Novel Mutations of TYK2 Leading to Divergent Clinical Phenotypes

TYK2 deficiency is a rare Primary immunodeficiency disease caused by loss of function mutations of TYK2 gene, which is initially proposed as a subset of Hyper IgE syndrome (HIES). However, accumulating evidence suggest TYK2 deficient patients do not necessarily present with HIES characteristics, indicating a vacuum of knowledge on the exact roles of TYK2 in human immune system. Here we describe five more TYK2 deficient cases presenting with or without hyper IgE levels, atopy and distinct pathogen infection profile, which are caused by novel TYK2 mutations. These mutations were all found by high throughout sequencing and confirmed by Sanger sequencing. Pathogenic effects were confirmed by qRT-PCR and western blot. Peripheral blood mononulear cells (PBMCs) from these patients showed heterogenous responses to various cytokines treatment, including IFN-a/b/g, IL-6, IL-10, IL12 and IL-23. The homeostasis of lymphocytes is also disrupted. Based on our findings, we propose that TYK2 works as a multi-tasker in orchestrating various cytokines signaling pathways, differentially combined defects of which account for the expressed clinical manifestations.

Four novel Picornaviruses detected in Magellanic Penguins (Spheniscus magellanicus) in Chile

Members of the Picornaviridae comprise a significant burden on the poultry industry, causing diseases such as gastroenteritis and hepatitis. However, with the advent of metagenomics, a number of picornaviruses have now been revealed in apparently healthy wild birds. In this study, we identified four novel viruses belonging to the family Picornaviridae in healthy Magellanic Penguins (Spheniscus magellanicus), a near threatened species found along the coastlines of temperate South America. We collected 107 faecal samples from 72 individual penguins. Twelve samples were initially sequenced by high throughout sequencing with metagenomics approach. All samples were subsequently screened by PCR for these new viruses, and approximately 20% of the penguins were infected with at least one of these viruses, and seven individuals were co-infected with two or more. The viruses were distantly related to members of the genera Hepatoviruses, Tremoviruses and unassigned viruses from Antarctic Penguins and Red-Crowned Cranes. Further, they had more than 60% amino acid divergence from other picornaviruses, and therefore likely constitute novel genera. That these four novel viruses were abundant among the sampled penguins, suggests Magellanic Penguins may be a reservoir for several picornaviruses belonging to different genera. Our results demonstrate the vast undersampling of wild birds for viruses, and we expect the discovery of numerous avian viruses that are related to Hepatoviruses and Tremoviruses in the future.ImportanceRecent work has demonstrated that Antarctic penguins of the genus Pygoscelis are hosts for an array of viral species. However, beyond these Antarctic penguin species, very little is known about the viral diversity or ecology in this highly charismatic avian order. Through metagenomics we identified four novel viruses belonging to the Picornaviridae family in faecal samples from Magellanic Penguins. These highly divergent viruses, each possibly representing novel genera, are related to members of the Hepatovirus, Tremovirus genera, and unassigned picornaviruses described from Antarctic Penguin and Red-crowned Cranes. By PCR these novel viruses were shown to be common in Magellanic Penguins, indicating that penguins may play a key role in their epidemiology and evolution. Overall, we encourage further sampling to reveal virus diversity, ecology, and evolution in these unique avian taxa.

UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughout sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalised. In particular, sequencing errors in the UMI sequence are often ignored, or else resolved in an ad-hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single cell RNA-Seq datasets. Reproducibility between iCLIP replicates and single cell RNA-Seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package (https://github.com/CGATOxford/UMI-tools).