Subject: Life Sciences, Biochemistry Keywords: SARS-CoV2; Biomathematics; vaccine; variants; mRNA; Fibonacci; Indian variants; B.1.617; B.1.617.2.
Online: 18 May 2021 (14:05:33 CEST)
ABSTRACT. In this paper, we run for all INDIA mutations and variants a biomathematical numerical method for analysing mRNA nucleotides sequences based on UA/CG Fibonacci numbers proportions (Perez, 2021). In this study, we limit ourselves to the analysis of whole genomes, all coming from the mutations and variants of SARS-CoV2 sequenced in India in 2020 and 2021. We then demonstrate - both on actual genomes of patients and on variants combining the most frequent mutations to the SARS-CoV2 Wuhan genomes and then to the B.1.617 variant - that the numerical Fibonacci AU / CG metastructures increase considerably in all cases analyzed in ratios of up to 8 times. We can affirm that this property contributes to a greater stability and lifespan of messenger RNAs, therefore, possibly also to a greater INFECTUOSITY of these variant genomes. Out of a total of 108 genomes analyzed: - None ("NONE") of them contained a number of metastructures LOWER than those of the reference SARS-CoV2 Wuhan genome. - Eleven (11) among them contained the same number of metastructures as the reference genome. - 97 of them contained a GREATER number of metastructures than the reference genome, ie 89.81% of cases. The average increase in the number of metastructures for the 97 cases studied is 4.35 times the number of SARS-CoV2 UA/CG 17711 Fibonacci metastructures. Finally, we put a focus on B.1.617.2 crucial exponential growth Indian variant. Then, we demonstrate, by analyzing the main worldwide 19 variants, both at the level of spikes and of whole genomes, how and why these UA / CG metastuctures increase overall in the variants compared to the 2 reference strains SARS-CoV2 Wuhan and D614G.
REVIEW | doi:10.20944/preprints202203.0376.v1
Subject: Life Sciences, Microbiology Keywords: SARS-CoV-2; Mutations; Omicron; Delta; Variants of Concern; Variants of Interest; Immunity Escape; Mechanisms
Online: 29 March 2022 (08:44:09 CEST)
With the emergence of COVID-19 pandemic in 2019, the world saw a humungous loss of human life and economic resources globally but also the rapid appearance of SARS-CoV-2 variants which have exhibited a higher transmissibility and/or virulence and which also evade immune system to such an extent that it raises a big question mark on the efficacy of current diagnostics, vaccines and convalescent plasma and mAb therapies. This has been attributed to the emergence of huge spectrum of mutations, especially in the virus’s spike (S) protein, occurring in regions harboring high concentration of B cell epitopes thus allowing neutralizing antibody escape. The mutations resulting in ACE 2 receptor recognition failure (T19R), unfavorable electrostatic interactions (E484K), structural change (∆69-70), disruption of hydrogen bonds, salt bridges or hydrophobic interactions (K417N, N501Y, ∆Y145) and change in orientation (N501Y) cause strong immune evasion by these variants. Further, the recent emergence of Omicron with more than 30 mutations in the S protein VOC allows it to escape and fail diagnosis as well as immune system and the protection generated by different vaccination regimes. Yet Omicron may not be the end of the story. This review presents an insight of the immunity escape and its mechanisms followed by different SARS-CoV-2 variant of concerns.
ARTICLE | doi:10.20944/preprints202105.0521.v1
Subject: Medicine & Pharmacology, Allergology Keywords: GH1, SOX3, TGIF1, HYPOPITUITARISM, ALLELIC VARIANTS
Online: 21 May 2021 (11:13:02 CEST)
We report four allelic variants (3 novel) in three genes previously established as causal for hypopituitarism or related disorders. A novel homozygous variant in the growth hormone gene, GH1 c.171delT (p. Phe 57Leufs * 43), was found in a male patient with severe isolated growth hormone deficiency (IGHD) born to consanguineous parents. A SOX3 allelic variant (p.Met304Ile) was found in a male patient with IGHD and hypoplastic anterior pituitary. YASARA, a tool to evaluate protein stability, suggests that p.Met304Ile destabilizes the SOX3 protein (ΔΔG = 2.49 kcal/mol). A rare, heterozygous missense variant in the TALE homeobox protein gene, TGIF1 (c.268C>T:p.Arg90Cys) was found in a patient with combined pituitary hormone deficiency (CPHD), diabetes insipidus, and syndromic features of holoprosencephaly (HPE). A novel heterozygous TGIF1 variant (c.82T>C:p.Ser28Pro) was identified in a patient with CPHD, pituitary aplasia and ectopic posterior lobe. Both TGIF1 variants have an autosomal dominant pattern of inheritance with incomplete penetrance. In conclusion, we have found allelic variants in 3 genes in hypopituitarism patients. We discuss these variants and associated patient phenotypes in relation to previously reported variants in these genes, expanding our knowledge of the phenotypic spectrum in patient populations.
ARTICLE | doi:10.20944/preprints202012.0671.v1
Subject: Medicine & Pharmacology, Allergology Keywords: HPV; E7; variants; molecular dynamics simulation
Online: 25 December 2020 (16:05:04 CET)
The oncogenic potential of high-risk HPVs is focused on producing the E6 and E7 oncoproteins responsible for disrupting the control of the cell cycle. Epidemiological studies propose the presence of the N29S and H51N variants of the HPV16 E7 protein as a significant association with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains unknown. Analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose for the first time a 3D structure of the E7 reference protein and two of its variants (N29S and H51N) and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.
ARTICLE | doi:10.20944/preprints202006.0184.v1
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.
ARTICLE | doi:10.20944/preprints202209.0241.v1
Online: 16 September 2022 (08:07:10 CEST)
SARS-CoV-2 is constantly evolving leading to new variants. We analysed data from 4,400 SARS-CoV-2-positive samples in order to continue variant surveillance in Italy to evaluate their epidemiological and relative impact on public health in the period April-December 2021. The main circulating strain (76.2%) was Delta followed by Alpha (13.3%), Omicron (5.3%) and Gamma variants (2.9%). B.1.1 lineages, Eta, Beta, Iota, Mu and Kappa variants represented around 1% of cases. Overall, 48.2% of subjects were not vaccinated with a lower median age compared to vaccinated subjects (47 vs. 61 years). An increasing number of infections in vaccinated subjects was observed overtime, with the highest proportion in November (85.2%). Variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed among Delta variant, while subjects harboring Gamma variant showed the highest proportion of asymptomatics (21.6%), albeit also of deaths (5.4%). The Omicron variant was only found in vac-cinated subjects, of which 47% were hospitalized. Diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at national and international level. Our study pro-vides data on the rapid changes in the epidemiological landscape of SARS-CoV-2 variants in Italy.
ARTICLE | doi:10.20944/preprints202108.0084.v1
Subject: Life Sciences, Biochemistry Keywords: Annotation; SNPs; Rare variants; Mendelian randomization; Algorithm
Online: 3 August 2021 (14:26:17 CEST)
Understanding the function of a locus is a challenge in molecular biology. Although numerous molecular data have been generated in the last decades, it remains difficult to grasp, how these data are related at a locus? In this study, we describe an analytical workflow that can solve this problem using the knowledge available at single-nucleotide polymorphisms (SNPs) level. The underlying algorithm uses SNPs as connectors to link omics data and identify correlation between them through a joint bioinformatical/statistical approach. We describe its application in finding the mechanism whereby a mutation causes a phenotype and in revealing the path whereby a gene is being regulated and impacts the phenotypes. We translated our workflow into freely available shell scripts that carry out the analyses. Our approach provides a basic framework to solve the information overload problem in biology.
ARTICLE | doi:10.20944/preprints202107.0654.v1
Online: 29 July 2021 (12:23:23 CEST)
The aim of this study was the reconstruction of SARS-CoV-2 evolutionary dynamics in time and space in Italy and Europe between February and June 2020. The cluster analysis showed that pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 entered Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, the reconstructed ancestral scenario suggests a central role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.
ARTICLE | doi:10.20944/preprints202104.0034.v5
Subject: Life Sciences, Biochemistry Keywords: SARS-CoV2; Biomathematics; vaccine; variants; mRNA; Fibonacci; numerical standing waves
Online: 20 April 2021 (10:05:55 CEST)
ABSTRACT. In this paper, we suggest a biomathematical numerical method for analysing mRNA nucleotides sequences based on UA/CG Fibonacci numbers proportions. This method is used to evaluate then compare the spike genes related to the main SARS-CoV2 VARIANTS currently circulating within the world population. The 10 main results proposed to be reproduced by peers are: 1/ SARS-CoV2 genome and spike evolution in one year 2020-2021. 2/ SARS-CoV2 Origins. 3/ Comparing 11 reference variants spikes. 4/ analysing 32 CAL.20C California variant patients spikes. 5/ Toward a meta mRNA Fibonacci gene end message code. 6/ Analysing S501 UK, S484 South Africa and « 2 mutations » INDIA variants. 7/ Suggesting a possible variants spike mRNA palindrome symmetry metastructure improving mRNA stability then infectiousness. 8/ Analysing Fibonacci Metastructures in the mRNA coding for the vaccines PFIZER and MODERNA. 9/ Does the CG-rich modification of the synonymous codons of the spikes of the 2 mRNA vaccines affect the expression and quantity of SARS-CoV2 antibodies? 10/ The exceptional case of the Brazilian variant P.1. Particularly, we suggest the following conjecture at mRNA folding level : CONJECTURE of SARS-CoV2 VARIANTS: The growth of long Fibonacci structures in the shape of "podiums" for almost all of the variants studied (UK, California, South Africa, India, etc.) suggests the probable folding of the Spike mRNA in the form of a "hairpin", which can strengthen the cohesion and the lifespan of this mRNA. Finally, we show that these kinds of Fibonacci matastructures disapear TOTALLY by analysing the published mRNA sequences of PFIZER and MODERNA vaccines. One fact is certain, the two mRNAs of the Moderna and Pfizer vaccines will result in a low functionality of the spike vaccine. This is because their designers by seeking greater stability, have doped to build CG rich sequences which, as soon as they are inserted into the human host, will, paradoxically, seek to mutate, like SARS-CoV2 variants, towards CG ==> UA forms in order to improve their STABILITY and LIFETIME. We conclude using new biomathematics theoretical methods (Master code and numerical standing waves), and comparing the Spikes of the two vaccines Moderna and Pfizer, that there will be very probable differences in stability and shelf life of the two respective mRNAs vaccines. However, “State of the Art” analyzes will disclose that their two protein sequences are strictly identical. By modified their synonymous codons using different strategies, no one can guarantee that the quantity of antibodies generated will be identical in the two cases. We wish to draw attention to the great ADAPTATION power - at the global scale of their genomes - of the most infectious VARIANTS, such as the BRAZIL 20J / 501Y.V3 variant (P.1). This is very worrying for the VACCINES <==> VARIANTS run: We demonstrate how the Brazilian variant P.1 which becomes uncontrollable in Brazil in April 2021 has a level of organization of long metastructures of 17,711 bases covering the genome which is 3.6 more important than that of the 2 reference genomes SARS-CoV2 and worldwide D614G. We suggest that this high level of overall structure of this variant contributes to the stability of this genome and, might explain its greater contagiousness.
ARTICLE | doi:10.20944/preprints202103.0400.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Lipid metabolism; NAFLD; genetic variants; PSRC1; HCC
Online: 15 March 2021 (16:30:15 CET)
Background and Aims: Dyslipidemia and cardiovascular diseases (CAD) are comorbidities of nonalcoholic fatty liver disease (NAFLD), which ranges from steatosis to hepatocellular carcinoma (HCC). The rs599839 A>G variant, in the CELSR2-PSRC1-SORT1 cluster, has been associated CAD, but its impact on metabolic traits and liver damage in NAFLD has not been investigated yet. Methods: We evaluated the effect of the rs599839 variant in 1426 NAFLD patients (Overall cohort) of whom 131 have HCC (NAFLD-HCC), in 500,000 individuals from the UK Biobank Cohort (UKBBC) and in 366 HCC samples from The Cancer Genome Atlas (TCGA). Hepatic PSRC1, SORT1 and CELSR2 expressions were evaluated by RNAseq (n=125). Results: The rs599839 variant was associated with reduced circulating LDL, carotid intima-media thickness, carotid plaques and hypertension (p<0.05) in NAFLD patients and with protection against dyslipidemia in UKBBC. The G allele was associated with higher risk of HCC and advanced tumor stage (p<0.05) in the Overall cohort. Hepatic PSRC1, SORT1 and CELSR2 expressions were increased in NAFLD patients carrying the rs599839 variant (p<0.0001). SORT1 mRNA levels negatively correlated with circulating lipids and with those of genes involved in lipoprotein turnover (p<0.0001). Conversely, PSRC1 expression was positively related to that of genes implicated in cell proliferation (p<0.0001). In TCGA, PSRC1 over-expression promoted more aggressive HCC development (p<0.05). Conclusions: In sum, the rs599839 A>G variant improves dyslipidemia thus protecting against CAD in NAFLD patients, but as one it might promote HCC development by modulating SORT1 and PSRC1 expressions which impact on lipid metabolism and cell proliferation, respectively
ARTICLE | doi:10.20944/preprints202005.0343.v1
Subject: Life Sciences, Other Keywords: GALAXY; Assembly; Annotation; Genomic Variants Discovery; Workflow
Online: 21 May 2020 (09:57:42 CEST)
Citizen Science has come up to perform analytics over the SARS-CoV-2 genome. Public GALAXY servers provide an automated platform for genomics analysis. Study includes design of GALAXY workflows for RNASEQ assembly and annotation as well as genomic variant discovery and perform analysis across four samples of SARS-CoV-2 infected humans obtained from the local population of Wuhan, China. It provides information about transcriptomics and genomic variants across the SARS-CoV-2 genome. Study can be extended to perform evolutionary and comparative study across each species of coronaviruses. Augmented and integrated study with cheminformatics and immunoinformatics will be a way forward for drug discovery and vaccine development.
ARTICLE | doi:10.20944/preprints202207.0174.v1
Subject: Life Sciences, Immunology Keywords: COVID-19; vaccine; booster; variants of concern; neutralization
Online: 12 July 2022 (07:43:56 CEST)
We determined the levels of neutralizing antibodies against the SARS-CoV-2 ancestral strain, Delta and Omicron variants of concern (VOCs) in 125 healthcare workers, who received Coro-naVac as their primary vaccination and later received either a single ChAdOx1 or a combination of two consecutive boosters using either two ChAdOx1 doses or a ChAdOx1 or BNT162b2 as the primary and second boosters, respectively, or 2 doses of BNT162b2. The titers 12 weeks after primary vaccination were inadequate to neutralize the all strains. After a single ChAdOx1 boost-er, the levels of neutralization at Day 30 varied significantly, only a small proportion of partici-pants developing neutralizing titers against Omicron at Day 7 and 30. The two doses of ChA-dOx1 as the booster induced lowest activity. A combination ChAdOx1 and BNT162b2 induced greater neutralization than by two doses of ChAdOx1. Two doses of BNT162b2 as the booster had the maximal activity against Omicron VOC.
ARTICLE | doi:10.20944/preprints202109.0101.v1
Subject: Life Sciences, Biophysics Keywords: E6; variants; MAGI-1; molecular dynamic simulation; docking
Online: 6 September 2021 (13:51:17 CEST)
Oncogenic protein E6 from Human Papilloma Virus 16 (HPV-16) mediates the degradation of Membrane-associated guanylate kinase with inverted domain structure-1 (MAGI-1), throughout the interaction of its protein binding motif (PBM) with the Discs-large homologous regions 1 (PDZ1) domain of MAG1-1. Generic variation in the E6 gene that translates to changes in the protein’s amino acidic sequence modifies the interaction of E6 with the cellular protein MAGI-1. MAGI-1 is a scaffolding protein found at tight junctions of epithelial cells, where it interacts with a variety of proteins regulating signaling pathways. MAGI-1 is a multidomain protein containing two WW (rsp-domain-9), one guanylate kinase-like, and six PDZ domains. PDZ domains played an important role in the function of MAGI-1 and served as targets for several viral proteins including the HPV-16 E6. The aim of this work was to evaluate, with an in silico approach, employing molecular dynamics simulation and protein-protein docking, the interaction of the intragenic variants E-G350 (L83V), E-C188/G350 (E29Q/L83V), E-A176/G350 (D25N/L83V), E6-AAa (Q14H/H78Y/83V) y E6-AAc (Q14H/I27RH78Y/L83V) and E6-reference of HPV-16 with MAGI-1. We found that variants E-G350, E-C188/G350, E-A176/G350, AAa and AAc increase their affinity to our two models of MAGI-1 compared to E6-reference.
ARTICLE | doi:10.20944/preprints202104.0216.v1
Subject: Life Sciences, Biochemistry Keywords: SARS-CoV-2; variants; co-circulation; dominance; vaccines
Online: 7 April 2021 (17:24:38 CEST)
Some emergent SARS-CoV-2 variants raise concerns due to their altered biological properties. For both B.1.1.7 and B.1351 variants, named as variants of concern (VOC), increased transmissibility was reported, whereas B.1.351 was more resistant to multiple monoclonal antibodies (mAbs), as well as convalescent and vaccination sera. To test this hypothesis, we examined the proportion of VOC over time across different geographic areas where the two VOC, B.1.1.7 and B.1.351, co-circulate. Our comparative analysis was based on the number of SARS-CoV-2 sequences on GISAID database. We report that B.1.1.7 dominates over B.1.351 in geographic areas where both variants co-circulate and the B.1.1.7 was the first variant introduced in the population. The only areas where B.1.351 was detected at higher proportion were South Africa and Mayotte in Africa, where this strain was associated with increased community transmission before the detection of B.1.1.7. The dominance of B.1.1.7 over B.1.351 could be important since B.1.351 was more resistant to certain mAbs, as well as heterologous convalescent and vaccination sera, thus suggesting that it may be transmitted more effectively in people with pre-existing immunity to other VOC. This scenario would lessen the effectiveness of vaccine and urge the need to update them with new strains.
REVIEW | doi:10.20944/preprints202209.0479.v1
Subject: Biology, Other Keywords: Posttranscriptional Modification; Alternative Splicing; Congenital Heart Defects; Transcriptome; Splicing Variants
Online: 30 September 2022 (08:23:54 CEST)
Advancements in genomics, bioinformatics and genome editing have uncovered new dimensions in gene regulation. Post-transcriptional modifications by the alternative splicing of mRNA transcripts are critical regulatory mechanisms of mammalian gene expression. In the heart, there is an expanding interest in elucidating the role of alternative splicing in transcriptome regulation. Substantial efforts have been directed towards investigating this process in heart development and failure. However, few studies have shed light on alternative splicing products and their dysregulation in congenital heart defects (CHDs). While elegant reports have shown the crucial roles of RNA binding proteins (RBPs) in orchestrating splicing transitions during heart development and failure, the impact of RBPs dysregulation or genetic variation on CHDs has been fully addressed. Herein, we review the current understanding of alternative splicing and RBPs’ roles in heart development and CHDs and discuss the impacts of perinatal splicing transition and its dysregulation in CHDs. We further summarize discoveries made of causal splicing variants in key transcription factors that have been implicated in CHDs. Improved understanding of the roles of alternative splicing in heart development and CHDs may potentially inform novel preventive and therapeutic advancements for newborn infants with CHDs.
ARTICLE | doi:10.20944/preprints202205.0131.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; Variants of Concern; Delta Variant; genomic surveillance.
Online: 10 May 2022 (09:44:11 CEST)
In this study, we analyzed sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which completely replaced other previously circulating variants in the country due to its transmission advantage. Among Delta sublineages detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these sublineages only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described, and phylogenetic analyses and haplotype networks were used to track their spread across the country. Other frequently detected sublineages include AY.3, AY.62, AY.103, and AY.113. Over time, the principal sublineages showed different geographical distributions, with AY.20 predominant in Central Mexico, AY.26 in the North, and AY.100 in the Northwest and South/Southeast. This work describes the circulation, from May to November 2021, of the primary sublineages of the Delta variants associated to the third wave of the COVID-19 pandemic in Mexico and reinforces the importance of SARS-CoV-2 genomic surveillance for timely identification of emerging variants that may impact public health.
REVIEW | doi:10.20944/preprints202202.0261.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2 variants; transmissibility; viral load; sensitivity to antisera
Online: 22 February 2022 (02:59:33 CET)
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic still persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host’s immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) increase of Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with increase of RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment of Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
ARTICLE | doi:10.20944/preprints202111.0134.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: HPV16; E7 variants; cervical cancer; transformation; wound healing; western blotting
Online: 8 November 2021 (12:28:30 CET)
The human papillomavirus (HPV) type 16 E7 oncogene is critical to carcinogenesis and highly conserved. Previous studies identified a preponderance of non-synonymous E7 variants amongst HPV16-positive cancer-free controls compared to those with cervical cancer. To investigate the function of E7 variants, we constructed full-length HPV16 E7 genes and tested variants at positions H9R, D21N, N29S, E33K, T56I, D62N, S63F, S63P, T64M, E80K, D81N, P92L, and P92S (found only in controls); D14E, N29H (CIN2), and P6L, H51N, R77S (CIN3). We determined the steady-state level of cytoplasmic and nuclear HPV16 E7 protein. All variants from the controls showed a reduced level of steady-state E7 protein, with 7/13 variants having deficient protein levels. In contrast, 2/3 variants from the CIN3 precancer group had near-normal E7 levels. We assayed the activity of representative variants in stably transfected NIH3T3 cells. The H9R, E33K, P92L, and P92S variants found in control subjects had lower transforming activity than D14E and N29H variants (CIN2); and the R77S (CIN3) had activity only slightly reduced from wildtype E7. In addition, R77S and WT E7 caused increased migration of NIH3T3 cells in a wound-healing assay as compared with H9R, E33K, P92L, and P92S (controls) and D14E (CIN2). These data provide evidence that the E7 variants found in HPV16-positive cancer-free women are partially defective for transformation and cell migration further demonstrating the importance of fully active E7 in clinical cancer development.
ARTICLE | doi:10.20944/preprints202103.0180.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: convolutional neural networks; activation functions; biomedical classification; ensembles; MeLU variants
Online: 5 March 2021 (10:05:38 CET)
Recently, much attention has been devoted to finding highly efficient and powerful activation functions for CNN layers. Because activation functions inject different nonlinearities between layers that affect performance, varying them is one method for building robust ensembles of CNNs. The objective of this study is to examine the performance of CNN ensembles made with different activation functions, including six new ones presented here: 2D Mexican ReLU, TanELU, MeLU+GaLU, Symmetric MeLU, Symmetric GaLU, and Flexible MeLU. The highest performing ensemble was built with CNNs having different activation layers that randomly replaced the standard ReLU. A comprehensive evaluation of the proposed approach was conducted across fifteen biomedical data sets representing various classification tasks. The proposed method was tested on two basic CNN architectures: Vgg16 and ResNet50. Results demonstrate the superiority in performance of this approach. The MATLAB source code for this study will be available at https://github.com/LorisNanni.
REVIEW | doi:10.20944/preprints201902.0090.v1
Subject: Life Sciences, Genetics Keywords: BRCA1; variants of uncertain clinical significance; VUS; germline variants; hereditary breast and ovarian cancer; breast cancer; genetic testing, ovarian cancer; variant classification; clinical annotation
Online: 11 February 2019 (16:12:03 CET)
Genetic testing allows for identification of germline DNA variations which are associated with a significant increase in risk of developing breast and ovarian cancer. Detection of a BRCA1 or BRCA2 pathogenic variant triggers several clinical management actions, which may include increased surveillance and prophylactic surgery for healthy carriers or treatment with PARP inhibitor therapy for carriers diagnosed with cancer. Thus, standardized validated criteria for annotation of BRCA1 and BRCA2 variants according to their pathogenicity are necessary to support clinical decision making and ensure improved outcomes. Upon detection, variants whose pathogenicity can be inferred by the genetic code are typically classified as pathogenic, likely pathogenic, likely benign, or benign. Variants whose impact on function cannot be directly inferred by the genetic code are labeled as Variants of Uncertain Clinical Significance (VUS) and are evaluated by multifactorial likelihood models that use personal and family history of cancer, segregation data, prediction tools, and co-occurrence with a pathogenic BRCA variant. Missense variants, coding alterations that replace a single amino acid residue with another, are a class of variants for which determination of clinical relevance is particularly challenging. Here, we discuss current issues in variant classification by following a typical life cycle of a BRCA1 missense variant through detection, annotation and information dissemination. Advances in massively parallel sequencing have led to a substantial increase in VUS findings. Although comprehensive assessment and classification of missense variants according to their pathogenicity remains the bottle neck, new developments in functional analysis, high throughput assays, data sharing, and statistical models are rapidly changing this scenario.
ARTICLE | doi:10.20944/preprints202205.0247.v1
Subject: Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Variants of Concern; Rapid screening; Mutations
Online: 19 May 2022 (03:31:36 CEST)
Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody mediated neutralization and were des-ignated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the dissemination of VOIs and VOCs in Venezuela during a year. A 614 nt genomic fragment was sequenced for the detection of some relevant mutations of these variants. Their presence was confirmed by complete genome sequencing, with a correlation higher than 99% between both methodologies. After the previously reported introduction of the Gamma VOC since the beginning of the year 2021, the variants Alpha VOC and Lambda VOI were detected as early as March 2021, at a very low frequency. In contrast, the Mu VOI, detected in May 2021, was able to circulate throughout the country. After the detection of Delta VOC in June 2021, it be-came the predominant circulating variant. With the arrival of the Omicron VOC in December, this variant was able to displace the Delta one in less than one month. This succession of variants was accompanied by a reduction in the Cycle threshold (Ct) values, in agreement with the in-crease in transmissibility described for these variants.
ARTICLE | doi:10.20944/preprints202204.0298.v1
Subject: Life Sciences, Microbiology Keywords: genome; accessory; core genome; Fusarium circinatum; structural variants; inversions; indels; pangenome
Online: 29 April 2022 (10:47:31 CEST)
Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates FSP34 and KS17. Multi-sample variant calling identified a total of 461683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. Variant density was higher on sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets affected by high impact variants. A core genome representing genomic elements conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements are present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help inform novel disease management strategies against the pathogen.
ARTICLE | doi:10.20944/preprints201909.0045.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Prostate cancer, post-GWAS, functional variants, pathway analysis, upstream analysis, Oncomine
Online: 4 September 2019 (14:13:15 CEST)
Understanding the role of risk regions identified by genome-wide association studies (GWAS) have made considerable progress lately referred to the post-GWAS era. Annotation of the genes to the GWAS and fine-mapped functional variants, and understanding their biological pathway/gene networks enrichments is expected to give rich dividend by elucidating the mechanisms underlying prostate cancer. To this aim, we compiled and analysed currently available post-GWAS data on genes identified through GWAS and validated through experimental studies in prostate cancer to investigate molecular biological pathways enriched for assigned functional genes. The results highlight some well-known cancer signalling pathways, antigen presentation process and enrichment in cell growth and development gene networks suggesting prostate cancer may result from the accumulation of the effects of functional variants through multiple gene sets and pathways. The upstream analysis identifies critical transcription factors, which supplements the results regarding the regulatory role of the post-GWAS genes. We also identified the common genes between post-GWAS and three well-annotated prostate cancer Oncomine data in patient samples in order to uncover possible main genes in prostate cancer development/progression. Post-GWAS generated knowledge of gene networks and pathways, if analysed further and targeted appropriately, will have an important impact on clinical management of the disease.
ARTICLE | doi:10.20944/preprints201710.0179.v1
Subject: Mathematics & Computer Science, General & Theoretical Computer Science Keywords: finite automata; games; PQ penny flip game; game variants; winning sequences
Online: 30 October 2017 (04:29:12 CET)
The meticulous study of finite automata has produced many important and useful results. Automata are simple yet efficient finite state machines that can be utilized in a plethora of situations. It comes, therefore, as no surprise that they have been used in classic game theory in order to model players and their actions. Game theory has recently been influenced by ideas from the field of quantum computation. As a result, quantum versions of classic games have already been introduced and studied. The PQ penny flip game is a famous quantum game introduced by Meyer in 1999. In this paper we investigate all possible finite games that can be played between the two players Q and Picard of the original PQ game. For this purpose we establish a rigorous connection between finite automata and the PQ game along with all its possible variations. Starting from the automaton that corresponds to the original game, we construct more elaborate automata for certain extensions of the game, before finally presenting a semiautomaton that captures the intrinsic behavior of all possible variants of the PQ game. What this means is that from the semiautomaton in question, by setting appropriate initial and accepting states, one can construct deterministic automata able to capture every possible finite game that can be played between the two players Q and Picard. Moreover, we introduce the new concepts of a winning automaton and complete automaton for either player.
ARTICLE | doi:10.20944/preprints202109.0415.v2
Subject: 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.
ARTICLE | doi:10.20944/preprints202202.0164.v1
Subject: Life Sciences, Genetics Keywords: rare variants; genome-wide association study; validation test; SNP chip; genomic selection
Online: 11 February 2022 (15:59:26 CET)
The experiments described in this research article were designed to test the effect of rare variants into genomic prediction in dairy cattle. Common polymorphisms are able to explain only a small proportion of the underlying genetic variation of complex phenotypes. Variants representing functional mutations with large effects on complex phenotypes are expected to be rare due to natural (humans) or artificial (livestock) selection pressure. Therefore, it is important to check whether the use of rare variants could increase the accuracy of ranking of animals by providing the tool for more precise differentiation among the bulls with high additive genetic merit. The goal of our study was to verify whether including rare variants in a genomic selection model allows for a more accurate description of the additive genetic background of traits under selection in dairy cattle. We used the linear mixed model for comparison SNP estimates for Holstein-Friesian cattle of the two data sets – a set containing only single nucleotide polymorphisms defined by minor allele frequency ≥ 0.01, which is routinely used in the Polish genomic evaluation system (46,216 SNPs), and a set containing SNPs selected based only on the call rate (54,378 SNPs). Based on the SNP estimates we also calculated DGV and GEBV and compared them between both data sets. In all the analyses we used production, fertility, conformation and udder health traits. We also assessed the time required for the two most computationally demanding components of genomic selection: preparing genotype data, and estimation of SNP effects between those two data sets. The results of our study indicated that the analysis including rare variants resulted in changes in the individual ranking of the top 100 male and female candidates, but had no effect on the outcome of the quality of EBV prediction as expressed by the Interbull validation test.
ARTICLE | doi:10.20944/preprints202107.0020.v1
Subject: Biology, Anatomy & Morphology Keywords: IBV; infectious bronchitis; variants; whole-genome sequencing, enteric tropism; runting-stunting syndrome
Online: 1 July 2021 (11:25:48 CEST)
Abstract: Infectious bronchitis virus (IBV) induces respiratory and urogenital disease in chickens. Although IBV replicates in the gastrointestinal tract, enteric lesions are uncommon. We have reported a case of runting-stunting syndrome in commercial broilers from which an IBV variant was isolated from the intestines. The isolate, CalEnt, demonstrated an enteric tissue tropism in chicken embryos and SPF chickens experimentally. Here, we determined the full genome of CalEnt and compared it to other IBV strains, in addition to comparing the pathobiology of CalEnt and M41 in commercial broilers. Despite the high whole-genome identity to other IBV strains, CalEnt is rather unique in nucleotide composition. The S gene phylogenetic analyses showed great similarity between CalEnt and Cal 99. Clinically, vent staining was slightly more frequent in CalEnt-infected birds than those challenged with M41. Furthermore, IBV IHC detection was more evident and the viral shedding in feces was overall higher with the CalEnt challenge compared with M41. Despite underlying intestinal lesions caused by coccidiosis and salmonellosis vaccination, microscopic lesions in CalEnt-infected chickens were more severe than in M41-infected chickens or controls, supporting the enteric tropism of CalEnt. Further studies in SPF chickens are needed to determine the pathogenesis of the virus, its molecular mechanisms for the enteric tropism, and its influence in intestinal health.
Subject: Keywords: SARS-CoV-2; Sequence analysis; Comparative genomic variants; Alternating Series; Covid-19
Online: 7 April 2021 (12:59:50 CEST)
A signal analysis of the genoma sequenced of coronavirus variants: B.1.1.7, B.1.135, B.1.429-B.1.427, B.1.525 and P1 is presented. We deal with a certain type of finite alternating sum series having independently distributed terms associated with binary (0,1) indicators for the nucleotide bases A,C,G,T. This method provides additional information to conventional Similarity comparisons and Power Spectrum approaches. It leads to uncover distinctive patterns regarding the intrinsic data organization of genomic sequences according to its progression along the nucleotide bases position. Hence, the method could be useful for survelliance of genoma variants.
ARTICLE | doi:10.20944/preprints202102.0040.v1
Subject: Life Sciences, Biochemistry Keywords: APCDD1; HDAC5; germline variants; familial colorectal cancer; whole exome sequencing; promoter activity
Online: 1 February 2021 (14:04:24 CET)
Germline mutations in predisposition genes account for only 20% of all familial colorectal cancer (CRC) and the remaining genetic burden may be due to rare high-to-moderate-penetrance germline variants that are not explored. With the aim of identifying such potential cancer predisposing variants, we performed whole exome sequencing on three CRC cases and three unaffected members of a Polish family and identified two novel heterozygous variants; a coding variant in APC down-regulated 1 gene (APCDD1, p.R299H) and a non-coding variant in the 5’ untranslated region (UTR) of histone deacetylase 5 gene (HDAC5). Sanger sequencing confirmed the variants segregating with the disease and Taqman assays revealed 8 additional APCDD1 variants in a cohort of 1705 familial CRC patients and no further HDAC5 variants. Proliferation assays indicated an insignificant proliferative impact for the APCDD1 variant. Luciferase reporter assays using the HDAC5 variant resulted in an enhanced promoter activity. Targeting of transcription factor binding sites of SNAI-2 and TCF4 interrupted by HDAC5 variant showed a significant impact of TCF4 on promoter activity of mutated HDAC5. Our findings contribute not only to the identification of unrecognized genetic causes of familial CRC but also underline the importance of 5´UTR variants affecting transcriptional regulation and the pathogenesis of complex disorders.
ARTICLE | doi:10.20944/preprints202206.0410.v1
Subject: Medicine & Pharmacology, Gastroenterology Keywords: COVID-19 variants; COVID-19 vaccine; IBD; ulcerative colitis; Crohn’s disease; anti-TNF
Online: 29 June 2022 (15:02:36 CEST)
Management of inflammatory bowel disease (IBD) often relies on biological and immunomodulatory agents for remission through immunosuppression, raising concerns regarding the SARS-CoV-2 vaccine's effectiveness. The emergent variants have hindered the vaccine neutralization capacity, and whether the third vaccine dose has the capacity to neutralize SARS-CoV-2 variants in this population remains unknown. This study aims to evaluate the humoral response of SARS-CoV-2 variants in patients with IBD 60 days after the third vaccine dose [BNT162b2 (Pfizer-BioNTech) or mRNA-1273 (Moderna)].56 su bjects with IBD and 12 healthy subjects were recruited. 90% of patients with IBD (49/56) were receiving biologics and/or immunomodulatory therapy. 24 subjects with IBD did not develop effective neutralizing capability against the Omicron variant. 70% (17/24) of those subjects were receiving anti-Tumor Necrosis Factor therapy [10= adalimumab, 7= infliximab], two of them had a history of COVID-19 infection, and one subject did not develop immune neutralization against three other variants: Gamma, Epsilon, and Kappa. All subjects in the control group developed detectable antibodies and effective neutralization against all seven SARS-CoV-2 variants. Our study shows that patients with IBD might not be protected against SARS-CoV-2 variants, and larger studies are needed to evaluate optimal immunity.
REVIEW | doi:10.20944/preprints202207.0100.v1
Subject: Life Sciences, Virology Keywords: omicron; alpha; delta; deltacron; recombination; RNA editing; intra-host variants; tropisms; ox-idative damage; Wuhan
Online: 6 July 2022 (15:27:32 CEST)
The successive waves of the Covid-19 pandemic are driven by SARS-CoV-2 variants that reached critical detection levels in different parts of the world. But how evolved the Wuhan virus since its detection in December 2019 into the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) variants of concern? This is a story of mice and men, of up to 1,000,000 infected cells in one person, where each cell produces between 105 and 106 viral RNAs, of immune-compromised patients, the digestive tract and viral recombination.
REVIEW | doi:10.20944/preprints202106.0060.v1
Subject: Biology, Anatomy & Morphology 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.
ARTICLE | doi:10.20944/preprints202209.0310.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: COVID-19; CoviRx.org; database; drugs; pandemic; repurposing; SARS-CoV-2; therapies; treatments; Variants of Concern (VOC)
Online: 20 September 2022 (15:00:48 CEST)
SARS-CoV-2, is the cause of the COVID-19 pandemic which has claimed more than six million lives worldwide, devastating the economy and overwhelming healthcare systems globally. The development of new drug molecules and vaccines has played a critical role in managing the pandemic; however, new variants of concern still pose a significant threat as the current vaccines cannot prevent all infections. This situation calls for the collaboration of biomedical scientists and healthcare workers across the world. Repurposing approved drugs is an effective way of fast-tracking new treatments for recently emerged diseases. To this end, we have assembled and curated a database consisting of 7817 compounds from the Compounds Australia Open Drug collection. We developed a set of eight filters based on indicators of efficacy and safety that were applied sequentially to down-select drugs that showed promise for drug repurposing efforts against SARS-CoV-2. Considerable effort was made to evaluate approximately 14000 assay data points for SARS-CoV-2 FDA/TGA-approved drugs and provide an average activity score for 3539 compounds. The filtering process identified 12 FDA approved molecules with established safety profiles that have a plausible mechanism for treating COVID-19 disease. The methodology developed in our study provides a template for prioritising repurposable drug candidates that are safe, efficacious, and cost-effective for the treatment of COVID-19, long COVID, or any other future disease. We present our database in an easy-to-use interactive interface (CoviRx, https://www.covirx.org/) that was also developed to enable scientific community to access to the data of over 7000 potential drugs and to implement alternative prioritisation and down-selection strategies.
BRIEF REPORT | doi:10.20944/preprints202105.0526.v1
Subject: Life Sciences, Biochemistry 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.
ARTICLE | doi:10.20944/preprints202204.0072.v1
Subject: Life Sciences, Immunology Keywords: SARS-CoV-2; Variants; COVID-19 vaccine; Chimeric adenovirus-vectored vaccine; GS linker; Neutralizing activity; Th1 immune responses
Online: 8 April 2022 (05:03:04 CEST)
Several COVID-19 platforms have been licensed across the world thus far, but vaccine platforms research that can lead to effective antigen delivery is still ongoing. Here, we constructed AdCLD-CoV19 that could modulate humoral immunity by harboring SARS-CoV-2 antigens onto a chimeric adenovirus 5/35 platform that was effective in cellular immunity. By replacing the S1/S2 furin cleavage sequence of the SARS-CoV-2 Spike (S) protein mounted on AdCLD-CoV19 with the linker sequence, high antigen expression was confirmed in various cell lines. The high levels of antigen expression contributed to antigen-specific antibody activity in mice and non-human primates (NHPs) with single vaccination of AdCLD-CoV19. Furthermore, the adenovirus-induced Th1 immune response was specifically raised for the S protein, and these immune responses protected the NHP against live viruses. While AdCLD-CoV19 maintained neutralizing antibody activity against various SARS-CoV-2 variants, it was reduced to single vaccination for β and ο variants, and the reduced neutralizing antibody activity was restored with booster shots. Hence, AdCLD-CoV19 can prevent SARS-CoV-2 with single vaccination, and the new vaccine administration strategy that responds to various variants can maintain the efficacy of the vaccine.
BRIEF REPORT | doi:10.20944/preprints202004.0407.v2
Subject: Life Sciences, Microbiology Keywords: covid; covid-19; SARS-CoV-2; zoonosis; ethnic disparities; health care disparities; virus strains; virus subtypes; virus variants
Online: 26 April 2020 (05:13:37 CEST)
A striking aspect of COVID-19 is the difference in the outcome of the infection between different countries, and different ethnic groups within one country. We surveyed the literature on SARS-CoV-2 complemented with comparative publications on SARS-CoV and other coronaviruses to capture the current understanding of virus – host interactions including virus subtypes, transmission, zoonotic aspects, and potential host determinants.
ARTICLE | doi:10.20944/preprints201612.0137.v1
Subject: Social Sciences, Econometrics & Statistics Keywords: cross-sectional heteroskedasticity; model specification strategy; Sargan-Hansen (incremental) tests; variants of t-tests; weighting matrices; Windmeijer-correction
Online: 29 December 2016 (07:32:36 CET)
Studies employing Arellano-Bond and Blundell-Bond GMM estimation for single linear dynamic panel data models are growing exponentially in number. However, for researchers it is hard to make a reasoned choice between many different possible implementations of these estimators and associated tests. By simulation the effects are examined of many options regarding: (i) reducing, extending or modifying the set of instruments; (ii) specifying the weighting matrix in relation to the type of heteroskedasticity; (iii) using (robustified) 1-step or (corrected) 2-step variance estimators; (iv) employing 1-step or 2-step residuals in Sargan-Hansen overall or incremental overidentification restrictions tests. This is all done for models in which some regressors may be either strictly exogenous, predetermined or endogenous. Surprisingly, particular asymptotically optimal and relatively robust weighting matrices are found to be superior in finite samples to ostensibly more appropriate versions. Most of the variants of tests for overidentification restrictions show serious deficiencies. A recently developed modification of GMM is found to have great potential when the cross-sectional heteroskedasticity is pronounced and the time-series dimension of the sample not too small. Finally all techniques are employed to actual data and lead to some profound insights.
REVIEW | doi:10.20944/preprints202011.0013.v1
Subject: Life Sciences, Biochemistry Keywords: APOBEC; RNA virus replication; DNA virus replication; AID; HIV-1 Vif; genome hypermutation; MMTV Rem; G-to-A mutations; viral variants
Online: 2 November 2020 (10:06:10 CET)
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to selection for viral variants.
Subject: Medicine & Pharmacology, Clinical Neurology Keywords: Parkinson’s disease; precision medicine; personalized medicine; GBA; Glucocerebrosidase; GCase; LRRK2; Leucine-rich repeat kinase-2; Dopamine; PD drug trials; PD risk variants
Online: 14 September 2020 (00:22:59 CEST)
Parkinson’s disease (PD) is characterized by motor deficits and a wide variety of non-motor symptoms. The age of onset, rate of disease progression and the precise profile of motor and non-motor symptoms display considerable individual variation. Neuropathologically, the loss of substantia nigra dopaminergic neurons is a key feature of PD. The vast majority of PD patients exhibit alpha-synuclein aggregates in several brain regions, but there is also great variability in the neuropathology between individuals. While the dopamine replacement therapies can reduce motor symptoms, current therapies do not modify the disease progression. Numerous clinical trials using a wide variety of approaches have failed to achieve disease modification. It has been suggested that the heterogeneity of PD is a major contributing factor to the failure of disease modification trials, and that it is unlikely that a single treatment will be effective in all patients. Precision medicine, using drugs designed to target the pathophysiology in a manner that is specific to each individual with PD, has been suggested as a way forward. PD patients can be stratified according to whether they carry one of the risk variants associated with elevated PD risk. In this review we assess current clinical trials targeting two enzymes, leucine-rich repeat kinase 2 (LRRK2) and glucocerebrosidase (GBA), which are encoded by two most common PD risk genes. Because the details of the pathogenic processes coupled to the different LRRK2and GBA risk variants are not fully understood, we ask if these precision medicine-based intervention strategies will prove “precise“ or “personalized“ enough to modify the disease process in PD patients. We also consider at what phases of the disease that such strategies might be effective, in light of the genes being primarily associated with the risk of developing disease in the first place, and less clearly linked to the rate of disease progression. Finally, we critically evaluate the notion that therapies targeting LRRK2 and GBA might be relevant to a wider segment of PD patients, beyond those that actually carry risk variants of these genes.
ARTICLE | doi:10.20944/preprints201705.0196.v1
Subject: Mathematics & Computer Science, Applied Mathematics Keywords: Boiling Water Reactors; density wave oscillations; stability monitor; Shannon Entropy; noise-assisted Empirical Mode Decomposition variants; mode-mixing; Hilbert-Huang transform; instantaneous frequency
Online: 29 May 2017 (10:28:28 CEST)
There are currently around 78 Nuclear Power Plants (NPP) in the world based on Boiling Water Reactors (BWR). The current parameter to assess BWR instability issues is the linear Decay Ratio (DR). However, it is well known that BWRs are complex non-linear dynamical systems that may even exhibit chaotic dynamics that normally preclude the use of the DR when the BWR is working at a specific operating point during instability. In this work a novel methodology based on an adaptive Shannon Entropy estimator and on Noise Assisted Empirical Mode Decomposition variants is presented. This methodology was developed for real-time implementation of a stability monitor. This methodology was applied to a set of signals stemming from several NPPs reactors (Ringhals-Sweden, Forsmark-Sweden and Laguna Verde-Mexico) under commercial operating conditions, that experienced instabilities events, each one of a different nature
HYPOTHESIS | doi:10.20944/preprints202208.0398.v1
Subject: Life Sciences, Immunology Keywords: rotavirus; coronavirus; vaccine; SARS-CoV-2; COVID-19; cross immunity; trained immunity; vaccinated breakthrough infections; COVID variants; long-Covid; post-viral syndrome; chronic fatigue; booster
Online: 23 August 2022 (10:50:57 CEST)
This proposal was prepared in the very first weeks of 2020 because of the outbreak of COVID-19.There is good reason to suppose that rotavirus vaccine can be used as protection tool to effectively and safely fight and mitigate SARS-CoV-2 infection and the impact caused by COVID-19 in adult humans, due to the development of cross and trained immunity following rotavirus vaccination. Up-to-date, some rotavirus vaccines are available and approved, two of them have a large experience in results and safety. Little experience has been achieved in the use of rotavirus vaccine in adults. However, it can be expected that it would be safe and effective in adults and in the elderly as well. This proposal explains the background.
REVIEW | doi:10.20944/preprints202001.0353.v1
Subject: Life Sciences, Genetics Keywords: chromothripsis; structural variants; DNA-repair; DNA-repair disorders; DNA-double strand breaks (DSBs); ataxia telangiectasia mutated (ATM); ataxia-telangiectasia and Rad3-related (ATR); TP53; micronuclei; chromosome pulverization.
Online: 29 January 2020 (11:58:58 CET)
Chromothripsis is a mutational mechanism leading to complex and relatively clustered chromosomal rearrangements resulting in diverse phenotypic outcomes depending on the involved genomic landscapes. It may occur both in the germ and the somatic cells resulting in congenital and developmental disorders and cancer, respectively. Asymptomatic individuals may be carriers of chromotriptic rearrangements and experience recurrent reproductive failures when two or more chromosomes are involved. Several mechanisms are postulated to underly chromothripsis. The most attractive hypothesis involves chromosome pulverization in micronuclei followed by incorrect reassembly of fragments through DNA repair to explain the clustered nature of the observed complex rearrangements. Moreover, exogenous or endogenous DNA damage induction and dicentric bridge formation may be involved. Chromosome instability is commonly observed in the cells of patients with DNA-repair disorders, such as ataxia telangiectasia, Nijmegen breakage syndrome and Bloom syndrome. In addition, germline variations of TP53 have been associated with chromothripsis in Sonic-Hedgehog medulloblastoma and acute myeloid leukemia. In the present review, we focus on the underlying mechanisms of chromothripsis and the involvement of defective DNA-repair genes resulting in chromosome instability and chromothripsis-like rearrangements.
ARTICLE | doi:10.20944/preprints201812.0185.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: Fluorescence in situ hybridization (FISH), Karyotype, array comparative genomic hybridization (aCGH), amniotic fluid (AF), chorionic villus sampling (CVS), aneuploidies, pathogenic copy number variants (pCNV), confined placental mosaicism (CPM), true fetal mosaicism (TFM), pseudo-mosaicism.
Online: 17 December 2018 (09:58:43 CET)
Current prenatal genetic evaluation showed a significantly increase in non-invasive screening and the reduction of invasive diagnostic procedures. To evaluate the diagnostic efficacy on detecting common aneuploidies, structural chromosomal rearrangements and pathogenic copy number variants (pCNV), we performed a retrospective analysis on a case series initially analyzed by aneuvysion fluorescence in situ hybridization (FISH) and karyotyping then followed by array comparative genomic hybridization (aCGH). Of the 386 cases retrieved from the past decade, common aneuploidies were detected in 137 cases (35.5%), other chromosomal structural rearrangements were detected in four cases (1%), and pCNV were detected in five cases (1.3%). The relative frequencies for common aneuploidies suggested a under detection of sex chromosome aneuploidies. Approximately 9.5% of cases with common aneuploidies showed a mosaic pattern. Inconsistent results between FISH and karyotyping were noted in cases with pseudo-mosaicism introduced by culture artifact or variable cellular proliferation from cells with mosaic karyotypic complements under in vitro cell culture. Based on findings from this case series, cell-based FISH and karyotyping should be performed to detect common aneuploidies, structural chromosomal abnormalities, and mosaic pattern. DNA-based aCGH and reflex FISH should be performed to detect and confirm genomic imbalances and pCNV. Practice points to ensure the diagnostic accuracy and efficacy were summarized.