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Rooibos (<i>Aspalathus linearis</i>) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South …
Read PDFMultiple anthelmintic drug resistance (MADR) is widespread in the canine hookworm Ancylostoma caninum in kenneled greyhounds in the USA and Australia with benzimidazole resistance being associated with the isotype-1 β-tubulin SNPs Q134H(CAA > CAT) and …
Read PDFAccurate and efficient whole-genome sequencing (WGS) is crucial for clinical diagnostics and surveillance of bacterial infections. Here, we investigate the potential of a new Oxford Nanopore Technologies (ONT) workflow for WGS of clinically relevant bacterial …
Read PDF<h4>Background</h4>Next generation sequencing (NGS) impacted on clinical algorithm of solid tumor patients. A heterogeneous series of NGS platforms have been implemented in clinical practice but challenging handling procedures, high technical costs, and scant affordability on …
Read PDFThe oral microbiome is a diverse ecosystem that plays a critical role in health and disease and contains numerous bacterial species capable of metabolizing host-derived glycans, particularly sialic acids. Sialidase enzymes can be produced by …
Read PDFThe present study describes an outbreak of Streptococcus canis (S.canis) infection in a commercial mink farm in West Macedonia, Greece, and investigates its clinical, pathological and microbiological features.In late February 2024, approximately 300 out of …
Read PDFWe report near-complete genome sequences of equine herpesvirus (EHV) 1, 3, and 4 from the USA. Hybrid assemblies combining Illumina and Oxford Nanopore reads yielded high-quality genomes, enhancing understanding of EHV diversity and evolution in …
Read PDFFungal DNA is systematically under-detected in shotgun metagenomics, likely due in part to physical barriers like melanized cell walls and complex DNA conformations. Additionally, Oxford Nanopore Technologies sequencing with native fungal DNA often results in …
Read PDFWe report the complete reference genome sequences of three <i>Haemophilus ducreyi</i> isolates (ITG3105, CIP76118, and TMA3542), generated using Oxford Nanopore and Illumina sequencing, and hybrid assemblies. Each genome has a closed circular chromosome; ITG3105 and …
Read PDFPolishing, the process of correcting base-level errors in genome assemblies, is a critical step for ensuring accuracy in downstream analyses, such as variant calling, gene annotation, and clinical genomics applications. While recent advances in long-read …
Read PDF<h4>Background</h4>Preimplantation genetic testing for structural rearrangements (PGT-SR) facilitates the selection of embryos with balanced karyotype prior to implantation. Currently, there is a critical need for reference materials (RMs) to ensure PGT-SR development.<h4>Results</h4>This study designed a …
Read PDF<h4>Introduction</h4>The occurrence and genomic context of the mobile colistin resistance gene <i>mcr-9.1</i> in the United Arab Emirates (UAE) food chain remain poorly characterized, with no previous reports identified from retail food products based on the …
Read PDF<i>Neisseria meningitidis</i> is a primary cause of bacterial meningitis and septicemia, which is a significant global public health concern. Here, we report Oxford Nanopore Technologies RNA sequencing for <i>N. meningitidis</i> serogroup B strain M0579. This …
Read PDFGenomic epidemiology was essential for characterizing SARS-CoV-2 transmission during the early COVID-19 pandemic. This systematic review examined how whole-genome sequencing was used in local outbreak investigations published between March 2020 and March 2021. Searches of …
Read PDFThis response addresses the comments raised by Souichi Oka and colleagues in their Letter to the Editor titled "Addressing biases and limitations in feature attribution for circRNA modification profiling." We clarify that two independent XGBoost …
Read PDF<h4>Motivation</h4>Allele typing for Human Leukocyte Antigen (HLA) genes has many important clinical applications. Popular short-read typing can only accurately distinguish alleles at the coding sequence level, which potentially limit our understanding of the effect of …
Read PDFH5 subtype high-pathogenicity avian influenza (HPAI) viruses continue to devastate the poultry industry and threaten food security and public health. The first outbreak of H5 HPAI in the Philippines was reported in 2017. Since then, …
Read PDFWe report two coding-complete genome sequences of porcine reproductive and respiratory syndrome virus 2 from field clinical samples obtained in 2021 (BA2021012A) and 2023 (ME20230008B-2) from the Philippines. BA2021012A (15,388 bp) is classified as a …
Read PDFWe report a coding-complete genome sequence of an African swine fever virus from an outbreak in 2021 among domestic pigs in Pangasinan, Philippines using Oxford Nanopore Technologies minION. The linear genome assembly is a single …
Read PDF<h4>Motivation</h4>Oxford Nanopore sequencing enables long-read analysis for diverse applications, but artefacts introduced by Nanopore barcoding are poorly characterized and can compromise demultiplexing accuracy and downstream analyses.<h4>Results</h4>Using a rapid barcoding experiment on 66 diagnostic samples, we …
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