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Deltas are densely populated industrialized regions, and home to important ports and navigation channels. Due to human interferences, the Yangtze Estuary has experienced a significant reduction in sediment load caused by the Three Gorges Dam (TGD), as well as adjustment to local morphodynamics by the Deep-water Navigation Channel (DNC). While the dramatic reduction in sediment triggers the increased channel erosion, the deposition flux of the DNC located at the estuary mouth has little change. To explore the physical mechanism of this phenomenon, a two-dimensional model is used to establish the relationship between sediment load and the sediment budget of channels based on the bathymetry in 2016. Model results show that the tidal reach and the inner estuary have a negative sediment budget. And the seasonal characteristics of water and sediment fluxes become less obvious downstream. Sensitivity analysis shows that the influence of upstream sediment load on deposition flux decreases along the channel, with a transition from deposition to erosion occurring in the tidal reach. For the last-level bifurcation, the annual siltation of sediment in the North Passage (NP) decreases by 4.5% with low sensitivity. This is attributed to the reduction of sediment load partially mitigated by riverbed erosion and cascade bifurcations. In addition, the lateral sediment supply, which accounts for 68% of the sediment input in the NP, is stable. Overall, this study strengthens the understanding of the relationship between sediment load and artificially deepened systems, thus allowing for better management of estuarine sediment and navigation channel. [ABSTRACT FROM AUTHOR]

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We aimed to evaluate the association between the humoral and cellular immune responses and symptomatic SARS‐CoV‐2 infection with Delta or Omicron BA.1 variants in fully vaccinated outpatients. Anti‐receptor binding domain (RBD) IgG levels and interferon‐gamma (IFN‐γ) release were evaluated at PCR‐diagnosis of SARS‐CoV‐2 in 636 samples from negative and positive patients during Delta and Omicron BA.1 periods. Median levels of anti‐RBD IgG in positive patients were significantly lower than in negative patients for both variants (p < 0.05). The frequency of Omicron BA.1 infection in patients with anti‐RBD IgG concentrations ≥1000 binding antibody units (BAU)/mL was 51.0% and decreased to 34.4% in patients with concentrations ≥3000 BAU/mL. For Delta infection, the frequency of infection was significantly lower when applying the same anti‐RBD IgG thresholds (13.3% and 5.3% respectively, p < 0.05). In addition, individuals in the hybrid immunity group had a 4.5 times lower risk of Delta infection compared to the homologous vaccination group (aOR = 0.22, 95% CI: [0.05−0.64]. No significant decrease in the risk of Omicron BA.1 infection was observed in the hybrid group compared to the homologous group, but the risk decreased within the hybrid group as anti‐RBD IgG titers increased (aOR = 0.08, 95% CI: [0.01−0.41], p = 0.008). IFN‐γ release post‐SARS‐CoV‐2 peptide stimulation was not different between samples from patients infected (either with Delta or Omicron BA.1 variant) or not (p > 0.05). Our results show that high circulating levels of anti‐RBD IgG and hybrid immunity were independently associated with a lower risk of symptomatic SARS‐CoV‐2 infection in outpatients with differences according to the infecting variant (www.clinicaltrials.gov; ID NCT05060939). [ABSTRACT FROM AUTHOR]

Background: Breakthrough infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are increasingly observed in vaccinated individuals. Immune responses towards SARS-CoV-2 variants, particularly Omicron-BA.5, are poorly understood. We investigated the humoral and cellular immune responses of hospitalized COVID-19 patients during Delta and Omicron infection waves. Methods: The corresponding SARS-CoV-2 variant of the respective patients were identified by whole genome sequencing. Humoral immune responses were analyzed by ELISA and a cell culture-based neutralization assay against SARSCoV-2 D614G isolate (wildtype), Alpha, Delta (AY.43) and Omicron (BA.1 and BA.5). Cellular immunity was evaluated with an IFN-g ELISpot assay. Results: On a cellular level, patients showed a minor IFN-g response after stimulating PBMCs with mutated regions of SARS-CoV-2 variants. Neutralizing antibody titers against Omicron-BA.1 and especially BA.5 were strongly reduced. Double-vaccinated patients with Delta breakthrough infection showed a significantly increased neutralizing antibody response against Delta compared to double-vaccinated uninfected controls (median complete neutralization titer (NT100) 640 versus 80, p<0.05). Omicron-BA.1 infection increased neutralization titers against BA.1 in double-vaccinated patients (median NT100 of 160 in patients versus 20 in controls, p=0.07) and patients that received booster vaccination (median NT100 of 50 in patients versus 20 in controls, p=0.68). For boosted patients with BA.5 breakthrough infection, we found no enhancing effect on humoral immunity against SARS-CoV-2 variants. Conclusion: Neutralizing antibody titers against Omicron-BA.1 and especially BA.5 were strongly reduced in SARS-CoV-2 breakthrough infections. Delta and Omicron-BA.1 but not Omicron-BA.5 infections boosted the humoral immunity in double-vaccinated patients and patients with booster vaccination. Despite BA.5 breakthrough infection, those patients may still be vulnerable for reinfections with BA.5 or other newly emerging variants of concern. [ABSTRACT FROM AUTHOR]

• A single Ad26.COV2.S booster given 45–75 or 90–240 days after 2 BBIBP-CorV doses was well tolerated. • Robust humoral and cell-mediated immune responses were measured at day 28 in both interval groups. • Humoral responses were strongest against ancestral virus, followed by delta then omicron variants. • T-cell–produced IFN-γ increased ≈10-fold in both groups after this heterologous booster dose. The inactivated COVID-19 whole-virus vaccine BBIBP-CorV has been extensively used worldwide. Heterologous boosting after primary vaccination can induce higher immune responses against SARS-CoV-2 than homologous boosting. The safety and immunogenicity after 28 days of a single Ad26.COV2.S booster dose given at different intervals after 2 doses of BBIBP-CorV are presented. This open-label phase 1/2 trial was conducted in healthy adults in Thailand who had completed 2-dose primary vaccination with BBIBP-CorV. Participants received a single booster dose of Ad26.COV2.S (5 × 1010 virus particles) 90–240 days (Group A1; n = 360) or 45–75 days (Group A2; n = 66) after the second BBIBP-CorV dose. Safety and immunogenicity were assessed over 28 days. Binding IgG antibodies to the full-length pre-fusion Spike and anti-nucleocapsid proteins of SARS-CoV-2 were measured by enzyme-linked immunosorbent assay. The SARS-CoV-2 pseudovirus neutralization assay and live virus microneutralization assay were used to quantify the neutralizing activity of antibodies against ancestral SARS-CoV-2 (Wuhan-Hu-1) and the delta (B.1.617.2) and omicron (B.1.1.529/BA.1 and BA.2) variants. The cell-mediated immune response was measured using a quantitative interferon (IFN)-γ release assay in whole blood. Solicited local and systemic adverse events (AEs) on days 0–7 were mostly mild, as were unsolicited vaccine-related AEs during days 0–28, with no serious AEs. On day 28, anti-Spike binding antibodies increased from baseline by 487- and 146-fold in Groups A1 and A2, and neutralizing antibodies against ancestral SARS-CoV-2 by 55- and 37-fold, respectively. Humoral responses were strongest against ancestral SARS-CoV-2, followed by the delta, then the omicron BA.2 and BA.1 variants. T-cell–produced interferon-γ increased approximately 10-fold in both groups. A single heterologous Ad26.COV2.S booster dose after two BBIBP-CorV doses was well tolerated and induced robust humoral and cell-mediated immune responses measured at day 28 in both interval groups. Clinical Trials Registration. NCT05109559. [ABSTRACT FROM AUTHOR]

The hepatitis D virus (HDV) or delta hepatitis is the most difficult form of viral hepatitis to treat. It is also the most aggressive, with the most rapid evolution to cirrhosis, hepatocellular carcinoma, and death. HDV is found globally with areas of greater prevalence, known as hotspots. Due to the dependence of HDV on the hepatitis B virus (HBV), it is likely that as HBV vaccination rates increase the population vulnerable to HDV will decrease. There is currently no HDV vaccine, leaving those infected with HBV vulnerable to HDV. HDV utilizes the host for almost all its replicative cycle, leading to a paucity of true antiviral targets. Diagnosis depends on accurate testing for HDV, and as testing has improved and expanded, the full extent of HDV has increasingly been appreciated. Although not satisfactory, the mainstay of therapy thus far has been interferon alpha and liver transplant where indicated. However, as the molecular virology of HDV has been unlocked, there has been a corresponding development of multiple therapeutic options. It is these therapeutic options that hold the promise of cure. Unmet needs include identifying patients infected with HDV, accurate noninvasive staging of their liver disease, and easy to administer curative therapies. It is hoped that the next decade will bring us substantively closer to meeting all unmet needs and closer towards the eradication of HDV. [ABSTRACT FROM AUTHOR]

Understanding the impact of climate change on the vegetation cover in the past is crucial for predicting the future warming scenario and its consequences. The present study integrates biotic (palynological analysis) and abiotic proxy (sediment chemistry, clay mineral assemblages and grain size end member (EM) analysis) records in a chronologically constrained sedimentary sequence from the southeastern part of the Mahanadi River delta to reconstruct the hydroclimate since 2600 years. The Mahanadi delta sediments are primarily derived from felsic rock source possibly composed of granites or granulites. The dominance of herbaceous taxa, high aridity index and deposition of fine grain (EM1) sediment possibly suggest a relatively cold and dry climate in the study region during ~2600–2100 cal yr BP corresponding to the Iron Age Cold Period (IACP). Presence of diverse mangrove and tree taxa, deposition of coarser sediment (EM3) and relatively high abundance of secondary clay minerals possibly indicate high precipitation associated with the Roman Warm Period (RWP, ~2100–1800 cal yr BP). A decline in mangroves, dominance of herbaceous taxa and high deposition of fine grain (EM2) sediment from ~1800 to 1300 cal yr BP may indicate a relatively drier climate coinciding with the Dark Age Cold Period (DACP). High moisture index and an increased value of Rb/Sr during ~1300 cal yr BP may suggest a wet phase with the onset of the Medieval Climatic Anomaly (MCA) and later shifted to an arid climate during ~1100–800 cal yr BP. After ~800 cal yr BP, a sharp decline in all weathering indices and vegetation cover, dominance of illite indicates a relatively dry climate which could mark the Little Ice Age (LIA, ~800–300 cal yr BP). A small increase in the terrestrial flux, as well as the weathering indices after ~300 cal yr BP, may suggest the onset of recent warming. [ABSTRACT FROM AUTHOR]

• This observational study included patients from the fifth to seventh COVID-19 epidemic waves in Japan. • We compared the clinical characteristics and outcomes between epidemic waves. • Lower critical outcomes were observed in the Omicron-dominated (sixth and seventh) waves. • COVID-19 vaccination may contribute to preventing respiratory failure. COVID-19 was severe in the Delta variant-dominated epidemic wave (fifth wave) in Japan. The clinical characteristics and effectiveness of COVID-19 vaccination are not fully understood in the Omicron variant-dominated wave (sixth and seventh waves), especially in hospitalized patients. We investigated the relationship between vaccination and disease severity in the Omicron-dominated wave and compared these variant-dominated waves. The nationwide COVID-19 database (Japan COVID-19 Task Force) was used to compare clinical characteristics and critical outcomes in patients hospitalized with Delta (fifth, N = 735) vs Omicron-dominated waves (sixth, N = 495; seventh, N = 128). Patients in the sixth and seventh waves had a lower incidence of critical outcomes and respiratory outcomes, and a higher incidence of bacterial infection, although the mortality rate did not differ significantly between waves. In the sixth and seventh waves, 138 (27.9%) and 29 (22.7%) patients with COVID-19 were unvaccinated, respectively. Multivariable analysis adjusted with previously reported factors revealed that the proportion of (1) critical outcomes and (2) respiratory outcomes decreased in a frequency-dependent manner. Thus, (1) (the number of vaccinations): 1-2 times: adjusted odds ratio (aOR) 0.37 (95% confidence interval [CI]; 0.20-0.69); 3-4 times: aOR 0.25 (95% CI; 0.11-0.58); and (2) 1-2 times: aOR 0.43 (95% CI; 0.27-0.66); 3-4 times: aOR 0.36 (95% CI; 0.21-0.60). Patients hospitalized with COVID-19 with Omicron infections showed a lower incidence of critical outcomes than those with Delta infections, and COVID-19 vaccination may contribute to preventing respiratory failure. [ABSTRACT FROM AUTHOR]

Although the SARS-CoV-2 Omicron variant is considered to induce less severe disease, there have been no consistent results on the extent of the decrease in severity. To compare the clinical outcomes of COVID-19–positive patients with Omicron and Delta variant infection. Searches were implemented up to 8 November 2022 in PubMed, Web of Science, BioRvix, and MedRvix. Eligible studies were cohort studies reporting the clinical outcomes of COVID-19–positive patients with Omicron and Delta variant infection, including hospitalization, intensive care unit (ICU) admission, receiving invasive mechanical ventilation (IMV), and death. COVID-19–positive patients with Omicron and Delta variant infection. Risk of bias was assessed employing the Newcastle-Ottawa Scale. Random-effect models were employed to pool the ORs and 95% CIs to compare the risk of clinical outcome. I2 was employed to evaluate the heterogeneity between studies. A total of 33 studies with 6 037 144 COVID-19–positive patients were included in this meta-analysis. In the general population of COVID-19–positive patients, compared with Delta, Omicron variant infection resulted in a decreased risk of hospitalization (10.24% vs. 4.14%, OR = 2.91, 95% CI = 2.35–3.60), ICU admission (3.67% vs. 0.48%, OR = 3.64, 95% CI = 2.63–5.04), receiving IMV (3.93% vs. 0.34%, OR = 3.11, 95% CI = 1.76–5.50), and death (2.40% vs. 0.46%, OR = 2.97, 95% CI = 2.17–4.08). In the hospitalized patients with COVID-19, compared with Delta, Omicron variant infection resulted in a decreased risk of ICU admission (20.70% vs. 12.90%, OR = 1.63, 95% CI = 1.32–2.02), receiving IMV (10.90% vs. 5.80%, OR = 1.65, 95% CI = 1.28–2.14), and death (10.72% vs. 7.10%, OR = 1.44, 95% CI = 1.22–1.71). Compared with Delta, the severity of Omicron variant infection decreased. [ABSTRACT FROM AUTHOR]

Traditionally, stylometry has been used to solve problems of authorship attribution. Quantitative attribution methods remain the last hope for researchers when reliable documentary evidence is unavailable. In the last 20 years, the Delta method, developed by John F. Burrows, has emerged as the leading attribution method. Overall, it has proven to be a reasonably reliable way of attributing texts in controversial cases. However, as our research shows, the case of Fernando Pessoa stands out, as he produced his texts "on behalf" of fictitious identities, commonly known as "heteronyms". It turns out that Delta does not identify these works as expected, that is, as texts belonging to the pen of a single person, Fernando Pessoa, but as texts from different authors. The article carries out a series of experiments to test the extent to which Pessoa manages to confuse the quantitative assessment of the authorship of his poetic texts. Pessoa's texts are examined as an independent corpus and against the background of the work of other Lusophone poets. In all cases, the distances between texts belonging to Pessoa's heteronyms are comparable to those between texts from different authors, much greater than the distances between texts from the same author. [ABSTRACT FROM AUTHOR]

Under § 7 of the federal Endangered Species Act (ESA or the Act),'federal agencies must ensure that actions they authorize, fund, or carry out are" not likely to jeopardize the continued existence of any endangered species or threatened species or result in the destruction or adverse modification of habitat of such species." 2 For species with low and declining populations, applying this standard is legally and scientifically difficult. 3 The US Fish and Wildlife Service (FWS) faced this problem in its recent biological opinion (BiOp) analyzing impacts to threatened Delta smelt from water project operations in the California Delta. FWS concluded the" species' recent abundance trends strongly suggest it is in the midst of demographic collapse," and most recent surveys to locate smelt have failed to find them.'Nevertheless, FWS approved agency actions that will likely increase extinction risk for Delta smelt.

With over 30% of current medications targeting this family of proteins, G-protein-coupled receptors (GPCRs) remain invaluable therapeutic targets. However, due to their unique physicochemical properties, their low abundance, and the lack of highly specific antibodies, GPCRs are still challenging to study in vivo. To overcome these limitations, we combined here transgenic mouse models and proteomic analyses in order to resolve the interactome of the δ-opioid receptor (DOPr) in its native in vivo environment. Given its analgesic properties and milder undesired effects than most clinically prescribed opioids, DOPr is a promising alternative therapeutic target for chronic pain management. However, the molecular and cellular mechanisms regulating its signaling and trafficking remain poorly characterized. We thus performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses on brain homogenates of our newly generated knockin mouse expressing a FLAG-tagged version of DOPr and revealed several endogenous DOPr interactors involved in protein folding, trafficking, and signal transduction. The interactions with a few identified partners such as VPS41, ARF6, Rabaptin-5, and Rab10 were validated. We report an approach to characterize in vivo interacting proteins of GPCRs, the largest family of membrane receptors with crucial implications in virtually all physiological systems.

Since the isolation of morphine from the opium poppy over 200 years ago, the molecular basis of opioid action has remained the subject of intense inquiry. The identification of specific receptors responsible for opioid function and the discovery of many chemically diverse molecules with unique opioid-like efficacies have provided glimpses into the molecular logic of opioid action. Recent revolutions in the structural biology of transmembrane proteins have, for the first time, yielded high-resolution views into the 3-dimensional shapes of all 4 opioid receptors. These studies have begun to decode the chemical logic that enables opioids to specifically bind and activate their receptor targets. A combination of spectroscopic experiments and computational simulations has provided a view into the molecular movements of the opioid receptors, which itself gives rise to the complex opioid pharmacology observed at the cellular and behavioral levels. Further diversity in opioid receptor structure is driven by both genetic variation and receptor oligomerization. These insights have enabled computational drug discovery efforts, with some evidence of success in the design of completely novel opioids with unique efficacies. The combined progress over the past few years provides hope for new, efficacious opioids devoid of the side effects that have made them the scourge of humanity for millennia.

Many fishes in the San Francisco Estuary have suffered declines in recent decades, as shown by numerous long-term monitoring programs. A long-term monitoring program, such as the Interagency Ecological Program, comprises a suite of surveys, each conducted by a state or federal agency or academic institution. These types of programs have produced rich data sets that are useful for tracking species trends over time. Problems arise from drawing conclusions based on one or few surveys because each survey samples a different subset of species or reflects different spatial or temporal trends in abundance. The challenges in using data sets from these surveys for comparative purposes stem from methodological differences, magnitude of data, incompatible data formats, and end-user preference for familiar surveys. To improve the utility of these data sets and encourage multi-survey analyses, we quantitatively rate these surveys based on their ability to represent species trends, present a methodology for integrating long-term data sets, and provide examples that highlight the importance of expanded analyses. We identify areas and species that are under-sampled, and compare fish salvage data from large water export facilities with survey data. Our analysis indicates that while surveys are redundant for some species, no two surveys are completely duplicative. Differing trends become evident when considering individual and aggregate survey data, because they imply spatial, seasonal, or gear-dependent catch. Our quantitative ratings and integrated data set allow for improved and better-informed comparisons of species trends across surveys, while highlighting the importance of the current array of sampling methodologies.

Summary Background One year after the coronavirus disease 2019 (COVID-19) pandemic, the focus of attention has shifted to the emergence and spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs). The aim of the study was to assess the frequency of VOCs in patients followed for COVID-19 at Kinshasa university hospital (KUH) during the 3rd and 4th waves of the pandemic in Kinshasa. Hospital mortality was compared to that of the first two waves. Method The present study included all patients in whom the diagnosis of SARS-CoV-2 infection was confirmed by the polymerase chain reaction (PCR). The laboratory team sequenced a subset of all SARS-CoV-2 positive samples with high viral loads define as Ct

Abstract Background The existence of mutated Delta (B.1.617.2) variants of SARS-CoV-2 causes rapid transmissibility, increase in virulence, and decrease in the effectiveness of public health. Majority of mutations are seen in the surface spike, and they are considered as antigenicity and immunogenicity of the virus. Hence, finding suitable cross antibody or natural antibody and understanding its biomolecular recognition for neutralizing surface spike are crucial for developing many clinically approved COVID-19 vaccines. Here, we aim to design SARS-CoV-2 variant and hence, to understand its mechanism, binding affinity and neutralization potential with several antibodies. Results In this study, we modelled six feasible spike protein (S1) configurations for Delta SARS-CoV-2 (B.1.617.2) and identified the best structure to interact with human antibodies. Initially, the impact of mutations at the receptor-binding domain (RBD) of B.1.617.2 was tested, and it is found that all mutations increase the stability of proteins (ΔΔG) and decrease the entropies. An exceptional case is noted for the mutation of G614D variant for which the vibration entropy change is found to be within the range of 0.133–0.004 kcal/mol/K. Temperature-dependent free energy change values (ΔG) for wild type is found to be − 0.1 kcal/mol, whereas all other cases exhibit values within the range of − 5.1 to − 5.5 kcal/mol. Mutation on spike increases the interaction with the glycoprotein antibody CR3022 and the binding affinity (CLUSpro energy = − 99.7 kcal/mol). The docked Delta variant with the following antibodies, etesevimab, bebtelovimab, BD-368–2, imdevimab, bamlanivimab, and casirivimab, exhibit a substantially decreased docking score (− 61.7 to − 112.0 kcal/mol) and the disappearance of several hydrogen bond interactions. Conclusion Characterization of antibody resistance for Delta variant with respect to the wild type gives understanding regarding why Delta variant endures the resistance boosted through several trademark vaccines. Several interactions with CR3022 have appeared compared to Wild for Delta variant, and hence, it is suggested that modification on the CR3022 antibody could further improve for the prevention of viral spread. Antibody resistance decreased significantly due to numerous hydrogen bond interactions which clearly indicate that these marketed/launched vaccines (etesevimab) will be effective for Delta variants. Graphical Abstract

The global demand for rapid identification of circulating SARS-CoV-2 variants of concern has led to a shortage of commercial kits. Therefore, this study aimed to develop and validate a rapid, cost-efficient genome sequencing protocol to identify circulating SARS-CoV-2 (variants of concern). Sets of primers flanking the SARS-CoV-2 spike gene were designed, verified and then validated using 282 nasopharyngeal positive samples for SARS-CoV-2. Protocol specificity was confirmed by comparing these results with SARS-CoV-2 whole-genome sequencing of the same samples. Out of 282 samples, 123 contained the alpha variant, 78 beta and 13 delta, which were indicted using in-house primers and next-generation sequencing; the numbers of variants found were 100% identical to the reference genome. This protocol is easily adaptable for detection of emerging variants during the pandemic.

Abstract Background Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome. Methods We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinION™ in Blantyre. Results We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p

Background: Studying the genomic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may help determine outbreak clusters and virus transmission advantages to aid public health efforts during the pandemic. Thus, we tracked the evolution of SARS-CoV-2 by variant epidemiology, breakthrough infection, and patient characteristics as the virus spread during the Delta and Omicron waves. We also conducted phylogenetic analyses to assess modes of transmission. Methods: Nasopharyngeal samples were collected from a cohort of 900 patients with positive polymerase chain reaction (PCR) test results confirming COVID-19 disease. Samples underwent real-time PCR detection using TaqPath assays. Sequencing was performed with Ion GeneStudio using the Ion AmpliSeq™ SARS-CoV-2 panel. Variant calling was performed with Torrent Suite™ on the Torrent Server. For phylogenetic analyses, the MAFFT tool was used for alignment and the maximum likelihood method with the IQ-TREE tool to build the phylogenetic tree. Data were analyzed using SAS statistical software. Analysis of variance or t tests were used to assess continuous variables, and χ2 tests were used to assess categorical variables. Univariate and multivariate logistic regression analyses were preformed to estimate odds ratios (ORs). Results: The predominant variants in our cohort of 900 patients were non–variants of concern (11.1 %), followed by Alpha (4.1 %), Beta (5.6 %), Delta (21.2 %), and Omicron (58 %). The Delta wave had more male than female cases (112 vs. 78), whereas the Omicron wave had more female than male cases (311 vs. 208). The oldest patients (mean age, 43.4 years) were infected with non–variants of concern; the youngest (mean age, 33.7 years), with Omicron. Younger patients were mostly unvaccinated, whereas elderly patients were mostly vaccinated, a statistically significant difference. The highest risk for breakthrough infection by age was for patients aged 30–39 years (OR = 12.4, CI 95 %: 6.6–23.2), followed by patients aged 40–49 years (OR = 11.2, CI 95 %: 6.1–23.1) and then 20–29 years (OR = 8.2, CI 95 %: 4.4–15.4). Phylogenetic analyses suggested the interaction of multiple cases related to outbreaks for breakthrough infections, healthcare workers, and intensive care unit admission. Conclusion: The findings of this study highlighted several major public health ramifications, including the distribution of variants over a wide range of demographic and clinical variables and by vaccination status.

The article describes the methodology for constructing digital elevation models for the vast delta areas of the Don and Volga rivers for further use in mathematical models of flooding from surges. The initial cartographic data and features of the delta regions are described. The methods of information processing are considered in detail. An algorithm for constructing a DEM has been developed to obtain highly detailed digital elevation models. The algorithm is based on combining the DEM of individual key features - land, the depths of the hydrographic network and the bathymetry of the receiving reservoir for the river. The topographic maps, maps of the navigable route depths, hydrographic maps, and satellite images Landsat-8 and Sentinel-2 were used to create the DEM of the Don and Volga river. To build individual DEMs, a raster of the absolute depth of the channels, a hydrography DEM, a land DEM, and a shelf DEM were created using geoinformation systems. To assess the possibility of using obtained DEMs in hydrological models based on HEC-RAS, we conducted training and verification calculations of water level during wind surge phenomena in Don Delta using different surface roughness coefficients. The calculation results show good reproducibility of observed water level fluctuation in the Don Delta using obtained DEM with a roughness coefficient of 0.0125. Also, we carried out similar calculations of storm surge phenomena in the Volga Delta using obtained DEM and combinations of various riverbed and not riverbed roughness coefficients. The combination of 0.007 for riverbed and 0.02 for not riverbed surfaces reproduces the observed water level fluctuation during storm surge phenomena in Volga Delta. The constructed DEMs for the Volga and Don deltas made it possible to reproduce the observed dynamics of river discharges and water level fluctuations during surge events. Such detailed DEMs, taking into account all the complexity of the coastal and delta relief, were created for the first time for the Volga and Don.

This study investigates the utility of satellite-based rainfall products and the performance of bias correction methods in one of the sub-basins of the Upper Blue Nile Basin (Main Beles basin). Four satellite rainfall products are used: Climate Prediction Center (CPC) MORPHing technique (CMORPH), Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN), Tropical Rainfall Measuring Mission Multi-Satellite Precipitation Analysis (TMPA) 3B42V7 (TMPA 3B42V7), and Climate Forecast System Reanalysis (CFSR). The performance of the satellite rainfall products (SRPs) was compared using three bias correction methods (Delta, Empirical Quantile Mapping (EQM), and Quantile Mapping (QM)) on five metrological stations. Six statistical criteria were used to evaluate these methods on the period 2003–2016 at daily and monthly scales. The results showed that SRPs and bias correction methods of CMORPH_QM (r = 0.538) and TMPA_3B42V7_EQM (r = 0.95) data showed good performance, while PERSIANN_EQM (r = 0.348) and PERSIANN_Delta (r = 0.83) performed worst at daily and monthly time scales, respectively. This study assessed the importance of SRPs and bias correction methods to use in data scarce regions for water resources planning and other related sectors. HIGHLIGHTS Four satellite rainfall products (CMORPH, CFSR, PERSIANN and TMPA_3B42V7) and three bias correction methods (i.e., Delta, Quantile Mapping (QM) and Empirical Quantile Mapping (EQM)) were evaluated.; Only CMORPH using QM and TMPA_3B42V7 using EQM data showed good performance, while PERSIANN using EQM and PERSIANN using Q3 Delta performed worst at daily and monthly time scales, respectively.;

Abstract Background Coronavirus Disease (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 virus is evolving continuously. The omicron variant of SARS-CoV-2 has the highest mutation in its spike protein, thus making the presently available vaccine ineffective or reducing its efficiency. Furthermore, the majority of the vaccines are constructed using a spike protein sequence from wild-type SARS-CoV-2. This raises the possibility of the virus evolving to the point where the vaccine's effectiveness is completely lost, even after booster doses. The study aims to develop a predictive vaccine as well as the epitopes for the updating of the vaccine sequences of currently available vaccines. In this study, following the immunoinformatics approach, predictive vaccine construction was done with the help of epitopes present on spike proteins of wild-type, delta, and omicron variants that encompass the majority of variants and possible new variants that arise from the combination of circulating variants. Results The vaccine that was constructed was stable and immunogenic. The vaccine was constructed with the help of 18 B-cell epitopes, 5 MHC class I epitopes, and 6 MHC class II epitopes. The epitope conservancy analysis suggests that the vaccine will work for the previously known variant of concern. The vaccine bound to TLR4, TLR2, B-cell receptor chains A and B, and ACE2 receptors with a z score of − 1.4, − 1.7, − 1.4, − 1.7, and − 1.4, respectively, with a cluster size of 121 highest for the ACE2 receptor and 46 lowest for B-cell receptor chain A. The C-ImmSim simulation results indicate that the vaccine is generating both humoral and cell-mediated responses at a sufficient level throughout the month upon injection of the vaccine as an antigen. Conclusion The study's findings indicate that the vaccine was both stable and immunogenic, providing a sufficient level of immunity. Following experimental validation, the vaccine can be used, and the epitopes can be employed for therapeutic purposes such as antibody synthesis. Graphical Abstract

We reconstructed the SARS-CoV-2 epidemic caused by Omicron variant in Puerto Rico by sampling genomes collected during October 2021–May 2022. Our study revealed that Omicron BA.1 emerged and replaced Delta as the predominant variant in December 2021. Increased transmission rates and a dynamic landscape of Omicron sublineage infections followed.

Objectives: This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program. Methods: COVID-19 samples that tested positive by reverse transcription polymerase chain reaction and with cycle threshold values

SARS-CoV-2 has caused the COVID-19 pandemic. B.1.617 variants (including Kappa and Delta) have been transmitted rapidly in India. The transmissibility, pathogenicity, and neutralization characteristics of these variants have received considerable interest. In this study, 22 pseudotyped viruses were constructed for B.1.617 variants and their corresponding single amino acid mutations. B.1.617 variants did not exhibit significant enhanced infectivity in human cells, but mutations T478K and E484Q in the receptor binding domain led to enhanced infectivity in mouse ACE2-overexpressing cells. Furin activities were slightly increased against B.1.617 variants and cell–cell fusion after infection of B.1.617 variants were enhanced. Furthermore, B.1.617 variants escaped neutralization by several mAbs, mainly because of mutations L452R, T478K, and E484Q in the receptor binding domain. The neutralization activities of sera from convalescent patients, inactivated vaccine-immunized volunteers, adenovirus vaccine-immunized volunteers, and SARS-CoV-2 immunized animals against pseudotyped B.1.617 variants were reduced by approximately twofold, compared with the D614G variant.

The Omicron BA.1 (B.1.1.529) SARS-CoV-2 variant is characterized by a high number of mutations in the viral genome, associated with immune escape and increased viral spread. It remains unclear whether milder COVID-19 disease progression observed after infection with Omicron BA.1 in humans is due to reduced pathogenicity of the virus or due to pre-existing immunity from vaccination or previous infection. Here, we inoculated hamsters with Omicron BA.1 to evaluate pathogenicity and kinetics of viral shedding, compared to Delta (B.1.617.2) and to animals re-challenged with Omicron BA.1 after previous SARS-CoV-2 614G infection. Omicron BA.1 infected animals showed reduced clinical signs, pathological changes, and viral shedding, compared to Delta-infected animals, but still showed gross- and histopathological evidence of pneumonia. Pre-existing immunity reduced viral shedding and protected against pneumonia. Our data indicate that the observed decrease of disease severity is in part due to intrinsic properties of the Omicron BA.1 variant.

Many strains of corona virus such as alpha, beta, gamma, delta, and omicron are still prevalent in various parts of the world. The new type of corona virus is called a variant when it is caused by more than one genetic mutation from the previous type of corona virus. Various strains around the world have come so far. The cough may persist for more than an hour or three or four times in 24 hours and body heat is high. You may not be able to feel the smell or taste. Researchers say that some people may have symptoms similar to those of a severe cold. In this paper, a multi threshold model was proposed to find the initial infection detection of COVID disease. Based on the initial health symptoms these methods observe the inputs of the patients. Then the observed symptoms are compared with the existing database and identify the spreading of the disease. This report was directly monitored by the patient and doctor. This model was helpful to provide the periodical monitoring and perfect treatments to the infected patients.

Abstract Background Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India. Results We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC. Conclusion Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance.

Background: The SARS-CoV-2 virus elicited a major public concern worldwide since December 2019 due to the high number of infections and deaths caused by COVID-19. The Omicron variant was detected in October 2021 which evolved from the wild-type SARS-CoV-2 and was found to possess many mutations. Omicron exhibited high transmissibility and immune evasion as well as reduced severity when compared to the earlier variants. Although vaccinated individuals were largely protected against infections in previous waves, the high prevalence of both reinfections and breakthrough infections with Omicron was observed. The aim of this review is to understand the effectiveness of previous infection on subsequent reinfection, given its significance in driving public health policy, including vaccination prioritization and lockdown requirements. Methods: A comprehensive literature search was conducted using several databases to target studies reporting data related to the effectiveness of the previous infection with SARS-CoV-2 in protecting against the Omicron variant. Screening of the studies, quality assessment and data extraction were conducted by two reviewers for each study. Results: Only 27 studies met our inclusion criteria. It was observed that previous infection was less effective in preventing reinfections with the Omicron variant compared to the Delta variant irrespective of vaccination status. Furthermore, being fully vaccinated with a booster dose provided additional protection from the Omicron variant. Additionally, most infections caused by Omicron were asymptomatic or mild and rarely resulted in hospitalizations or death in comparison to the Delta wave. Conclusion: A majority of the studies reached a consensus that although previous infection provides some degree of immunity against Omicron reinfection, it is much lower in comparison to Delta. Full vaccination with two doses was more protective against Delta than Omicron. Receiving a booster dose provided additional protection against Omicron. It is therefore clear that neither vaccination nor previous infection alone provide optimal protection; hybrid immunity has shown the best results in terms of protecting against either Omicron or Delta variants. However, additional research is needed to quantify how long immunity from vaccination versus previous infection lasts and whether individuals will benefit from variant-specific vaccinations to enhance protection from infection. [ABSTRACT FROM AUTHOR]

Health care workers (HCW) have a higher exposure to SARS-CoV-2 virus than other professionals and to protect both HCW and patients, HCW have been prioritized for vaccination against SARS-CoV-2 in many countries. Estimating the COVID-19 vaccine effectiveness among HCW is important to provide recommendations to protect risk groups. We estimated vaccine effectiveness against SARS-CoV-2 infections using Cox proportional hazard models among HCW with comparisons in the general population, from 1 August 2021 to 28 January 2022. Vaccine status is specified as a time-varying covariate and all models incorporated explicit time and were adjusted for age, sex, comorbidities, county of residence, country of birth, and living conditions. Data from the adult Norwegian population (aged 18–67 years) and HCW workplace data (as registered 1 January 2021) were collated from the National Preparedness Register for COVID-19 (Beredt C19). Vaccine effectiveness was higher for Delta than for the Omicron variant in HCW (71 % compared to 19 %) as well as in non-HCW (69 % compared to −32 %). For the Omicron variant a 3rd dose provides significantly better protection against infection than 2 doses in both HCW (33 %) and non-HCW (10 %). Further, HCW seem to have better vaccine effectiveness than non-HCW for the Omicron, but not for the Delta variant. Vaccine effectiveness were comparable between HCW and non-HCW for the delta variant, but significantly higher in HCW than non-HCW for the omicron variant. Both HCW and non-HCW got increased protection from a third dose. [ABSTRACT FROM AUTHOR]

The upper and middle interval of the third member of Shahejie Formation is important target strata for oil and gas exploration and development on the northern area of Gudao Uplift in Zhanhua Sag. Therefore, it is critical to have a thorough understanding of the sedimentary system of the target strata, which has long been considered as nearshore subaqueous fan or fan delta systems sourced by Gudao Uplift. However, through systematic core observation and logging facies analysis, it has been found that medium-fine sandstone and siltstone are the main composition of the strata, and well logging show typical coarsening-upward delta-front facies, which indicate delta front subfacies. Microfacies such as subaqueous distributary channel, interdistributary bay, mouth bar, sheet sand can be recognized. Based on correlation of connected wells, paleogeomorphology reconstruction and the multi-attribute analysis of seismic data, including root-mean-square (RMS) and amplitude, the plane distribution of sand bodies in 4~1 sand groups were analyzed, under the guidance of delta front sedimentary model. According to sand body distribution, plane distribution map of sedimentary microfacies were made. It is clear that subaqueous distributary channel and mouth bar distributed in leaf shape and extend from southeast to northwest are more favorable to oil reservoir. New understandings provide geological basis for fine oil and gas exploration and development, based on which drilling ratio increases dramatically in Gubei area. [ABSTRACT FROM AUTHOR]

Background: The aim of this study is to determine the prognostic value of the prognostic nutritional index (PNI), the neutrophil to lymphocyte ratio (NLR), and the platelet to lymphocyte ratio (PLR) and their dynamic changes on survival outcomes in metastatic colorectal cancers (mCRC). Methods: The data of 199 patients with mCRC were retrospectively analyzed. To evaluate the temporal relation between the PNI, NLR, and PLR values and survival, pre-chemotherapy PNI, NLR, and PLR levels were assessed from peripheral blood cell counts on admission; post-chemotherapy PNI, NLR, and PLR levels were assessed with follow-up blood cell counts within two weeks after chemotherapy; and the difference between pre-chemotherapy PNI, NLR, and PLR levels and post-chemotherapy PNI, NLR, and PLR levels was evaluated as delta PNI, delta NLR, and delta PLR. Results: The median PNI, PLR, and NLR were 39.01, 150.2 and 2.53 before chemotherapy and 38.2, 146.6, and 3.31 after chemotherapy, respectively. The median OS was 23.7 months (95%CI:17.8–29.7) and 28.9 months (95%CI:24.8–33.08) for pre-chemotherapy PNI level < 39.01 vs. PNI level ≥ 39.01, respectively(p = 0.035) The positive delta PNI was significantly higher for OS than the negative delta PNI(p < 0.009). Delta PLR and delta NLR were not significant for OS and PFS(p > 0.05 for all). Conclusions: The results of this study clearly show that the negative delta PNI to be an independent predictor of poor OS and poor PFS in patients with colon cancer who received first line treatment. In addition, delta NLR and delta PLR were shown not to predict survival outcomes. [ABSTRACT FROM AUTHOR]

This article discusses a fragment of a model of a tower house found on the surface at Kom el-Gir in the central northwestern Delta. The settlement of Kom el-Gir, which was used at least from the Ptolemaic to the Late Roman Periods, showed a dense occupation of tower houses, based on magnetic prospection. A reconstruction of what the house model may have looked like is suggested and the possible uses of such house models are discussed. [ABSTRACT FROM AUTHOR]

Copyright of Acta Infologica is the property of Acta Infologica and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We examine the hypothesis that internal dual-energy X-ray absorptiometry (DXA) structural variables measured at the femoral neck and trochanter cross sections will improve prediction of fractures at these sites in addition to areal BMD (aBMD). We present an analysis of the internal distribution of bone at the site of these fractures using baseline hip DXA measurement of 1151 participants, mean age (SD) 75 (3) years, in the 14.5-year Perth Longitudinal Study of Aging in Women. Structural differences at the femoral neck (FN) and trochanter (TR) cross sections were compared in 69 participants who went on to sustain femoral neck fracture (FNF) and 59 participants who went on to sustain trochanter fracture (TRF), on average 10 years later, to those who did not fracture. The new structural variables, in addition to aBMD and bone width (W), were Sigma (distribution of bone within scanned area) and Delta (distance between center-of-mineral mass and geometric center), which can be assessed by current DXA programs. At baseline, compared with nonfracture cases, FNF cases had a FNaBMD 7% lower, a FNWidth 3% higher and a FNDelta 29% higher, associated with reduced bone in the superior segment. In FNF Cox proportional hazard analysis, age (hazard ratio [HR 1.39]), total hip aBMD (THaBMD; 0.79), and Delta (1.70) were significant. Addition of FN Delta to the base case of THaBMD and age improved the C statistic from 0.62 to 0.69, p = 0.01. At baseline, TRF cases had a 15% lower TRaBMD with minor differences in Sigma (1%) and Width (2%). In TRF Cox analysis, neither addition of Sigma nor Width improved the model that included age and THaBMD as predictors and did not alter the C-statistic of 0.81. In conclusion, adding measurement of FN Delta, an assessment of superior sector bone loss, to hip aBMD and age substantially improved clinical FNF prediction in older women. [ABSTRACT FROM AUTHOR]

Copyright of Acta Sedimentologica Sinica is the property of Acta Sedimentologica Sinica Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The Omicron variant was first detected in October 2021, which evolved from the original SARS‐CoV‐2 strain and was found to possess many mutations. Immune evasion was one of the notable consequences of these mutations. Despite Omicron exhibiting increased transmissibility, the rates of hospitalizations and deaths among patients infected with this variant were substantially lower when compared to other strains. However, concluding that the Omicron variant is less severe than other variants of SARS‐CoV‐2 requires consideration of multiple factors, including the vaccination status of infected patients as well as any previous infections with other variants. This review compiled data about any reported indicators of severity in Omicron‐infected patients, including studies comparing Omicron with other variants while adjusting for confounders. A comprehensive search was conducted using different databases to target any studies about Omicron. In total, 62 studies met our inclusion criteria and were included in this study. Many studies reported a significantly reduced risk of hospitalization, ICU admission, need for oxygenation/ventilation, and death in Omicron‐infected patients compared to patients infected with other variants, such as Delta. Some studies, however, reported comparable severity in Omicron infected patients as to other variants emphasizing a substantial risk for severe illness. Furthermore, the COVID‐19 vaccines were less effective against Omicron relative to previous lineages, except after receiving the booster dose. One study recommended vaccination during pregnancy, which may help prevent future cases of severe SARS‐CoV‐2 pneumonia in neonates and young infants due to the transfer of humoral response from the mother. [ABSTRACT FROM AUTHOR]

River delta soils are the final spatial units of the matter flow within the whole river catchment. Due to their spatial position in the catchment and due to their fine grain size composition, river delta soils are important matter sinks in general, especially for heavy metals. The article presents the results of spectrometric analysis of heavy metals in the soils of the Ili River Delta and State Natural Reserve "Ili-Balkhash" in 2021. This area is included in the list of wetlands of international importance under the Convention on Wetlands. Heavy metals in the samples were determined using the flame atomic absorption spectrometric method using the AA-7000 atomic absorption spectrophotometer. The spatial distribution of the metals was visualized in the ArcGIS 10.5 environment. Copper concentrations were measured in the soils of the dry steppe, semi-desert and desert zones with average values up to 28.5 mg kg−1 and a maximum level of 75.1 mg kg−1. The concentrations of lead are 8.0–15.9 mg kg−1. The cadmium content exceeds the standards from 2.1 to 6.5 mg kg−1 on the whole territory at MPC 2.0 mg kg−1, reaching up to 3.3 MPC (Maximum Permissible Concentration). The cobalt concentration ranges from 6.7 to 20.6 mg kg−1, and nickel ranges from 11.3 to 22.2 mg kg−1. Soil contamination due to cobalt and nickel is observed in the northern and eastern parts of the study area. The received data about pollution of the soil cover by heavy metals makes it possible to assess the degree of anthropogenic load of the unique natural environment in the Ili River Delta and natural reserve. [ABSTRACT FROM AUTHOR]

• The BNT162b2 vaccine was less effective against any Omicron infection than Delta. • The effectiveness decreased with time since vaccination for both Delta and Omicron. • We did not observe a protective effect against Omicron infection after one dose. • The vaccine effectiveness against Delta peaked at 93% in 35-62 days after the second dose. • The vaccine effectiveness against Omicron peaked at 53% in 7-34 days after the second dose. We estimated the BNT162b2 vaccine effectiveness (VE) against any (symptomatic or not) SARS-CoV-2 Delta and Omicron infection among adolescents (aged 12-17 years) in Norway from August 2021 to January 2022. We used Cox proportional hazard models, where vaccine status was included as a time-varying covariate and models were adjusted for age, sex, comorbidities, residence county, birth country, and living conditions. The VE against Delta infection peaked at 68% (95% confidence interval [CI]: 64-71%) and 62% (95% CI: 57-66%) in days 21-48 after the first dose among those aged 12-15 years and 16-17 years, respectively. Among those aged 16-17 years who received two doses, the VE against Delta infection peaked at 93% (95% CI: 90-95%) in days 35-62 and decreased to 84% (95% CI: 76-89%) in ≥63 days after vaccination. We did not observe a protective effect against Omicron infection after receiving one dose. Among those aged 16-17 years, the VE against Omicron infection peaked at 53% (95% CI: 43-62%) in 7-34 days after the second dose and decreased to 23% (95% CI: 3-40%) in ≥63 days after vaccination. We found a reduced protection after two BNT162b2 vaccine doses against any Omicron infection compared to Delta. Effectiveness decreased with time from vaccination for both variants. The impact of vaccination among adolescents on reducing infection and thus transmission is limited during the Omicron dominance. [ABSTRACT FROM AUTHOR]

Aim: Structure-based identification of natural compounds against SARS-CoV-2, Delta and Omicron target proteins. Materials & methods: Several known antiviral natural compounds were subjected to molecular docking and MD simulation against SARS-CoV-2 Mpro, Helicase and Spike, including Delta and Omicron Spikes. Results: Of the docked ligands, 20 selected for each complex exhibited overall good binding affinities (-7.79 to -5.06 kcal/mol) with acceptable physiochemistry following Lipinski's rule. Finally, two best ligands from each complex upon simulation showed structural stability and compactness. Conclusion: Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A were identified as potential inhibitors of SARS-CoV-2 Mpro, Helicase and Spike, while Orientin and Obetrioside also showed good binding affinities with Omicron Spike. Catechin and Neridienone A formed stable complexes with Delta Spike. Mutant strains of SARS-CoV-2 called 'variants of concern' (VOCs) are linked to a good ability to infect, re-infect and spread among people. They are also linked to poor ability to fight the disease and reduced effectiveness of vaccines. Delta and Omicron are important VOCs because they are difficult to control and treat. Specific resistance to some drugs used to treat COVID-19 poses a further challenge. Therefore, discovering natural or plant-derived drugs with no known resistance would be valuable to the treatment of COVID-19. In this study, we screen and identify seven plant-derived compounds that may be useful to treating COVID-19 – we identify Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A as potential candidates. Orientin, Obetrioside, Catechin and Neridienone A are identified as candidates against Delta and Omicron for the first time. We report structure-based identification of natural compounds viz., Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A against SARS-CoV-2 Mpro, Helicase and Spike as well as Delta and Omicron Spike proteins. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 2 tests and t tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations' associations with clinical outcomes. [ABSTRACT FROM AUTHOR]

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern are associated with increased infectivity, severity, and mortality of coronavirus disease 2019 (COVID-19) and have been increasingly detected in clinical and wastewater surveillance in Canada and internationally. In this study, we present a real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay for detection of the N gene D377Y mutation associated with the SARS-CoV-2 Delta variant in wastewater. Methods: Wastewater samples (n=980) were collected from six cities and 17 rural communities across Canada from July to November 2021 and screened for the D377Y mutation. Results: The Delta variant was detected in all major Canadian cities and northern remote regions, and half of the southern rural communities. The sensitivity and specificity of this assay were sufficient for detection and quantitation of the Delta variant in wastewater to aid in rapid population-level screening and surveillance. Conclusion: This study demonstrates a novel cost-effective RT-qPCR assay for tracking the spread of the SARS-CoV-2 Delta variant. This rapid assay can be easily integrated into current wastewater surveillance programs to aid in population-level variant tracking. [ABSTRACT FROM AUTHOR]