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

Does the giant wood spider Nephila pilipes respond to prey variation by altering web or silk properties?

Recent studies demonstrated that orb-weaving spiders may alter web architectures, the amount of silk in webs, or the protein composition of silks in response to variation in amount or type of prey. In this study, we conducted food manipulations to examine three mechanisms by which orb-weaving spiders may adjust the performance of webs to variation in prey by altering the architectures of webs, making structural changes to the diameters of silk threads, and manipulating the material properties or amino acid composition of silk fibers. We fed Nephila pilipes two different types of prey, crickets or flies, and then compared orb structure and the chemical and physical properties of major ampullate (MA) silk between groups. Prey type did not affect orb structures in N. pilipes, except for mesh size. However, MA silk diameter and the stiffness of orbs constructed by spiders fed crickets were significantly greater than for the fly group. MA fibers forcibly silked from N. pilipes fed crickets was significantly thicker, but less stiff, than silk from spiders fed flies. Spiders in the cricket treatment also produced MA silk with slightly, but statistically significantly, more serine than silk from spiders in the fly treatment. Percentages of other major amino acids (proline, glycine, and glutamine) did not differ between treatments. This study demonstrated that orb-weaving spiders can simultaneously alter some structural and material properties of MA silk, as well as the physical characteristics of webs, in response to different types of prey

Phylogeny of the orb‐weaving spider family Araneidae (Araneae: Araneoidea)

We present a new phylogeny of the spider family Araneidae based on five genes (28S, 18S, COI, H3 and 16S) for 158 taxa, identified and mainly sequenced by us. This includes 25 outgroups and 133 araneid ingroups representing the subfamilies Zygiellinae Simon, 1929, Nephilinae Simon, 1894, and the typical araneids, here informally named the “ARA Clade”. The araneid genera analysed here include roughly 90% of all currently named araneid species. The ARA Clade is the primary focus of this analysis. In taxonomic terms, outgroups comprise 22 genera and 11 families, and the ingroup comprises three Zygiellinae and four Nephilinae genera, and 85 ARA Clade genera (ten new). Within the ARA Clade, we recognize ten informal groups that contain at least three genera each and are supported under Bayesian posterior probabilities (≥ 0.95): “Caerostrines” (Caerostris, Gnolus and Testudinaria), “Micrathenines” (Acacesia, Micrathena, Ocrepeira, Scoloderus and Verrucosa), “Eriophorines” (Acanthepeira, Alpaida, Eriophora, Parawixia and Wagneriana), “Backobourkiines” (Acroaspis, Backobourkia, Carepalxis, Novakiella, Parawixia, Plebs, Singa and three new genera), “Argiopines” (Arachnura, Acusilas, Argiope, Cyrtophora, Gea, Lariniaria and Mecynogea), “Cyrtarachnines” (Aranoethra, Cyrtarachne, Paraplectana, Pasilobus and Poecilopachys), “Mastophorines” (Celaenia, Exechocentrus and Mastophora,), “Nuctenines” (Larinia, Larinioides and Nuctenea), “Zealaraneines” (Colaranea, Cryptaranea, Paralarinia, Zealaranea and two new genera) and “Gasteracanthines” (Augusta, Acrosomoides, Austracantha, Gasteracantha, Isoxya, Macracantha, Madacantha, Parmatergus and Thelacantha). Few of these groups are currently corroborated by morphology, behaviour, natural history or biogeography. We also include the large genus Araneus, along with Aculepeira, Agalenatea, Anepsion, Araniella, Cercidia, Chorizopes, Cyclosa, Dolophones, Eriovixia, Eustala, Gibbaranea, Hingstepeira, Hypognatha, Kaira, Larinia, Mangora, Metazygia, Metepeira, Neoscona, Paraplectanoides, Perilla, Poltys, Pycnacantha, Spilasma and Telaprocera, but the placement of these genera was generally ambiguous, except for Paraplectanoides, which is strongly supported as sister to traditional Nephilinae. Araneus, Argiope, Eriophora and Larinia are polyphyletic, Araneus implying nine new taxa of genus rank, and Eriophora and Larinia two each. In Araneus and Eriophora, polyphyly was usually due to north temperate generic concepts being used as dumping grounds for species from southern hemisphere regions, e.g. South-East Asia, Australia or New Zealand. Although Araneidae is one of the better studied spider families, too little natural history and/or morphological data are available across these terminals to draw any strong evolutionary conclusions. However, the classical orb web is reconstructed as plesiomorphic for Araneidae, with a single loss in “cyrtarachnines”–“mastophorines”. Web decorations (collectively known as stabilimenta) evolved perhaps five times. Sexual dimorphism generally results from female body size increase with few exceptions; dimorphic taxa are not monophyletic and revert to monomorphism in a few cases

The survival of patients with heart failure with preserved or reduced left ventricular ejection fraction: an individual patient data meta-analysis

Aims A substantial proportion of patients with heart failure have preserved left ventricular ejection fraction (HF-PEF). Previous studies have reported mixed results whether survival is similar to those patients with heart failure and reduced EF (HF-REF). Methods and results We compared survival in patients with HF-PEF with that in patients with HF-REF in a meta-analysis using individual patient data. Preserved EF was defined as an EF = 50%. The 31 studies included 41 972 patients: 10 347 with HF-PEF and 31 625 with HF-REF. Compared with patients with HF-REF, those with HF-PEF were older (mean age 71 vs. 66 years), were more often women (50 vs. 28%), and have a history of hypertension (51 vs. 41%). Ischaemic aetiology was less common (43 vs. 59%) in patients with HF-PEF. There were 121 [95% confidence interval (CI): 117, 126] deaths per 1000 patient-years in those with HF-PEF and 141 (95% CI: 138, 144) deaths per 1000 patient-years in those with HF-REF. Patients with HF-PEF had lower mortality than those with HF-REF (adjusted for age, gender, aetiology, and history of hypertension, diabetes, and atrial fibrillation); hazard ratio 0.68 (95% CI: 0.64, 0.71). The risk of death did not increase notably until EF fell below 40%. Conclusion Patients with HF-PEF have a lower risk of death than patients with HF-REF, and this difference is seen regardless of age, gender, and aetiology of HF. However, absolute mortality is still high in patients with HF-PEF highlighting the need for a treatment to improve prognosis