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Metagenomic Sequencing samples - Europe PMC

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Last Updated: 27 January 2022

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Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya.

We investigated the effectiveness of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing on respiratory samples that were non-positive for the common respiratory pathogens by a local standard diagnostic panel. In 35 and 23 samples, respectively, among 95 hospitalized pneumonia patients and 95 household-cohort patients, the study of viral NGS revealed at least one respiratory-associated virus in 95 hospitalized pneumonia patients and 95 household-cohort individuals. Assay results, molecular causes of missed diagnoses, and reveal holes in the respiratory virus set used for local screening assays could be aided by regular application of such viral NGS.

Source link: https://europepmc.org/article/MED/34997042


Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing.

This is the first analysis to determine the results of various sequencing techniques for profiling bovine vaginal metagenomic samples. We compared Oxford Nanopore Technologies adaptive sequencing, which can be used to target or eliminate specific sequences, to standard ONT sequencing, Illumina 16S rDNA amplicon sequencing, and Illumina shotgun sequencing. A higher number of metagenomic results were obtained by ONT adaptive sequencing with a greater number of metagenomic sequences per 1 Gb of sequence results than the other methods per 1 Gb of sequence data. The increased sequencing sensitivity of ONT adaptive sequencing has consequently reduced the number of raw data required to ensure adequate coverage for the metagenomic samples with high host-to-microbe DNA ratios, which also reduced the volume of raw data needed to ensure appropriate coverage for the metagenomic samples with high host-to-microbe DNA ratios. This study illustrates the benefits of ONT adaptive sequencing in increasing the number of metagenomic data extracted from microbiome samples with high host-to-microbe DNA ratios, as well as the benefits of long reads in preserving intact data for accurate annotations.

Source link: https://europepmc.org/article/MED/34791313


Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.

The aim of this report was to determine the results of nanopore-Independent Single Primer Amplification's for the detection and analysis of SARS-CoV-2. Methods We performed mNGS on clinical samples and created a diagnostic classifier that corrects for barcode crosstalk between specimens. Our assay yielded 100% specificity and 92% sensitivity for specimens with a RT-PCR cycle threshold value less than 30 degrees. 10/11 specimens from British Columbia had a closest relationship to another British Columbian specimen, according to a phylogenetic review. We found 100% concordance between phylogenetic lineage assignment and Variant of Concern PCR results. Our assay was able to distinguish between the Alpha and Gamma versions, which was not possible with the new international standard VOC PCR being used in British Columbia, which was not possible with the current standard VOC PCR being used in British Columbia. Conclusions This research supports future research into the wider use of nanopore mNGS as a diagnostic tool for the detection and characterization of viral pathogens.

Source link: https://europepmc.org/article/MED/34793508


The Application of Metagenomic Next-Generation Sequencing in Detection of Pathogen in Bronchoalveolar Lavage Fluid and Sputum Samples of Patients with Pulmonary Infection.

Mission: To determine the application of metagenomic next-generation sequencing in the detection of pathogen in bronchoalveolar lavage fluid and sputum samples, the aim is to determine the use of the procedure in bronchoalveolar lavage fluid and sputum samples. Conclusions The pathogen culture findings were favorable in 9 patients and negative in 13 patients. In two kinds of samples, no statistical differences were found regarding the sensitivity and specificity of mNGS diagnosis in bacteria and fungus. Both patients' two samples were positive, 13 patients' two samples were negative, 7 patients were only positive in BALF samples, and two patients' sputum samples were positive, as shown by mNGS detection. The EB virus, human adenovirus 5, herpes simplex virus type 1, and human cytomegalovirus were among the common viruses mNGS found in EB virus, human adenovirus 5, herpes simplex virus type 1, and human cytomegalovirus type 1. mNGS showed no statistical differences in the sensitivity and specificity of pathogen detection in BALF and sputum samples, according to the authors. Sputum samples may be more suitable for pathogen detection under certain circumstances, due to the invasiveness of BALF samples under certain circumstances.

Source link: https://europepmc.org/article/MED/34790254


Metagenomic Sequencing Characterizes a Wide Diversity of Viruses in Field Mosquito Samples in Nigeria

Mosquito vectors, a significant public health risk globally, are a significant public health threat, with one out of six diseases worldwide being vector-borne transmitted mainly by mosquitoes. In several places in N. . ia, active Yellow fever virus outbreaks have existed for a few years, and nationwide, entomological surveillance has been a major attempt to recognize these outbreaks. In this research, we used a metagenomic sequencing technique to identify viruses present in vector samples collected during multiple outbreaks of Yellow fever in N. . ia between 2017 and 2020. Mosquito samples were divided into one to fifty mosquitoe ponds, each depending on species, sex, and location. Aedes spp and one pool of Anopheles spp obtained from nine states were sequenced and metagenomic analysis was carried out. The Fako virus, Phasi Charoen-like virus, Verdadero virus, Chaq like-virus, Aedes aegypti totivirus, cell fusing agent virus, and Tesano Aedes virus were among the seven common viruses found: Fako virus, Phasi Charoen-like virus, Chaptypti jaune virus, Aegypti proteovirus, cell fusing agent virus, the virus, the virus, Pha, Phasi Charo zi zir-virus, Chaq Virus, Chaq Virus, Ae virus, Ae virus, Ae virus, cell Virus, Tesan-virus, Ae virus, Tesan-Virus, Testi Virus,.

Source link: https://europepmc.org/article/PPR/PPR415193

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions