Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
PLoS One
; 16(10): e0259277, 2021.
Article
in English
| MEDLINE | ID: covidwho-1496534
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
ABSTRACT
Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Pandemics
/
Nanopore Sequencing
/
SARS-CoV-2
/
COVID-19
Type of study:
Diagnostic study
/
Experimental Studies
Topics:
Long Covid
/
Variants
Limits:
Humans
Language:
English
Journal:
PLoS One
Journal subject:
Science
/
Medicine
Year:
2021
Document Type:
Article
Similar
MEDLINE
...
LILACS
LIS