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Super spreading events are considered important contributors to the spread of COVID−19, but the extent to which superspreading varies by transmission setting is unclear. Here, the authors demonstrate heterogeneity in superspreading and the generation interval between COVID−19 cases in different settings using data from Hong Kong.

Hong Kong experienced a large wave of COVID-19 in early 2022 driven by Omicron BA.2. Here, the authors describe the epidemiological dynamics of this wave and show discordant inferences based on genomic and epidemiological data that underscore the need to improve near real-time epidemic growth estimates.

Based on two waves of data collection from 748 households in Hong Kong, this analysis sheds light on the number of transmission events that occurred before manifestation of symptoms in influenza A and B cases.

Lin et al. investigate the immune response in severely ill H7N9 patients and its link to early-life influenza imprinting. They find that individuals first exposed to H2N2 develop faster, higher-avidity cross-reactive antibodies and tend to experience less severe illness.

Coral reefs are declining globally, but regional degradation drivers are poorly quantified. This study reveals that coral loss in the northern South China Sea is predominantly linked to human coastal activities, suggesting that tailored local management may effectively reduce reef collapse.

Cases linked to superspreading events are estimated to account for 80% of all local transmission of SARS-CoV-2 in Hong Kong in a study with implications for public health policies.

Antiviral treatment with nirmatrelvir-ritonavir has been associated with improved post-COVID outcomes. Here, the authors perform a retrospective cohort study using electronic health record data from Hong Kong to investigate the importance of timing of treatment.

While antivirals like nirmatrelvir/ritonavir and molnupiravir are known to reduce severe COVID-19, their impact on cardiovascular outcomes is unclear. Here, the authors use a target trial emulation design to show that nirmatrelvir/ritonavir significantly lowers long-term cardiovascular risks among hospitalized patients, highlighting its potentials over molnupiravir for mitigating post-COVID-19 cardiovascular complications.

Robustness checks and reproduction of analyses with existing and updated data based on 110 articles in economics and political science journals with data and code-sharing requirements found high levels of robustness and reproducibility and determined that robustness was not dependent on author characteristics or data availability.

Forecasting influenza activity in tropical/subtropical regions such as Hong Kong is complicated by irregular seasonality and variability in epidemic onset time. Here, the authors show that forecasting accuracy can be improved by combining individual models in an adaptive ensemble that allows dynamic updating of model weights.

SARS-CoV-2 rebound is a recurrence of symptoms or return to test positivity after initial recovery. Here, the authors demonstrate an association between SARS-CoV-2 rebound and post-acute COVID conditions using data from Hong Kong.

The time-varying effective reproductive number (Rt) is useful for monitoring transmission of infections such as COVID-19, but reporting delays impact case count-based estimation methods. Here, the authors demonstrate and validate a method for estimation of Rt based on viral load data from Hong Kong that does not require accurate daily counts.

The Global Flourishing Study provides a comprehensive view of the distribution and determinants of well-being by assessing domains such as health, happiness, meaning, character, relationships and financial security. Initial findings reveal significant variations in flourishing across countries and demographic groups, with factors such as age, marital status and religious service attendance showing strong associations with well-being.

Urban redevelopment is a key government policy and planning strategy to address various urban challenges. This study investigates where, how and to what extent China’s city hierarchy influences redevelopment activities within China’s rapidly evolving urban landscape.

This study leverages single-nucleus multiomics to map cellular senescence atlas in aging human skeletal muscle and uncovers potential targets and senotherapeutics for treating age-associated sarcopenia.

Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD), underscoring the power of the presented analysis to minimize false assignments of disease risk.

Relevance of indirect protection of household members of vaccinees is unclear. Here, Tsang et al. quantify the direct and indirect protection of vaccination in a randomized controlled trial and show that benefits of individual vaccination remain important even when other household members are vaccinated.

Serological classification of influenza infection has classically been based on a four-fold or higher increase in antibody levels, but this approach may not be optimal. Here, the authors develop a Bayesian model to improve identification of infections in serological samples by accounting for individual antibody dynamics.

The pathogenicity and transmissibility of SARS-CoV-2 in golden (Syrian) hamsters resemble features of COVID-19 in human patients, suggesting that these hamsters could be used to model this disease.

Whole-gene sequencing of microdissected gastric glands from individuals with and without gastric cancer reveals distinct patterns of somatic mutations and provides insights into influences on the somatic evolution of the gastric epithelium.

An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

This study of magic-angle twisted trilayer graphene moiré superconductors using scanning tunnelling microscopy and spectroscopy identifies two energy gaps that develop from many-body resonance in this highly tunable class of materials.

Nasopharyngeal carcinoma (NPC) lacks effective diagnostic and therapeutic strategies, in particular at advanced stages. Here, the authors show that expression of the somatostatin receptor 2 is induced by Epstein-Barr virus in NPC and has a key role in the diagnosis, imaging, targeted therapies and prognosis of NPC.

CDK4/6 inhibitors are promising treatments for ER+ breast cancer, however resistance remains a challenge. Here, the authors analyse the NeoPalANA cohort and indicate that a 33 gene signature was predictive of response to neoadjuvant anastrozole and palbociclib.

Influenza A virus must package eight separate genomic segments, called viral ribonucleoproteins (vRNPs). Using in situ cryo-electron tomography, the authors visualize how vRNPs are clustered on cell membranes containing the viral glycoprotein hemagglutinin or neuraminidase, and how the matrix protein M1 forms intracellular structures that reorganize during budding to support packaging.

The lack of appropriate models restricts pre-clinical research for nasopharyngeal carcinoma (NPC). Here the authors report the development and characterization of NPC patient-derived xenografts (PDXs), and EBV positive NPC cell line from patient tumor, and suggest their potential use in future NPC research.

The authors find subtype-specific influenza cross-reactivity patterns, including rapid declines for A(H3N2) within 6 years, sustained responses for A(H1N1)pdm09 and increased cross-reactive responses in humans after repeated A(H3N2) exposure.

RNA editing provides epigenetic diversity and is thought to be decreased in cancer. However, this report describes a phenomenon of increased RNA editing associated with malignancy in human liver tumors. The increased editing of AZIN1 is facilitated by the correlative increase in the editing enzyme ADAR1 and induces an amino acid change that leads to subcellular relocalization, increased stability and affinity for antizyme. This effect impairs antizyme's function and increases the stability of its target oncoproteins, providing protumorigenic functions. The hyperediting of AZIN1 is a protumorigenic event in liver cancer pathogenesis.

A genome-wide association study including over 76,000 individuals with schizophrenia and over 243,000 control individuals identifies common variant associations at 287 genomic loci, and further fine-mapping analyses highlight the importance of genes involved in synaptic processes.

This Review discusses the mechanisms underlying both cavitation and folding amniogenesis and provides an overview of the various recent stem cell-based human embryo models that have been developed to elucidate amniotic formation and function.

In this study, the authors assessed influenza-specific antibody responses in a cohort of seasonally vaccinated children and report that seasonal vaccination is beneficial by enhancing pandemic influenza virus-specific antibodies and cross-reactive effector functions.

Lam et al. evaluate a self-report scale and eight BERT-family large language models trained on clinical interview transcripts to detect clinician-rated depression in people with and without alexithymia. All models detect depression more accurately than the self-report scales in detecting depression, particularly in those with alexithymia.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

There are distinct hypermethylation patterns in gene promoters in hepatocellular carcinomas (HCCs). Here, the authors show that the enhancer of C/EBPβ is recurrently hypomethylated in human HCCs, recapitulating this in a transgenic murine model and linking aberrant enhancer hypomethylation to hepatocarcinogenesis.

Neutralizing antibody titers are considered possible correlates of protection against SARS-CoV-2, but vaccine efficacy for Omicron infections is high despite reduced titers. Here, the authors investigate the relationship between neutralizing antibody titers and vaccine effectiveness/efficacy through a meta-analysis and statistical modeling.

It is unclear whether somatic mutation rates are elevated in Lynch Syndrome (LS), which is the most common cause of hereditary colorectal cancer. Here, the authors use whole-genome sequencing and organoid cultures to show that normal tissues in LS patients are genomically stable, while ancestor cells of neoplastic tissues undergo multiple cycles of clonal evolution.

Genomic analyses applied to 14 childhood- and adult-onset psychiatric disorders identifies five underlying genomic factors that explain the majority of the genetic variance of the individual disorders.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.