Regional importation and asymmetric within-country spread of SARS-CoV-2 variants of concern in the Netherlands

Variants of concern (VOCs) of SARS-CoV-2 have caused resurging waves of infections worldwide. In the Netherlands, Alpha, Beta, Gamma and Delta variants circulated widely between September 2020 and August 2021. To understand how various control measures had impacted the spread of these VOCs, we analyzed 39,844 SARS-CoV-2 genomes collected under the Dutch national surveillance program. We found that all four VOCs were introduced before targeted flight restrictions were imposed on countries where the VOCs first emerged. Importantly, foreign introductions, predominantly from other European countries, continued during these restrictions. Our findings show that flight restrictions had limited effectiveness in deterring VOC introductions due to the strength of regional land travel importation risks. We also found that the Alpha and Delta variants largely circulated more populous regions with international connections after their respective introduction before asymmetric bidirectional transmissions occurred with the rest of the country and the variant dominated infections in the Netherlands. As countries consider scaling down SARS-CoV-2 surveillance efforts in the post-crisis phase of the pandemic, our results highlight that robust surveillance in regions of early spread is important for providing timely information for variant detection and outbreak control.

IgG1 responses following SARS-CoV-2 infection are polyclonal and highly personalized, whereby each donor and each clone displays a distinct pattern of cross-reactivity against SARS-CoV-2 variants

Using a recently introduced efficient mass spectrometry-based approach we monitored individual donors IgG1 clonal responses in molecular detail, examining SARS-CoV-2 spike-protein-specific IgG1 repertoires. We monitored the plasma clonal IgG1 profiles of 8 donors (4 male and 4 female) who had recently experienced an infection by either the wild type Wuhan Hu-1 virus or one of 3 VOCs (Alpha, Beta and Gamma). In these donors we charted the full plasma IgG1 repertoires as well as the IgG1 repertoires targeting the SARS-CoV-2 spike protein trimer as antigen. We observed that shortly after infection in between <0.1% to almost 10% of all IgG1 antibody molecules present in plasma did bind to the spike protein. Each donor displayed a unique plasma IgG1 repertoire, but also each donor displayed a unique and polyclonal antibody response against the SARS-CoV-2 spike-protein variants. Our analyses revealed that certain clones exhibit (alike) binding affinity towards all four tested spike-protein variants, whereas other clones displayed strong unique mutant-specific affinity. We conclude that each infected person generates a unique polyclonal response following infection, whereby some of these clones can bind multiple viral variants, whereas other clones do not display such cross-reactivity. In general, by assessing IgG1 repertoires following infection it becomes possible to identify and select fully matured human plasma antibodies that target specific antigens, and display either high specificity or cross-reactivity versus mutated versions of the antigen, which will aid in selecting antibodies that may be developed into biotherapeutics.

Increased risk of infection with SARS-CoV-2 Omicron compared to Delta in vaccinated and previously infected individuals, the Netherlands, 22 November to 19 December 2021

Infections by the Omicron SARS-CoV-2 variant are rapidly increasing worldwide. Among 70,983 infected individuals (age [≥] 12 years), we observed an increased risk of S-gene target failure, predictive of the Omicron variant, in fully vaccinated (odds ratio: 5.0; 95% confidence interval: 4.0-6.1) and previously infected individuals (OR: 4.9: 95% CI: 3.1-7.7) compared with infected naive individuals. This suggests a substantial decrease in protection from vaccine- or infection-induced immunity against SARS-CoV-2 infections caused by the Omicron variant compared with the Delta variant.

Declining SARS-CoV-2 PCR sensitivity with time and dependence on clinical features: consequences for control

Real-time reverse transcription-polymerase chain reaction (RT-PCR) on upper respiratory tract (URT) samples is the primary method to diagnose SARS-CoV-2 infections and guide public health measures, with a supportive role for serology. However, the clinical sensitivity of RT-PCR remains uncertain. In the present study, Bayesian statistical modeling was used to retrospectively determine the sensitivity of RT-PCR using SARS-CoV-2 serology in 644 COVID-19-suspected patients with varying degrees of disease severity and duration. The sensitivity of RTPCR ranged between 79-95%; while increasing with disease severity, it decreased rapidly over time in mild COVID-19 cases. Negative URT RT-PCR results should therefore be interpreted in the context of clinical characteristics, especially with regard to containment of viral transmission based on the test, trace and isolate principle.

Comparison of commercial RT-PCR diagnostic kits for COVID-19

The final months of 2019 witnessed the emergence of a novel coronavirus in the human population. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has since spread across the globe and is posing a major burden on society. Measures taken to reduce its spread critically depend on timely and accurate identification of virus-infected individuals by the most sensitive and specific method available, i.e. real-time reverse transcriptase PCR (RT-PCR). Many commercial kits have recently become available, but their performance has not yet been independently assessed. The aim of this study was to compare basic analytical and clinical performance of selected RT-PCR kits from seven different manufacturers (Altona Diagnostics, BGI, CerTest Biotec, KH Medical, PrimerDesign, R-Biopharm AG, and Seegene). We used serial dilutions of viral RNA to establish PCR efficiency and estimate the 95% limit of detection (LOD95%). Furthermore, we ran a panel of SARS-CoV-2-positive clinical samples (n=16) for a preliminary evaluation of clinical sensitivity. Finally, we used clinical samples positive for non-coronavirus respiratory viral infections (n=6) and a panel of RNA from related human coronaviruses to evaluate assay specificity. PCR efficiency was [≥]96% for all assays and the estimated LOD95% varied within a 6-fold range. Using clinical samples, we observed some variations in detection rate between kits. Importantly, none of the assays showed cross-reactivity with other respiratory (corona)viruses, except as expected for the SARS-CoV-1 E-gene. We conclude that all RT-PCR kits assessed in this study may be used for routine diagnostics of COVID-19 in patients by experienced molecular diagnostic laboratories.

Microstructure and properties of crystalline bioglass compositions prepared by polymeric route.

The standard bioglass composition GS45 as well as with excess silica GS50 or with the addition of 5% titanium oxide GS45+Ti5, were prepared by the polymeric route. The different glass components were added to the formed polymer. Firing at 700 degrees C gave an amorphous product with microporous texture that readily crystallizes out at 900 degrees C. The prepared materials were highly porous with two modes of pore system micro-pores and macro-pores with a size ranging between 100 microm to 0.006 microm and a porosity reaching 73%. The measured bulk density was between 0.36 to 1.1g/cm3. The fired material preserved the former structure of the polymer precursor. Biocompatibility was verified in vitro and vivo. IR of the specimens previously immersed in SBF revealed the formation of apatite like layer. While the histology sections of implants in rate femurs showed new bone tissue or bone trabeculae after 21 days.

Temperature calibration of Pico-Rad detectors for radon measurement.

A simple mathematical equation linking the activity of adsorbed radon in the vials to the time and temperature of its exposure is discussed. The calibration coefficient--Ks, defined as activity measured in cpm after saturation time, corresponding to radon air concentration of 1 Bq m-3, was determined for four temperatures: 284, 291, 294 and 298 K. A linear relationship of ln Ks values versus T-1 was found. The relatively high difference in Ks values: 2.12 and 1.24 cpm/Bq m-3 for the temperatures of 284 and 298 K, respectively, was observed. It indicates that temperature fluctuations during Pico-Rad vial exposure may lead to erroneous results if the constant average temperature of exposure is introduced into a commonly used computer programme for calculating Rn concentration.

The monitoring of cadmium, zinc and copper in the kidneys and liver of humans deceased in the region of Cracow (Poland).

Cadmium, zinc and copper levels were determined in the renal cortex and liver of 60 inhabitants of Cracow, Poland. Cadmium levels in the renal cortex were contained in broad limits of 5-176 µg/g, mean 50.6 µg/g (wet weight). Maximum levels were found in the age group of about 50-60 years. The levels were slightly higher in men (53 µg/g) than in women (45 µg/g), with no effect of location within the region. The levels in smokers (62 µg/g) were much higher than in non-smokers (32 µg/g). The above relations were less pronounced for cadmium levels in the liver. Whole body retention of cadmium followed the pattern of cadmium in renal cortex. The level of zinc in renal cortex reflected those of cadmium. A significant proportion of the population (54% in smokers, 9% in non-smokers) showed cadmium levels in renal cortex exceeding the reference level of 50 µg/g recently accepted for general population. In the view of the authors the exposure to cadmium of the population of Cracow is excessive and calls for attention.

Cadmium, zinc, and copper levels in the kidneys and liver of the inhabitants of north-eastern Poland.

Concentrations of Cd, Zn, and Cu were determined in the renal cortex and the liver of 79 persons who died in 1991 in Bialystok and its vicinity. The mean concentrations were: 30.5 +/- 27.7 micrograms Cd/g, 37.6 +/- 18.5 micrograms Zn/g, 2.6 +/- 2.5 micrograms Cu/g, and 2.1 +/- 2.2 micrograms Cd/g, 52.4 +/- 20.5 micrograms Zn/g, 4.0 +/- 2.1 micrograms Cu/g, respectively, in the renal cortex and the liver, at the mean age of 51.1 +/- 19.1 years. Smokers showed almost twice higher Cd levels in the cortex than non-smokers. The mean whole body retention calculated for cadmium was 18.9 +/- 15.9 mg. Smoking increases it by about 60%--from 13.7 mg in non-smokers to 22.8 mg in smokers. In the inhabitants of the investigated region cadmium levels (kidney, liver, whole body retention) were lower than in persons from Lodz and Katowice regions.

Cadmium, zinc, copper, and metallothionein levels in the kidney and liver of inhabitants of upper Silesia (Poland).

The levels of Cd, Zn, Cu and metallothionein (MT) were determined in renal cortex and liver of 75 subjects decreased in the period 1986-1989 in the area of Upper Silesia (Katowice). The mean age of the population studied was 53.6 +/- 14.6 years. The determined levels (mean +/- SD) were: 43.1 +/- 23.5 micrograms Cd/g; 52.5 +/- 17.4 micrograms Zn/g; 2.2 +/- 0.7 microgram Cu/g; 0.80 +/- 0.36 mumol Hg/g in renal cortex and 3.5 +/- 2.5 micrograms Cd/g; 82.8 +/- 34.3 micrograms Zn/g; 4.5 +/- 2.6 micrograms Cu/g; 0.69 +/- 0.44 mumol Hg/g in the liver. The level of Cd in renal cortex was 40% higher in smokers compared to nonsmokers and was independent of the gender. Whole-body retention of Cd was 34.1 +/- 18.5 mg; smoking elevated the value from 27.1 to 38.2 mg. Compared with a similar study made in central Poland (Lódz), a significant difference was found only regarding the level of Zn and MT in the liver, pointing to the possibility that exposure to this element in the region of Upper Silesia may be higher.

Cadmium, zinc, copper and metallothionein levels in the kidney and liver of humans from central Poland.

Cd, Zn, Cu, and metallothionein (MT) levels have been determined in the renal cortex and liver of 70 persons who died in Lodz and its surroundings in the years 1985-1989. The mean concentrations were: 44.9±28.6 µg Cd/g, 52.0±16.7 µg Zn/g, 2.4±1.0 µg Cu/g, 0.79±0.40 µmol Hg/g, and 3.5±1.8 µg Cd/g, 66.7±30.5 µg Zn/g, 4.9±2.1 µg Cu/g, 0.50±0.38 µmol Hg/g wet tissue in renal cortex and liver, respectively, with mean age 54.0±13.8. Smokers showed 2.4 times higher levels of Cd in the renal cortex than non-smokers. The mean body burden of Cd was 33.4±17.3 mg. Smoking increases it twofold from 22.0 mg in non-smokers to 41.8 mg in smokers.

Renal binding of cadmium in the rat following intragastric exposure.

Renal binding of cadmium was compared in groups of rats administered cadmium intragastrically or subcutaneously in doses resulting in similar renal cadmium concentrations. In rats administered cadmium intragastrically the renal concentrations of copper and metallothionein were lower, suggesting disturbance in copper metabolism. These changes were alleviated gradually in the post-exposure period. In experiments with 64Cu it has been shown that intragastric exposure to cadmium reduced copper absorption to about 21% of that in the control rats, thus explaining the poor copper availability for renal binding of cadmium in the form of Cd,Cu-metallothionein. Changes in zinc uptake were less strongly marked and were limited to slight decrease of zinc content in the kidneys.

Cadmium and metallothionein levels in the liver of humans exposed to environmental cadmium in Upper Silesia, Poland.

The area of Upper Silesia is the most industrialized region in Poland. The concentrations of cadmium (Cd), zinc (Zn), copper (Cu) and metallothionein (MT) in autopsy samples (n = 29) of liver from the inhabitants of that area were determined. The metal levels varied in the ranges of 0.5-11.9 micrograms Cd/g, 45.3-221.6 micrograms Zn/g, 1.4-10.3 micrograms Cu/g. The concentration of MT determined by the Hg-method was high: 0.38-2.86 mumol Hg/g. A positive linear relationship was observed between Zn and MT levels.

Cadmium, zinc, copper and metallothionein levels in human liver.

The concentrations of cadmium, zinc, copper and metallothionein in the autopsy samples of liver among the inhabitants of Lódz (Poland) were determined. The cadmium levels were low in the range of 1.5 to 5.8 micrograms/g. The concentration of metallothionein determined by the Hg-method was high (0.160-1.665 mumol Hg/g); it was mainly a Zn-thionein. The percentage of hepatic zinc bound in the MT-fraction increased with the overall content of zinc in the liver. The elevation of zinc in the liver occurs in the proportion required for the saturation of metal-binding ligands of metallothionein. The role of cadmium remains less clear. Our results suggest that the metallothionein level in the liver increase significantly in response to elevated cadmium concentrations. This response, however, is in high excess to the demand which is justified stoichiometrically.

Influence of mercury (II), cadmium (II), methylmercury, and phenylmercury on the kinetic properties of rat liver glutathione peroxidase.

The effect of phenylmercury and methylmercury on rat liver glutathione peroxidase (GSH X Px) is investigated and compared with that of Hg(II) and with some previously reported results for Cd(II). Analysis of the kinetics of metal binding to the enzyme gives apparent inhibition rate constants: kc = 9.7 mM-1 min-1 for all three mercury compounds and 75 mM-1 min-1 for CdCl2. Glutathione (0.2 mM) protects the enzyme from metal inhibition, decreasing the apparent inhibition rate constants (kc) by 3.6 times for mercury compounds and 4.4 times for CdCl2. KI for the three mercury compounds is found to be 53 microM. It is unexpected that the same value of KI exists for all three forms of mercury studied and that inhibition of the enzyme by the metals is a relatively slow process. For Cd(II) the value of KI is 8.5 microM. It is suggested that inhibition of GSH X Px enzyme activity by cadmium, mercury, and organic mercury salts may not be due to simple complexation of the active site selenium moiety but may be due to a slower process, e.g., an alteration of the enzyme tertiary or quaternary structure.

The tissue disposition of zinc and copper following repeated administration of cadmium and selenium to rats.

Female rats were divided into four groups of five rats each including one control group (C). The animals were administered Na2SeO3 (Se), (CdCl2 Cd), and Na2SeO3 + CdCl2 (Cd + Se). Sodium selenite was given intragastrically at a dose of 0.5 mg Se/kg every day and cadmium chloride was injected subcutaneously every other day at a dose of 0.3 mg Cd/kg for 2 weeks. Exposure of rats to Cd caused an increase in the concentration of copper in the kidneys, blood, and liver and a decrease in the lung, but increased the concentration of zinc in the liver and brain and diminished it in the muscles and bones. In animals exposed to Se an increase in the copper concentration was observed in blood and brain; zinc was increased in the blood, heart, brain, and stomach, but decreased in the kidneys. Exposure of rats to Cd + Se resulted in an increase of copper in the kidneys and a decrease in the spleen, lungs, stomach, muscles and bones. Se prevented the cadmium-induced diminution of the zinc levels in the muscles and bones.

Organ and subcellular distribution of cadmium in rats exposed to cadmium, mercury, and selenium.

Four groups of rats were given: cadmium chloride (Cd), cadmium chloride and mercuric chloride (Cd + Hg), cadmium chloride and sodium selenite (Cd + Se), or cadmium chloride, mercuric chloride, and sodium selenite (Cd + Hg + Se). All animals received subcutaneous doses of 115mCdCl2 (0.3 mg Cd/kg) every other day for 2 weeks. Mercuric chloride was administered intravenously at doses of 0.5 mg Hg/kg every other day, and Na2 75SeO3 intragastrically at doses of 0.1 mg Se/kg every day for a fortnight. The whole-body and organ retention of cadmium changed slightly with the type of exposure. A significant interaction effect of the examined elements was noted in the nuclear and soluble fractions of the liver and kidneys. Mercury decreased the cadmium concentration in both the nuclear and soluble fractions of the kidneys and diminished the effect of selenium on the cadmium level in the soluble fraction of the kidneys. In the liver the presence of mercury contrary to selenium, lowered the cadmium level in the nuclear fraction. The pattern of cadmium binding to proteins of the soluble fraction of the kidneys and liver remained the same in all groups of animals.

Organ and subcellular distribution of selenium in rats exposed to cadmium, mercury, and selenium.

Three groups of rats were given sodium selenite (Se), sodium selenite and cadmium chloride (Se + Cd), or sodium selenite, cadmium chloride, and mercuric chloride (Se + Cd + Hg), respectively. All animals received subcutaneous doses of 115CdCl2 (0.3 mg Cd/kg) every other day for a fortnight. Mercuric chloride was administered intravenously at doses of 0.5 mg Hg/kg every other day and Na2 75SeO3 intragastrically at doses of 0.1 mg Se/kg every other day for 2 weeks. The whole-body retention of selenium was slightly elevated by cadmium and increased threefold by cadmium with mercury (mainly blood, liver, and kidneys). Cadmium did not affect subcellular levels of selenium in the kidneys and slightly increased the selenium content in the soluble fraction of the liver. On the other hand, combined administration of mercury and cadmium induced a significant elevation of the selenium content in all subcellular fraction of the kidneys and in the nuclear and mitochondrial fractions of the liver. In all animal groups selenium was bound in the soluble fractions of both the liver and kidneys by high-molecular-weight proteins.

Determination of selenium in the environment and in biological material.

This paper reviews the following problems, sampling, decomposition procedures and most important analytical methods used for selenium determination, e.g., neutron activation analysis, atomic absorption spectrometry, gas-liquid chromatography, spectrophotometry, fluorimetry, and x-ray fluorescence. This review covers the literature mainly from 1975 to 1977.