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

Editorial overview: recommendations for the promotion of a resilient linefishery in the Anthropocene

‘Linefish’ is a uniquely South African term used to describe marine fishes that are captured using hook and line. The South African linefishery is a complex socio-ecological system that has a considerable impact on the coastal marine environment while generating social and economic benefits for commercial, small-scale and recreational fishers. Like many fisheries, this complex system is under threat from the combined impacts of increasing levels of exploitation and climate change associated with the Anthropocene. The Southern African Marine Linefish Symposium (SAMLS) provides a platform for linefish scientists, managers, conservation officers, individuals from nongovernmental organisations, and other stakeholders to meet and exchange knowledge about the state and development of linefisheries. This overview discusses some of the long-term trends in linefish research during the last five symposia and highlights salient outcomes of the 5th SAMLS, which was held in July 2019. While the recovery and management success for some of South Africa’s commercial linefish species are recognised, the lack of policy and management in the recreational sector will not only undermine the implementation of the country’s new small-scale fisheries policy, but also the resilience of the socio-ecological system. To promote a resilient linefishery in the Anthropocene it is recommended that the fishery policies be strengthened to cover all sectors in the linefishery and that the general principles of the ecosystem approach to fisheries, including the incorporation of the human dimension and the implementation of co-management, are promoted. Improved communication between fishers, scientists, and managers is necessary, and recreational permit revenue should be used for research and monitoring to improve the management and stock assessment of species important to the recreational and small-scale sectors. Keywords: line fishing, Linefish Management Protocol, management, research priorit

South African marine citizen science – benefits, challenges and future directions

South Africa has a long history of engagement in citizen science (CS), particularly marine CS. This review examines the contributions made by marine CS, from the 1930s through to the current era, where websites, social media and mobile apps provide a wide range of opportunities. Largescale marine CS projects, such as the Oceanographic Research Institute’s Cooperative Fish Tagging Project, have made enormous contributions to marine scientific research. Individual citizen scientists have also made considerable contributions, particularly in taxonomy and the publication of field guides. Marine CS has also contributed towards the  popularisation of science and improved scientific literacy through the active engagement of many citizens. These benefits align well with the visions of policies that currently guide the South African marine research agenda. However, marine CS in the developing world is not without challenges, and practitioners should be cognisant of the time and effort required to initiate and maintain viable CS initiatives. Especially, long-term successful CS projects depend on secure, ongoing funding, institutional support and enthusiastic champions. Participation by almost exclusively the urban and middle-class sectors of society is also of concern. These challenges can be addressed through stakeholder-inclusive planning, development of novel methods that engage with broader sectors of society, and regular critical evaluations of CS projects. Where global projects on the intended taxa/subject of study already exist, it may also be preferable to enter into collaborative data-sharing agreements with these to reduce operational costs and avoid duplication

The characterization of lactic acid production bacteria from the rumen of dairy cattle grazing on improved pasture supplemented with wheat and barley grain

Aims: To identify and characterize the major lactic acid bacteria in the rumen of dairy cattle grazing improved pasture of rye grass and white clover and receiving a maize silage and grain supplement with and without virginiamycin. Methods and Results: Eighty-five bacterial isolates were obtained from the rumen of 16 Holstein-Friesian dairy cows. The isolates were initially grouped on the basis of their Gram morphology and by restriction fragment length polymorphism analysis of the PCR amplified 16S rDNA. A more definitive analysis was undertaken by comparing the 16S rDNA sequences. Many of the isolates were closely related to other previously characterized rumen bacteria, including Streptococcus bovis, Lactobacillus vitulinus, Butyrivibrio fibrisolvens, Prevotella bryantii and Selenomonas ruminantium. The in vitro production of l- and/or d-lactate was seen with all but five of the isolates examined, many of which were also resistant to virginiamycin. Conclusion: Supplementation of grain with virginiamycin may reduce the risk of acidosis but does not prevent its occurrence in dairy cattle grazing improved pasture. Significance and Impact of the Study: This study shows that lactic acid production is caused, not only by various thoroughly researched types of bacteria, but also by others previously identified in the rumen but not further characterized