Search Results (14)

During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPath^TM COVID-19 CE-IVD RT-PCR Kit for large-scale routine diagnostic testing in Switzerland and the principality of Liechtenstein. The TaqPath Kit is a widely used multiplex assay targeting three genes (i.e., ORF1AB, N, S). With emergence of the B.1.1.7 (Alpha) variant, a diagnostic flaw became apparent as the amplification of the S-gene target was absent in these samples due to a deletion (ΔH69/V70) in the Alpha variant genome. This S-gene target failure (SGTF) was the earliest indication of a new variant emerging and was also observed in subsequent variants such as Omicron BA.1 and BA4/BA.5. The Delta variant and Omicron BA.2 did not present with SGTF. From September 2020 to November 2022, we investigated the applicability of the SGTF as a surrogate marker for emerging variants such as B.1.1.7, B.1.617.2 (Delta), and Omicron BA.1, BA.2, and BA.4/BA.5 in samples with cycle threshold (Ct) values < 30. Next to true SGTF-positive and SGTF-negative samples, there were also samples presenting with delayed-type S-gene amplification (higher Ct value for S-gene than ORF1ab gene). Among these, a difference of 3.8 Ct values between the S- and ORF1ab genes was found to best distinguish between “true” SGTF and the cycle threshold variability of the assay. Samples above the cutoff were subsequently termed partial SGTF (pSGTF). Variant confirmation was performed by whole-genome sequencing (Oxford Nanopore Technology, Oxford, UK) or mutation-specific PCR (TIB MOLBIOL). In total, 17,724 (7.4%) samples among 240,896 positives were variant-confirmed, resulting in an overall sensitivity and specificity of 93.2% [92.7%, 93.7%] and 99.3% [99.2%, 99.5%], respectively. Sensitivity was increased to 98.2% [97.9% to 98.4%] and specificity lowered to 98.9% [98.6% to 99.1%] when samples with pSGTF were included. Furthermore, weekly logistic growth rates (α) and sigmoid’s midpoint (t₀) were calculated based on SGTF data and did not significantly differ from calculations based on comprehensive data from GISAID. The SGTF therefore allowed for a valid real-time estimate for the introduction of all dominant variants in Switzerland and Liechtenstein. Full article

At the end of 2021, the SARS-CoV-2 Omicron variant of concern (VOC) displaced the previously dominant Delta VOC and enhanced diagnostic and therapeutic challenges worldwide. Respiratory specimens submitted to the Riga East University Hospital Laboratory Service by the central and regional hospitals of Latvia from January to March 2022 that were positive for SARS-CoV-2 RNA were tested by commercial multiplexed RT-qPCR targeting three of the Omicron VOC signature mutations: ΔH69/V70, E484A, and N501Y. Of the specimens tested and analyzed in parallel by whole-genome sequencing (WGS), 964 passed the internal quality criteria (genome coverage ≥90%, read depth ≥400×) and the Nextstrain’s quality threshold for “good”. We validated the detection accuracy of RT-qPCR for each target individually by using WGS as a control. The results were concordant with both approaches for 938 specimens, with the correct classification rate exceeding 96% for each target (CI 95%); however, the presumptive WHO label was misassigned for 21 specimens. The RT-qPCR genotyping provided an acceptable means to pre-monitor the prevalence of the two presumptive Omicron VOC sublineages, BA.1 and BA.2. Full article

The study presented in this paper follows the line of research created by the fact that by employing the monomiality principle, new outcomes are produced. This article deals with the inducement of ${\Delta }_h$ tangent-based Appell polynomials and derivation of certain of its characterizations such as explicit form, determinant form, monomiality principle, etc. These polynomials are designed to exhibit certain symmetries themselves or to capture and describe symmetrical patterns in mathematical structures. Further, certain members of ${\Delta }_h$ Appell polynomials such as ${\Delta }_h$ Bernoulli, Euler, and Genocchi polynomials are taken, and their corresponding results are obtained. Full article

This study follows the line of research that by employing the monomiality principle, new outcomes are produced. Thus, in line with prior facts, our aim is to introduce the ${\mathrm{\Delta }}_h$ multi-variate Hermite Appell polynomials ${}_{{\mathrm{\Delta }}_h}{}_{\mathfrak{H}}{\mathfrak{A}}_m^{\left[r\right]}(q_1,q_2,\cdots ,q_r;h)$. Further, we obtain their recurrence sort of relations by using difference operators. Furthermore, symmetric identities satisfied by these polynomials are established. The operational rules are helpful in demonstrating the novel characteristics of the polynomial families and thus operational principle satisfied by these polynomials is derived and will prove beneficial for future observations. Further, a few members of the ${\mathrm{\Delta }}_h$ Appell polynomial family are considered and their corresponding results are derived accordingly. Full article

The development of certain aspects of special polynomials in line with the monomiality principle, operational rules, and other properties and their aspects is obvious and indisputable. The study presented in this paper follows this line of research. By using the monomiality principle, new outcomes are produced, and their differential equation and series representation is obtained, which are important in several branches of mathematics and physics. Thus, in line with prior facts, our aim is to introduce the ${\Delta }_h$ hybrid special polynomials associated with Hermite polynomials denoted by ${}_{{\Delta }_{h}H}{Q}_m(u,v,w;h)$. Further, we obtain some well-known main properties and explicit forms satisfied by these polynomials. Full article

Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants of concern (VOC) because they have resulted in an increased number of cases, posing a strong risk to public health. Thus far, five VOCs have been designated, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), including their sublineages. Next-generation sequencing (NGS) can produce a significant amount of information facilitating the study of variants; however, NGS is time-consuming and costly and not efficient during outbreaks, when rapid identification of VOCs is urgently needed. In such periods, there is a need for fast and accurate methods, such as real-time reverse transcription PCR in combination with probes, which can be used for monitoring and screening of the population for these variants. Thus, we developed a molecular beacon-based real-time RT-PCR assay according to the principles of spectral genotyping. This assay employs five molecular beacons that target ORF1a:ΔS3675/G3676/F3677, S:ΔH69/V70, S:ΔE156/F157, S:ΔΝ211, S:ins214EPE, and S:ΔL242/A243/L244, deletions and an insertion found in SARS-CoV-2 VOCs. This assay targets deletions/insertions because they inherently provide higher discrimination capacity. Here, the design process of the molecular beacon-based real-time RT-PCR assay for detection and discrimination of SARS-CoV-2 is presented, and experimental testing using SARS-CoV-2 VOC samples from reference strains (cultured virus) and clinical patient samples (nasopharyngeal samples), which have been previously classified using NGS, were evaluated. Based on the results, it was shown that all molecular beacons can be used under the same real-time RT-PCR conditions, consequently improving the time and cost efficiency of the assay. Furthermore, this assay was able to confirm the genotype of each of the tested samples from various VOCs, thereby constituting an accurate and reliable method for VOC detection and discrimination. Overall, this assay is a valuable tool that can be used for screening and monitoring the population for VOCs or other emerging variants, contributing to limiting their spread and protecting public health. Full article

Non-B nucleic acids structures have arisen as key contributors to genetic variation in SARS-CoV-2. Herein, we investigated the presence of defining spike protein mutations falling within inverted repeats (IRs) for 18 SARS-CoV-2 variants, discussed the potential roles of G-quadruplexes (G4s) in SARS-CoV-2 biology, and identified potential pseudoknots within the SARS-CoV-2 genome. Surprisingly, there was a large variation in the number of defining spike protein mutations arising within IRs between variants and these were more likely to occur in the stem region of the predicted hairpin stem-loop secondary structure. Notably, mutations implicated in ACE2 binding and propagation (e.g., ΔH69/V70, N501Y, and D614G) were likely to occur within IRs, whilst mutations involved in antibody neutralization and reduced vaccine efficacy (e.g., T19R, ΔE156, ΔF157, R158G, and G446S) were rarely found within IRs. We also predicted that RNA pseudoknots could predominantly be found within, or next to, 29 mutations found in the SARS-CoV-2 spike protein. Finally, the Omicron variants BA.2, BA.4, BA.5, BA.2.12.1, and BA.2.75 appear to have lost two of the predicted G4-forming sequences found in other variants. These were found in nsp2 and the sequence complementary to the conserved stem-loop II-like motif (S2M) in the 3′ untranslated region (UTR). Taken together, non-B nucleic acids structures likely play an integral role in SARS-CoV-2 evolution and genetic diversity. Full article

As a biologically active peptide, L-carnosine has been widely used in the pharmaceutical, cosmetic and health care industries due to its various physiological properties. However, relatively little research is available regarding L-carnosine’s enzymatic synthesis function. In this study, a potential enzyme sequence with the function of carnosine synthesizing was screened out using the ancestral sequence reconstruction (ASR) technique. Identified with L-carnosine synthesis activity, this enzyme was further confirmed using autoproteolytic phenomenon via Western blot and N-terminal sequencing. After purification, the enzymatic properties of LUCA–DmpA were characterized. The melting temperature (T_m) and denaturation enthalpy (ΔH) of LUCA–DmpA were 60.27 ± 1.24 °C and 1306.00 ± 26.73 kJ·mol⁻¹, respectively. Circular dichroism (CD) spectroscopy results showed that this ancestral enzyme was composed of α-helix (35.23 ± 0.06%), β-sheet (11.06 ± 0.06%), β-turn (23.67 ± 0.06%) and random coil (32.03 ± 0.06%). The enzyme was characterized with the optimal temperature and pH of 45 °C and 9.0, respectively. Notably, LUCA–DmpA was also characterized with remarkable pH tolerance based on the observation of more than 85% remaining enzymatic activity after incubation at different pH buffers (pH = 6–11) for 12 h. Additionally, rather than being improved or inhibited by metal ions, its enzymatic activity was found to be promoted by introducing organic solvent with a larger log P value. Based on these homology modeling results, the screened LUCA–DmpA is suggested to have further optimization potential, and thereafter to be offered as a promising candidate for real industrial applications. Full article

For the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson–Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark set of duplexes used to generate the parameters were GC-rich in the shorter duplexes and AU-rich in the longer duplexes, and the length of the majority of the duplexes ranged between 6 and 8 bps. We were curious if other models would generate similar results and whether adding longer duplexes of 17 bps would affect the conclusions. We developed a gradient-descent fitting program for obtaining free-energy parameters—the changes in Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), and the melting temperature (Tm)—directly from the experimental melting curves. Using gradient descent and a genetic algorithm, the duplex melting results were combined with the standard benchmark data to obtain bp parameters. Both the standard (Turner) model and a new model that includes length-dependent terms were tested. Both models could fit the standard benchmark data; however, the new model could handle longer sequences better. We developed an updated strategy for fitting the duplex melting data. Full article

Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR screening assay. In this study, we evaluated one RT-PCR kit for this screening (ID SARS-CoV-2/UK/SA Variant Triplex^®, ID Solutions, Grabels, France) on 2207 nasopharyngeal samples that were positive for SARS-CoV-2. Using ID Solutions kit, 4.1% (92/2207) of samples were suspected to belonged to B.1.351 or P.1 variants. Next-generation sequencing that was performed on 67.4% (62/92) of these samples confirmed the presence of a B.1.351 variant in only 75.8% of the samples (47/62). Thirteen samples belonged to the UK variant (B.1.1.7), and two to A.27 with N501Y mutation. The thirteen with the UK variant presented one mutation in the S-gene, near the ΔH69/ΔV70 deletion (S71F or A67S), which impacted the detection of ΔH69/ΔV70 deletion. Using another screening kit (PKampVariantDetect SARS-CoV-2 RT-PCR combination 1 and 3^® PerkinElmer, Waltham, MA, USA) on the misidentified samples, we observed that the two mutations, S71F or A67S, did not impact the detection of the UK variant. In conclusion, this study highlights the limitations of the screening strategy based on the detection of few mutations/deletions as well as it not being able to follow the virus evolution. Full article

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island. Full article

Serine/threonine protein phosphatase-5 (PP5; PPP5C) is a member of the phosphoprotein phosphatase (PPP) gene family. The PPP catalytic domains feature a bimetal system (M₁/M₂), an associated bridge hydroxide (W¹(OH⁻)), an M₁-bound water/hydroxide (W²), and a highly conserved core sequence. The PPPs are presumed to share a common mechanism: The seryl/threonyl phosphoryl group of the phosphoprotein coordinates the metal ions, W¹(OH⁻) attacks the central phosphorous atom, rupturing the antipodal phosphoester bond and releasing the phosphate-free protein. Also, a histidine/aspartate tandem is responsible for protonating the exiting seryl/threonyl alkoxide. Here, we employed quantum-based computations on a large section of the PP5 catalytic site. A 33-residue, ONIOM(UB3LYP/6-31G(d):UPM7) model was built to perform computations using methylphosphate dianion as a stand-in substrate for phosphoserine/phosphothreonine. We present a concerted transition state (TS) in which W¹(OH⁻) attacks the phosphate center at the same time that the exiting seryl/threonyl alkoxide is protonated directly by the His³⁰⁴/Asp²⁷⁴ tandem, with W² assigned as a water molecule: W²(H₂O). Arg²⁷⁵, proximal to M₁, stabilizes the substrate and TS by binding both the ester oxygen (O^γ) and a phosphoryl oxygen (O¹) in a bidentate fashion; in the product state, Tyr⁴⁵¹ aids in decoupling Arg²⁷⁵ from O¹ of the product phosphate ion. The reaction is exothermic (ΔH = −2.0 kcal/mol), occurs in a single step, and has a low activation barrier (ΔH^‡ = +10.0 kcal/mol). Our work is an improvement over an earlier computational study that also found bond rupture and alkoxide protonation to be concerted, but concluded that Arg²⁷⁵ is deprotonated during the reactant and TS stages of the pathway. In that earlier study, the critical electron-withdrawal role that Arg²⁷⁵ plays during the hydroxide attack was not correctly accounted for. Full article

As a country that is poor in petroleum yet rich in coal, it is significant for China to develop direct coal liquefaction (DCL) technology to relieve the pressure from petroleum shortages to guarantee national energy security. To improve the efficiency of the direct coal liquefaction process, scientists and researchers have made great contributions to studying and developing highly efficient hydrogen donor (H-donor) solvents. Nevertheless, the details of hydrogen donation and the transfer pathways of H-donor solvents are still unclear. The present work examined hydrogen donation and transfer pathways using a model H-donor solvent, tetralin, by density functional theory (DFT) calculation. The reaction condition and state of the solvent (gas or liquid) were considered, and the specific elementary reaction routes for hydrogen donation and transfer were calculated. In the DCL process, the dominant hydrogen donation mechanism was the concerted mechanism. The sequence of tetralin donating hydrogen atoms was α-H (C₁–H) > δ-H (C₄–H) > β-H (C₂–H) > γ-H (C₃–H). Compared to methyl, it was relatively hard for benzyl to obtain the first hydrogen atom from tetralin, while it was relatively easy to obtain the second and third hydrogen atoms from tetralin. Comparatively, it was easier for coal radicals to capture hydrogen atoms from the H-donor solvent than to obtain hydrogen atoms from hydrogen gas. Full article

The Minimum Mutual Information (MinMI) Principle provides the least committed, maximum-joint-entropy (ME) inferential law that is compatible with prescribed marginal distributions and empirical cross constraints. Here, we estimate MI bounds (the MinMI values) generated by constraining sets T_cr comprehended by m_cr linear and/or nonlinear joint expectations, computed from samples of N iid outcomes. Marginals (and their entropy) are imposed by single morphisms of the original random variables. N-asymptotic formulas are given both for the distribution of cross expectation’s estimation errors, the MinMI estimation bias, its variance and distribution. A growing T_cr leads to an increasing MinMI, converging eventually to the total MI. Under N-sized samples, the MinMI increment relative to two encapsulated sets T_cr1 ⊂ T_cr2 (with numbers of constraints mcr1<mcr2 ) is the test-difference δH = H_{max 1, N} - H_{max 2, N} ≥ 0 between the two respective estimated MEs. Asymptotically, δH follows a Chi-Squared distribution ¹/_2NΧ2 (m_cr2-m_cr1) whose upper quantiles determine if constraints in T_cr2/T_cr1 explain significant extra MI. As an example, we have set marginals to being normally distributed (Gaussian) and have built a sequence of MI bounds, associated to successive non-linear correlations due to joint non-Gaussianity. Noting that in real-world situations available sample sizes can be rather low, the relationship between MinMI bias, probability density over-fitting and outliers is put in evidence for under-sampled data. Full article