Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness.
J Clin Virol
; 131: 104594, 2020 Oct.
Article
in English
| MEDLINE | ID: covidwho-726610
ABSTRACT
INTRODUCTION:
The SARS-CoV-2 pandemic of 2020 is a prime example of the omnipresent threat of emerging viruses that can infect humans. A protocol for the identification of novel coronaviruses by viral metagenomic sequencing in diagnostic laboratories may contribute to pandemic preparedness.AIM:
The aim of this study is to validate a metagenomic virus discovery protocol as a tool for coronavirus pandemic preparedness.METHODS:
The performance of a viral metagenomic protocol in a clinical setting for the identification of novel coronaviruses was tested using clinical samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, in combination with databases generated to contain only viruses of before the discovery dates of these coronaviruses, to mimic virus discovery.RESULTS:
Classification of NGS reads using Centrifuge and Genome Detective resulted in assignment of the reads to the closest relatives of the emerging coronaviruses. Low nucleotide and amino acid identity (81% and 84%, respectively, for SARS-CoV-2) in combination with up to 98% genome coverage were indicative for a related, novel coronavirus. Capture probes targeting vertebrate viruses, designed in 2015, enhanced both sequencing depth and coverage of the SARS-CoV-2 genome, the latter increasing from 71% to 98%.CONCLUSION:
The model used for simulation of virus discovery enabled validation of the metagenomic sequencing protocol. The metagenomic protocol with virus probes designed before the pandemic, can assist the detection and identification of novel coronaviruses directly in clinical samples.Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Pneumonia, Viral
/
Genome, Viral
/
Coronavirus Infections
/
Metagenomics
/
High-Throughput Nucleotide Sequencing
Type of study:
Diagnostic study
/
Prognostic study
Limits:
Humans
Language:
English
Journal:
J Clin Virol
Journal subject:
Virology
Year:
2020
Document Type:
Article
Similar
MEDLINE
...
LILACS
LIS