Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens DOI Creative Commons
Chaney C. Kalinich, Freddy L. Gonzalez,

Alice Osmaston

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 20, 2024

Abstract Pathogen sequencing is an important tool for disease surveillance and demonstrated its high value during the COVID-19 pandemic. Viral pandemic allowed us to track spread, quickly identify new variants, guide development of vaccines. Tiled amplicon sequencing, in which a panel primers used multiplex amplification fragments across entire genome, was cornerstone SARS-CoV-2 sequencing. The speed, reliability, cost-effectiveness this method led implementation academic public health laboratories world adaptation broad range viral pathogens. However, similar methods are not available larger bacterial genomes, whole-genome typically requires vitro culture. This increases costs, error rates turnaround times. need culture poses particular problems medically bacteria such as Mycobacterium tuberculosis, slow grow challenging As proof concept, we developed two novel panels M. tuberculosis Streptococcus pneumoniae . Applying our clinical samples, show ability classify pathogen subgroups reliably markers drug resistance without culturing. Development work settings has potential dramatically reduce time diagnosis multiple drugs parallel, enabling earlier intervention priority

Language: Английский

First identification of the SARS-COV-2/XBB.1.5 sublineage among indigenous COVID-19 cases through the influenza sentinel surveillance system in Niger DOI Creative Commons
Adamou Lagaré, Martin Faye,

Moussa Issa

et al.

Heliyon, Journal Year: 2023, Volume and Issue: 9(11), P. e20916 - e20916

Published: Oct. 19, 2023

The emergence of the Omicron variant in November 2021, has caused panic worldwide due to rapid evolution and ability virus escape immune system. Since, several sublineages (BA.1 BA.5) their descendent recombinant lineages have been circulating worldwide. Furthermore, December 2022, a new subvariant XBB.1.5 characterized by an unusual mutation spike protein evolved United States rapidly spread other continents. Our study reports on first cases sublineage among indigenous Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) positive detected through influenza sentinel surveillance system Niger. All suspected were tested for both SARS-COV-2 using Centre Disease Control prevention (CDC) Influenza Multiplex quantitative Reverse-Transcription Polymerase Chain Reaction (qRT-PCR) Assay. samples with cycle threshold ≤28 selected whole genome sequencing subsequently Oxford Nanopore Midnight protocol barcoding MinIon MK1B device. A total 51 confirmed between 2022 March 2023. We successfully obtained 19 sequences predominance XBB.1/XBB.1.5 (73.7 %). In addition, XBD sequence was also first-ever identified early findings support need strengthen routine Coronavirus 2019 (COVID-19) variants monitoring

Language: Английский

Citations

2
SARS-CoV-2 Genotyping Highlights the Challenges in Spike Protein Drift Independent of Other Essential Proteins DOI Creative Commons
Jeremy W. Prokop,

Sheryl Alberta,

Martin Witteveen‐Lane

et al.

Microorganisms, Journal Year: 2024, Volume and Issue: 12(9), P. 1863 - 1863

Published: Sept. 9, 2024

As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative any species was initiated combat the tracking changes over time at a full virus base-pair resolution. represents unique opportunity understand selective pressures viral evolution but requires cross-disciplinary approaches from epidemiology functional protein biology. Within this work, we integrate two-year genotyping window with structural biology explore on insights. Although genotype Spike (Surface Glycoprotein) continue drift, most proteins have had few amino acid alterations. Spike, high rate acids involved in antibody evasion also corresponds within ACE2 binding pocket that undergone multiple maintain binding. suggests pressure receptor specificity could confer risk. Mapping structures co-transcriptional complex (nsp7-nsp14), nsp3 (papain-like protease), nsp5 (cysteine protease) suggest they remain critical factors drug development will be sustainable, unlike those strategies targeting Spike.

Language: Английский

Citations

0
Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens DOI Creative Commons
Chaney C. Kalinich, Freddy L. Gonzalez,

Alice Osmaston

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 20, 2024

Abstract Pathogen sequencing is an important tool for disease surveillance and demonstrated its high value during the COVID-19 pandemic. Viral pandemic allowed us to track spread, quickly identify new variants, guide development of vaccines. Tiled amplicon sequencing, in which a panel primers used multiplex amplification fragments across entire genome, was cornerstone SARS-CoV-2 sequencing. The speed, reliability, cost-effectiveness this method led implementation academic public health laboratories world adaptation broad range viral pathogens. However, similar methods are not available larger bacterial genomes, whole-genome typically requires vitro culture. This increases costs, error rates turnaround times. need culture poses particular problems medically bacteria such as Mycobacterium tuberculosis, slow grow challenging As proof concept, we developed two novel panels M. tuberculosis Streptococcus pneumoniae . Applying our clinical samples, show ability classify pathogen subgroups reliably markers drug resistance without culturing. Development work settings has potential dramatically reduce time diagnosis multiple drugs parallel, enabling earlier intervention priority

Language: Английский

Citations

0