Comparative analysis of within-host diversity among vaccinated COVID-19 patients infected with different SARS-CoV-2 variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly evolving RNA virus that mutates within hosts and exists as viral quasispecies. Here, we evaluated the within-host diversity among vaccinated and unvaccinated individuals (n = 379) infected with different SARS-CoV-2 Variants of Concern. The majority of samples harbored less than 14 intra-host single-nucleotide variants (iSNVs). A deep analysis revealed a significantly higher intra-host diversity in Omicron samples than in other variants (p value < 0.05). Vaccination status and type had a limited impact on intra-host diversity except for Beta-B.1.315 and Delta-B.1.617.2 vaccinees, who exhibited higher diversity than unvaccinated individuals (p values: <0.0001 and <0.0021, respectively). Three immune-escape mutations were identified: S255F in Delta and R346K and T376A in Omicron-B.1.1.529. The latter 2 mutations were fixed in BA.1 and BA.2 genomes, respectively. Overall, the relatively higher intra-host diversity among vaccinated individuals and the detection of immune-escape mutations, despite being rare, suggest a potential vaccine-induced immune pressure in vaccinated individuals.The authors are grateful for the leadership and assistance provided by the Ministry of Public Health in Qatar, the virology laboratory staff at Hamad Medical Corporation, and Qatar Biobank (QBB) team. This project was funded by Qatar National Research Fund (QNRF; Project number UREP28-164-3-048) and Qatar University (Project number QUCG-BRC-22/23-547). The article processing charges were paid from grant no. QUCG-BRC-2022/23-578

Traditional knowledge of wild edible plants used in Palestine (Northern West Bank): A comparative study

<p>Abstract</p> <p>Background</p> <p>A comparative food ethnobotanical study was carried out in fifteen local communities distributed in five districts in the Palestinian Authority, PA (northern West Bank), six of which were located in Nablus, two in Jenin, two in Salfit, three in Qalqilia, and two in Tulkarm. These are among the areas in the PA whose rural inhabitants primarily subsisted on agriculture and therefore still preserve the traditional knowledge on wild edible plants.</p> <p>Methods</p> <p>Data on the use of wild edible plants were collected for one-year period, through informed consent semi-structured interviews with 190 local informants. A semi-quantitative approach was used to document use diversity, and relative importance of each species.</p> <p>Results and discussion</p> <p>The study recorded 100 wild edible plant species, seventy six of which were mentioned by three informants and above and were distributed across 70 genera and 26 families. The most significant species include <it>Majorana syriaca, Foeniculum vulgare, Malvasylvestris</it>, <it>Salvia fruticosa, Cyclamen persicum, Micromeria fruticosa, Arum palaestinum, Trigonella foenum-graecum</it>, <it>Gundelia tournefortii</it>, and <it>Matricaria aurea</it>. All the ten species with the highest mean cultural importance values (mCI), were cited in all five areas. Moreover, most were important in every region. A common cultural background may explain these similarities. One taxon (<it>Majoranasyriaca</it>) in particular was found to be among the most quoted species in almost all areas surveyed. CI values, as a measure of traditional botanical knowledge, for edible species in relatively remote and isolated areas (Qalqilia, and Salfit) were generally higher than for the same species in other areas. This can be attributed to the fact that local knowledge of wild edible plants and plant gathering are more spread in remote or isolated areas.</p> <p>Conclusion</p> <p>Gathering, processing and consuming wild edible plants are still practiced in all the studied Palestinian areas. About 26 % (26/100) of the recorded wild botanicals including the most quoted and with highest mCI values, are currently gathered and utilized in all the areas, demonstrating that there are ethnobotanical contact points among the various Palestinian regions. The habit of using wild edible plants is still alive in the PA, but is disappearing. Therefore, the recording, preserving, and infusing of this knowledge to future generations is pressing and fundamental.</p

Immune Imprinting and Protection against Repeat Reinfection with SARS-CoV-2

More than 2 years into the coronavirus disease 2019 (Covid-19) pandemic, the global population carries heterogeneous immune histories derived from various exposures to infection, viral variants, and vaccination.1 Evidence at the level of binding and neutralizing antibodies and B-cell and T-cell immunity suggests that a history of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can have a negative effect on subsequent protective immunity.1 In particular, the immune response to B.1.1.529 (omicron) subvariants could be compromised by differential immune imprinting in persons who have had a previous infection with the original virus or the B.1.1.7 (alpha) variant.

Protection against the omicron variant from previous SARS-CoV-2 infection

Natural infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) elicits strong protection against reinfection with the B.1.1.7 (alpha),1,2 B.1.351 (beta),1 and B.1.617.2 (delta)3 variants. However, the B.1.1.529 (omicron) variant harbors multiple mutations that can mediate immune evasion. We estimated the effectiveness of previous infection in preventing symptomatic new cases caused by omicron and other SARS-CoV-2 variants in Qatar. In this study, we extracted data regarding coronavirus disease 2019 (Covid-19) laboratory testing, vaccination, clinical infection data, and related demographic details from the national SARS-CoV-2 databases, which include all results of polymerase-chain-reaction (PCR) testing, vaccinations, and hospitalizations and deaths for Covid-19 in Qatar since the start of the pandemic

Waning of BNT162b2 Vaccine Protection against SARS-CoV-2 Infection in Qatar.

BACKGROUND: Waning of vaccine protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or coronavirus disease 2019 (Covid-19) is a concern. The persistence of BNT162b2 (Pfizer-BioNTech) vaccine effectiveness against infection and disease in Qatar, where the B.1.351 (or beta) and B.1.617.2 (or delta) variants have dominated incidence and polymerase-chain-reaction testing is done on a mass scale, is unclear. METHODS: We used a matched test-negative, case-control study design to estimate vaccine effectiveness against any SARS-CoV-2 infection and against any severe, critical, or fatal case of Covid-19, from January 1 to September 5, 2021. RESULTS: Estimated BNT162b2 effectiveness against any SARS-CoV-2 infection was negligible in the first 2 weeks after the first dose. It increased to 36.8% (95% confidence interval [CI], 33.2 to 40.2) in the third week after the first dose and reached its peak at 77.5% (95% CI, 76.4 to 78.6) in the first month after the second dose. Effectiveness declined gradually thereafter, with the decline accelerating after the fourth month to reach approximately 20% in months 5 through 7 after the second dose. Effectiveness against symptomatic infection was higher than effectiveness against asymptomatic infection but waned similarly. Variant-specific effectiveness waned in the same pattern. Effectiveness against any severe, critical, or fatal case of Covid-19 increased rapidly to 66.1% (95% CI, 56.8 to 73.5) by the third week after the first dose and reached 96% or higher in the first 2 months after the second dose; effectiveness persisted at approximately this level for 6 months. CONCLUSIONS: BNT162b2-induced protection against SARS-CoV-2 infection appeared to wane rapidly following its peak after the second dose, but protection against hospitalization and death persisted at a robust level for 6 months after the second dose. (Funded by Weill Cornell Medicine-Qatar and others.)

Bivalent mRNA-1273.214 vaccine effectiveness against SARS-CoV-2 omicron XBB* infections

In October of 2022, Qatar introduced COVID-19 bivalent vaccination for persons ≥ 12 years using the 50-μg mRNA-1273.214 vaccine combining SARS-CoV-2 ancestral and omicron BA.1 strains.1 We estimated this vaccine’s effectiveness against SARS-CoV-2 infection. Using Qatar’s national SARS-CoV-2 databases, we conducted a matched, retrospective, cohort study to compare infection incidence in the national cohort of persons who received the vaccine (bivalent cohort) to that in the national cohort of Qatar residents whose last vaccination was ≥6 months before follow-up start (no-recent-vaccination cohort; Supplementary Appendix 1). The 6-month cut-off was chosen because of negligible effectiveness of first-generation vaccines against omicron infection ≥ 6 months after vaccination.2 Incidence of infection was defined as the first SARS-CoV-2 PCR-positive or rapid-antigen-positive test after the start of follow-up, regardless of symptoms. Cohorts were balanced on observed confounders through exact matching. Follow-up started 7 days after the person in the bivalent cohort received their vaccine dose. Associations were estimated using Cox proportional-hazards models adjusted for the matching factors and testing rate

Iron and cobalt salicylaldimine complexes as catalysts for epoxide and carbon dioxide coupling: effects of substituents on catalytic activity

The synthesis and characterization of substituted ONNO-donor salen-type Schiff base complexes of general formula [MIII(L)Cl] (L�=�Schiff base ligand, M�=�Fe, Co) is reported. The complexes have been applied as catalysts for the coupling of carbon dioxide and styrene oxide in the presence of tetrabutylammonium bromide as a co-catalyst. The reactions were carried out under relatively low-pressure and solvent-free conditions. The effects of the metal center, ligands, and various substituents on the peripheral sites of the ligand on the coupling reaction were investigated. The catalyst systems were found to be selective for the coupling of CO2 and styrene oxide, resulting in cyclic styrene carbonate. The cobalt(III) complex with no substituents on the ligand showed higher activity (TON�=�1297) than the corresponding iron(III) complex (TON�=�814); however, the iron(III)-based catalysts bearing electron-withdrawing substituents on the salen ligands (NEt3, TON�=�1732) showed the highest catalytic activity under similar reaction conditions. The activity of one of the cobalt(III) complexes toward the coupling of 1-butene oxide, cyclohexene oxide and propylene oxide with CO2 was evaluated, revealing a notable activity for the coupling of 1-butene oxide.Scopu

Design, Synthesis and in Vivo Evaluation of Novel Glycosylated Sulfonylureas as Antihyperglycemic Agents

Sulphonylurea compounds have versatile activities such as antidiabetic, diuretic, herbicide, oncolytic, antimalarial, antifungal and anticancer. The present study describes the design, synthesis and in vivo testing of novel glycosylated aryl sulfonylurea compounds as antihyperglycaemic agents in streptozocine-induced diabetic mice. The rational for the introduction of the glucosamine moiety is to enhance selective drug uptake by pancreatic β-cells in order to decrease the cardiotoxic side effect commonly associated with sulfonylurea agents. 2-Deoxy-2-(4-chlorophenylsulfonylurea)-d-glucopyranose was found to be the most potent antihyperglycaemic agents among the synthesized compounds in diabetic mice. This investigation indicates the importance of this novel class as potential antihyperglycaemic agents

Data for: The reconstruction of long-term cyanobacterial dynamics using lake sediment DNA in relation to experimental eutrophication, acidification, and climate change

This repository includes the normalized ddPCR gene copy numbers (copies/g), raw ddPCR results (copies/uL), annual phytoplankton data, relative abundance data used in the analyses, annual climate data, and annual nutrient data for study lakes 227, 223, 224, and 442. </p