Global disparities in SARS-CoV-2 genomic surveillance

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity

Mapping and Functional Characterisation of a CTCF-Dependent Insulator Element at the 3′ Border of the Murine Scl Transcriptional Domain

The Scl gene encodes a transcription factor essential for haematopoietic development. Scl transcription is regulated by a panel of cis-elements spread over 55 kb with the most distal 3′ element being located downstream of the neighbouring gene Map17, which is co-regulated with Scl in haematopoietic cells. The Scl/Map17 domain is flanked upstream by the ubiquitously expressed Sil gene and downstream by a cluster of Cyp genes active in liver, but the mechanisms responsible for delineating the domain boundaries remain unclear. Here we report identification of a DNaseI hypersensitive site at the 3′ end of the Scl/Map17 domain and 45 kb downstream of the Scl transcription start site. This element is located at the boundary of active and inactive chromatin, does not function as a classical tissue-specific enhancer, binds CTCF and is both necessary and sufficient for insulator function in haematopoietic cells in vitro. Moreover, in a transgenic reporter assay, tissue-specific expression of the Scl promoter in brain was increased by incorporation of 350 bp flanking fragments from the +45 element. Our data suggests that the +45 region functions as a boundary element that separates the Scl/Map17 and Cyp transcriptional domains, and raise the possibility that this element may be useful for improving tissue-specific expression of transgenic constructs

Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1-3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods - recursive partitioning and regression - to pinpoint disease susceptibility to the MHC class I genes HLA-B and HLA-A (risk ratios >1.5; Pcombined = 2.01 × 10-19 and 2.35 × 10-13, respectively) in addition to the established associations of the MHC class II genes. Other loci with smaller and/or rarer effects might also be involved, but to find these, future searches must take into account both the HLA class II and class I genes and use even larger samples. Taken together with previous studies, we conclude that MHC-class-I-mediated events, principally involving HLA-B*39, contribute to the aetiology of type 1 diabetes. ©2007 Nature Publishing Group

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Identification and functional analysis of a novel 1.76 kb Scl element located 45 kb downstream from Scl promoter.

<p>(<b>A</b>) DNaseI hypersensitive profiles across 130 kb (NCBI37/mm9 chr4:114,670,057–114,799,426) of the extended Scl locus in 3 cell types: mouse haematopoietic progenitors (416B), mouse embryonic stem cells (mES) and primary mouse thymocytes. The location of the 4 genes at the locus are represented at the top of the figure (Sil, Scl, Map17 and Cyp4x) with direction of transcription indicated by the arrows and translated and untranslated exons represented by wide and narrow bars respectively. The location of known key regulatory elements is indicated by the red bars (Sil promoter, Scl promoter, Scl+19, Scl+23, Map17 promoter, Scl+40, and Cyp promoter), and the location of the putative +45 element is indicated with a dashed red line. The data presented is a representative experiment showing fold enrichment over non-enriched input plotted (log₂) against genomic position. (<b>B</b>) Luciferase activity is increased in 416B cells stably transfected with constructs containing the +45 element (SV/Luc/+45, Map17/Luc/+45 and Scl/Luc/+45) when compared to promoter alone. The 350 bp core region of the +45 element (Scl/Luc/+45del350) is necessary but not sufficient for full transcriptional enhancement from the Scl/Luc/+45 construct. The left panel represents the constructs diagrammatically. Luciferase activity was calculated as fold increase over the promoter only construct. The data representing mean +/− SD relative luciferase activity from 5 independent experiments, each performed in triplicate. ** indicated p<0.01 compared to promoter alone.</p

ChIP-chip profiles mapping of H3K9ac (A) and H3K27me3 (B) across 150 kb of the extended Scl locus in 3 cell types, 416B (mouse haematopoietic progenitor cells), mouse embryonic stem cells (mES) and primary mouse thymocytes.

<p>The location of the 4 genes at the locus are represented at the top of the figure (Sil, Scl, Map17 and Cyp4x) with direction of transcription indicated by the arrows and translated and untranslated exons represented by wide and narrow bars respectively. The location of known key regulatory elements is indicated by the red bars (Sil promoter, Scl promoter, Scl+19, Scl+23, Map17 promoter,Scl+40 and Cyp promoter), and the location of the putative +45 element is indicated with a dashed red line. Representative experiments showing fold enrichment over non-enriched input plotted (log₂) against genomic position. In the cell types studied, the +45 element is located at a boundary between chromatin domains carrying transcriptionally active and/or repressive histone marks, while the H3 proteins at the +45 element itself are neither acetylated at H3K9 nor methylated at H3K27.</p

The 350 kb core region of the +45 element improves tissue-specific expression of transgenes.

<p>The 350/Scl/LacZ/350 transgenic embryos consistently expressed LacZ in mid and hind brain (white arrow), reflecting endogenous expression pattern of Scl in brain, Scl/LacZ transgenic embryos show ectopic expression (grey arrow). The transgenic constructs are depicted diagrammatically on the left panel, with photographs of 3 representative transgenic embryos presented on the right.</p

The 350 bp core region of the +45 element insulates transgenic constructs and improves tissue-specific expression from the Scl promoter.

<p>The total number of F0 transgenic embryos obtained with each construct was determined by PCR using specific primers. Upon ß-galactosidase staining, transgenic embryos were visually inspected and scored as either LacZ+ or LacZ- and the percentage of LacZ+ embryos calculated.</p>*<p>p<0.05 compared to SV/LacZ. The expression pattern of Scl/LacZ and 350/Scl/LacZ/350 transgenic embryos is considered ectopic if beyond the mid and hind brain, the expected expression pattern for the Scl promoter alone.</p>**<p>p<0.01 compared to Scl/LacZ.</p

The +45 element function as an insulator and this activity is dependent on the 57FPR.

<p>The left panel represents the different constructs diagrammatically. Data is presented as K562 colony numbers relative to the control pNI construct containing only the ß-globin HS2 enhancer and the neomycin resistance promoter. The positive control (1.2 kb fragment containing the chicken HSIV insulator) reduces the number of colonies by 50%, with similar insulation observed from the 1.76 kb +45 element containing the 350 bp core element and the 57FPR. Deletion of either the 350 bp core from the +45 or deletion of the 57FPR from the 350 bp core, both removed the insulator function of the elements. Furthermore, mutation of the CTCF-binding site in the 350 bp core element significantly reduced the insulator function of the 350 bp core element. The data represents the mean ±SD of relative colony numbers from 3 independent experiments each performed in triplicate. * p<0.05, ** p<0.01 when compared to pNI.</p