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Transcriptomic and proteomic profiling of blood samples from individuals with COVID-19 reveals immune cell and hematopoietic progenitor cell alterations that are differentially associated with disease severity.

The spike protein of the Omicron variant of SARS-CoV-2 has a higher affinity for ACE2 than Delta, and a marked change in its antigenicity increases Omicron’s evasion of therapeutic and vaccine-elicited neutralizing antibodies.

A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.

Mutation of the human genePHF8, encoding a histone demethylase, is linked to cognitive defects but its role in development is unclear. Here, the authors show that Phf8deletion in mice causes no overt developmental defects but confers resilience to depression, likely through increased serotonin signalling.

Openshaw and colleagues find myeloid inflammation and complement activation signatures in patients with long COVID who were previously hospitalized.

Schistosomiasis control strategies rely on mass drug administration (MDA) using praziquantel. Here, Berger et al. perform whole-genome sequencing of larvae from infected children across Ugandan regions with differing MDA histories. They find extensive gene flow with limited positive selection suggesting minimal change post MDA.

The Omicron variant evades vaccine-induced neutralization but also fails to form syncytia, shows reduced replication in human lung cells and preferentially uses a TMPRSS2-independent cell entry pathway, which may contribute to enhanced replication in cells of the upper airway. Altered fusion and cell entry characteristics are linked to distinct regions of the Omicron spike protein.

The long-noted association of red meat with an increased risk of cardiovascular disease may be due to ingestion of a specific compound found in red meat, l-carnitine. The ability of this compound to promote atherosclerosis in mice requires that it be further metabolized by the gut microbiota. In humans, omnivores but not vegans or vegetarians metabolize l-carnitine in this manner, a difference which may be explained by effects of diet on the presence of specific types of bacteria in the gut.

Pulsed doses of antibiotics increased the incidence of type 1 diabetes in non-obese diabetic (NOD) mice. This was associated with altered gut microbial composition, lipid metabolism, host cholesterol biosynthetic gene expression and Th17 and Treg cell proportions.

Motile and non-motile cilia have distinct functions and protein complexes associated with them. Here, the authors show the conserved protein CFAP20 is important for both motile and non-motile cilia and is distinct from other ciliopathy-associated domains or macromolecular complexes.

The authors document unexpectedly high levels of biodiversity in algal habitats between the coral reefs in the Great Barrier Reef.

Jan Brosens and his colleagues have found that deregulation of a single kinase—SGK1, a kinase involved in fluid balance—in two distinct cellular compartments of the endometrium is linked to two different forms of reproductive failure in humans. Using gain- and loss-of-function approaches in mice, the group confirmed the importance of these expression changes in such pathologies.

It remains unclear how rapid antibiotic switching affects the evolution of antibiotic resistance in individual patients. Here, Chung et al. combine short- and long-read sequencing and resistance phenotyping of 420 serial isolates of Pseudomonas aeruginosa collected from the onset of respiratory infection, and show that rare resistance mutations can increase by nearly 40-fold over 5–12 days in response to antibiotic changes, while mutations conferring resistance to antibiotics not administered diminish and even go to extinction.

Reduced fitness of the tumor microenvironment is mediated by a long non-coding RNA expressed in tumors.

This large, multi-ethnic genome-wide association study identifies 97 loci significantly associated with atrial fibrillation. These loci are enriched for genes involved in cardiac development, electrophysiology, structure and contractile function.

Targeted liquid chromatography–tandem mass spectrometry-based metabolomics using in vitro (organoids) and in vivo (gnotobiotic mice colonized with mono- or multi-species bacterial cultures) systems examines the role of specific microbially driven pathways of the mammalian gut–brain axis.

Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.

Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.

Genome-wide association meta-analyses identify more than 350 loci associated with atrial fibrillation. A polygenic score derived from these results improves atrial fibrillation risk prediction compared to published clinical and polygenic scores.

The authors discovered that proinflammatory senescent myeloid cells may recruit peripheral immune cells in the aged mouse brain. Their findings implicate senescent cell clearance as a strategy to counter aged brain inflammation and cognitive decline.

This Perspective discusses how addressing disparities in genomics can drive improvements in health equity more broadly.

The QT interval is a heritable electrocardiographic measure associated with arrhythmia risk when prolonged. Here, the authors used a series of genetic analyses to identify genetic loci, pathways, therapeutic targets, and relationships with cardiovascular disease.

New methods and larger sample groups are used to precisely determine the alleles in the HLA complex which contribute susceptibility to type 1 diabetes.

Interleukin-2 (IL-2) is a T-cell proliferating factor used for cancer immunotherapy. Here, the authors develop a long-lived variant of IL-2 that, mutated in its binding domain, drives a much more potent tumour regression by depleting CD25⁺ CD4⁺regulatory T-cells via targeting them for phagocytosis.

Interleukin-13 receptor alpha 2 is highly expressed in glioblastoma multiforme but its role in this malignancy is unclear. Here the authors show that this receptor interacts with mutant EGFR, stimulating its kinase activity, thus inducing proliferation.

An exciting genome-wide association study in the British population for seven common diseases. This analysis confirms previously identified loci and provides strong evidence for many novel disease susceptibility loci.

Although observations of volcanic deposits on Mars are more accessible than ever, constraining Martian eruption styles remains a challenge. Here, the authors show that volcanic eruption style can be characterized through X-ray diffraction analysis of groundmass crystallinity in basaltic volcanic deposits.

Two PD-1 directed checkpoint inhibitors have recently been approved for squamous cell carcinoma of the head and neck (SCCHN). Further checkpoint inhibitors, as well as other molecularly targeted agents and cytokine-based immunotherapies, are currently in the late-stage pipeline and are poised to change the treatment paradigm for SCCHN.

Susanne Kohl and colleagues report mutations in ATF6, a regulator of the unfolded protein response pathway, that cause a familial form of achromatopsia. Their results indicate a role for ATF6 in foveal development rather than a direct role in the cone phototransduction pathway.

Copy number variants (CNVs) account for a major proportion of human genetic diversity and may contribute to genetic susceptibility to disease. Here, a large, genome-wide study of association between common CNVs and eight common human diseases is presented. The study provides a wealth of technical insights that will inform future study design and analysis. The results also indicate that common CNVs that can be 'typed' on existing platforms are unlikely to contribute much to the genetic basis of common diseases.

As phase 1 of the Earth Microbiome Project, analysis of 16S ribosomal RNA sequences from more than 27,000 environmental samples delivers a global picture of the basic structure and drivers of microbial distribution.

1000 Genomes imputation can increase the power of genome-wide association studies to detect genetic variants associated with human traits and diseases. Here, the authors develop a method to integrate and analyse low-coverage sequence data and SNP array data, and show that it improves imputation performance.

This report from the 1000 Genomes Project describes the genomes of 1,092 individuals from 14 human populations, providing a resource for common and low-frequency variant analysis in individuals from diverse populations; hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites, can be found in each individual.

The cellular heterogeneity in brain obscures the identification of robust cellular regulatory networks. Here the authors integrate genome-wide chromosome conformation data from sorted neurons and glia, with transcriptomic and enhancer profiles, to characterize cell-type-specific gene regulatory landscapes in the human brain, and provide insights into cell-type-specific gene regulatory networks in brain disorders.