Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

The long-term effects of fire regime on primary production of montane grasslands in South Africa

Natural grasslands deliver essential ecosystem services through plant production, which enhances water supply, nutrient cycling, soil retention and greenhouse gas mitigation. Although the condition of montane grasslands for provision of ecosystem services is maintained by regular annual or biennial burning, controversy exists over the impact of different frequencies and seasons of burning on grassland productivity. The objective of this study was to determine the long-term effects of different burning regimes on primary production and quality of the montane grasslands of the KwaZulu-Natal Drakensberg. There were no significant differences in the mean standing live mass between 30 years of annual winter and biennial spring burning. However, in unburnt areas productivity was 20% lower (118.2 g m−2) than in  regularly burnt grassland (144.7–154.5 g m−2). Crude protein did not vary between the annual winter and biennial spring treatments (95–113 kg ha−1), but was  significantly lower in unburned areas (45 kg ha−1). However, an infrequent fire in a protected area caused a temporary spike in crude protein (16%) compared with regular burning (5–10%), which can benefit wildlife. We conclude that montane grasslands can be burnt annually or biennially in the dormant season to promote long-term productivity.Keywords: aboveground dry matter, crude fibre, crude protein, standing dea

The Applicability of the Cosmic Ray Neutron Sensor to Simultaneously Monitor Soil Water Content and Biomass in an Acacia mearnsii Forest

Soil water content is an important hydrological parameter, which is difficult to measure at a field scale due to its spatial and temporal heterogeneity. The Cosmic Ray Neutron Sensor (CRNS) is a novel and innovative approach to estimate area-averaged soil water content at an intermediate scale, which has been implemented across the globe. The CRNS is moderated by all hydrogen sources within its measurement footprint. In order to isolate the soil water content signal from the neutron intensity, the other sources of hydrogen need to be accounted for. The CRNS’s applications are not only limited to soil water content estimation, as it can potentially be used to monitor biomass. The Two-Streams clear-felling provided the unique opportunity to monitor the cosmic ray neutron intensities before, during, and after the clear-felling. The cadmium-difference method was used to obtain the pure thermal and epithermal neutron intensities from the bare and moderated detectors. The study concluded that the presence of biomass within the site reduced the epithermal neutron intensity by 12.43% and the N0 value by 13.8%. The use of the neutron ratio to monitor biomass was evaluated and changes in the neutron ratio coincided with biomass changes and resulted in a high correlation (R2 of 0.868) with the normalized difference vegetation index (NDVI) and (R2 of 0.817) leaf area index (LAI). The use of the CRNS to simultaneously monitor soil water content and biomass will be beneficial in providing more reliable soil water content estimates, provide biomass estimates at a field scale, and aid in understanding the dynamics between soil water content and vegetation

The population dynamics of four grass species in relation to burning in the KwaZulu-Natal Drakensberg

Marked tillers of Heteropogon contortus, Trachypogon spicatus, Tristachya leucothrix and Harpochloa falx were sampled regularly over a two-year period in Highland Sourveld burnt annually in winter and biennially in spring. Parameters recorded were height of shoot apex, tiller mass, number of new lateral tillers and time of flowering. Monitoring of marked tillers before and after each burn enabled the life history of populations of tillers to be followed. In all species investigated, flowering was found to be of minimal importance with most tillers remaining vegetative until death. Shoot apices remained close to the soil surface (<20 mm) enabling them to survive frequentburns. All species exhibited smooth survivorship curves, suggesting that dramatic fluctuations in climate and severe defoliation, as by fire, had little impact on mortality. The differential response of the four grass species was explained by their different reproductive capacities and reproductive rates. The predicted responses to fire regime were verified by changes that took place at the study area from 1981 to 2019, showing the importance of applying appropriate burning regimes to maintain the bud bank. A biennial spring burn was best for maintaining these important grass species at current levels of abundance in the KwaZulu-Natal Drakensberg. Keywords: bud banks, Leslie matrix, mortality, survivorshi

Frequent burning maintained a stable grassland over four decades in the Drakensberg, South Africa

The mesic montane grasslands of the uKhahlamba-Drakensberg, which produce cured flammable fuel, have evolved under and are sustained by recurrent fires. The Brotherton burning trial (12 replicated treatments) was established at Cathedral Peak (1 890 m asl) in 1980 to understand how burn season and frequency control the composition and diversity of the montane catchment grassland. Multivariate methods were used to examine the long-term (almost 40 years). compositional stability under different burning regimes. The species composition deviated steadily and markedly from the initial state (Bray–Curtis dissimilarity) by 43.4 ± 9.32% with quinquennial burning (alternating autumn/spring) and by 64.6 ± 2.24% with attempted fire exclusion (three unplanned burns). Composition was rapidly transformed (by 53.1 ± 4.6%) by biennial summer burning (discontinued in 1991). Dominance shifted from Themeda triandra to other grasses (Stiburus alopecuroides, Tristachya leucothrix, Harpochloa falx) with biennial summer and infrequent burning. In contrast, regular dormant season burning annually or biennially (in autumn, winter, or spring) maintained a stable grassland close to the original composition (mean deviation 23.08%). Burning homogenised the composition, overriding the initial extant small-scale spatial variation. Results support the current practice to burn biennially in the dormant season to maintain stable grassland in the Drakensberg catchments. Keywords: change, dominance, montane, species composition, stabilit

The Applicability of the Cosmic Ray Neutron Sensor to Simultaneously Monitor Soil Water Content and Biomass in an Acacia mearnsii Forest

Soil water content is an important hydrological parameter, which is difficult to measure at a field scale due to its spatial and temporal heterogeneity. The Cosmic Ray Neutron Sensor (CRNS) is a novel and innovative approach to estimate area-averaged soil water content at an intermediate scale, which has been implemented across the globe. The CRNS is moderated by all hydrogen sources within its measurement footprint. In order to isolate the soil water content signal from the neutron intensity, the other sources of hydrogen need to be accounted for. The CRNS’s applications are not only limited to soil water content estimation, as it can potentially be used to monitor biomass. The Two-Streams clear-felling provided the unique opportunity to monitor the cosmic ray neutron intensities before, during, and after the clear-felling. The cadmium-difference method was used to obtain the pure thermal and epithermal neutron intensities from the bare and moderated detectors. The study concluded that the presence of biomass within the site reduced the epithermal neutron intensity by 12.43% and the N0 value by 13.8%. The use of the neutron ratio to monitor biomass was evaluated and changes in the neutron ratio coincided with biomass changes and resulted in a high correlation (R2 of 0.868) with the normalized difference vegetation index (NDVI) and (R2 of 0.817) leaf area index (LAI). The use of the CRNS to simultaneously monitor soil water content and biomass will be beneficial in providing more reliable soil water content estimates, provide biomass estimates at a field scale, and aid in understanding the dynamics between soil water content and vegetation

Modelling annual evapotranspiration in a semi-arid, African savanna: functional convergence theory, MODIS LAI and the Penman–Monteith equation

Accurately measuring evapotranspiration (ET) is essential if we are to derive reasonable estimates of production and water use for semi-arid savannas. Estimates of ET are also important in defining the health of an ecosystem and the quantity of water used by the vegetation when preparing a catchment-scale water balance. We derived ET0 from an automatic weather station 30 km west of Skukuza, Kruger National Park, South Africa using the Penman– Monteith equation, and then used the MODIS LAI to inform the model of canopy phenological dynamics. This result was compared with 173 days of ET measurements from the eddy covariance (ETec) system near Skukuza in 2007 as well as from the ET recorded by a large-aperture scintillometer at the same site in 2005. The model compared favourably with both sets of measured data and, when used independently of the eddy covariance data, ETMODIS predicted an annual ET of 378 mm in 2007 for the semi-arid savanna around the Skukuza flux site.Keywords: LAI, modelling, plant production, remote sensin

Water use and potential hydrological implications of fast-growing Eucalyptus grandis x Eucalyptus urophylla hybrid in northern Zululand, South Africa

We measured the tree transpiration of 9-year-old, Eucalyptus grandis x Eucalyptus urophylla clonal hybrid (GU) trees in the commercial forestry area of northern KwaZulu-Natal, South Africa. Transpiration was measured using the heat ratio method over two consecutive hydrological years (2019/20 and 2020/21) and up-scaled to a stand level. Leaf area index (LAI), quadratic mean diameter, and soil water content (SWC) were measured over the same period using an LAI 2200 plant canopy analyser, manual dendrometers and CS616 sensors, respectively. The depth to groundwater was estimated to be approx. 28 m, using a borehole next to our study site. Results showed that transpiration followed a seasonal pattern, with daily mean of 2.3 mm‧tree−1‧day−1 (range: 0.18 to 4.55 mm‧tree−1‧day−1) and 3.3 mm‧tree−1‧day−1 (range: 0.06 to 6.6 mm‧tree−1‧day−1) for 2019/20 and 2020/21, respectively. Annual GU transpiration was higher than that found by international studies under similar conditions, but was within the same transpiration range as Eucalyptus genotypes in the KwaMbonambi area. Plantation water productivity, calculated as a ratio of stand volume to transpiration, was higher than for other published studies, which was attributed to a very high productive potential of the study site. Multiple regression using the random forests predictive model indicated that solar radiation, SWC and air temperature highly influence transpiration. There is a high possibility that our GU tree rooting system extracted water in the unsaturated zone during the dry season. Due to the use of short-term results in this study, the impact of GU on water resources could not be quantified; however, previous long-term paired catchment studies in South Africa concluded that Eucalyptus has a negative impact on water resources. Further research is suggested with long-term measurements of transpiration and total evaporation and an isotope study to confirm the use of water by GU trees in the unsaturated zone

Modelling annual evapotranspiration in a semi-arid, African savanna: functional convergence theory, MODIS LAI and the Penman–Monteith equation

Accurately measuring evapotranspiration (ET) is essential if we are to derive reasonable estimates of production and water use for semi-arid savannas. Estimates of ET are also important in defining the health of an ecosystem and the quantity of water used by the vegetation when preparing a catchment-scale water balance. We derived ET0 from an automatic weather station 30 km west of Skukuza, Kruger National Park, South Africa using the Penman– Monteith equation, and then used the MODIS LAI to inform the model of canopy phenological dynamics. This result was compared with 173 days of ET measurements from the eddy covariance (ETec) system near Skukuza in 2007 as well as from the ET recorded by a large-aperture scintillometer at the same site in 2005. The model compared favourably with both sets of measured data and, when used independently of the eddy covariance data, ETMODIS predicted an annual ET of 378 mm in 2007 for the semi-arid savanna around the Skukuza flux site