampling size. We use these results to study the statistical fluctuation of correlations, distinguishability and irreversibility of maximum entropy Markov chains. We illustrate these applications using simple examples where the large deviation rate function is explicitly obtained for maximum entropy models of relevance in this field.
ARTICLE | doi:10.20944/preprints202103.0055.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Fractional complex moment; SARS-CoV-2; coronaviruses; spike protein sequence; Pearson correlation coefficient; semi-covariance coefficient; positive-correlative and negative-correlative domains
Online: 2 March 2021 (09:30:12 CET)
Complex modeling has received significant attention in recent years and is increasingly used to explain the statistical phenomenon with increasing and decreasing fluctuations such as the similarity or difference of spike protein charge patterns of coronaviruses. Different from the existing covariance or correlation coefficient methods in traditional integer dimension construction, this study proposes a simplified novel fractional dimension derivation with the exact Excel tool algorithm. It involves the fractional center moment extension to covariance, which ends up a complex covariance coefficient that is better than the Pearson correlation coefficient, in the sense that the nonlinearity relationship can be further depicted. The spike protein sequences of coronaviruses were obtained from the GenBank and GISAID database, including the coronaviruses from pangolin, bat, canine, swine (three variants), feline, tiger, SARS-CoV-1, MERS, and SARS-CoV-2 (including the strains of Wuhan, Beijing, New York, German, and UK variant B.1.1.7) were used as the representative examples in this study. By examining the values above and below the average/mean based on the positive and negative charge patterns of the amino acid residues of the spike proteins from coronaviruses, the proposed algorithm provides deep insights into the nonlinear evolving trends of spike proteins for understanding the viral evolution and identifying the protein characteristics associated with viral fatality. The calculation results demonstrate that the complex covariance coefficient analyzed by this algorithm is capable of distinguishing the subtle nonlinear differences in the spike protein charge patterns with reference to Wuhan strain SARS-CoV-2 for which the Pearson correlation coefficient may overlook. Our analysis reveals the unique convergent (positive correlative) to divergent (negative correlative) domain center positions of each virus. The convergent or conserved region may be critical to the viral stability or viability; while the divergent region is highly variable between coronaviruses suggesting high frequency of mutations in this region. The analyses show that the conserved center region of SARS-CoV-1 spike protein is located at amino acid residues 900, but shifted to the amino acid residues 700 in MERS spike protein, and then to amino acid residues 600 in SARS-COV-2 spike protein, indicating the evolvement of the coronaviruses. Interestingly, the conserved center region of the spike protein in SARS-COV-2 variant B.1.1.7 shifted back to amino acid residues 700, suggesting this variant is more virulent than the original SARS-COV-2 strain. Another important characteristic our study reveals is that the distance between the divergent mean and the maximal divergent point in each of the viruses (MERS>SARS-CoV-1>SARS-CoV-2) is proportional to viral fatality rate. This algorithm may help to understand and analyze the evolving trends and critical characteristics of SARS-COV-2 variants, other coronaviral proteins and viruses.
REVIEW | doi:10.20944/preprints202307.1198.v1
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: myocarditis; sudden death; chest pain; autopsy; necropsy; COVID-19; COVID-19 vaccines; mRNA; SARS-CoV-2 vaccination; death; excess mortality; spike protein; organ system
Online: 18 July 2023 (09:34:51 CEST)
Background: COVID-19 vaccines have been linked to myocarditis which in some circumstances can be fatal. This systematic review aims to investigate potential causal links between COVID-19 vaccines and death from myocarditis using post-mortem analysis. Methods: We performed a systematic review of all published autopsy reports involving COVID-19 vaccination-related myocarditis through July 3rd, 2023. All autopsy studies that include COVID-19 vaccine-induced myocarditis as a possible cause of death were included, without imposing any additional restrictions. Causality in each case was determined by three independent reviewers with cardiac pathology experience and expertise. Results: We initially identified 1,691 studies and, after screening for our inclusion criteria, included 14 papers that contained 28 autopsy cases. The cardiovascular system was the only organ system affected in 26 cases. In 2 cases, myocarditis was characterized as a consequence from multisystem inflammatory syndrome (MIS). The mean and median number of days from last COVID-19 vaccination until death was 6.2 and 3 days, respectively. Most of the deaths occurred within a week from the last injection. We established that all 28 deaths were causally linked to COVID-19 vaccination by independent adjudication. Conclusions: The temporal relationship, internal and external consistency seen among cases in this review with known COVID-19 vaccine-induced myocarditis, its pathobiological mechanisms and related excess death, complemented with autopsy confirmation, independent adjudication, and application of the Bradford Hill criteria to the overall epidemiology of vaccine myocarditis, suggests there is a high likelihood of a causal link between COVID-19 vaccines and death from suspected myocarditis in cases where sudden, unexpected death has occurred in a vaccinated person. Urgent investigation is required for the purpose of risk stratification and mitigation in order to reduce the population occurrence of fatal COVID-19 vaccine-induced myocarditis.
ARTICLE | doi:10.20944/preprints202203.0411.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: COVID-19; SARS-CoV-2; Vaccines; anti-SARS-CoV-2 spike total antibodies; Surrogate viral neutralizing antibody; T-cell immune response; CoronaVac; ChAdOx1; BNT162b2; booster
Online: 31 March 2022 (14:28:11 CEST)
Inactivated SARS-CoV-2 vaccine (CoronaVac) is commonly used in national immunization programs. However, the immune response significantly declined within a few months. Our study assessed the immune response against SARS-CoV-2 after receiving booster shots of BNT162b2 or ChAdOx1 among health care workers who previously received CoronaVac as their primary immunization. Fifty-six participants received ChAdOx1 and forty-two participants received BNT162b2 were enrolled into this study which evaluated the immune responses including anti-SARS-CoV-2 spike total antibodies (Elecsys®), surrogated viral neutralization test (sVNT) to ancestral strain (cPass™; GenScript) and five variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) (Luminex; multiplex sVNT) and the ELISpot with spike (S1 and S2) peptide pool against the ancestral SARS-CoV-2 strain. The samples were analyzed at baseline, 4, and 12 weeks after primary immunization as well as 4 and 12 weeks after receiving the booster. This study showed a significantly higher B-cell response among the BNT162b2 than the ChAdOx1 booster group, particularly against the Omicron variant, as well as a trend of good T-cell immune response in the BNT162b2 group. Moreover, the immune response rapidly declined at 12 weeks after the booster. A fourth dose or a second booster should be recommended, especially for reducing Omicron severity.
REVIEW | doi:10.20944/preprints202306.0329.v1
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: SARS-CoV-2 vaccine side effect; vaccines and Heart rhythm disorders; Spike Protein and cardiac arrhythmias; ACE system and heart conduction; Angiotensin II and cardiac arrhythmias
Online: 5 June 2023 (13:40:58 CEST)
-529391451442Citation: To be added by editorial staff during production. Academic Editor: Firstname Lastname Received: date Revised: date Accepted: date Published: date Copyright: © 2023 by the authors. Submitted for possible open access publication under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).0Citation: To be added by editorial staff during production. Academic Editor: Firstname Lastname Received: date Revised: date Accepted: date Published: date Copyright: © 2023 by the authors. Submitted for possible open access publication under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).Abstract: SARS-CoV-2 vaccination offered the opportunity to get out of the pandemic and thereby worldwide health, social, and economic disasters. However, in addition to efficacy, safety is an important issue for any vaccine. The mRNA-based vaccine platform is considered to be safe but side effects are being reported more frequently as more and more people around the world become treated. Myo-pericarditis is the major, but not the only cardiovascular complication of this vaccine, hence it is important not to underestimate other side effects. We report a case series of patients affected by cardiac arrhythmias post mRNA vaccine from our clinical practice and the literature. Reviewing the official vigilance database emerged that heart rhythm disorders after Covid vaccination are not uncommon and deserve more clinical and scientific attention. Since Covid vaccine is the only vaccination to have been related to this side effect questions arose about whether these vaccines could affect heart conduction. Although the risk-benefit is clearly in favor of vaccination heart rhythm disorders are not a negligible issue and there are red flags in the literature about the risk of post-vaccination malignant arrhythmias in some predisposed patients. In light of these findings, we investigated the potential mechanism for the Covid vaccine to impact on cardiac electrophysiology and cause heart rhythm disorders.
COMMUNICATION | doi:10.20944/preprints202106.0091.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2 variant; lateral flow immunoassay; spike protein; receptor binding domain (RBD); neutralizing antibody; therapeutic antibody cocktail; epitope binning; rapid neutralization test; ACE2
Online: 2 June 2021 (16:11:29 CEST)
Identifying anti-spike antibodies that exhibit strong neutralizing activity against current dominant circulating variants and antibodies that are escaped by these variants have important implications in the development of therapeutic and diagnostic solutions as well as in improving understanding of the humoral response to SARS-CoV-2 infection. We characterized seven anti-RBD monoclonal antibodies for their binding activity, pairing capability and neutralization activity to SARS-CoV-2 and three variant RBDs (UK, SA and BR P.1) via lateral flow immunoassays. The results allowed us to group these antibodies into three distinct epitope bins. Our studies showed that two antibodies had broadly potent neutralizing activity against SARS-CoV-2 and these variant RBDs and that one antibody did not neutralize the SA and BR P.1 RBDs. The antibody escaped by the SA and BR P.1 RBDs retained binding activity to SA and BR P.1 RBDs but was unable to induce neutralization. Further, we demonstrated that the lateral flow immunoassay can be a rapid and effective tool for antibody characterization, including epitope classification and antibody neutralization kinetics. From these studies, the potential contributions of the mutations (N501Y, E484K and K417N/T) contained in these variants’ RBDs on antibody pairing capability, neutralization activity and therapeutic antibody targeting strategy are discussed.
ARTICLE | doi:10.20944/preprints202109.0415.v2
Subject: Biology And Life Sciences, Virology Keywords: Delta variant; Variants of concern; Variants of interest; SARS-CoV-2; Spike protein; Nested RT-PCR; Sanger sequencing; Amino acid mutations; ACE2 RBD; N-terminal domain (NTD)
Online: 2 November 2021 (10:40:46 CET)
As SARS-CoV-2 continues to spread among human populations, genetic changes occur and accumulate in the circulating virus. Some of these genetic changes have caused amino acid mutations, including deletions, which may have potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics. Considerable efforts have been made to categorize the amino acid mutations of the angiotensin-converting enzyme 2 (ACE2) receptor binding domain (RBD) of the spike (S) protein along with certain mutations in other regions within the S protein as specific variants in an attempt to study the relationship between these mutations and the biological behavior of the virus. However, the currently used whole genome sequencing surveillance technologies can test only a small fraction of the positive specimens with high viral loads and often generate uncertainties in nucleic acid sequencing that needs additional verification for precision determination of mutations. This article introduces a generic protocol to routinely sequence a 437-bp nested RT-PCR cDNA amplicon of the ACE2 RBD and a 490-bp nested RT-PCR cDNA amplicon of the N-terminal domain (NTD) of the S gene for detection of the amino acid mutations needed for accurate determination of all variants of concern and variants of interest according to the definitions published by the U.S. Centers for Disease Control and Prevention. This protocol was able to amplify both nucleic acid targets into cDNA amplicons to be used as templates for Sanger sequencing on all 16 clinical specimens that were positive for SARS-CoV-2.