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 hospitalization2–4 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

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

Reproductive aspects of the Purple-throated Euphonia, Euphonia chlorotica (Aves: Fringillidae) in southeastern Brazil, and first record of the species nesting inside a vespiary

Despite the fact that E. chlorotica (Linnaeus, 1766) is common and widely distributed in South America, the reproductive aspects of the species are poorly documented. Here we present data on 18 active nests found from August to February, between 2007 and 2012. Nests were globular with a lateral entrance, and measured 97.9 ± 14.4 mm in outside height, 110.6 ± 11.6 mm in outside diameter, and were 4.88 ± 2.09 m above ground. They were often supported from bellow and were composed mainly of tiny dry leafs and leaflets, fine petioles, and plumed seeds, all compacted with spider web silk. Eggs were laid on consecutive days or with one day interval, and clutch size varied from 1–3 eggs (2.1 ± 0.6, n = 9 nests). Only females incubated the eggs, but both sexes were involved in nest construction and nestling attendance at similar rates. Incubation and nestling periods were 14 and 21 days, respectively, and overall nest survival probability was 5%. A vespiary used for nesting was not occupied by wasps and nest material was deposited only to form the incubatory chamber. Although nesting near wasps or bees is a widespread strategy among birds in general, nesting inside the nests of social insects is a poorly documented behavior

First complete description of nest, eggs, and nestlings of the Squamate Antbird, Myrmoderus squamosus (Aves: Thamnophilidae)

Even though nest architecture has been useful for phylogenetic inferences among the Thamnophilidae (Aves: Passeriformes), the nests of only three out of five species of Myrmoderus (Ridgway, 1909) are known to science. Here we describe the nests, eggs, and nestling of the Squamate Antbird Myrmoderus squamosus (Pelzeln, 1868). Two nests were bulky bottom-supported cups, measuring 7.3 and 12 cm in maximum outside diameter, with a noticeably smaller egg cup, and they were placed within the crown of short, broad-leafed plants. Eggs were short-oval, with chalky white background color, and purple blotches and streaks more concentrated in the large end. One nestling was dark reddish grey, with bluish white feet, pinkish gray tarsi, and a blackish bill with bright yellow rictal flanges. In face of the great diversity of nest types found among the Thamnophilidae, we concluded that the nest of M. squamosus was similar to those of other congeners, giving support to this currently phylogenetically-defined genus

Successional stage effect on the availability of tree cavities for cavity-nesting birds in an Atlantic Forest park from the state of São Paulo, Brazil

<div><p>Abstract The availability of suitable cavities and substrate for hole construction can limit the populations of birds that rely on tree hollows to reproduce. Several studies have focused on the effects of types of habitats, and types of human disturbances on cavities abundance, but the effect of successional stages in the Atlantic Forest has been poorly addressed. In this study we aimed to compare the availability and biometric characteristics of tree cavities between primary and mid-successional stage sites in an Atlantic Forest area from southeastern Brazil. Based on nest characteristics described in the literature, we inferred if hollows present in secondary sites could harbor the large secondary-nester Atlantic Forest birds, with special attention to toucans and hawks. From September 2016 to April 2017, 96 cavities were sampled, 67 in the primary, and 29 in the secondary plots. Our data revealed that the communities of cavity-nester birds in mid-successional stage areas may be more affected by the reduced cavity availability than by cavities quality, as the number of cavities in these sites was less than half than that found in mature forests. We also provide evidences that the largest cavity nesters, such as the biggest hawks, might have limited nesting possibilities in mid-successional stage areas especially due to small cavity entrances, which may have important reflects in conservation strategies.</p></div

Testing camera traps as a potential tool for detecting nest predation of birds in a tropical rainforest environment

Identification of the predators of bird nests is essential to test ecological and evolutionary hypotheses and to make practical management decisions. A variety of nest monitoring devices have been proposed but many remain difficult to set up in the field. The aim of this study was to test camera traps as a potential tool to study predation of natural nests in a tropical rainforest environment. Specifically, we registered the predators, assessed their size range, and we compared the use of one and two cameras per nest. Of 122 nests from 24 bird species, 45 (37%) were depredated, and the cameras recorded the predator species in 29 of the total of depredated nests (64%). We identified predators in eight of 16 depredated nests (50%) in which we used one camera trap per nest, and we identified predators in 21 of 29 depredated nests (72%) when we used two camera traps per nest. The predators included six species of birds and six species of mammals, with body masses varying from 20 g to 16.5 kg. Causes for 10 of the 16 detection failures were identified and are discussed. These results suggest that camera traps are viable tools to investigate nest predation in a tropical rainforest area