ARTICLE | doi:10.20944/preprints202209.0318.v1
Subject: Life Sciences, Virology Keywords: BA.2.75 variant; Gibbs energy of binding; binding rate; infectivity; SARS-CoV-2
Online: 21 September 2022 (09:44:34 CEST)
Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermodynamic properties have changed comparing to earlier variants. In this paper Gibbs energy of binding and antigen-receptor binding rate is reported for the BA.2.75 variant. Gibbs energy of binding (driving force of binding) of Omicron BA.2.75 variant is more negative than that of the competing variants BA.2 and BA.5.
ARTICLE | doi:10.20944/preprints202206.0192.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: eCDC; WHO; Sanger sequencing; Omicron variant; minor subvariants; BA.4/BA.5; BA.2; mul-ti-allelic; SNPs; recombinant
Online: 14 June 2022 (04:30:41 CEST)
Large population passages of the SARS-CoV-2 in the past two and a half years have allowed the circulating virus to accumulate an increasing number of mutations in its genome. The most recently emerging Omicron subvariants have the highest number of mutations in the Spike (S) protein gene and these mutations mainly occur in the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the S gene. The eCDC and the WHO recommend partial Sanger sequencing of the SARS-CoV-2 S gene RBD and NTD on the PCR-positive samples in diagnostic laboratories as a practical means of determining the variants of concern to monitor a possible increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them. The author’s diagnostic laboratory has implemented the eCDC/WHO recommendation by sequencing a 398-base segment of the N gene for the definitive detection of SARS-CoV-2 in clinical samples, and sequencing a 445-base segment of the RBD and a 490-509-base segment of the NTD for variant determination. This paper presents 5 selective cases to illustrate the challenges of using Sanger sequencing to diagnose Omicron subvariant when the samples harbor a high level of co-existing minor subvariant sequences with multi-allelic single nucleotide polymorphisms (SNPs) or possible recombinant Omicron subvariants containing a BA.1 NTD and a BA.2 RBD, which can only be detected by using specially designed PCR primers. The current large-scale surveillance programs using next-generation sequencing (NGS) do not face similar problems because NGS focuses on deriving consensus sequence.
ARTICLE | doi:10.20944/preprints202204.0120.v1
Online: 13 April 2022 (08:31:45 CEST)
BA.2, a sublineage of Omicron BA.1, is now prominent in many parts of the world. Early reports indicate that BA.2 is more infectious than BA.1. To gain insight into BA.2 mutation profile and the resulting impact of mutations on interaction with receptor and/or monoclonal antibodies, we analyzed available se-quences, structures of Spike/receptor, and Spike/antibody complexes, and conducted molecular dynamics simulations. The results showed that BA.2 has 50 high-prevalent mutations compared to 48 in BA.1. Seventeen BA.1 mutations are not present in BA.2. Instead, BA.2 has 19 unique mutations and a signature Delta variant mutation (G142D). Intriguingly, the BA.2 has 28 signature mutations in Spike, compared to 30 in BA.1. This is due to two revertant mutations S446G and S496G in the receptor-binding domain (RBD), making BA.2 somewhat similar to Wuhan-Hu-1 (WT), which has G446 and G496. The molecular dynamics simulations showed that the RBD consisting of G446/G496 is more stable than S446/S496 containing RBD. Thus, our analyses suggest that BA.2 has evolved with novel mutations (i) to maintain receptor binding similar to WT, (ii) evade the antibody binding greater than BA.1, and (iii) acquire mutation of the Delta variant that may be associated with the high infectivity.
ARTICLE | doi:10.20944/preprints202207.0223.v1
Subject: Life Sciences, Virology Keywords: Monoclonal antibodies; Sotrovimab; COVID-19; Omicron; BA.2
Online: 14 July 2022 (12:22:21 CEST)
Coronavirus disease 19 (COVID-19) continues to spread worldwide as a severe pandemic. The Omicron BA.2 became the predominant variant and the protagonist of the ongoing surge. As the virus continues to mutate, using of approved drugs or developing new therapeutic or prophylactic therapies against COVID-19 could be more complex. Sotrovimab is a monoclonal antibody (mAb) targeting the conserved epitope on the spike protein receptor; the most recent studies observed that it has substantially decreased in vitro activity against the Omicron BA.2 subvariant, but real-life data are still scarce. We describe the outcome of a case series of outpatients with BA.1 or BA.2 infection treated with sotrovimab. We conducted a retrospective observational study including all non-hospitalized adult patients treated with sotrovimab, for which a Sanger sequencing of SARS-CoV-2 was performed within a regional genomic surveillance program. Eleven (50%) patients with BA.1 infection and eleven (50%) with BA.2 infection were considered. Most patients were immunocompromised. During the follow-up period, no patient died and only one with BA.1 infection was hospitalized for severe COVID-19 pneumonia onset. One month after treatment, 90.9% of patients were completely asymptomatic in each group. We demonstrated that patients carrying the BA.2 variant treated with sotrovimab did not evolve to severe COVID-19, showing a similar outcome to BA.1 infected patients. Further studies are needed to prove that vaccination or the presumably high doses of mAbs used can protect this group of patients at high risk of progression.
BRIEF REPORT | doi:10.20944/preprints202205.0018.v2
Online: 6 May 2022 (11:55:20 CEST)
The rapid emergence and worldwide detection of the SARS-CoV-2 omicron variant underscore the importance of robust genomic surveillance systems and prompt information sharing among global public health partners. The Omicron variant has rapidly replaced the delta variant as a dominating SARS-CoV-2 variant because of natural selection, favoring the variant with higher infectivity and more strong vaccine breakthrough ability. Also known as B.1.1.529, Omicron has four sub-variants, BA.1, BA.2, BA.3, and BA.4. Among them, BA.1 is the currently prevailing sub-variant, BA.2 is found to be able to alarmingly re-infect patients initially infected by omicron BA.1. BA.3 sub-variants is a combination of mutations of BA.1 and BA.2, especially in the spike protein. Today emerging is the BA.4, herein described and first detected in Italy, harboring a new mutation, specifically a deletion in the ORF 1 ab gene, corresponding to KSF141_del in non-structural protein 1 (nsp1), a critical virulence factor able to suppress host translation. The bioinformatics comparison analysis with the other three sub-variants pointed out that the deletion was not present previously and was never reported until now. Therefore, we can speculate that omicron BA.4; will become a new dominating “variant of concern” and might also break vaccine protection . On the other hand, we show that other proteins are mutated in the BA.4 in particular, seven mutations are recognized in the nucleocapsid (N) protein, the capability of five different types of rapid antigenic tests to recognize it.
ARTICLE | doi:10.20944/preprints202002.0038.v1
Subject: Life Sciences, Molecular Biology Keywords: allele specific expression; 6-BA; DNA methylation; long noncoding RNA; siRNA; poplar
Online: 4 February 2020 (05:22:28 CET)
The cytokinins play important roles in plant growth and development by regulating gene expression at genome wide level. DNA methylation is responsive to the external environment, but whether DNA methylation changes in response to cytokinin treatment to regulate gene expression is still unclear. Here, we used bisulfite sequencing and RNA sequencing to examine genome-wide DNA methylation and gene expression patterns in poplar (Populus tomentosa) after treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 566 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 501 protein-coding genes, 262 long non-coding RNAs, and 15,793 24-nt small interfering RNAs were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa. Combined DNA methylation and gene expression analysis demonstrated that DNA methylation plays an important role in regulating allele-specific gene expression. To further investigate the relationship between these 6-BA-responsive genes and phenotypic variation, we performed SNP analysis of 507 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa and identified 206 SNPs that were significantly associated with growth and wood properties. Association analysis indicated that 53% of loci with allele-specific expression had primarily dominant effects on poplar traits. Our comprehensive analyses of P. tomentosa DNA methylation and the regulation of allele-specific gene expression suggest that DNA methylation is an important regulator of imbalanced expression between allelic loci.
ARTICLE | doi:10.20944/preprints201905.0129.v1
Subject: Materials Science, Other Keywords: Alkaline copper quat (ACQ); Boric acid (BA); Micronized copper quat (MCQ); Nano boron (NB); Corrosion test
Online: 10 May 2019 (14:36:07 CEST)
In this study, the corrosion performances of ammonium copper quat (ACQ) and boric acid (BA) wood preservatives were investigated, with micronized copper quat (MCQ) and nano boron (NB) used as reference materials. In the study, Scots pine (Pinus sylvestris L.) wood samples were impregnated according to the full-cell process method with ACQ at 2.4% concentration, BA at 4% and MCQ and NB at 1%. The ACQ- and BA-impregnated samples were then impregnated for a second time using five different water-repellent materials: tall oil, linseed oil, sodium silicate, methyl hydrogen silicone and N'-N- (1, 8-Naphthalyl) hydroxylamine. Polyethylene glycol (PEG) 600 and aluminum sulfate were introduced as single impregnations in the form of homogeneous mixtures with the ACQ and BA. The corrosion properties of the impregnated and control samples, including metal weight loss (MWL) and corrosion depth, were examined. As a result, the MWL values of the ACQ-impregnated samples showed an increase compared to the control group. The MWL values of the MCQ-impregnated samples were lower than those of the samples impregnated with ACQ, whilst the MWL values of the BA-impregnated samples were higher than those of the samples impregnated with NB.
ARTICLE | doi:10.20944/preprints202209.0017.v1
Subject: Chemistry, Applied Chemistry Keywords: Bonding agents (BA); composite solid rocket propellants (CSRP); Reichardt’s ET(30) polarity scale; mechanical properties of CSRP.
Online: 1 September 2022 (09:25:21 CEST)
Bonding agents (BA) are key compounding ingredients for the correct formulation of composite solid rocket propellants (CSRP). In particular, the addition of BA is essential to achieve suitable mechanical properties of CSRP in terms of adequate tensile strength and elongation at break. It is shown that the polarity of each conventional BA as well as new potential BA can be measured through the Reichardt’s ET(30) polarity scale. Using this criteria it was possible to find a substitute for MAPO (tris-(methylaziridinyl)-phosphine oxide), a conventional BA with the drawback of high toxicity and high reactivity, with TTPT (tris-(pyrrolidine)-phosphine oxide), a completely safe and effective BA. In this work, many other potential BA were evaluated through the Reichardt’s ET(30) polarity scale but only a selection of the potential BA were effectively tested in a standard CSRP. Particular interesting was the evaluation of TTPT vs MAPO showing the ability of the former BA to match the mechanical properties of the latter BA.
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: photogrammetry; metrology; underwater 3D reconstruction; structure-from-motion; navigation fusion; multi-objective BA; laser scalers; Monte-Carlo simulation; uncertainty estimation; scale drift evaluation; laser spot detection
Online: 15 July 2019 (05:22:16 CEST)
Rapid developments in the field of underwater photogrammetry have given scientists1the ability to produce accurate 3-dimensional (3D) models which are now increasingly used in the representation and study of local areas of interest. This paper addresses the lack of systematic analysis of 3D reconstruction and navigation fusion strategies, as well as associated error evaluation of models produced at larger scales in GPS-denied environments using a monocular camera (often in deep-sea scenarios). Based on our prior work on automatic scale estimation of Structure from Motion (SfM)-based 3D models using laser scalers, an automatic scale accuracy framework is presented. The confidence level for each of the scale error estimates is independently assessed through the propagation of the uncertainties associated with image features and laser spot detections using a Monte Carlo simulation. The number of iterations used in the simulation was validated through the analysis of the final estimate behaviour. To facilitate the detection and uncertainty estimation of even greatly attenuated laser beams, an automatic laser spot detection method, mitigating the effects of scene texture, was developed, with the main novelty of estimating the uncertainties based on the recovered characteristic shapes of laser spots with radially decreasing1 intensities. The effects of four different reconstruction strategies resulting from the combinations of Incremental/GlobalSfM, and thea priori/a posterioriuse of navigation data were analyzed using two distinct survey scenarios captured during the SUBSAINTES 2017 cruise (doi: 10.17600/17001000). The study demonstrates that surveys with multiple overlaps of non-sequential images result in a nearly identical solution regardless of the strategy (SfM or navigation fusion), while surveys with weakly connected sequentially acquired images are prone to produce broad-scale deformation (doming effect) when navigation is not included in the optimization. Thus the scenarios with complex survey patterns substantially benefit from using multi-objective BA navigation fusion. In all cases, the errors in the models are inferior to 5%, with errors often being around 1%. The effects of combining data from multiple surveys were also evaluated. The introduction of additional vectors in the optimization of multi-survey problems successfully accounted for offset changes present in the underwater USBL-based navigation data and thus minimize the effect of contradicting navigation priors. Our results also illustrate the importance of collecting a multitude of evaluation data at different locations and moments during the survey.