Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections - a survival analysis

BACKGROUND: The extent to which the reduced risk of severe disease seen with SARS-CoV-2 Omicron is due to a decrease in variant virulence, or higher levels of population immunity, is currently not clear. METHODS: RdRp target delay (RTD) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from 1 November to 14 December 2021 in the Western Cape Province, South Africa, public sector. Vaccination status and prior diagnosed infection, were adjusted for. RESULTS: 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted Hazard Ratio [aHR] of 0.56, 95%CI 0.34-0.91). Complete vaccination was protective of admission with an aHR of 0.45 (95%CI 0.26-0.77). CONCLUSION: Omicron has resulted in a lower risk of hospital admission, compared to contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence

Modelling the impact of toxic and disturbance stress on white-tailed eagle (Haliaeetus albicilla) populations

Several studies have related breeding success and survival of sea eagles to toxic or non-toxic stress separately. In the present investigation, we analysed single and combined impacts of both toxic and disturbance stress on populations of white-tailed eagle (Haliaeetus albicilla), using an analytical single-species model. Chemical and eco(toxico)logical data reported from laboratory and field studies were used to parameterise and validate the model. The model was applied to assess the impact of ∑PCB, DDE and disturbance stress on the white-tailed eagle population in The Netherlands. Disturbance stress was incorporated through a 1.6% reduction in survival and a 10–50% reduction in reproduction. ∑PCB contamination from 1950 up to 1987 was found to be too high to allow the return of white-tailed eagle as a breeding species in that period. ∑PCB and population trends simulated for 2006–2050 suggest that future population growth is still reduced. Disturbance stress resulted in a reduced population development. The combination of both toxic and disturbance stress varied from a slower population development to a catastrophical reduction in population size, where the main cause was attributed to the reduction in reproduction of 50%. Application of the model was restricted by the current lack of quantitative dose–response relationships between non-toxic stress and survival and reproduction. Nevertheless, the model provides a first step towards integrating and quantifying the impacts of multiple stressors on white-tailed eagle populations

Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study.

Background: The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant’s disease severity in other settings, particularly in an African context, and when compared to the Beta variant. Methods: A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene AllplexTM 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. Results: A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). Conclusion: RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting

Neutron star parameter constraints for accretion-powered millisecond pulsars from the simulated IXPE data

We have simulated the X-ray polarization data that can be obtained with the Imaging X-ray Polarimetry Explorer, when observing accretion-powered millisecond pulsars. We estimated the necessary exposure times for SAX J1808.4-3658 in order to obtain different accuracy in the measured time-dependent Stokes profiles integrated over all energy channels. We found that the measured relative errors strongly depend on the relative configuration of the observer and the emitting hotspot. The improvement in the minimum relative error in Stokes Q and U parameters as a function of observing time t scales as 1/√ t, and it spans the range from 30-90% with a 200 ks exposure time to 20-60% with a 500 ks exposure time (in the case of data binned in 19 phase bins). The simulated data were also used to predict how accurate measurements of the geometrical parameters of the neutron star can be made when modelling only Q and U parameters, but not the flux. We found that the observer inclination and the hotspot co-latitude could be determined with better than 10° accuracy for most of the cases we considered. In addition, we show that the position of a secondary hotspot can also be constrained when the spot is not obscured by an accretion disc. These measurements can be used to further constrain the neutron star mass and radius when combined with modelling of the X-ray pulse profile

Effects of metal pollution on earthworm communities in a contaminated floodplain area: Linking biomarker, community and functional responses

Effects on earthworms in the contaminated floodplain area the Biesbosch, the Netherlands, were determined at different levels of organization using a combination of field and laboratory tests. The species Lumbricus rubellus, collected from different polluted sites in the Biesbosch, showed reduced values for the biomarker neutral red retention time (NRRT), mainly explained by high metal concentrations in the soil and the resulting high internal copper concentrations in the earthworms. Organic pollutant levels in earthworms were low and did not explain reduced NRRTs. Earthworm abundance and biomass were not correlated with pollutant levels in the soil. Litterbag decomposition and bait-lamina feeding activity, measures of the functional role of earthworms, were not affected by metal pollution and did not show any correlation with metal concentrations in soil or earthworms nor with NRRT. Effects at the biochemical level therefore did not result in a reduced functioning of earthworm communities. © 2008 Elsevier Ltd. All rights reserved

Effect of uneven sampling along an environmental gradient on transfer-function performance

We investigate the effect that uneven sampling of the environmental gradient has on transfer-function performance using simulated community data. We find that cross-validated estimates of the root mean squared error of prediction can be strongly biased if the observations are very unevenly distributed along the environmental gradient. This biased occurs because species optima are more precisely known (and more analogues are available) in the part of the gradient with most observations, hence estimates are most precise here, and compensate for the less precise estimates in the less well sampled parts of the gradient. We find that weighted averaging and the modern analogue technique are more sensitive to this problem than maximum likelihood, and suggest a way to remove the bias via a segment-wise RMSEP procedure