We present a protocol to efficiently sequence genomes of the MPXV-causing mpox. This enables researchers and public health agencies to acquire high-quality genomic data using a rapid and cost-effective approach. Genomic data can be used to conduct surveillance and investigate mpox outbreaks. We present 91 mpox genomes that show the diversity of the 2022 mpox outbreak in Ontario, Canada.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10783113 | PMC |
http://dx.doi.org/10.1128/spectrum.02979-23 | DOI Listing |
Ann Clin Microbiol Antimicrob
January 2025
Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France.
Aim: Located in the Southwest Indian Ocean area (SIOA), the two French overseas territories (FOTs) of Reunion and Mayotte islands are heavily impacted by antimicrobial resistance. The aim of this study was to investigate all cases of NDM-5 and OXA-181 carbapenemase-producing Escherichia coli (CPEc) in these two FOTs between 2015 and 2020, to better understand the regional spread of these last-line treatment resistant bacteria.
Methods: All E.
BMC Genomics
January 2025
Department of Virology, Norwegian Institute of Public Health, Oslo, 0456, Norway.
The COVID-19 pandemic has underscored the importance of virus surveillance in public health and wastewater-based epidemiology (WBE) has emerged as a non-invasive, cost-effective method for monitoring SARS-CoV-2 and its variants at the community level. Unfortunately, current variant surveillance methods depend heavily on updated genomic databases with data derived from clinical samples, which can become less sensitive and representative as clinical testing and sequencing efforts decline.In this paper, we introduce HERCULES (High-throughput Epidemiological Reconstruction and Clustering for Uncovering Lineages from Environmental SARS-CoV-2), an unsupervised method that uses long-read sequencing of a single 1 Kb fragment of the Spike gene.
View Article and Find Full Text PDFSci Rep
January 2025
MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
Bulk ATAC-seq assays have been used to map and profile the chromatin accessibility of regulatory elements such as enhancers, promoters, and insulators. This has provided great insight into the regulation of gene expression in many cell types in a variety of organisms. To date, ATAC-seq has most often been used to provide an average evaluation of chromatin accessibility in populations of cells.
View Article and Find Full Text PDFNature
January 2025
Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives, are not equitably represented in large-scale gut microbiome research. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa.
View Article and Find Full Text PDFNature
January 2025
Department of Mathematics & Computer Science, Freie Universität Berlin, Berlin, Germany.
Since the onset of the pandemic, many SARS-CoV-2 variants have emerged, exhibiting substantial evolution in the virus' spike protein, the main target of neutralizing antibodies. A plausible hypothesis proposes that the virus evolves to evade antibody-mediated neutralization (vaccine- or infection-induced) to maximize its ability to infect an immunologically experienced population. Because viral infection induces neutralizing antibodies, viral evolution may thus navigate on a dynamic immune landscape that is shaped by local infection history.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!