A Low-cost High-throughput Targeted Sequencing for the Accurate Detection of Respiratory Tract Pathogen DOI Open Access

Ju Changyan,

Zhou Chengbosen,

Deng Zhezhi

et al.

International Journal of Clinical Virology, Journal Year: 2024, Volume and Issue: 8(1), P. 001 - 007

Published: March 12, 2024

Introduction: The current gold standard for SARS-CoV-2 diagnosis by real-time RT-PCR has limitations of gene numbers that can be detected. In this study, we developed a low-cost and high-throughput next-generation sequencing technology overcome the RT-PCR. Methodology: A targeted panel (TSP) consisting approximately 500 amplicons was designed simultaneously detect broad range loci genes most common viruses respiratory infectious in single run up to 96 samples. 448 samples 31 control were examined independently with both TSP RT-PCR, results compared accuracy other indicators. Results: identified 50 positive 99.33% match results. It is not surprising also multiple viral infections from samples, whereas could not. demonstrated its ability conclude those undecided tests. Conclusion: Our data fast accurate test detecting pathogen tract.

Language: Английский

Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy DOI Creative Commons
Michele Equestre, Cinzia Marcantonio, Nadia Marascio

et al.

Microorganisms, Journal Year: 2023, Volume and Issue: 11(11), P. 2711 - 2711

Published: Nov. 5, 2023

We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy order classify viral isolates a potential hotspot for virus spread. Positive samples were subjected Next-Generation Sequencing (NGS) of the whole genome Sanger sequencing spike coding region. Phylogenetic analysis classified traced their evolutionary relationships. Clusters identified using 70% cut-off. methods yielded comparable results terms variant classification. In 2021, we several variants, including B.1.258 (4/67), B.1.177 (9/67), Alpha (B.1.1.7, 9/67), Gamma (P.1.1, 4/67), Delta (4/67). only Omicron its sub-lineage observed (37/67). screened detect naturally occurring resistance genomic regions, target new therapies, comparing them Wuhan Hu-1 reference strain. Interestingly, 2/30 non-Omicron carried G15S 3CLpro substitution responsible reduced susceptibility protease inhibitors. On other hand, unusual substitutions A1803V, D1809N, A949T on PLpro, D216N 3CLpro. Finally, P323L RdRp regions was not associated with mutational pattern related polymerase inhibitor resistance. This study highlights importance continuous surveillance monitor evolution general population, as well restricted communities.

Language: Английский

Citations

10
Navigating the New Norm: The FDA's Final Rule on Laboratory Developed Tests (LDTs) and Its Impact on Clinical Laboratory Operations DOI Creative Commons
Rob E. Carpenter

Clinical Microbiology Newsletter, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

Citations

3
Dataset for a Validated Method of Non-Invasive Urine Collection Using Sodium Polyacrylate-Based Diapers for PCR Detection of Uropathogens DOI Creative Commons
Tyler Vine, Rob E. Carpenter,

Debbie Bridges

et al.

Data in Brief, Journal Year: 2024, Volume and Issue: 57, P. 111036 - 111036

Published: Oct. 18, 2024

Language: Английский

Citations

2
Precision Metagenomic Next-Generation Sequencing Data of Respiratory Infection DOI Open Access
Sadia Almas, Rob E. Carpenter, Vaibhav K. Tamrakar

et al.

Published: Oct. 3, 2023

Understanding microbial composition in upper respiratory infections (URIs) is critical for effective diagnosis and treatment. Precision Metagenomic next-generation sequencing p(mNGS) can provide a comprehensive yet clinically relevant profile of infection. The hybridization capture-based targeted generated precision metagenomics 29 patients with acute URIs. Nasopharyngeal samples were collected from the subjects suspected infection, was performed using Illumina®/IDbyDNA Respiratory Pathogen ID/AMR Panel (RPIP). dataset obtained mNGS analysis contains wealth information on URI microbiota, including relative abundance known pathogens potential clinical implications. represents valuable resource future research endeavors medicine, infectious disease epidemiology, therapeutic interventions. In addition, offers significant reuse integration other omics datasets. nature data allows exploration associations between microbiota host factors such as outcomes, immune responses, or genetic predisposition. Combining this datasets, transcriptomics metabolomics, could deeper understanding complex interactions

Language: Английский

Citations

1
Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania DOI Open Access

Jemila Deida,

Nasserdine Papa Mze,

Mamadou Beye

et al.

Genes, Journal Year: 2024, Volume and Issue: 15(3), P. 361 - 361

Published: March 14, 2024

The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite presence virus Mauritania, only one study described its genomic variation course epidemic. purpose present was to document pattern SARS-CoV-2 variants from clinical isolates COVID-19 outbreak September November 2021. whole genomes 54 strains detected nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and Illumina protocol. mean genome coverage (±standard deviation) 96.8% (±3.7). most commonly identified clade 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), 20B (9.2%). At level lineages, majority samples Delta sub-lineage AY.34 (or B.1.617.2.34). Among that sequenced, 33 (61.1%) came vaccinated individuals, 21 (38.9%) unvaccinated individuals. Several Mauritania between As like many West African countries, is resource-limited regarding viral facilities, establishment mutualized sub-regional platforms will be necessary ensure continuous monitoring mutations track potential reduction vaccine efficacy, increased transmissibility, severity.

Language: Английский

Citations

0
A Low-cost High-throughput Targeted Sequencing for the Accurate Detection of Respiratory Tract Pathogen DOI Open Access

Ju Changyan,

Zhou Chengbosen,

Deng Zhezhi

et al.

International Journal of Clinical Virology, Journal Year: 2024, Volume and Issue: 8(1), P. 001 - 007

Published: March 12, 2024

Introduction: The current gold standard for SARS-CoV-2 diagnosis by real-time RT-PCR has limitations of gene numbers that can be detected. In this study, we developed a low-cost and high-throughput next-generation sequencing technology overcome the RT-PCR. Methodology: A targeted panel (TSP) consisting approximately 500 amplicons was designed simultaneously detect broad range loci genes most common viruses respiratory infectious in single run up to 96 samples. 448 samples 31 control were examined independently with both TSP RT-PCR, results compared accuracy other indicators. Results: identified 50 positive 99.33% match results. It is not surprising also multiple viral infections from samples, whereas could not. demonstrated its ability conclude those undecided tests. Conclusion: Our data fast accurate test detecting pathogen tract.

Language: Английский

Citations

0