Rapid Identification of Relevant Microbial Strains by Identifying Multiple Marker Single Nucleotide Polymorphisms via Amplicon Sequencing: Epidemic Monkeypox Virus as a Proof of Concept-Reference-Cited by-同舟云学术

Rapid Identification of Relevant Microbial Strains by Identifying Multiple Marker Single Nucleotide Polymorphisms via Amplicon Sequencing: Epidemic Monkeypox Virus as a Proof of Concept

Published:2023-02-14 Issue:1 Volume:11 Page:
ISSN:2165-0497
Container-title:Microbiology Spectrum
language:en
Short-container-title:Microbiol Spectr

Author:

Buenestado-Serrano Sergio¹²³,Herranz Marta¹²,Palomino-Cabrera Rosalía¹²,Rodríguez-Grande Cristina¹²,Peñas-Utrilla Daniel¹²,Molero-Salinas Andrea¹²,Veintimilla Cristina¹²^ORCID,Catalán Pilar¹²,Alonso Roberto¹²⁴^ORCID,Muñoz Patricia¹²⁵⁴^ORCID,Pérez-Lago Laura¹²^ORCID,García de Viedma Darío¹²⁵^ORCID

Affiliation:

1. Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain

2. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain

3. Escuela de Doctorado, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain

4. Departamento de Medicina, Universidad Complutense, Madrid, Spain

5. CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III (CIBERES), Madrid, Spain

Abstract

Nanopore sequencing of multiple amplicons harboring signature single nucleotide polymorphisms (SNPs) escapes the targeting limitations of strain-specific PCRs and offers a powerful alternative to systematic whole-genome analysis, paving the way to real-time genomic epidemiology and making immediate intervention possible to finally optimize transmission control.

Funder

Instituto de Investigación Sanitaria Gregorio Marañón

MEC | Instituto de Salud Carlos III

Publisher

American Society for Microbiology

Subject

Infectious Diseases,Cell Biology,Microbiology (medical),Genetics,General Immunology and Microbiology,Ecology,Physiology

Link

https://journals.asm.org/doi/pdf/10.1128/spectrum.04196-22

Reference10 articles.

1. Global landscape of SARS-CoV-2 genomic surveillance and data sharing

2. Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus

3. The never-ending global emergence of viral zoonoses after COVID-19? The rising concern of monkeypox in Europe, North America and beyond

4. Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage?

5. Fast and low-cost decentralized surveillance of transmission of tuberculosis based on strain-specific PCRs tailored from whole genome sequencing data: a pilot study

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