Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Activity of some plant oils and extracts against Collectotrichum gloeosporioides

The antifungal effects of a range of plant extracts and oils were studied in a series of in vitro experiments against Colletotrichum gloeosporioides isolated from black pepper (Piper nigrum L.). Spore germination of the fungus was completely inhibited by cinnamon (Cinnamomum zeylanicum Blume.) oils as well as by water or ethanol extracts from galangal (Alpinia galanga L. Willd.) rhizomes and cardamom (Elettaria cardamomum Maton.) leaves. Ethanol extracts were more efficient in inhibiting spore germination than water extracts. Phytotoxicity symptoms were not observed or were minimal on pepper leaves and berries or red pepper fruits when treated with cardamom extract and galangal extract and a group of oils of cardamom, Eucalyptus, lesser galangal, lemon grass, lemon myrtle, neem, pepper black and tea-tree, but were pronounced with cinnamon oils. Cardamon oil was non toxic, but was required in higher concentrations to completely inhibit germination

A laboratory study of application of basalt dust to highly weathered soils: effect on soil cation chemistry

Surface (0–10 cm) samples from 7 highly weathered soils in tropical coastal Queensland were incubated for 3 months at room temperature and at field moisture capacity with basalt dust applied in 2 size fractions: <150 μm and 40 μm. The basalt application was mixed at 0, 1, 5, 25, and 50 t/ha to cover situations of moderate applications as well as where the amendment might be banded to achieve high local concentrations. Basalt dust application caused desirable increases in soil pH, reduced the content of exchangeable acidic cations, increased soil cation exchange capacity, and increased the content of base cations in all soils. By determining fundamental surface charge characteristics of these variable charge soils, it was possible to show that the additional base cations released from the basalt dust were present as exchangeable cations, and that the amounts released were controlled by the number of negatively charged sites available, i.e. soil cation exchange capacity. Selected treatments were then subjected to a strong leaching environment to assess the longevity of the effects obtained. Soil properties remained virtually unchanged by the leaching treatment, except that significant amounts of monovalent K and Na were removed. At the higher rates of application, the amounts of base cations released from the basalt were small in comparison with the actual amounts applied, indicating that the amendment could be effective over a considerable period of time

Antifungal activity of selected aromatic and volatile oils and plant extracts on putative plant pathogens

A range of aromatic and volatile plant oils (0.1-3% concentration) were shown to inhibit spore germination of putative pathogens isolated from black pepper, cinnamon and\ud turmeric. Cinnamon and clove bark and leaf oils were more efficient inhibitors than the synthetic fungicide Amistar TM\ud used at recommended field concentrations. Cinnamon oils were\ud usually completely inhibitory of spore germination at low\ud concentrations. Garlic oil completely inhibited Phoma, but was less effective on all other fungal species. Oils of lemon grass leaf, lesser galangal rhizome, cardamom seed, and lemon myrtle leaf restricted spore germination at relatively high concentrations (0.5-1%). Lemongrass leaf oil completely inhibited spore germination of Pestalotiopsis cf. versicolor isolated from cinnamon leaves at all concentrations tested. Extracts from galangal rhizomes and cardamom leaves inhibited spore germination. Ethanol extracts had a greater ability to inhibit spore germination than corresponding water extracts. Ethanol extracts from galangal stem and cinnamon bark were particularly inhibitory. Meanwhile, cinnamon bark extract\ud tended to inhibit both putative pathogens and saprophytic fungi but it was less efficient on Pestaiotiopsis sp. isolated from cinnamon leaves

Amending highly weathered soils with finely ground basalt rock

Surface (0–10 cm) samples of 7 soils from tropical coastal Queensland were incubated at room temperature and at field capacity with finely ground (<150 μ) basalt rock for 3 months. The amendment was applied at 0, 1, 5, 25 and 50 t/ha to cover situations of moderate application rates to that where the amendment might be banded to produce high local concentrations. Having an abrasion pH of about 9, the amendment was able to reduce both active acidity (as estimated by an increase in soil pH) and reserve acidity (reduction in % Al saturation of the CEC). Increases in soil pH resulted in increased CEC, depending on the variable charge nature of each soil, accompanied by increases in exchangeable Ca, Mg, and K supplied by the basalt. The amounts of basic cations converted to exchangeable form constituted only a fraction of the amounts applied. Thus the cations held in reserve ensure that the effect of cation enrichment will be prolonged. In some soils phosphate sorption was significantly reduced by crushed basalt application. Furthermore, ‘available’ P as measured by extraction with 0.005 M H2SO4 was increased. These effects appear to be due to the release of silicate from the basalt as well as modest amounts of phosphate in the rock. Three extractants commonly used for estimating Si availability in sugarcane production indicated that all 7 soils contained sub-optimal levels of the element. Application of crushed basalt rock increased extractable Si levels above what is considered sufficient for this crop. The incubated soils were placed in columns and leached with the equivalent of 2750-mm (average wet season) rainfall. Re-analysis showed that the favourable chemical soil properties imparted by the amendment were retained. These results add further support to the contention that the effects of amelioration will continue for some tim

Maintenance of fruit quality in organically-grown bananas under modified atmosphere conditions

The effects of modified atmosphere packaging at low storage temperature on the quality of organic bananas (cv. Cavendish) were investigated. Polybags, with or without an ethylene scavenger, significantly reduced (p<0.05) the total weight loss of bananas during storage for 25 days and fruit firmness was favoured by packaging. Bags containing a scavenger prevented the peel colour changing beyond the classification ‘greener than yellow’ over 25 days and total soluble solids were lower than in unwrapped fruit. The fruit was not treated with fungicide yet disease levels were relatively low at 25 days. Shelf life extension to 62 days was possible in polybags containing potassium permanganate when held at 14?C. When the scavenger was omitted, storage life was 55 days, yet acceptable taste and other quality were maintained